Continuation Part Eight: Discussion of the Amanda Knox/Raffaele Sollecito case

[Samson]

A young woman's view

Over the course of the past school term I decided to reread the Harry Potter series. What struck me most was how the level of violence and torture, largely against children, ratchets up as the series approaches its conclusion. People will always do nasty things to others, and I'm not holding these books, or any others up as inspirational reference material for would-be sadists (wasn't A Clockwork Orange banned or requested as such in the UK?) but AK didn't just read the series, she appeared to have a fixation with them. For all we know, her sympathies may have lain entirely with Dumbledore's Army. But there is a central theme of genocide/ ethnic cleansing to the Deatheaters' thrust, and a sense, not mine alone, that there was a racial aspect to Meredith's murder. No, the manga didn't "make" RS do it, but those images of torture could have been in his mind as he looked at her body.

From pmf to reinvent the ordinary offspring of ordinary people into caricatures.

 

[js202]

A young woman's view

Over the course of the past school term I decided to reread the Harry Potter series. What struck me most was how the level of violence and torture, largely against children, ratchets up as the series approaches its conclusion. People will always do nasty things to others, and I'm not holding these books, or any others up as inspirational reference material for would-be sadists (wasn't A Clockwork Orange banned or requested as such in the UK?) but AK didn't just read the series, she appeared to have a fixation with them. For all we know, her sympathies may have lain entirely with Dumbledore's Army. But there is a central theme of genocide/ ethnic cleansing to the Deatheaters' thrust, and a sense, not mine alone, that there was a racial aspect to Meredith's murder. No, the manga didn't "make" RS do it, but those images of torture could have been in his mind as he looked at her body.

From pmf to reinvent the ordinary offspring of ordinary people into caricatures.

Truly an insane case of projection.

 

[Desert Fox]

A young woman's view

Over the course of the past school term I decided to reread the Harry Potter series. What struck me most was how the level of violence and torture, largely against children, ratchets up as the series approaches its conclusion. People will always do nasty things to others, and I'm not holding these books, or any others up as inspirational reference material for would-be sadists (wasn't A Clockwork Orange banned or requested as such in the UK?) but AK didn't just read the series, she appeared to have a fixation with them. For all we know, her sympathies may have lain entirely with Dumbledore's Army. But there is a central theme of genocide/ ethnic cleansing to the Deatheaters' thrust, and a sense, not mine alone, that there was a racial aspect to Meredith's murder. No, the manga didn't "make" RS do it, but those images of torture could have been in his mind as he looked at her body.

From pmf to reinvent the ordinary offspring of ordinary people into caricatures.

This whole thing is strange.
I am curious why somebody who is racist would want to go to Italy where a great many people are "Dusky." We all likely have to fight with racism and I have my own struggles.
My parents though were racist, at least my mother was. Amanda was raised in almost the most liberal place in the country with quite liberal parents.
Almost all fiction has elements of stuff you just simply would not want to do in real life.

I get a feeling the young women you quoted does not see herself as a geek and is in effect has a hatred of geeks.

 

[Diocletus]

I love how Doctor Stefanoni kept retesting the knife
[qimg]http://imagizer.imageshack.us/v2/xq90/13/vcdb.jpg[/qimg]
until she got the desired results,
don't you?

Was this the only item she kept re-testing and re-testing?

Why didn't she do so with that apparent semen stain?
Or those 2 blonde hairs found? Or underneath Meredith's fingernails?

Link:
http://www.injusticeinperugia.org/TheKnife.html

Those "too low" entries refer to the results of quantification via Qubit Flourometer for a series of different samples. Many of them returned the same result: "too low."

Quantification is important for a couple of reasons: 1) to make sure that you are putting the right amount of DNA into the amplification reaction, and 2) to tell you when you are working with a small amount of DNA that requires special handling, in particular, multiple amplifications.

The problem with the Qubit Flourometer is that given the configuration that Stefanoni was using (i.e., diluting the template by 200:1), it was not sufficiently sensitive and virtually useless for either of these purposes. Hence, all of the "too low" results. In effect, 36b and a number of other items effectively were never quantified.

