Continuation Part 12: Amanda Knox/Raffaele Sollecito

[Numbers]

When did the defense become aware that Stef was working with Low template DNA? only very late in the first trial, no? They did move to invalidate the trial though, because the DNA evidence was misrepresented before Micheli, din't they, or have I confused things?

I just think its flawed reasoning to suggest there is anything the defense could have done to get a fair verdict from a biased process.

Let's remember that early on (pre-trial proceedings) "Doctor" Stefanoni claimed the DNA sample from the knife blade was about 400 pg, IIRC. {She said "a few hundred picograms}
ETA: Stefanoni testimony:

Question – But in your opinion was it in the order of a few nanograms or almost [at the level of] picograms?
Answer –Yes, it was in the order of a few hundred picograms, yes, for the total quantity.

Question: After which you passed to the quantification phase?
Answer: Yes.
Question: Quantification which you did with Real Time, I imagine?
Answer: Indeed yes

This was false. She didn't use Real Time PCR. She used the Qubit Fluorometer and it failed to register (=too low; means there may be NO DNA in the sample!).

ETA2: So the defense did not know until much later, as Carbonjam points out, that LCN DNA was involved. This was a clear perjury by Stefanoni and a clear violation of Convention Article 6.

 

[carbonjam72]

No, they knew from well before the trial that the "evidence" was low template level. What they didn't know was exactly how minuscule it was, and nor of course did they have the EDFs to properly understand the magnitudes, amplifications and noise levels/artifacts.

In my view, in the Massei trial they should have put an Italian DNA scientist with an international reputation on the stand to point all this out: 1) we categorically do not have the data to allow us to conduct a proper defence; 2) regardless of that, we know that the quanta of DNA being presented are well within the low-template range; 3) that being the case, a whole different - and much more stringent - set of rules applies to the admissibility and reliability of such DNA evidence; 4) we can show conclusively to the court that these rules have categorically not been followed in this case; and therefore 5) the courts should not be considering any of the DNA evidence reliable, and in fact should consider it inadmissible.

And you believe that had the defense done this, Massei would have recognized the merit of the argument, and incorporated it into his opinion?

Do you believe massei's verdict is honestly stupid, or fatally biased?

 

[carbonjam72]

Let's remember that early on (pre-trial proceedings) "Doctor" Stefanoni claimed the DNA sample from the knife blade was about 400 pg, IIRC.

That's similar to what I recall, and I believe it was that claim by Stef that helped keep Amanda and Raf incarcerated? And/Or was it also one of the reasons that Micheli certified the case for trial, and therefore when the defense found out it was false, they moved for a mistrial, because the trial crtification was based on an erroneous fact?

 

[LondonJohn]

Let's remember that early on (pre-trial proceedings) "Doctor" Stefanoni claimed the DNA sample from the knife blade was about 400 pg, IIRC. {She said "a few hundred picograms}
ETA: Stefanoni testimony:

Question – But in your opinion was it in the order of a few nanograms or almost [at the level of] picograms?
Answer –Yes, it was in the order of a few hundred picograms, yes, for the total quantity.

Question: After which you passed to the quantification phase?
Answer: Yes.
Question: Quantification which you did with Real Time, I imagine?
Answer: Indeed yes

This was false. She didn't use Real Time PCR. She used the Qubit Fluorometer and it failed to register (=too low; means there may be NO DNA in the sample!).

ETA2: So the defense did not know until much later, as Carbonjam points out, that LCN DNA was involved. This was a clear perjury by Stefanoni and a clear violation of Convention Article 6.

I entirely agree - but this was all in the pre-trial hearings, no? Isn't it correct that by the time that the Massei trial started in 2009, the defence teams were well aware that the prosecution was talking about tiny levels of DNA that definitely fell into the low-template range, even if they still weren't being told exactly how tiny the amounts were?

 

[Numbers]

No, they knew from well before the trial that the "evidence" was low template level. What they didn't know was exactly how minuscule it was, and nor of course did they have the EDFs to properly understand the magnitudes, amplifications and noise levels/artifacts.

