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

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Why the soft approach? I want a headline on the evening news saying "Amanda Knox filed suit tioday in U.S court against the American manufacturer and Italian police for negligence in generating bogus DNA results used to falsely convict her for the murder of her British roommate. Knox's suit seeks $100 million damages from the parties involved."

I know that most of the major organizations such as the ACLU, FFREF, and other similar organization which argue church and state issues will usually start with a sternly worded letter.

This is one of those "need to ask a lawyer" issues.
 
PCR amplification of DNA

I'm going to throw a monkey wrench into what Diocletus has said are problems with Batch 5. Diocletus says that there is 5 times as much DNA in these samples as there is supposed to be. That doesn't seem right to me. These are "positive samples of DNA" . correct? The are being put in a machine that is supposed to "grow" the DNA in each well by the temperature rising and falling cycles...correct? So wouldn't we expect the DNA to in fact do just that...increase in amount? If they were negative control samples, we would expect the DNA not to increase...but positive control samples should show growth?

Or do I just not understand this? Someone??
acbytesla,

In each PCR cycle, the maximum amount of growth in the amount of DNA is twofold. Once the cycling stops, there cannot be further growth. The other issue is the question of how much DNA one starts with. If all else is held equal, two reactions that start with the same amount of DNA will have approximately the same amount of DNA at the end of each cycle, although there is some experimental error. Does this help?
 
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I suppose another law suit could be aimed at the manufacturer of the read only device the Perugian Police used to clone hard drives in a forensically safe way. You know, the one that allowed the police to destroy one hard drive after another without apparently being aware they were doing so.

Cody
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I think both you and Strozzi have excellent ideas. The worst case scenario with either idea is the gross incompetence is brought into the light, if not outright corruption, fraud, and framing .
 
acbytesla,

In each PCR cycle, the maximum amount of growth in the amount of DNA is twofold. Once the cycling stops, there cannot be further growth. The other issue is the question of how much DNA one starts with. If all else is held equal, two reactions that start with the same amount of DNA will have approximately the same amount of DNA at the end of each cycle, although there is some experimental error. Does this help?

Do you know how many cycles were performed Chris? If there were 23 to start with, then one cycle would mean about 46 and two cycles would mean about 92. 3 cycles around 184 and so on. Am I on track? Or maybe doubling is not the right factor??
 
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I'm going to throw a monkey wrench into what Diocletus has said are problems with Batch 5. Diocletus says that there is 5 times as much DNA in these samples as there is supposed to be. That doesn't seem right to me. These are "positive samples of DNA" . correct? The are being put in a machine that is supposed to "grow" the DNA in each well by the temperature rising and falling cycles...correct? So wouldn't we expect the DNA to in fact do just that...increase in amount? If they were negative control samples, we would expect the DNA not to increase...but positive control samples should show growth?

Or do I just not understand this? Someone??


Did you not read my earlier post where I went to the trouble of explaining how this works in in quite simple terms? The Ct(s) being higher means that the DNA in the sample is lower, much lower in fact, than in a normal run. This is bad because the reference samples are not there just for a feel good confirmation that the machine is working. The machine uses those results to construct a calibration curve for each run. It took 4 extra cycles to amplify the references up to the threshold compared to the norm seen in prior runs. Since the DNA almost doubles every cycle, that means that all of the reference samples were diluted by a factor of 16 to 1. When this bogus calibration is applied to the Ct values of the unknown samples, they will be reported as containing 16 times as much DNA over what there really is.


(* doubling is a first order approximation and not strictly correct. the actual factor could be computed from the reference data but that involves math which most people would not understand. If anyone is really interested, they can do the calculation themselves.)
 
I know that most of the major organizations such as the ACLU, FFREF, and other similar organization which argue church and state issues will usually start with a sternly worded letter.

This is one of those "need to ask a lawyer" issues.

I agree. I think it is also one of those "need to ask a media advisor" issues and also one of those "need to ask an extradition expert" issues. I can't imagine either of the latter saying "No. Keep a low profile. Don't let it be the opening news story on the evening news. Write a letter instead."
 
