Continuation Part 2 - Discussion of the Amanda Knox case

[daydreamer]

Steve Moore is reporting the the knife handle was opened and no blood found. This is the first I heard of that, does anybody have confirmation?

"Additionally, and interestingly, when the handles were taken off the blade of the knife, no blood was found. Starch was found. Starch? Yes, as in the type of starch found in the water of boiling pots of pasta. If blood had EVER been on that knife, the starch would have absorbed it and preserved it. That knife has never even touched blood."

http://gmancasefile.blogspot.com/2011/06/beginning-of-end.html

 

[Chris_Halkides]

DNA in skin and dust

The report is referencing Toothman 2008 study about DNA in household dust, pointng out that no samples of ambient dust were tested for comparison to prove that the contamination didn't come from it. I got a feeling I've seen it mentioned before. Was is on this forum ?

The artifact was recovered 46 days after the crime, in an environment highly suggestive of contamination . The risk of incorrectly interpreting environmental contaminants such dust could be minimized only by having the foresight to establish very strict control procedures, including analysis of extracts from sterile cotton swabs soaked in sterile buffer passed to pick up on environmental surfaces dust samples, a procedure that has not been implemented; (google)

Katody Matrass,

I may have been the first person to quote this article, and I contacted the lead author for clarification. Kestrel started a thread on DNA in skin cells that also dealt with the Toothman study. I have sometimes wondered whether or not a little of the DNA on the clasp came from dust.

 

[Diocletus]

Diocletus,

This is a very insightful comment.

And let me also echo LondonJohn's praise of Italy's automatic appeal system with its presumption of innocence, which is looking pretty good right now.

Thank you. I will be most interested to read your analysis of the report when you have a chance to put something together, as I have found your prior work on this case to be excellent.

I'm afraid that I can't share the praise of Italy's two-trial system. Systems built like this tend to encourage error in the first go-round, because the first group knows that the error can be fixed later. This case, and the fates of the inncocent defendants, show why there needs to be a premium on getting it right the first time. The absence of a speedy trial safeguard compounds the problem, IMHO.

In the US and UK, assuming the same initial errors, there also would also have been two trials, because the first trial would have been thrown out by the appellate court. The trial and re-trial would have happened much more quickly then the two trials in this case.

 

[RoseMontague]

Steve Moore is reporting the the knife handle was opened and no blood found. This is the first I heard of that, does anybody have confirmation?

"Additionally, and interestingly, when the handles were taken off the blade of the knife, no blood was found. Starch was found. Starch? Yes, as in the type of starch found in the water of boiling pots of pasta. If blood had EVER been on that knife, the starch would have absorbed it and preserved it. That knife has never even touched blood."

http://gmancasefile.blogspot.com/2011/06/beginning-of-end.html

I believe it said the starch was found on the part of the blade next to the handle, I haven't seen anything saying the handle was removed/taken apart.

 

[RoseMontague]

The toolkit doesn't know how to handle tags within text so these have to be moved to between sentences. Keeping the original page numbers (ie: [403]) and attempting to preserve the look with hard newlines helps tremendously when comparing the converted text to the original. The toolkit could be a lot better if it did some of this mechanical stuff automatically. Somebody should write Google and tell them

It is also helpful to have a glossary of names that shouldn't be translated and technical terms that should have a specific translation. I can convert the Kercher Case People list from the wiki into the format needed for the glossary. Anybody else that wants to submit a list of terms used in these documents and their translation, I'll create a page to keep the master list.

I tried a few things this morning with no success although I did create a 700 page html version. LOL. I am letting this one rest for awhile.

 

[RoseMontague]

Here is a translation by thoughtful on this issue:

It emerges from the SAL that on Exhibit 165B [bra clasp] the generic test for blood was not performed[...] nor was any lab investigation made with the goal of proving the presence of non-blood biological material.

It is held that it would have been necessary to proceed with a morphological analysis for the possible presence of cells, using coloring with one of the reactive agents usually employed in histology (hematoxylin). Such investigations are simple and fast and would have required only a minimal quantity of material, which would not in any way have compromised the further lab investigations, but could have clarified the nature of the material taken from the exhibit and examined.

In spite of these omitted investigations for the existence of cells (and thus the lack of identification of the material taken from exhibit 165B), the C.T. [Stefanoni] hypothesized the presence of "presumed exfoliation cells" on this exhibit.

