Kaosium
Philosopher
- Joined
- Oct 12, 2010
- Messages
- 6,695
Let's stop here first, and answer this point alone to avoid too long posts.
Well, no, no no. I think you develop your own concept of “contamination issue”, and probably that's the problem.
It would be better instead to look at what Stefanoni says altogether; and it’s better to use the information for building arguments that make sense. Stefanoni says some other, very different things, where she explains how negative controls work, she explains that the possibility of contamination in reagents - whether you see it as "contamination" by a whole profile or instead by single drop-in allele - in negative controls, is something that can always happen. This kind of contamination happens, the possibility of contamination is something “normal”, therefore the negative controls are part of the work.
Let's quote Stefanoni (Oct. 4. 2008). Sorry, I must quote he testimony in Italian:
Here is that passage as rendered by google translate:
50
I do not agree ... the methodology, we negative controls we use in our laboratory practice but have a different meaning, for example, we use them in any stage of the process from the extraction of the biological sample to the analysis electrophoretic why? Because in that case we are interested in two things: one see the goodness of the execution by the operator on methods that prevent possible pollution and therefore a possible transfer of its DNA operator to find, because even this can inadvertently do, despite all precautions, and to this end, each operator is typed fact that you know its genetic profile so that if, as often happens, the genetic profiles of people are unknown to us, we can definitely rule out that the genetic profile of the unknown is not even a technical operator or another any person who is coming in contact with the sample. Then another control that we put as negative, which we call "white" is a control that is used to verify that practically, as it were, the reagents used - because you use chemicals at all stages of processing, of course, because it is a chemical process is the extraction that DNA analysis - Has not itself of accidental contamination due to previous sampling operations, for example of a rate, because the reagents are obviously not single-dose, reagents must be taken each time by the operator from a test tube, a sheath because you use in very small amount in the order of micro liter! are a millionth of a liter so a thing absolutely very small so that the tube is used several times, for which our negative control, for example in the amplification step, is to observe having put all chemical reagents except the DNA, we do not any kind of DNA, that the sample once analyzed gives no signal of DNA of course (...)
I do not agree ... the methodology, we negative controls we use in our laboratory practice but have a different meaning, for example, we use them in any stage of the process from the extraction of the biological sample to the analysis electrophoretic why? Because in that case we are interested in two things: one see the goodness of the execution by the operator on methods that prevent possible pollution and therefore a possible transfer of its DNA operator to find, because even this can inadvertently do, despite all precautions, and to this end, each operator is typed fact that you know its genetic profile so that if, as often happens, the genetic profiles of people are unknown to us, we can definitely rule out that the genetic profile of the unknown is not even a technical operator or another any person who is coming in contact with the sample. Then another control that we put as negative, which we call "white" is a control that is used to verify that practically, as it were, the reagents used - because you use chemicals at all stages of processing, of course, because it is a chemical process is the extraction that DNA analysis - Has not itself of accidental contamination due to previous sampling operations, for example of a rate, because the reagents are obviously not single-dose, reagents must be taken each time by the operator from a test tube, a sheath because you use in very small amount in the order of micro liter! are a millionth of a liter so a thing absolutely very small so that the tube is used several times, for which our negative control, for example in the amplification step, is to observe having put all chemical reagents except the DNA, we do not any kind of DNA, that the sample once analyzed gives no signal of DNA of course (...)
It has her saying the opposite of what you claim, she's agreeing with me (and everyone else) in saying that there should be no DNA in the negative control. This should be obvious to the most casual observer: if the negative control registers DNA then by definition there's lab contamination. It could have come from no where else, being as there's supposed to be strict controls and methods employed to ensure that none of the equipment or reagents being used have any DNA at all.
I think you're mistaking the fact that low level DNA ('stray alleles') can often be found in samples, the 'environmental contamination' which Dr Balding referred to, and while 'always' would be an exaggeration, 'most of the time' would not be inaccurate for samples taken from a typical crime scene. If you read through the Ct column for these five charts you'll see that most all of the samples have a number below 50 in the Ct column, meaning human DNA was found at that cycle of the process, but that some did go 50 cycles without finding anything and that all the other negative controls did go 50 cycles without registering DNA. You'll also be able to see that this information isn't available for batch 2 (the one embedded in 'these' above) and almost 90% of those profiles were withheld to this day, nor is there quantification data (the 'Ct column') for that batch, which is the one where the knife blade was processed.
That's because it's just lab contamination, there was never any DNA of Meredith Kercher on that knife, it was an empty sample which showed the background DNA of Meredith Kercher due to the fact that lab had recently amplified and processed dozens of samples with her DNA present and her methods to control contamination weren't up to snuff for LT/LCN DNA.