In my view, in the Massei trial they should have put an Italian DNA scientist with an international reputation on the stand to point all this out: 1) we categorically do not have the data to allow us to conduct a proper defence; 2) regardless of that, we know that the quanta of DNA being presented are well within the low-template range; 3) that being the case, a whole different - and much more stringent - set of rules applies to the admissibility and reliability of such DNA evidence; 4) we can show conclusively to the court that these rules have categorically not been followed in this case; and therefore 5) the courts should not be considering any of the DNA evidence reliable, and in fact should consider it inadmissible.

{Highlighting added to quote.}

How did they know about the LCN DNA? When were the defense provided with the quantification - the real data, that is, not Stefanoni's perjury that it was hundreds of picograms? (The upper limit for LCN DNA is debatable - but IIUC is generally taken to be 100 or sometimes 200 pg.)

 

[tsig]

The Rock

As far as I can tell, there would be no difference as far as evidence between staged or not staged if the rock being thrown from out. Effectively, the argument "staged" can no longer be used.
It has to be obviously staged for them to argue guilt.

It:

Goes in and out the window,
Goes in and out the window,
Goes in and out the window,
As if has done before.

 

[LondonJohn]

And you believe that had the defense done this, Massei would have recognized the merit of the argument, and incorporated it into his opinion?

Do you believe massei's verdict is honestly stupid, or fatally biased?

I think it's a bit of both, to be honest.
I think that Massei was clearly improperly inclined to take the prosecution argument as objective "truth", and that unless and until the defence teams could explicitly disprove any element of it, then that element would be considered correct.

I think that this attitude is a hangover from the inquisitorial system, and I strongly suspect that it's an endemic problem in Italian criminal justice. I think that the prevailing reactionary (and unlawful) position of many Italian judges is that the prosecution is utterly disinterested and is a "friend of the court", while the defence is the only "side" that is considered partisan.

But that being said, I do think that the defence (collectively) did a pretty dreadful job in the Massei trial. There were a number of things that screamed out to be argued, which the defence either obfuscated, minimised or simply ignored. But of course even then a competent court should have seen the prosecution case for what it was. Unfortunately - and very possibly owing the phenomenon I suggested in the previous paragraph - Massei's court chose to essentially take Mignini's horribly flawed position as the starting point, and then chose to embellish it with his own special stardust......

 

[anglolawyer]

I had explained validation to a small extent in a post lost due to my clumsy skills at the keyboard.

Validation, in general, is a statistically valid exercise - a study that involves the actual physical processes - that demonstrates a process or method is fit for use.

For example, in DNA work, one should do repeated analyses de novo (from a starting point known to be validated) on known DNA samples, using a statistical model to determine the appropriate number of repetitions and of various types of DNA materials, and check that the DNA method produces the expected result and noting any statistical variation (statistical error), with quantification of the statistical error rate and assurance that such error rate is less than or equal to some predetermined acceptable limit.

The point is that physical processes - such as lab tests or manufacturing methods - have some potential for variation, or even producing fully erroneous results or products. One needs to assure that what results from the process meets the expectations of use. For forensics in a criminal case, the standard must be essentially certainty that the DNA profile is indeed what was present in the sample. There are many artifacts that can occur in DNA profiling, and those artifacts are larger in number and more severe in effect on interpretation for LCN DNA.

Exactly - and I think that courts (particularly, it would appear, in Italy....) simply have not yet come to grasp the concept that the problems of reliability are magnified disproportionately greatly in low template DNA analysis compared with "standard" PCR DNA work.

I think that courts (particularly, it would appear, in Italy....) have become comfortable with the issues surrounding "standard" DNA evidence, and erroneously think that the same rules and standards apply to low template DNA evidence - or if not exactly the same rules and standards, then only a small tweak. In reality, an entire new set of much, much more stringent rules and standards is required in order to allow the admission of low template DNA evidence.