The hypothesis formulated by the C.T. on the nature of the material under analysis (hypothesis confirmed [by her] in the GUP hearings and in the Assize Court) is absolutely arbitrary, in that it is absolutely not supported by any scientifically objective

thoughtful also indicates that there is mention in the report that Stefanoni did not run negative controls.

Very interesting information coming out of the report.

 

[Katody Matrass]

Katody Matrass,

I may have been the first person to quote this article, and I contacted the lead author for clarification. Kestrel started a thread on DNA in skin cells that also dealt with the Toothman study. I have sometimes wondered whether or not a little of the DNA on the clasp came from dust.

Exactly, it does look like the independent experts swallowed your FOA talking points hook, line, and sinker

There are many potential paths of contamination, none of which can we exclude due to outstanding work and documentation of Scientifica. I suspect a "non-scientific" cop handling items of clothing or underwear in Amanda's room and then picking up and throwing away the clasp is as possible as transfer from the door handle or yes - simply dust.

 

[Diocletus]

Here is another fascinating item from Thoughtful:

"As for accuracy, I doubt that there is one single inaccurate statement in Conti-Vecchiotti's report (unless Stefanoni has documentation that she didn't send on, but that seems unlikely at this point). Conti and Vecchiotti date every document they received from her, and clearly she was sending them documents little by little and only on specific demand, as they were still receiving further documents on April 29 and May 11. I'm sure they requested and received the complete SAL."

(my emphasis)

 

[Bruce Fischer]

Steve Moore is reporting the the knife handle was opened and no blood found. This is the first I heard of that, does anybody have confirmation?

"Additionally, and interestingly, when the handles were taken off the blade of the knife, no blood was found. Starch was found. Starch? Yes, as in the type of starch found in the water of boiling pots of pasta. If blood had EVER been on that knife, the starch would have absorbed it and preserved it. That knife has never even touched blood."

http://gmancasefile.blogspot.com/2011/06/beginning-of-end.html

Steve is incorrect to say the knife was taken apart but the basis of his statement is sound. They found starch in the seam where the handle meets the blade. His statement: "If blood had EVER been on that knife, the starch would have absorbed it and preserved it. That knife has never even touched blood" is absolutely true.

 

[RoseMontague]

Here is another fascinating item from Thoughtful:

"As for accuracy, I doubt that there is one single inaccurate statement in Conti-Vecchiotti's report (unless Stefanoni has documentation that she didn't send on, but that seems unlikely at this point). Conti and Vecchiotti date every document they received from her, and clearly she was sending them documents little by little and only on specific demand, as they were still receiving further documents on April 29 and May 11. I'm sure they requested and received the complete SAL."

(my emphasis)

I have to say that I am somewhat surprised that thoughtful is going through the report with so little objection (from other posters there). Another quote:

Pages 122-126 show a graphic analysis of several bits of the electropherogram from the bra clasp.

They quote Stefanoni as correctly citing the rules for declaring whether small-looking peaks in the graph are actual alleles or "stutter" (bumps in the graph due to background noise). The rules are basically:

1) a peak is not stutter if it's more than 50 RFU in height

2) a peak is not stutter if its height is greater than 15% of the height of the following peak (on the right)

3) a peak is not stutter if it is the last peak on the right in a group of peaks (stutter peaks always occur to the left of allele peaks)

They then give four specific places in the electropherogram where Stefanoni qualified as "stutter" peaks which according to the above 3 rules should have been taken to be alleles.

Quote:
Regarding the evaluation of stutter, it should be noted that while the C.T. [Stefanoni] asserted that there are "recommendations for correct interpretation, which are really guidelines", in practice she did not correctly apply the recommendations given in the guidelines of the ISFG.


They note that these remarks were already made to Dr. Stefanoni in court and quote her response as being: "As you rightly point out, the height, or rather the indications, as you correctly point out to me, have not been written down for certain peaks appearing in this electropherogram, that's obviously correct, I mean we can see that they are not there, but it's for the simple reason that having interpreted this mixture, obviously I took it as my responsibility to consider these alleles, so to speak, these peaks as not significant because from my point of view they are stutter, they are artifacts which have been described, measured and quantified both in the literature and in the kit that I'm using."

They then add that Stefanoni did not respect one of the guidelines which states that "in cases where alleles and stutter are indistinguishable, results must also include those alleles in stutter position which do not support the position of the prosecution", and also that even if one were to consider as stutter those peaks in stutter position but which are higher than 50 RFU, one still gets a much more complex interpretation of the electropherogram than Stefanoni's, with one major contributor and several minor ones.

