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

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LondonJohn said:
Yes, that's exactly what I took from that exchange as reported as well. It's not Italian standards/protocols per se that are the problem at all. It's the fact that Stefanoni manifestly didn't apply proper Italian (and, by extension, international) standards and protocols in her work.

By contrast, the Carabinieri scientists appear both to have understood and followed all the necessary standards and protocols. It's these standards and protocols that they are defending - not Stefanoni's incompetent and mendacious warping/ignorance of them.
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Yep, of course the RIS scientists are not going to say "Italian standards are rubbish", because they would be attacking their own work! The whole thrust of their carefully written report is to show by example that Italian standards for DNA testing are very good and in line with international standards. Nowhere do they directly attack Stefanoni, but it could be said their report indirectly attacks her work by defending the high standards used in Italian DNA testing - no wonder, since this is their livelihood. Barbie, of course, got the wrong end of the stick.
 
Letters...

Hi all,
it sounds like a good day in court for the defence!
I look forward to reading here about more of what transpired today...

Anyways, as I'm wide awake at 4:00am right now here in Southern California,
I was reading elsewhere and found this photo of Rudy Guede's newest hand written letter to the court:



Seeing Guede's handwritting reminded me of his last letter during the Appeals Trial, which allowed Amanda Knox and Raffaele Sollecito to go free.

You might remember this letter, Rudy Guede supposedly wrote it BUT didn't PM Mignini read it to the court, as Guede apparently couldn't read the words or something like that? Which many of us thought was because Guede did not write it.

It would be fun to compare the handwriting of these 2 hand written letters.
Does anyone gotta link to that Appeals Trial letter?
thanks, RW
 
RoseMontague said:
LOL. yes. She does not even mention it. Period. Too funny.
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She must be very confused. She thought the whole discussion today was going to be about whether Amanda's DNA got on the handle because she used it while cooking or during the murder. No wonder she's deleted that comment and replaced it with a report about Sollecito.
 
katy_did said:
To be fair, I would say that "at least two" implies "preferably more, but two at a minimum". IIRC the recommended standard for LCN is three, but because that's often not practical due to the material being very scarce, two tests are accepted instead.
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Because of the prevalence of drop outs and the difficulty in distinguishing sometimes whether some peaks are actual alleles or stutter/noise/drop-ins, when doing LT DNA analysis they usually repeat the test and check to see if they get all the same peaks in the same places. If there's some that don't show up they'll do a third and the ones that appear twice are considered legit, 'best two out of three.' If the first two show the same collection of alleles then there would be no point to doing the third test, they've already shown up twice.

I assume that's what they're getting at by 'at least two.' Sometimes three is necessary but a repeat of the same results with the second test precludes the necessity of doing the third.
 
RandyN said:
Actually neither do I but I still think it was stupid. Just as I think trying to get Kerchers permission to visit is stupid. I cant imagine either has a real desire to actually visit the grave of someone they knew for a few weeks. This could be just me though since I don't do graves...in fact I think they are a needless waste of valuable real estate. Which is why I have a directive...burn me up and flush if you cant think of a better idea...:-) If you want to remember me...go to the orchard I funded with the money saved on funeral expenses...I am still working on details of a beer tree...pick a beer and enjoy it and smile that you knew a crazy guy like me...a great guy who says stupid things all the time...but still a great guy.
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I have been thinking the same, since cremating my father when he was relatively young some time ago, he has been permanently located in the dodgy real estate between my ears, but cultural mores remain. Interesting that Amanda says she is an atheist, why do we know, and why should she be scrutinised?
 
Kaosium said:
Because of the prevalence of drop outs and the difficulty in distinguishing sometimes whether some peaks are actual alleles or stutter/noise/drop-ins, when doing LT DNA analysis they usually repeat the test and check to see if they get all the same peaks in the same places. If there's some that don't show up they'll do a third and the ones that appear twice are considered legit, 'best two out of three.' If the first two show the same collection of alleles then there would be no point to doing the third test, they've already shown up twice.

I assume that's what they're getting at by 'at least two.' Sometimes three is necessary but a repeat of the same results with the second test precludes the necessity of doing the third.
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Thanks. I think I was remembering this part from C & V:

Most scientists who work with LCN stress the need to perform 2-3 replications and state that an allele must be observed at least twice to be denominated as such (Taberlet P. et al., 1996, even invoke up to 7 replications to increase the reliability of allele denomination): allele redundancy in replicates is therefore the cornerstone of reliable LCN typing. [...]