Unfortunately, I once again lay a certain amount of blame in this specific case at the feet of the defence lawyers in the Massei trial. They could (and easily should) have produced an expert in DNA analysis to show the court unequivocally that 1) the standards required for low template analysis are dramatically different from those required for "standard" DNA analysis, and 2) the low template evidence in this case manifestly and definitively came nowhere even close to meeting those standards.

PS: Pi to 10 dp is 3.1415926536 - one of my strange party tricks is an ability to recite Pi to 50 dp (3.14159265358979323846264338327950288419716939937511 since you ask )

PPS: for non-mathematicians who might be slightly confused, the reason why the last digit of Pi to 10dp is 6 rather than 5 is that the following dp is >=5 (it is in fact 5) - this means that to 10dp one needs to round up the 5 to a 6.....

can we dumb it down just a teeny bit more?

 

[Chris_Halkides]

imbalance in peak heights

When did the defense become aware that Stef was working with Low template DNA? only very late in the first trial, no? They did move to invalidate the trial though, because the DNA evidence was misrepresented before Micheli, din't they, or have I confused things?

I just think its flawed reasoning to suggest there is anything the defense could have done to get a fair verdict from a biased process.

Carbonjam72,

Just by looking at the gram, you can see that the peaks within a single locus (location) are imbalanced in height, which is one definition of the low template region. There are other indications, such as two drop-in peaks (as Numbers mentioned) and one peak dropped out.

I am not saying that the defense was perfect, but I am sympathetic to the view in your last sentence.

 

[Bill Williams]

I think it's a bit of both, to be honest.
I think that Massei was clearly improperly inclined to take the prosecution argument as objective "truth", and that unless and until the defence teams could explicitly disprove any element of it, then that element would be considered correct.

I think that this attitude is a hangover from the inquisitorial system, and I strongly suspect that it's an endemic problem in Italian criminal justice. I think that the prevailing reactionary (and unlawful) position of many Italian judges is that the prosecution is utterly disinterested and is a "friend of the court", while the defence is the only "side" that is considered partisan.

But that being said, I do think that the defence (collectively) did a pretty dreadful job in the Massei trial. There were a number of things that screamed out to be argued, which the defence either obfuscated, minimised or simply ignored. But of course even then a competent court should have seen the prosecution case for what it was. Unfortunately - and very possibly owing the phenomenon I suggested in the previous paragraph - Massei's court chose to essentially take Mignini's horribly flawed position as the starting point, and then chose to embellish it with his own special stardust......

Strangely this is CNN cub-reporter, Barbie Nadeau's assessment back to CNN headquarters on the night of the Dec 2009 conviction. "The prosecution case was weak, but the defence case was weaker. This could very well be overturned at appeal."

No one at CNN that night seemed to pick up on that if the prosecution case was weak, who cares about the defence case?

Massei's motivations report consistently takes prosecution experts at their word, regardless. What is remarkable are the numerous issues Massei reinvents straight out of thin air, some stuff in contradiction to what Mignini was advancing.

 

[Numbers]

can we dumb it down just a teeny bit more?

Perhaps this can help. Of course, it is general.

The basic simplest idea of validation for a DNA profile test for forensic criminal work:

Accumulate a number of DNA specimens of the various DNA types - with variations in the STRs typical of what would be encountered.

Subject a given number of each type to all the processes involved in the test.

(The number tested should be determined based upon statistical model concepts of how many should be tested to assure that potential error rates of less than a certain level can be estimated with some level of confidence.)

Compare the results, including observed variations, to the expectations based on other testing or other information known with confidence. Determine and characterize variation in the results; determine error rates and compare them to the predetermined maximum error rate considered allowable. Determine if there are any limitations for the test methods, such as minimum and maximum amounts of DNA required to produce acceptable (interpretable) results.


http://en.wikipedia.org/wiki/Test_method

Test Method Validation

Test methods are often scrutinized for their validity, applicability, and accuracy. It is very important that the scope of the test method be clearly defined, and any aspect included in the scope is shown to be accurate and repeatable through validation.