At this point they don't openly address the question of whether Sollecito can be determined to be one of the minor contributors with certainty. You'd think it would be important enough to mention!

 

[JREF2010]

Here is a translation by thoughtful on this issue:



thoughtful also indicates that there is mention in the report that Stefanoni did not run negative controls.

Very interesting information coming out of the report.

thats as bad as not recording, or transcribing, the interrogation.

to NOT run a simple "blank run", negative control, to ensure the tool is ready for the next sample, and all previous residual traces are cleared is hard to believe, even from a novice let alone a expert.

this possible residual, as I read, is why the equipment designer recommends a RFU limit too. Too Low is like trying to decipher music from a fuzzzy-radio station.

i'm not one for conspiracy's in general, but I do believe solo humans often lie and are biased. they might ignore data and justify their actions because they truly believe in their "team's goal".

makes me wonder if she ran negatives, like the interrogation tape, they realized it wasn't good info and it disappeared.

or I'm wrong again...and its common practice in the DNA world, not to run controls before running the sample.

this is huge. without the knife, there is absolutely nothing to place Amanda in Merediths room, not even Rudys "partial truths" support Amanda in the bedroom.

will the Guilters attack Raffaele now? They always seem to put Rudy on the pedestal as his words are believed the two students were there.



thanks Rose, great info..

 

[Bruce Fischer]

In the next few days it would be nice to see those, who have been involved in this heated debate, to take a step back and look at what the DNA report actually says. This debate has gone on for so long that it appears the online debate has become the focus rather than the actual people involved. Right now I see a lot of spin regarding the report which is to be expected for those determined to win their online shouting match, but not very realistic for those looking at this case based on the real lives being destroyed.

The knife and the clasp are gone. They will no longer be viewed as credible after the July hearing. The independent experts were appointed by the court and their results will be accepted.

The spin goes like this; "the DNA is only a small part of the 'mountain of evidence' to convict the two 'love birds.' The 'staged' break in is really what convicted them in the first place"

There is no credible evidence to prove a staged break in but Massei (the judge that refused additional testing on the DNA) said it was staged so that's good enough for those in spin mode now. If that's all you have to secure convictions then it's really time to walk away from the debate.

 

[lane99]

If this is a meta-comment on how criminal litigation has seeped into the popular culture as entertainment, then it's brilliant. However, seeing the thread about education that the poster started, I fear this may not be satire at all...

Yea, satire was the first thing that occured to me. I was expecting a follow up post that, channeling the spirt of Gilda Radner, said simply:

"Nevermind"

 

[komponisto]

I predict a huge come back of one of the more idiotic arguments, i.e. "where is the proof of contamination?"

Oh, it's already happening. But it's futile -- this is addressed in the report, as you know. Here is p. 136, regarding the bra clasp:

Regarding the reliability of the item with specific reference to "possible contamination", we find it appropriate to examine the means by which and cirmustances under which Item 165B was acquired.

The item was recovered 46 days after the crime, in a context highly suggestive of environmental contamination.

The DNA obtained, though sufficient in quantity to permit analysis, does not satsify the mimimum quality requirements, due to clear environmental contamination.

Various peaks (cf. table of autosomic STRs and Y-chromosome haplotype) which should have been considered alleles until proven otherwise, were not taken into consideration in the analyses; yet their presence was indicative of the fact that, besides Kercher and Sollecito, other unidentified individuals were represented in the genetic traces found at the crime scene. In this regard, it was necessary to proceed to further amplifications of the extracted DNA in order to conferm the presence of the various haplotypes present at the crime scene -- something which was not done, even though a sufficient amount of extracted material was available (cf. SAL: 50μl of extracted material).

Furthermore, the documentation regarding possible contamination of the item, both before and after recovery, is inadequate. The mere fact that the amplification control -- which was not provided -- was negative is not enough to rule out environmental contamination of the item previous to the extraction and amplification of the DNA. It would have been necessary to obtain the allele profiles present in the surrounding environment.

The item was recovered on the floor, where it predictably had contact with ambient dust, which, in closed enviroments frequented by humans, is composed to a large extent of elements of human origin (cells, hairs, etc.).

It has been demonstrated that dust from closed environments can contain tens of micrograms of DNA per gram, with the amount of DNA depending on the level of frequentation by individuals and on the amount of dust that accumulates in the relevant environment.