In practice, it needs to be considered that performing more than 2-3 replications is often not possible; therefore most interpretation guidelines and degree of reliability assertions must be applied and declared based on the analysis of 2-3 replicates.
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ETA: A bit more here, obviously the source for C&V's statements:

Most practitioners of LCN typing advocate 2-3 replicate analyses and that an allele must be observed twice to be sufficient for recording it as an allele. Taberlet et al (34) advocated more (up to 7) replicates to increase the confidence of allele calls. Thus, redundancy of alleles in replicates is the basis for reliability in LCN typing. Obviously, the more replicates that show the same allele(s) will increase the confidence that the observation is less likely due to laboratory contamination. [...] However, there is a practical realization that more than 2-3 replicates may not be possible with a limited sample. Therefore, most interpretation guidelines and degree of confidence assessments must be predicated on 2-3 replicate analyses. Presumably, the more replicates that show the same alleles at a locus are more reliable than less redundancy.
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It sounds from this that basically the more tests the better, and if you get a result repeated three times then great, but two is the minimum. Based on this I'm not sure that doing a third test would be redundant though? (i.e. you don't bother with it if you already have 2 repeated results).
 
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LondonJohn said:
Yup :)




Could be close to game over for the knife.......
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katy_did said:
(snip)



And...game over for the knife.
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Let's hope so, more than two years ago with the release of the Conti-Vecchiotti Report I posted a picture of the Tiber to Pilot as I'd thought that ridiculous knife had finally been committed to it by the professors from Rome. However it appears a bedraggled bunny fished it out of there and brought it to Florence, so (hopefully) the final resting place of perhaps the most absurd 'murder knife' in modern criminal forensics will be at the bottom of the Arno instead.



​

That's a pretty river isn't it? Better looking than the Tiber it appears to me. If I was a kitchen knife pressed into service as a faux murder knife I'd be happy rusting away at the bottom of that river. :)
 
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LondonJohn said:
Hilariously (and rather pathetically), a certain pro-guilt commentator is trying to claim that the phrase "at least two" - as apparently spoken by the Carabinieri expert in response to how many duplicate low-template DNA tests are required for validation of the results - actually suggests three tests and really implies three :D :D

However, back in the normal, rational world, "at least two" means " a minimum of two", which means "two or more". Therefore it means that two would be sufficient, and so would three, four, five etc.

Some total loss of rational thinking ability among certain pro-guilt commentators, I think :p
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I have a question. Did Stefanoni ever do multiple amplifications/electropherograms of ANY samples?
 
Mary, Mary

“I never knew Rudy Guede and I barely knew Meredith. It does not make sense that I had any interest in taking part in the atrocious crime against a girl just 20 years old. This has been going forward for too many years. My life has been totally changed.”

:p
 
RoseMontague said:
The key question is how will the judge and jury interpret the new DNA test results? Much will hinge on the Nov. 6 arguments. As I have cautioned in the past, all reports previously released to Nov. 6 arguments should be considered incomplete, as it is the day of the hearing and the debate that commences before the judge and jury that really matters. Watch here for updates.
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RoseMontague said:
If you read Vogt's report, it is almost as if DNA was not even discussed.

http://thefreelancedesk.com/front_featured/amanda-knox-appeal-2/
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There won't be much time left to bug Machiavelli and Andrea Vogt, so we have to get it in now....

One wonders how Machiavelli will assemble what promises to be a last round of dietrology in defence of Mignini and Vogt....

To recap, Machiavelli has started throwing everyone else under buses... Barbie Nadeau is an "approximate reporter", John Kercher is just "mistaken, and the only reason we're talking about Mignini's original *****ic R*t* theory anyway is because of one of the early, procedural judges...

What I want to know is this.... the ISC set out more stuff than the (now non-existant) DNA on the knife, Aviello, and (what was the first thing that landed with a thud for the prosecution?)......

.... so why are they already talking about closing this thing up, with two more hearing days, summations in January, then a verdict?

I mean, if this is it - there's been nothing at all positive for the new Florentine prosecution, at all!

Hell, even Andrea has stopped talking about the DNA - and presumably the knife, altogether!

Where's Machiavelli when we need him to explain why any of this is vindication for Mr. Mignini; but why is this (seemingly) now winding up, what with all the uproar last March when the ISC thought Galati had just written a new book for the New Testament?
 
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katy_did said:
She must be very confused. She thought the whole discussion today was going to be about whether Amanda's DNA got on the handle because she used it while cooking or during the murder. No wonder she's deleted that comment and replaced it with a report about Sollecito.
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Andrea Vogt seems to be the last believer who is not completely nutso..... at least she (seems to be) discontinuing flogging dead horses.... and doing her journalistic equivalent of saying, "O Look, squirrel...."
 