Had Stefanoni employed proper quantification and other lab practices, then she would have found that 36b was of such slight quantity, that special contamination precautions and multiple amplifications were required in order to derive a reliable piece of evidence (i.e., like the Carabinieri did when they tested 36i). She didn't do any of the right things.

In terms of "cranking up" the machine, what she might have done is raise the number of amplification cycles that she used (e.g., from 28 to 31 or even 34), which would be an LCN methodology showing a need for multiple amplifications, but we have no evidence either way on this because she didn't produce her amplification records.

I would be interested to know whether there has ever been a case where an LCN sample has been used to convict in a situation where (i) tissue analysis was negative and a demonstrably contaminated lab performed no quantification, there was no repeat amplification, and the lab is not set up or certified for LCN analysis, (ii) the lab report contains material errors of fact and the lab technician's authenticating testimony was proved false, (iii) there was virtually no discovery in the case, such that almost all protocols, contamination logs and underlying data are unknown to the defendants, (iv) the courts placed the burden on the defendants to prove contamination notwithstanding the defendants' successful proof of (i)-(iii), above.

 

[Bill Williams]

I think we need to see the complete document. It's not my understanding that she kept re-testing the knife until she got the desired result. This is the same as the 'cranking up' point. Her procedures, insofar as recorded, are described in Conti-Vechiotti and did not include repeated testing of the same samples. The thing about the 'too low' results is that she chose to ignore them, relying on the same mystical intuition that inspired the selection of the knife in the first place.

This mystical intuition is the coin of the realm in this case.

Nencini agrees with Conti-Vecchiotti (!) that there are four samples of Y-genetic "somethings" on the bra-clasp other than Meredith's samples. Put aside the two alleged female Y-samples..... Nencini uses mystical intuition to make a "judicial fact" that Y-sample #2 is Meredith's boyfriend's. (Of course guilters will refute this by supplying the testing on that sample which proves it was Meredtih's boyfriend's, won't they! Actually they won't, because like the bleach receipt, there was no testing. Nencini just makes it up.)

Massei in 2010 writes that there must have been a clean-up - in the hall space between Meredith's room and the bathroom - or else he's confounded as to how the bathmat foot-track got there. There's no evidence of a clean-up (no swirls, no luminol hits on bleach, etc.) so this must be mystical intuition.

A Roman investigator solves this crime on mystical intuition before the "evidence" comes it - eating a pizza, swiveling hips and saying "Oooopla", and crying at the wrong times.

Postal Police Battistelli uses a better form of intuition when he looks into Filomena's room and says, "this is no burglary....", because whatever Rudy intended in climbing in through her window to gain access to the cottage, got sidetracked once Meredith (tragically) came home at the wrong time.

However, there was the mystical intuition that focussed solely on a keyholder as a perp, and completely abandoning the break-in as doable.... mainly because old, fat investigators couldn't themselves have done it...

Where do I get this mystical intuition? I'm off to Vegas next week!

 

[Kestrel]

I get a feeling the young women you quoted does not see herself as a geek and is in effect has a hatred of geeks.

There are some fundamentalist Christian groups that see the Harry Potter books as an evil influence. Harry Potter not only uses witchcraft, he also violates rules and defies authority figures. That he does so to protect his friends doesn't seem to matter.

I worry far more about people getting bad ideas from reading the Bible.

 

[Chris_Halkides]

some problems with the bra clasp profile

By contrast, the issue with the bra clasp in the Kercher case involves tiny (low template) amounts of DNA, where investigators were demonstrably contaminating the crime scene, where the bra clasp was demonstrably moved around repeatedly and mixed in with a jumble of debris, and where the manner in which the clasp was finally collected was demonstrably improper and pro-contamination (dirty gloves, inexplicably passing the clasp round the group hand-to-hand then placing it back on the floor). And of course the other difference is that the defendant in question here (Sollecito) had a totally valid reason for his DNA to have been in the cottage (though not of course directly upon the bra clasp), and would almost certainly have deposited small amounts of his DNA on Kercher's bedroom door and its handle on the morning of 2nd November.

I agree. The PG commenters typically focus on gap of about 46 days, while ignoring the lack of a sealed crime scene and the other problems you list. In addition, and perhaps most importantly, they have no good explanation for the other DNA found on the clasp. Unless one believes that 2-4 additional men took part in the assault, the presence of these donors greatly weakens the probative value of the clasp even on its own.