It has been thoroughly demonstrated that the presence of ambient dust constitutes a significant source of contamination in forensic investigations, since the DNA deriving from such dust can present itself in the form of alleles in analyses of polymorphisms.

(more to come...)

 

[HumanityBlues]

In the next few days it would be nice to see those, who have been involved in this heated debate, to take a step back and look at what the DNA report actually says. This debate has gone on for so long that it appears the online debate has become the focus rather than the actual people involved. Right now I see a lot of spin regarding the report which is to be expected for those determined to win their online shouting match, but not very realistic for those looking at this case based on the real lives being destroyed.

The knife and the clasp are gone. They will no longer be viewed as credible after the July hearing. The independent experts were appointed by the court and their results will be accepted.

The spin goes like this; "the DNA is only a small part of the 'mountain of evidence' to convict the two 'love birds.' The 'staged' break in is really what convicted them in the first place"

There is no credible evidence to prove a staged break in but Massei (the judge that refused additional testing on the DNA) said it was staged so that's good enough for those in spin mode now. If that's all you have to secure convictions then it's really time to walk away from the debate.

Does this mean we can't make fun of Kermit's open letter to the independent experts?

 

[komponisto]

contamination of bra clasp, continued...

p. 137:

The risk of incorrectly interpreting such enviromental contaminants can be minimized only by instituting extremely strict control protocols, including, the analysis of extracts from sterile cotton swabs soaked with sterile buffer that have passed on ambient surfaces to take dust samples (Toothman MH et al., 2008).

In any case, the allele profiles obtained from ambient dust, or from samples contaminated with ambient dust, can be indicative of the individuals who have frequented that environment.

Nevertheless, the aforementioned authors explain that it is diffiult to generalize to a direct correlation between human frequentation and levels of dust with the quantity and quality of human DNA therein present, because of the potential effects of other uncontrolled factors. Indeed, environmental variables, including light, heat, and humidity can degrade DNA, and residues of detergents (such as bleach) can destroy the DNA. Moreover, the ventilation system can act as a vehicle for transferring dust among different rooms, introducing DNA from individuals that have not necessarily frequented a specific environment (Toothman MH. et al., 2008).

In order to advance interpretive hypotheses, it would have been necessary, in our opinion, to proceed to multiple amplifications on item 165B, whose alleles should have been compared with the alleles obtained from multiple amplifications performed on extracts from multiple samples of ambient dust.

Only alleles found on Item 165B, and not in ambient dust, could be considered of possible evidentiary value -- independently of the height and area of the corresponding peaks. This [comparison] not having been done, the allele profiles of item 165B should not, in our opinion, be considered evidence.

 

[Rolfe]

I'm pleased to see this development, because it makes sense.

I simply couldn't see how the time of death evidence could possibly fit with the murder having happened much after 9 o'clock. By the way, I discussed that evidence with a colleague who is FRCPath, and her reaction was that she was mildly surprised there had been no transit to the duodenum by 9 o'clock, and was quite adamant that death must have occurred soon after the victim was last seen alive under the circumstances described. She also gave the opinion that while some artefactual slippage from the pylorus into the duodenum might happen if care wasn't taken, for duodenal contents to slip well down into the jejunum by accident, leaving an empty duodenum, was well-nigh impossible.

For the time of death to be much later than nine o'clock, we'd have to shift the time of the meal to after the film was watched, or even to after Meredith returned home, or we'd have to show that the post mortem results as reported were in error. The testimony of the friends as to the time of the meal seems clear enough that it was eaten before the film was watched, and I understand the post mortem examination was videoed and showed correct procedure with results as reported. Thus the time of death has to have been shortly after Meredith returned home. Which is conveniently consistent with the evidence in her home, indicating that she didn't do anything else once she got there, not even phone her mother.

I couldn't get much sense out of those posters supporting guilt on this point. Handwaving about "google time of death", and assertions that we had no idea at all when Meredith ate, really didn't help at all. As far as I could see what was actually being said was that the DNA evidence placed Knox and Sollecito at the scene of the crime, so if they couldn't have been there shortly after nine, the murder must have happened significantly later.

As I said, I couldn't see how the time of death could possibly be shifted, on the evidence as it stood. However, while I am not a molecular biologist and do not even play one on TV, I do have a molecular biology lab two doors down from my office. And I am occasionally on the receiving end of highly vocal ire from the technicians there for daring to step into their "clean lab", because of the risk of contamination. We don't want you in here, you might shed skin cells! Go away! Please, take the pipette and don't give it back because we don't want it again if you've touched it!