Test method validations often encompass the following considerations:

Accuracy and precision: Demonstration of accuracy may require the creation of a reference value if none is yet available.
Repeatability and Reproducibility, sometimes in the form of a Gauge R&R.
Range, or a continuum scale over which the test method would be considered accurate. Example: 10 N to 100 N force test.
Measurement resolution, be it spatial, temporal, or otherwise.
Curve fitting, typically for linearity, which justifies interpolation between calibrated reference points.
Robustness, or the insensitivity to potentially subtle variables in the test environment or setup which may be difficult to control.
Usefulness to predict end-use characteristics and performance
Measurement uncertainty
Interlaboratory or round robin tests
other types of measurement systems analysis


Content of a Test Method

Quality management systems usually require full documentation of the procedures used in a test. The document for a test method might include:

Descriptive title
Scope over which class(es) of materials or articles may be evaluated
Date of last effective revision and revision designation
Reference to most recent test method validation
Person, office, or agency responsible for questions on the test method, updates, and deviations.
The significance or importance of the test method and its intended use.
Terminology and definitions to clarify the meanings of the test method
A listing of the types of apparatus and measuring instrument (sometimes the specific device) required to conduct the test
Safety precautions
Required calibrations and metrology systems
Environmental concerns and considerations
Sampling procedures: How samples are to be obtained, and Number of samples (sample size).
Conditioning or required environmental chamber: temperature, humidity, etc., including tolerances
Preparation of samples for the test and test fixtures
Detailed procedure for conducting the test
Calculations and analysis of data
Interpretation of data and test method output
Report: format, content, data, etc.

 

[Numbers]

can we dumb it down just a teeny bit more?

There is also this set of definitions from the FBI DNA lab standards document:

http://www.fbi.gov/about-us/lab/biometric-analysis/codis/stds_testlabs

(ff) Validation is a process by which a procedure is evaluated to determine its efficacy and reliability for forensic casework analysis and includes:

(1) Developmental validation is the acquisition of test data and determination of conditions and limitations of a new or novel DNA methodology for use on forensic samples.
(2) Internal validation is an accumulation of test data within the laboratory to demonstrate that established methods and procedures perform as expected in the laboratory.

ETA: ENFSI has a document on validation as well. See: www.enfsi.eu

Recommended Minimum Criteria for the Validation of Various
Aspects of the DNA Profiling Process

 

[Numbers]

can we dumb it down just a teeny bit more?

From ENSFI:

One of the requirements of EN ISO/IEC 17025 is that methods used in testing laboratories should be validated. As EN ISO/IEC 17025 only determines a general standard it is the role of the experts in a given field to give more detailed recommendations.

The ENFSI DNA Working Group has agreed upon the minimum validation criteria as laid down in this document. This paper can only serve as a recommendation because each DNA testing laboratory has its own duties and workflows. There might be other approaches to validate a certain protocol or instrument. Whatever the criteria are to validate a system, they must give evidence that the procedures and instrument are suitable for the purpose they are used for according to EN ISO/IEC 17025. It is also an absolute necessity that the results are in concordance with the international standards to ensure that DNA profiles are comparable between laboratories.

These recommendations only apply to standard situations in a laboratory (internal validation). However, if a testing laboratory develops new methods or technologies, the validation efforts have to be far more extensive and considered as developmental validation (see below).

General prescriptions
Any change in technique (reagents, kits, apparatus ...) with a potential influence on the results, requires an internal validation (see below). It is essential to show that profiles obtained using the new regime are of the same, or better, quality than those obtained under the previous regime.

Ref code: ENFSI DNA WORKING GROUP Issue No. 001 Page: 2/11

 

[Numbers]

can we dumb it down just a teeny bit more?

Here's a validation issue and a test lab integrity issue.

Something strange - a malfunction or a malpractice (cheating) was happening with Stefanoni's Real Time PCR quantification equipment.