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Did you not read my earlier post where I went to the trouble of explaining how this works in in quite simple terms? The Ct(s) being higher means that the DNA in the sample is lower, much lower in fact, than in a normal run. This is bad because the reference samples are not there just for a feel good confirmation that the machine is working. The machine uses those results to construct a calibration curve for each run. It took 4 extra cycles to amplify the references up to the threshold compared to the norm seen in prior runs. Since the DNA almost doubles every cycle, that means that all of the reference samples were diluted by a factor of 16 to 1. When this bogus calibration is applied to the Ct values of the unknown samples, they will be reported as containing 16 times as much DNA over what there really is.


(* doubling is a first order approximation and not strictly correct. the actual factor could be computed from the reference data but that involves math which most people would not understand. If anyone is really interested, they can do the calculation themselves.)

I must have missed it Dan. Thanks for this clarification. My apologies, I'm still trying to get a handle on this. So? What did Stefanoni say the quantification was and in your opinion, what was it actually?
 
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Did you not read my earlier post where I went to the trouble of explaining how this works in in quite simple terms? The Ct(s) being higher means that the DNA in the sample is lower, much lower in fact, than in a normal run. This is bad because the reference samples are not there just for a feel good confirmation that the machine is working. The machine uses those results to construct a calibration curve for each run. It took 4 extra cycles to amplify the references up to the threshold compared to the norm seen in prior runs. Since the DNA almost doubles every cycle, that means that all of the reference samples were diluted by a factor of 16 to 1. When this bogus calibration is applied to the Ct values of the unknown samples, they will be reported as containing 16 times as much DNA over what there really is.


(* doubling is a first order approximation and not strictly correct. the actual factor could be computed from the reference data but that involves math which most people would not understand. If anyone is really interested, they can do the calculation themselves.)

Great explanation, Dan O. And I contend that the machine software should identify/flag anything like this and that the printed data should alert to it and warn that something atypical or abnormal is occurring. A red warning message needs to be included in the data field of any printed result.

I see it as a product design defect when something that can be misconstrued by the machine operator or data analyst is allowed to occur without a warning message hightlighting it.

The manufacturer knows his device is being used by police labs to prepare evidence to send people to prison. There should be no design leeway for anything untoward to occur.
 
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I agree. I think it is also one of those "need to ask a media advisor" issues and also one of those "need to ask an extradition expert" issues. I can't imagine either of the latter saying "No. Keep a low profile. Don't let it be the opening news story on the evening news. Write a letter instead."

They might advise abuse of process though (as a collateral attack on the Italian proceedings).
 
Great explanation, Dan O. And I contend that the machine software should identify/flag anything like this and that the printed data should alert to it and warn that something atypical or abnormal is occurring. A red warning message needs to be included in the data field of any printed result.

I see it as a product design defect when something that can be misconstrued by the machine operator or data analyst is allowed to occur without a warning message hightlighting it.

The manufacturer knows his device is being used by police labs to prepare evidence to send people to prison. There should be no design leeway for anything untoward to occur.
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Since the lab stopped using the ABI 7700 after Batch 5, I wonder if it was sent to the manufacturer or one of their representatives for repair and/or calibration? That information should be available from the manufacturer, I would think.

Cody
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Since the lab stopped using the ABI 7700 after Batch 5, I wonder if it was sent to the manufacturer or one of their representatives for repair and/or calibration? That information should be available from the manufacturer, I would think.

Cody
.

Maybe Stefanoni sent it for cleaning. :p
 
I'm going to throw a monkey wrench into what Diocletus has said are problems with Batch 5. Diocletus says that there is 5 times as much DNA in these samples as there is supposed to be. That doesn't seem right to me. These are "positive samples of DNA" . correct? The are being put in a machine that is supposed to "grow" the DNA in each well by the temperature rising and falling cycles...correct? So wouldn't we expect the DNA to in fact do just that...increase in amount? If they were negative control samples, we would expect the DNA not to increase...but positive control samples should show growth?

Or do I just not understand this? Someone??

This is where I am with this.... given that when it comes to DNA and subsequent forensic analysis I am a simpleton.

I've also discovered that I share a question with The Machine/Harry Rag, you know Harry Rag, he's the guy who for 6 years has carpet bombed every-and-sundry comments' section of every on-line newspiece and Amazon book reviews with lurid tales of FOA PR Supertankers, mixed blood "in abundance" at the cottage, etc., etc.