So yes, it occurred to me that those suggesting the DNA results were the weaker side of the argument might well be right. It's still a bit of a shocker that a forensic lab could be so wrong, and a forensic scientist stand up and defend such bad procedure in court.

The danger of forensic scientists who work on police cases starting to see themselves as part of the prosecution team instead of impartial seekers after truth is well-recognised. Somebody needs to tell the Italian criminal justice system about this phenomenon.

Rolfe.

 

[Chris_Halkides]

contamination from amplified DNA

Thoughtful also translated a section that dealt with the need to run the reference samples after the evidence samples and the need to do LCN work in a separate facility. These are not new issues to readers of the first Knox thread. Mark Waterbury quoted the Crown’s guidelines with reference to having a separate facility with special precautions. Donald Riley’s excellent introductory article has two sections on contamination. This article alerted me to the problem of an amplified sample’s potentially contaminating an unamplified one, and I have quoted from it liberally on many occasions.
EDT
Dr. Riley's article discusses the problem of the PCR-amplified product of one reaction contaminating another sample that is yet to be amplified. He also draws an analogy between sterile technique and PCR (polymerase chain reaction) technique and notes its limitations.

 

[quadraginta]

Speaking of Casey Anthony.

Did anyone see yesterday's testimony of a traumatologist who explained how different people, especially at a young age (20-25), deal with grief, sorrow and other strong emotions?

Yep.

She would be a good witness for the defense in Amanda's trial. The woman said that there are hundreds of different reactions when a person is struck by a trauma, such as the loss of a daughter(in Anthony's case it's obviously a little bit different, since she killed her baby) or a friend, or a member of the family. And then she went on to explain that it's no wonder some people choose to laugh or act in an unusual way and some simply cry. All deal with the sorrow in their own way.

She'd be a good witness for nearly anybody ... and was. Or either not much good at all.

When questioned by Jose Baez, the defense attorney, her testimony in essence was that any type of reaction at all could be expressed by someone experiencing deep grief.

When cross-examined by the SA she testified with equal equanimity that the same could be true of someone experiencing deep guilt.

Taken as a whole her professional opinion appeared to be that anyone could express nearly anything in nearly any way at all.

It was yet another WTF moment in the trial, as in, "WTF is the point of this testimony?"

The prosecution's case in this trial would probably have be as strong if the defense had called fewer witnesses. I think 'Dr. Grief' might be an example. Not one of the best ones, since her testimony on cross wasn't outright detrimental to the defendant (as was that of some of the other defense witnesses), but I expect it left the jury wondering what the hell Baez was trying to do.

 

[Ampulla of Vater]

Some posters at PMF were making a big stink about the report making reference to "international standards," the implication being how dare they defer to these international standards when Italy is an advanced nation with its own justice system, etc., etc. This got me thinking.

First, I think it's clear from the conclusions that the indepenent experts looked at the overall picture, and were absolutely horrified at what happened, from evidence collection all the way through to testing. I think they thought to themselves that "people cannot be sent to jail in Italy based on work like this." And then they must have thought "Patrizia Stefanoni is one of our best scientists in this field--how can this have happened? . . ."

And they looked around, and they found that in reality, Italy doesn't have clear standards governing much of what was done in this case. And they asked "if this is happening here, in this high-profile case with a good scientist, what is going on in other cases? Are we routinely locking away people based on work like this? Momma mia."

But then they thought: "we are Italy's leading scientists in this field. We are La Sapienza. We are internationally known and respected. People will listen to us, and this case is a big stage. Let's do something about this."

So what we ended up with is a report that is half about this case, and half statement to the justice system. The part that is statement to the justice system cites extensively to international standards and says that they must be followed. The experts know that this report will be widely publicized and discussed in the forensics community in Italy, and they know that if the report is accepted by the court, then the standards and practices advocated by the report will become de facto standards in Italy.

These experts together have said to the Italian justice system "this new science is a valuable tool, but you must use it properly or you will destroy lives. Here is how we will use it." So in my view, this report may very well have a very powerful and important message that reaches well beyond the narrow boundaries of this case. And, taking a broader view, this is a very good thing for Italy.

And I sincerely hope this will be Amanda's and Rafaelle's legacy so they can live the rest of their lives knowing something positive came out of this entire fiasco. A protocol for the testing of DNA called the Knox-Sollecito standards maybe?