So she changed over to the Qubit, which is a very different, and less accurate device using an interpolation over only two points to quantify DNA concentration. (RT-PCR uses 6 points, IIRC). She found that a number of sample registered "too low" on the Qubit - meaning the Qubit could not truly give an accurate concentration value for the sample, perhaps there was no DNA in the sample at all. Note that the Qubit and RT-PCR have as an inescapable artifact a certain level of noise in their measurement, which is more readily discerned from signal (of real DNA) in RT-PCR than for the Qubit.

Now Stefanoni tested by DNA profiling and reported on some of the "too low" samples, tested by DNA profiling and did not report on many other "too low" samples, and apparently did not test some other "too low" DNA samples.

The sample from the knife blade, alleged to contain Meredith Kercher's DNA, was one of the samples quantified as "too low" on the Qubit, concentrated by vacuum pump (which can introduce contamination into a sample), and then DNA profiled and reported. And there were similar samples* mysteriously not reported. Why? Because the sample reported somehow showed Meredith's DNA, and others did not?

ETA: *from the knife blade

 

[Desert Fox]

It:

Goes in and out the window,
Goes in and out the window,
Goes in and out the window,
As if has done before.

What does that even mean?

 

[sept79]

When did the defense become aware that Stef was working with Low template DNA? only very late in the first trial, no? They did move to invalidate the trial though, because the DNA evidence was misrepresented before Micheli, didn't they, or have I confused things?
.
.

Per Andrea Vogt's 13 Sept. 2009 article (during Massei's trial):

". . . the court recessed for the summer in mid-July with a request of additional information about the DNA from police forensic scientist, Patrizia Stefanoni.

The detailed information provided by Stefanoni formed the basis for a number of significant concerns raised by Monday's witness, Professor Adriano Tagliabracci, director of the Forensic Institute of Ancona and president of the Italian Association of Forensic Genetics,
Tagliabracci raised doubts about several of the DNA results presented by Stefanoni last May and pointed out missing data, potential protocol missteps and at least one glaring inconsistency.

Specifically, he took Stefanoni to task for incomplete documentation of her scientific process and even produced a daily registry from the machine that detected Knox's and the victim's DNA on the knife and showed where Stefanoni had handwritten "too low" four times. "It could be contamination of the laboratory. It could have been anything," Tagliabracci said. "'Too low' means it should not have been used for analysis."

He also pointed out contradictions between the results and what Stefanoni actually wrote in her technical report. Specifially, Stefanoni wrote that a mattress cover from the downstairs apartment had tested positive for cat blood and negative for human DNA, when the actual results showed a positive result for human DNA.

He also criticized Stefanoni for positively attributing DNA to Sollecito, despite what many labs would consider a "low copy number." The odds that the genetic profile was Sollecito's were such that it could have matched 500 people in the city of Perugia, population 360,000, he said. But he also later argued the clasp could have been contaminated in the course of the 47 days after Kercerh's death that it was left behind at the crime scene. That prompted the Kercher family's attorney, Francesco Maresca to note an inconsistency: Tagliabracci argued that he DNA didn't match Sollecito's, yet later also noted the clasp could have been contaminated with Sollecito's DNA.

Stefanoni, seated between prosecutors Manuela Comodi and Giuliano Mignini, appeared agitated at times, twirling her long black hair repeatedly around her finger and gesturing as she listened. Comodi objected several times, at one point calling some of defensive attorneys' suggestions insulting.
The hearing began with a surprise defense request to have the charges (or at least the DNA evidence) against the two thrown out, because the new, detailed information was only provided July 30, too late, they argued to allow for preparation of a proper defense strategy."


A couple other significant points

--Stefanoni lied to Micheli's 'grand jury' that the knife sample size was considerably in excess of LCN.

--If Stefanoni hadn't lied about the sample size, would the defense have been able to mount a significant argument preventing Micheli from sending the case to a trial of first instance--i.e., Massie?