Harry Rag/The Machine leads the leagues as a hater - and yet strangely he posed a question that (when separated from his obsessive hatred) deserves to be asked.

Why is this surfacing now, if this is DNA-forensics that has been available to folks since the git-go?

Was this part of the copious number of defence requests for testing that kept getting shot down by various judges? Judge Nencini warned-off one of Amanda's lawyers from pursuing a line of questioning about the interrogation, because it bordered on accusing the interrogators of wrongdoing, and the Public Minister (the prosecutor) controlled the keys to charging someone (even defence lawyers) with a crime....

Is this what's happened with the DNA stuff? Is Stefanoni a criminal herself, or just incompetent? Or both?

What I've learned from my own 2 1/2 years reading around the edges of this is that Italian judges don't like (or accept into evidence) the fact that the investigators themselves may be the criminals.

And the following is one thing I found that shows this - it's from the Massei motivations report, about why (even if they'd actually done an audit of the DNA testing machine) why Massei would believe Stefanoni.....

Massei p 298 said:
"Nor, as has already been said, is it possible to hypothesise a contamination in the laboratory since, as was declared by Dr. Stefanoni, during the course of all the analyses, no anomaly occurred, and the fact that all due controls, precautions and procedures of good laboratory practice were complied with necessarily leads us to rule out the possibility of such contamination in the laboratory."​

So what Judge Massei wrote back in 2010 is that there was no contamination or misuse of equipment in Stefanoni's lab. Why? Because Stefanoni told him so.
Yet some people are saying that anomalies DID occur.

So perhaps a partial answer to my own (and The Machine/Harry Rag's) question is..... they DID ask for some sort of audit, and Massei denied it.

What remains of this denial is this notation in Massei's report that he saw no reason to continue in court with such pesky requests from the defence which impugned the professionalism of Stefanoni. I say "what remains" is because if it had not been challenged, why did Massei need to specifically say be believed Stefanoni, if no one was asking the question about machine/labratory-contamination?

Why give an apology for something, if no one was complaining?

What I fear will come up as Cassazione is set to declare two innocent people "murderers" is that Cassazione sees it as more important to keep the status quo of its own hopelessly broken system, rather than free one of its own citizens and declare innocent a woman from Seattle....

So maybe, I don't go fully with The Machine/Harry Rag, which is a little bit of a relief, believe you me.
 
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Just noticed this on IIP and thought it deserved to be ported over here.

Edward McCall's fake wiki is either:

1) not up to date or
2) telling lies​

in relation to the climb in though Filomena's window. Key to the prosecution claim of a "staged break-in" is the claim that it was impossible for Rudy (or anyone else) to seek entry through that window.

This is the way Edward McCall's fake wiki puts it.... "An ad hoc attempt to determine if the entry was possible was made by a member of the defense team who was a couple of inches taller than Rudy: he was able to get his hands on the window ledge but did not get any further, nor gain entry through the window.

To date, there is no recorded instance of anyone successfully entering the house through that window."


A while ago, Channel 5 in England showed this demonstration. You judge for yourself.


Note bars on window that were not there in 2007.... I wonder why they thought to put bars on THAT window!
 
If the window were locked, how could the lawyer enter?

IIUC when the lawyer did his climbing demonstration, the window was locked. The fake wiki is playing very fast and very loose with the facts, but it is cleverly worded.
 
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Ok, one last one....

Here is BBC4 interviewing Giancarol Costagliola (prosecutor) as to why the defence request to test the presumed semen stain was declined.

"Because if it pointed to someone unknown to us, it would have led us down the wrong path of investigation. Meredith Kercher was known to have an active sex life."


Strangely, the text of this piece (there is BBC audio as well), suggests that this issue is one of the points of "separation" between Knox and Sollecito!!!

The BBC piece wrongly states that Knox "waited 14 days" to retract the Lumumba "confessions", and sees this as somehow incriminatory.... but the separation between co-accused over the stain....

It starts out with a strawman argument....

Why is Knox dithering on the semen stain tests?

Amanda Knox defence relies upon the single attacker theory. On twitter Knox supporters claim any semen stain tests are futile because they must be from Rudy Guede (not very bright the average Knox supporter).

On the one hand, Knox supporters want tests but only to the extent that they prove their single attacker theory was correct all along. . Sellecito wants the tests to find the second killer (this makes more sense) for some reason all sides fear tests… the million dollar question is why?