 

[Desert Fox]

There are some fundamentalist Christian groups that see the Harry Potter books as an evil influence. Harry Potter not only uses witchcraft, he also violates rules and defies authority figures. That he does so to protect his friends doesn't seem to matter.

I worry far more about people getting bad ideas from reading the Bible.

We both agree on that. I don't know what Raff is but I know that Amanda, at least as of the time of writing her book, she is a non believer. Many religious try to say that non believers have no morals.

 

[js202]

Those "too low" entries refer to the results of quantification via Qubit Flourometer for a series of different samples. Many of them returned the same result: "too low."

Quantification is important for a couple of reasons: 1) to make sure that you are putting the right amount of DNA into the amplification reaction, and 2) to tell you when you are working with a small amount of DNA that requires special handling, in particular, multiple amplifications.

The problem with the Qubit Flourometer is that given the configuration that Stefanoni was using (i.e., diluting the template by 200:1), it was not sufficiently sensitive and virtually useless for either of these purposes. Hence, all of the "too low" results. In effect, 36b and a number of other items effectively were never quantified.

Had Stefanoni employed proper quantification and other lab practices, then she would have found that 36b was of such slight quantity, that special contamination precautions and multiple amplifications were required in order to derive a reliable piece of evidence (i.e., like the Carabinieri did when they tested 36i). She didn't do any of the right things.

In terms of "cranking up" the machine, what she might have done is raise the number of amplification cycles that she used (e.g., from 28 to 31 or even 34), which would be an LCN methodology showing a need for multiple amplifications, but we have no evidence either way on this because she didn't produce her amplification records.

I would be interested to know whether there has ever been a case where an LCN sample has been used to convict in a situation where (i) tissue analysis was negative and a demonstrably contaminated lab performed no quantification, there was no repeat amplification, and the lab is not set up or certified for LCN analysis, (ii) the lab report contains material errors of fact and the lab technician's authenticating testimony was proved false, (iii) there was virtually no discovery in the case, such that almost all protocols, contamination logs and underlying data are unknown to the defendants, (iv) the courts placed the burden on the defendants to prove contamination notwithstanding the defendants' successful proof of (i)-(iii), above.

Lucidly and cogently argued and expressed. Maybe it's because I've now done something approaching adequate homework on this material, but I fairly effortlessly followed this on the first pass.

 

[acbytesla]

There are some fundamentalist Christian groups that see the Harry Potter books as an evil influence. Harry Potter not only uses witchcraft, he also violates rules and defies authority figures. That he does so to protect his friends doesn't seem to matter.

I worry far more about people getting bad ideas from reading the Bible.

Harry Potter, the FreeMasons, Wiccan, VooDoo. You have to keep in mind that Christianity and it's different sects are like most religions that basically insist that their God is the only true God and belief in anything else not only is wrong but a perversion led by the devil. "Infidels" for example Muslims would say. Look back through Christian history and watch the fact that Christians did the same thing to non-believers and worshipers of other religions as was done to them. In about a 50 year span in Italy, one could be executed for being a Christian to being executed for not being a Christian. Catholics burned people at the stake for saying the Sun was the center of the Solar System or translating the bible into other languages. The Freemasons a civic group is demonized in Italy because they are not Catholic and therefore must be the work of the devil.. So they are devil worshippers...Same for Wiccans and African Voodoo.

 

[acbytesla]

How does the Qubit work in comparison to the Real Time machine. I thought the default with the Real Time is 50 cycles and it stops for each well when it shows a DNA result above the background noise or 50. So how does the Qubit work?

 

[Strozzi]

There are some fundamentalist Christian groups that see the Harry Potter books as an evil influence. Harry Potter not only uses witchcraft, he also violates rules and defies authority figures. That he does so to protect his friends doesn't seem to matter.

I worry far more about people getting bad ideas from reading the Bible.

How are things in Iraq between the Sunni and Shia sects of Islam? Or between Mignini's authoritarian defenders of provincial Catholic life looking for satanic influence and the Masons?