--In spite of Stefanoni's lying and various other fraudulent activities, Massie refused the defense's request for an independent review of the DNA

--The additional information supplied by Stefanoni during the summer break of 2009 revealed the negative blood results obtained via TMB testing of the hallway footprints.

 

[Bill Williams]

Per Andrea Vogt's 13 Sept. 2009 article (during Massei's trial):

". . . the court recessed for the summer in mid-July with a request of additional information about the DNA from police forensic scientist, Patrizia Stefanoni.

The detailed information provided by Stefanoni formed the basis for a number of significant concerns raised by Monday's witness, Professor Adriano Tagliabracci, director of the Forensic Institute of Ancona and president of the Italian Association of Forensic Genetics,
Tagliabracci raised doubts about several of the DNA results presented by Stefanoni last May and pointed out missing data, potential protocol missteps and at least one glaring inconsistency.

Specifically, he took Stefanoni to task for incomplete documentation of her scientific process and even produced a daily registry from the machine that detected Knox's and the victim's DNA on the knife and showed where Stefanoni had handwritten "too low" four times. "It could be contamination of the laboratory. It could have been anything," Tagliabracci said. "'Too low' means it should not have been used for analysis."

He also pointed out contradictions between the results and what Stefanoni actually wrote in her technical report. Specifially, Stefanoni wrote that a mattress cover from the downstairs apartment had tested positive for cat blood and negative for human DNA, when the actual results showed a positive result for human DNA.

He also criticized Stefanoni for positively attributing DNA to Sollecito, despite what many labs would consider a "low copy number." The odds that the genetic profile was Sollecito's were such that it could have matched 500 people in the city of Perugia, population 360,000, he said. But he also later argued the clasp could have been contaminated in the course of the 47 days after Kercerh's death that it was left behind at the crime scene. That prompted the Kercher family's attorney, Francesco Maresca to note an inconsistency: Tagliabracci argued that he DNA didn't match Sollecito's, yet later also noted the clasp could have been contaminated with Sollecito's DNA.

Stefanoni, seated between prosecutors Manuela Comodi and Giuliano Mignini, appeared agitated at times, twirling her long black hair repeatedly around her finger and gesturing as she listened. Comodi objected several times, at one point calling some of defensive attorneys' suggestions insulting.
The hearing began with a surprise defense request to have the charges (or at least the DNA evidence) against the two thrown out, because the new, detailed information was only provided July 30, too late, they argued to allow for preparation of a proper defense strategy."


A couple other significant points

--Stefanoni lied to Micheli's 'grand jury' that the knife sample size was considerably in excess of LCN.

--If Stefanoni hadn't lied about the sample size, would the defense have been able to mount a significant argument preventing Micheli from sending the case to a trial of first instance--i.e., Massie?

--In spite of Stefanoni's lying and various other fraudulent activities, Massie refused the defense's request for an independent review of the DNA

--The additional information supplied by Stefanoni during the summer break of 2009 revealed the negative blood results obtained via TMB testing of the hallway footprints.

Holy moley. Maybe now Machiavelli will start calling Andrea Vogt, an "approximate reporter"!!

 

[Ampulla of Vater]

But, as we know, science is different in Italy. As Grinder used to say, 'three compatibles equals a match' and I used to add ' and nobody may be accused of lying' to which Grinder would then say 'it's an opera' and I would reply, 'panto'.

How is old Grinder doing these days? I do miss having him around.

 

[anglolawyer]

How is old Grinder doing these days? I do miss having him around.

Good, I think. Me too.

 

[christianahannah]

Their argument is that it was staged backwards by first trashing Filomena's room and then breaking the window. But where is the evidence? The prosecutions own photographs don't show this.

Wasn't the evidence, in part, the testimony of Filomena and the police officer(s) who entered the room before Meredith's body was found? The room had been disrupted by Filomena picking up items which had glass fragments on top of them. So the investigative photos wouldn't necessarily show every part of the room as it was before it was entered by Filomena and the police.

Very early in the investigation it was being reported in the journals that the police believed the break-in was simulated. I don't recall if there were specifics as to why this was thought.