So... here we have a defence request to test the stain denied, and this piece says ALL sides fear its testing?
 
Remember how the cops went to get the bra clasp as soon as they learned that the Sollecitos had rubbished the shoe prints?

Check this out: http://murderofmeredithkercher.com/batch-5-bra-clasp-contamination-undocumented-re-run-tampering/

Wow. Just wow.

Not only did the Polizia Scientifica fail to find any evidence of Raffaele and Amanda on their first (and only objective) forensic analysis done directly after the murder, they found nothing initially on their second trip out six weeks later. Then they did another run and 'found' what they needed and then withheld half the results (I count 16 I may have missed one) that definitely showed DNA.

There's no excuse whatsoever for not revealing the EDFs, even more so now. Those sixteen or so withheld results from plate 410 which definitely show DNA are the smoking gun to show contamination or fraud. They either show DNA from any number of people not involved in the murder but who were at the cottage before and after the discovery, (just like Raffaele was) or they're Rudy's but found somewhere inconvenient to the prosecution case. In either instance they're evidence of withholding exculpatory evidence and/or a more proactive form of fraud.

I can think of an innocent explanation for some of those other oddities suggested by that page, but there is not one possible for withholding sixteen or so positive hits and making the claims the prosecution did regarding the bra clasp and knife in this case.

I presume we have you to thank for this discovery, at least in part? Major kudos to you. I recall a (relatively) recent extradition case the US was involved in where the requested nation demanded to see some files of a prosecutor interview, the US demurred, probably because the contents of it would destroy the case for extradition which was subsequently denied. This may very well be the equivalent, evidence withheld by the requesting nation which would destroy their case and can never be revealed because it would prove the pandemic fraud on the part of the prosecution suggested by those results.

As a result we will never see the EDFs from this case, however eventually it will dawn on people that without them being available (in any case) the 'science' of forensic DNA analysis amounts to little more than allowing a police lab tech to scribble 'guilty' on piece of paper with crayon.
 
I really want to read an expert weigh in about Diocletus's discovery. I think his work has been very impressive. Maybe it is just my nature to believe that things that are too good to be true usually are makes me a bit skeptical.

Instead of just jumping on the bandwagon that this is the smoking gun, I'd much rather see us try and shoot holes in this discovery and then if it comes through unscathed, we know we have a winner.

Where is Grinder when we need him? LOL...

Dan explained to me that this is evidence that there was 16 times more DNA than there should have been . I am struggling to understand that. I find the second run of the bra clasp to be even more suspicious than this, but I also think it is the kind of thing where Stefanoni would provide an answer that an Italian judge would find plausible.

C'mon all you skeptics lets try and shoot holes in this...and then if we can't someone (Diocletus...hint hint) needs to prepare an article that could be peer reviewed by forensic scientists and for the public.
 
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This is where I am with this.... given that when it comes to DNA and subsequent forensic analysis I am a simpleton.

I've also discovered that I share a question with The Machine/Harry Rag, you know Harry Rag, he's the guy who for 6 years has carpet bombed every-and-sundry comments' section of every on-line newspiece and Amazon book reviews with lurid tales of FOA PR Supertankers, mixed blood "in abundance" at the cottage, etc., etc.

Harry Rag/The Machine leads the leagues as a hater - and yet strangely he posed a question that (when separated from his obsessive hatred) deserves to be asked.

Why is this surfacing now, if this is DNA-forensics that has been available to folks since the git-go?
This too is my question, Bill. I feel like Diocletus is me with the cell phone evidence. I went after that like a pit bull terrier because I was thoroughly convinced that the 10:13 call absolutely positively could not have been made from within the cottage. And after doing all my research I could only say that it very probably wasn't made from the cottage, not that it was as definitive as I earlier thought.

Has he jumped to a conclusion that is something that he just misunderstands as proof and excitedly sharing that with us? (nothing wrong with that)

There is nothing more I want then solid indisputable proof of contamination and or corruption...since I'm convinced that either or both exists. But I don't want to make it up..just because that fits my belief.
 
I would argue that there is some level of corruption but just how deep does it go is the question. Is it widespread or it is just a few examples of dishonesty and nobody willing to turn the boat around.
 
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