 

[xinonix]

to understand this case one has to understand the Italian style of respect for authority.
Its like in The Godfather II. Vito Corleone's father insulted the Don. He got wacked. Vito's older brother could not keep his mouth shut, vowed to get revenge and then had the nerve to attend his dad's burial. He got shot. Vito snuck out of Sicily and went to America.
You may not feel respect for the Don, but you have to act like you respect him, or suffer the consequences. The Don has the authority to decide if you live or die.
You may not respect Prosecutor Mignini or the judge and jury he worked with, but if you were in Perugia you would have to act like you did. Amanda's Lawyer may think Mignini is a liar and he is crazy, but he won't say that in court because it would be disrespectful, and he has to maintain a relationship with the judges and juries of Perugia.
Amanda was given a break during her appeal, and she got to go home.
That was all the forgiveness they were gonna give her.
After that Amanda wrote a book that was full of insults about the Italian justice system.
We can do that in America as long as what we say is true. That is not allowed in Italy.

 

[Desert Fox]

to understand this case one has to understand the Italian style of respect for authority.
Its like in The Godfather II. Vito Corleone's father insulted the Don. He got wacked. Vito's older brother could not keep his mouth shut, vowed to get revenge and then had the nerve to attend his dad's burial. He got shot. Vito snuck out of Sicily and went to America.
You may not feel respect for the Don, but you have to act like you respect him, or suffer the consequences. The Don has the authority to decide if you live or die.
You may not respect Prosecutor Mignini or the judge and jury he worked with, but if you were in Perugia you would have to act like you did. Amanda's Lawyer may think Mignini is a liar and he is crazy, but he won't say that in court because it would be disrespectful, and he has to maintain a relationship with the judges and juries of Perugia.
Amanda was given a break during her appeal, and she got to go home.
That was all the forgiveness they were gonna give her.
After that Amanda wrote a book that was full of insults about the Italian justice system.
We can do that in America as long as what we say is true. That is not allowed in Italy.

As much as I may disagree with you on some, I think some of what you wrote here may very well hit close to home.

 

[acbytesla]

to understand this case one has to understand the Italian style of respect for authority.
Its like in The Godfather II. Vito Corleone's father insulted the Don. He got wacked. Vito's older brother could not keep his mouth shut, vowed to get revenge and then had the nerve to attend his dad's burial. He got shot. Vito snuck out of Sicily and went to America.
You may not feel respect for the Don, but you have to act like you respect him, or suffer the consequences. The Don has the authority to decide if you live or die.
You may not respect Prosecutor Mignini or the judge and jury he worked with, but if you were in Perugia you would have to act like you did. Amanda's Lawyer may think Mignini is a liar and he is crazy, but he won't say that in court because it would be disrespectful, and he has to maintain a relationship with the judges and juries of Perugia.
Amanda was given a break during her appeal, and she got to go home.
That was all the forgiveness they were gonna give her.
After that Amanda wrote a book that was full of insults about the Italian justice system.
We can do that in America as long as what we say is true. That is not allowed in Italy.

Shockingly Xionix, we agree on something. This is about what Americans would say is "questioning authority" part of the American DNA and for Italians, this "questioning" is in fact an insult to their very soul.

 

[Chris_Halkides]

DNA quantitation

How does the Qubit work in comparison to the Real Time machine. I thought the default with the Real Time is 50 cycles and it stops for each well when it shows a DNA result above the background noise or 50. So how does the Qubit work?

A common method to quantitate DNA is to use a fluorescent dye. I have not yet been able to find a good discussion pitched at the right level. This article is probably good, but it is behind a paywall: Curr Protoc Mol Biol. 2006 Nov;Appendix 3:Appendix 3D. doi: 10.1002/0471142727.mba03ds76.
Quantitation of DNA and RNA with absorption and fluorescence spectroscopy.
Gallagher SR1, Desjardins PR.