I don’t know what “contamination issue” would mean according to you (and I don’t think the defence lawyer has a precise, technical meaning in mind neither), but what I understand from Stefanoni’s explanation, is two things: first, that the contamination of a testing tube with an extra-profile (from a technician for example) or with the drop-in from an “aliquota” (a modicum, a small fraction) of the reagent that was used in the previous test with the same test tube, is to be considered relatively “normal” possibility (not something that you don’t meet for seven years). Second, as an implication of this, the meaning I understand she gives to a concept like “contamination issue”, is that you can deduce from what she explain, to say a DNA finding in the laboratory was due to “laboratory contamination” (there is an issue) is something that does not equate to mere “presence of an allele peak in a negative control”. You can well infer from what she says that, in order to say “this profile was contamination”, you need to have in your negative control something that yields a positive result that is significant, and possibly about the profile itself; it means that the profile extracted from the sample analysis (or most of it) is found in the negative control as well, so that you may conclude: the DNA did not come from the sample, it is found everywhere in controls so the reason must have been the reagent that was not “clean”.
I provided a link regarding contamination in LT/LCN samples in my last post and did so again above. If your negative control is contaminated as you detail above then the proper response is to throw all of that out and clean your lab and materials, not withhold 90% of the results from that batch as well as the negative controls and then produce that lab contamination as 'evidence' and dare the defense to disprove it when you know they can't because all the evidence necessary to do that has been withheld as well.
Cough up the EDFs and we'll talk.
I don’t think anything like that comes out anywhere in the DNA findings.
I also know that prof. Novelli testified that he analyzed a sequence of 105 tests carried on within a week with the machine that tested the knife, and he found no trace contamination. I also know that nobody, either Vecchiotti or the defences could disprove or dispute Novelli’s statement.
How do you know this? What exactly did he say and where did he say it?
So, what I see is that you are making up technical meanings, creating conditions, which in reality they do not belong to the true technical meaning. You say "in a negative control and there should be no DNA in it at all", and this appears to be just plain false. You use this false premise in order to build a conspiracy theory (at the same time, you delete parts from the meaning of what Stefanoni said). Don’t misunderstand me: by putting this objection to you about the flawed premise, I am not just limiting the focus on considering what Stefanoni says, I am not picking up the corret premise from Stefanoni alone; you could equally deduce the same, more correct premise regarding drop-in alleles in negative controls, by picking quotes from Vecchiotti as she quotes Caragine et al (translation of C-V report, p. 94):
Purportedly C&V page 94 said:Moreover the experiments done have shown that, despite the scrupulous application of adequate protocols in order to minimize the possible sources of alleles drop-in within the laboratory, anyway we should always expect to observe a few extra alleles in negative controls.
You can see Vecchiotti quotes Caragine, saying - read carefully the wording - one should always expect to find a few extra alleles in negative controls.
If you have DNA in your negative controls then you have contamination in your lab. I was unable to find your quote in the C&V translation that I use which doesn't have page numbers. I went to where I know they quoted Caragine and I didn't find it there. Could you post a link to that translation? That string only returns your post for that exact wording with a google search and considering how it is phrased I suspect a mistranslation.
Always. This as for Caragine and Vecchiotti seems to agree.
I doubt it, not for the negative controls at least. Those should be completely free of DNA, otherwise it was introduced in the lab itself and shows that there's contamination.
Vecchiotti also pointed out that currently no protocols have been developed in order to how to "count" the drop in alleles to the date in order to assess the quality of negative controls (p. 90):
So your first assumption, that "there should be no of DNA trace at all", not even a single drop-in allele in a negative control (I believe actually B11 is a negative sample rather than a negative control but it makes no big difference), is simply false. The ngative controls should have a good quality, but you should always expect to find a few drop in alleles (this is what I can read in reports and testimonies).
Last thing, I point out that there are no DNA profiles that were "withheld". Not even one. All documentation about all results that was requested - and btw all of what was requested was requested anyway late according to what the procedure code provides for - was all given. What was not given is what had just never been requested, certainly not within the timings and fashion in which it was offered according to the procedure code.
Read through those links I provided and you'll see just how much information Stefanoni withheld. The EDFs would provide the missing data and show just how much contamination was in that lab, specifically regarding the knife blade and also the curiosities surrounding the processing of the bra clasp. If there was nothing there then there would have been no reason for Stefanoni to so selectively withhold it, even defying a judges order. Pretending the defense didn't ask when there's copious evidence of them demanding all the files necessary and specifically requesting the EDFs when they were not provided both to Massei and the independent experts (who also asked for them) is pathetic and evidence of a corrupt prosecution.
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