From Vogt:

RIS REPORT

The RIS Wednesday deposited their forensic report on trace 36i, a spot of DNA identified (but not earlier tested) on the kitchen knife alleged to be the murder weapon. “Cento Percento” (100 percent) said Major Berti, discussing compatibility. The RIS found that the DNA was compatible with Amanda Knox, and excluded that it was that of Sollecito, Guede or Kercher. The RIS expert was asked only a few questions from attorneys and the judge. The judge asked why the RIS had done two amplications of the DNA and not 3 or 4. Major Berti described that two is considered the minimum number of amplifications necessary, according to today’s forensic standards, doing less (or more) might have diminished the reliability of the results. The judge also asked about the age of the equipment used. Berti responded that the forensic kit used this time has been commercialized since 2010 and available for use since 2011. At one point the judge stopped a line of questioning by Knox’s Rome attorney Carlo Dalla Vedova, who was asking why the RIS described Knox’s DNA as “fluids” when a prior expert had said the trace did not come from blood. Nencini said: That question was not put to the RIS by this court, it was not their job to determine that. The other experts’ reports are in the case files for everyone to read, he noted, adding: “We cannot put words in the mouth of this expert that were said by another expert.”

Well it looks like no love lost between RIS and Steffy.
 
katy_did said:
Thanks. I think I was remembering this part from C & V:



ETA: A bit more here, obviously the source for C&V's statements:


It sounds from this that basically the more tests the better, and if you get a result repeated three times then great, but two is the minimum. Based on this I'm not sure that doing a third test would be redundant though? (i.e. you don't bother with it if you already have 2 repeated results).
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I agree that (generally) the more tests the better, though for those using the common 'consensus profiling method' two is all you need, so if you have the same alleles in the first two no matter what shows up in the third you've satisfied the conditions for that methodology.
 
A pro-guilt commentator demonstrates that he does not understand DNA testing science properly (or perhaps he DOES understand it, but is being deliberately misleading...):

For 36b the sample was not divided. The RIS is correct that having only run one undivided sample is less reliable but not in a meaningful way for 36b. The reason you divide the sample and do it twice is to ensure against stutters being interpreted as genuine alleles. If a peak is present on one but not the second then you shouldn't consider it in your analysis. This becomes significant when dealing with mixed samples and when dealing with partial profiles where you only have a few loci. It does not apply to the 36b where there is only Kercher's DNA and where you have a complete profile.
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The highlighted part is just plain wrong. It doesn't matter at all whether there's just one putative profile on the sample or several, or whether it's a partial or fuller match. The whole point is that the extreme amplification of low-template samples can easily result in noise and other artifacts rendering as false alleles in the amplified sample. This means that if you think you've got a match at a certain allele, you can't be at all sure whether the peak on your graph at that allele is genuinely from the DNA of the person being matched, or whether it's the product of noise/stutter/drop-in etc.

That's why it's mandatory to do a second test, including a full re-amplification of the original sample. If this second amplified sample also has a peak (or peaks) at the same places as the first, then it's likely (for evidential purposes) that this peak(s) is indeed from the DNA of the person being matched. If, however, matching peaks that are present in the first sample are not present in the second sample, then it's pretty likely that these peaks are the result of noise amplification rather than a genuine DNA match. It's at that point you do a third test, again amplifying from the original sample. If this also shows differing peaks, then you can conclude that you don't have a true match to the person being assessed - otherwise their DNA alleles would have constantly shown up as peaks on all three graphs.

Again, this is all totally irrespective of whether you're looking at a sample with multiple peaks (potentially corresponding to multiple people plus noise) or a sample with fewer peaks (potentially corresponding to just one person plus noise). Noise is noise. Two or more tests are required. End of story. End of 36B. End of knife.
 
LondonJohn said:
That's why it's mandatory to do a second test, including a full re-amplification of the original sample. If this second amplified sample also has a peak (or peaks) at the same places as the first, then it's likely (for evidential purposes) that this peak(s) is indeed from the DNA of the person being matched. If, however, matching peaks that are present in the first sample are not present in the second sample, then it's pretty likely that these peaks are the result of noise amplification rather than a genuine DNA match. It's at that point you do a third test, again amplifying from the original sample. If this also shows differing peaks, then you can conclude that you don't have a true match to the person being assessed - otherwise their DNA alleles would have constantly shown up as peaks on all three graphs.
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Hmmm, are you sure this is the sequence LJ? My assumption would be that they have to make a decision initially as to how the sample is going to be divided - into two or three (or more) separate parts, depending on how much material is available - and that they then analyze all the samples they have, comparing the results at the end of the process. Given the uncertainty of LCN in general, it seems odd that they would leave a third sample untested if it was available and just say "We have two, that'll do". But I'm just guessing here.
 
katy_did said:
Hmmm, are you sure this is the sequence LJ? My assumption would be that they have to make a decision initially as to how the sample is going to be divided - into two or three (or more) separate parts, depending on how much material is available - and that they then analyze all the samples they have, comparing the results at the end of the process. Given the uncertainty of LCN in general, it seems odd that they would leave a third sample untested if it was available and just say "We have two, that'll do". But I'm just guessing here.
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That's an interesting question, because of their limited sample they may have just decided to run the two tests and consider only alleles that showed up both times, because splitting it into another sample would have made each one of them significantly smaller--which also impacts the reliability of results.
 
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