Abstract
Quantitation of nucleic acids is a fundamental tool in molecular biology that requires accuracy, reliability, and the use of increasingly smaller sample volumes. This unit describes the traditional absorbance measurement at 260 nm and three more sensitive fluorescence techniques, as well as three microvolume methods that use fiber optic technology in specialized cells or instrumentation. These procedures allow quantitation of DNA solutions ranging from 1 pg/l to 50 mg/ml.
PMID: 18265369 [PubMed - indexed for MEDLINE]

 

[Desert Fox]

to understand this case one has to understand the Italian style of respect for authority.
Its like in The Godfather II. Vito Corleone's father insulted the Don. He got wacked. Vito's older brother could not keep his mouth shut, vowed to get revenge and then had the nerve to attend his dad's burial. He got shot. Vito snuck out of Sicily and went to America.
You may not feel respect for the Don, but you have to act like you respect him, or suffer the consequences. The Don has the authority to decide if you live or die.
You may not respect Prosecutor Mignini or the judge and jury he worked with, but if you were in Perugia you would have to act like you did. Amanda's Lawyer may think Mignini is a liar and he is crazy, but he won't say that in court because it would be disrespectful, and he has to maintain a relationship with the judges and juries of Perugia.
Amanda was given a break during her appeal, and she got to go home.
That was all the forgiveness they were gonna give her.
After that Amanda wrote a book that was full of insults about the Italian justice system.
We can do that in America as long as what we say is true. That is not allowed in Italy.

As much as I may disagree with you on some, I think some of what you wrote here may very well hit close to home.

Shockingly Xionix, we agree on something. This is about what Americans would say is "questioning authority" part of the American DNA and for Italians, this "questioning" is in fact an insult to their very soul.

Assuming that this is on the right track, if it gets to the European Court of Appeals, Amanda better get a new lawyer. I don't think that the rest of Europe has this respect.

 

[acbytesla]

A common method to quantitate DNA is to use a fluorescent dye. I have not yet been able to find a good discussion pitched at the right level. This article is probably good, but it is behind a paywall: Curr Protoc Mol Biol. 2006 Nov;Appendix 3:Appendix 3D. doi: 10.1002/0471142727.mba03ds76.
Quantitation of DNA and RNA with absorption and fluorescence spectroscopy.
Gallagher SR1, Desjardins PR.

Abstract
Quantitation of nucleic acids is a fundamental tool in molecular biology that requires accuracy, reliability, and the use of increasingly smaller sample volumes. This unit describes the traditional absorbance measurement at 260 nm and three more sensitive fluorescence techniques, as well as three microvolume methods that use fiber optic technology in specialized cells or instrumentation. These procedures allow quantitation of DNA solutions ranging from 1 pg/l to 50 mg/ml.
PMID: 18265369 [PubMed - indexed for MEDLINE]

I thought a fluorescent die is used in both or maybe all quantitation methodologies? From my understanding the die is added to each well with the Real Time machine and it goes through a warm up cool down cycle (each cycled causing the DNA to go through mitosis and this increases the amount of protein in the well that would react to the fluorescent dye. And that the number of cycles would stop when the spectroscopy would determine that the protein level or DNA had increased to the point that fluorescent dye had created a visible reaction.

Of course I might be misunderstand this process..but that is how I understand the Real Time PCR quantitation machine operates. I guess I have to go back and read the Qubit Flourimeter's manual

 

[Kaosium]

I thought a fluorescent die is used in both or maybe all quantitation methodologies? From my understanding the die is added to each well with the Real Time machine and it goes through a warm up cool down cycle (each cycled causing the DNA to go through mitosis and this increases the amount of protein in the well that would react to the fluorescent dye. And that the number of cycles would stop when the spectroscopy would determine that the protein level or DNA had increased to the point that fluorescent dye had created a visible reaction.

Of course I might be misunderstand this process..but that is how I understand the Real Time PCR quantitation machine operates. I guess I have to go back and read the Qubit Flourimeter's manual

Essentially yes, the difference being with Real Time that the sample is amplified (making it easier to count) and then they figure backwards from there to determine how much they started with.

 

[Chris_Halkides]

the Qubit does not use DNA replication

acbytesla,

Both processes use fluorescent dyes, but they do so in very different ways. Quantitating DNA by the real-time PCR method uses the polymerase chain reaction (PCR) to increase the amount of DNA in a repetitive manner (mitosis is not an accurate description of the process). The Qubit fluorometer does not use PCR at all, but there is a dye that is specific for binding to double stranded DNA. If I have time this evening, I will come back to this subject.