The Trials of Amanda Knox and Raffaele Sollecito: Part 24

[Bill Williams]

Originally Posted by jsfisher

Thirty-six posts on religion have been excised from this thread. This thread is not about religion. We have an entire section of the forum set aside for the discussion of religion and related topics. Here is not that place. If you'd like to rekindle the discussion, feel free to do so, but in a proper thread of its on in the proper section of the forum. Once again, here is not that place.

Posted By:jsfisher

Thank God!

[Chris_Halkides]

DNA can be degraded by bleach (NaClO) or hydrogen peroxide, which is also an oxidant. I have discussed this study previously, but I will try to attach a file of an electropherogram that shows this effect. See how the peak heights slope downward from left to right, which is from shorter to longer DNA fragments. When DNA degradation is random, one expects this sort of downward slope. This is a figure from "An Investigation of the Effect of DNA Degradation and Inhibition on PCR Amplification of Single Source and Mixed Forensic Samples." The authors of this study are Bruce McCord, Kerry Opel, Maribel Funes, Silvia Zoppis, and Lee Meadows Jantz. I cannot detect such a slope in profile 36B (the knife profile). There is a great deal of variation in peak height in 36B, but this is to be expected when the amount of DNA is very small. Therefore I strongly doubt that 36B arose from a bloody knife cleaned with bleach or hydrogen peroxide.

[acbytesla]

Originally Posted by jsfisher

Thirty-six posts on religion have been excised from this thread. This thread is not about religion. We have an entire section of the forum set aside for the discussion of religion and related topics. Here is not that place. If you'd like to rekindle the discussion, feel free to do so, but in a proper thread of its on in the proper section of the forum. Once again, here is not that place.

Posted By:jsfisher

That's right people. Time to get back to the serious game of whack a mole.

[Stacyhs]

Originally Posted by Stacyhs

This is a lie. During a discussion of when the bra was removed, a newcomer was asking about the aspirated blood on Meredith's chest showing she was still alive after her bra had been cut off. The "woman" offered to send him a picture via PM showing the aspirated drops. Since you can only PM someone who "follows" you, she suggested he follow her, which he did. I have seen the picture and it did NOT show her "naked torso" as you claim, but a very heavily censored photo that had the body completely obscured by a blue photoshop paint job with the torso simply outlined. The only part of the body visible was a small square area that showed the aspirated blood droplets. That's it.

Nor did this "woman" write "'I'm sure Mez wouldn't mind'. In fact, this is her tweet to him:

"Follow me & I will message you. Is from Frank Sfarzo's old site. The pro-guilt peeps will be up in arms but hey! MK understands."

As for the mention of "brazilians", that is another lie as nothing about brazilians was ever sent to the Kerchers...at least by this "woman". Present evidence of this or stop telling these lies.Do you REALLY think this type of behavior is acceptable? Do you, Vixen, do you?

Vixen, I am still waiting for you to provide evidence that "the woman" sent anything regarding "Brazilians" to the Kerchers. Should I expect a long wait?

Since my comment with the photo of the claimed "naked torso" has been moved, I'll include it here.

[Numbers]

Originally Posted by Chris_Halkides

Or perhaps Hellman was simply outvoted by the lay judges and had to come up with a rationale. Who knows?

Originally Posted by Bill Williams

Then again even the 2015 ISC said that Knox wss interrogated in a context "institutionally immune" from pressure - so even the Marasca-Bruno panel seemed to back the notion that on some things a PM can do no wrong.

1. I strongly suspect the legal logic, if not the actual verdict, is controlled by the two professional judges and not by the lay judges.

2. See Sections 2.2 and 2.3 for the reasoning of the Chieffi CSC panel. This is from Section 2.3: "the conclusion that there was no evidence of a link between Lumumba and Meredith was disconnected from the information which emerged at trial, and in particular from information given by Lumumba himself, who claimed to have met Kercher, via Knox. The passage of the ruling in which it is argued that Knox must have been certain of Lumumba’s innocence, even if [herself] far from the crime scene (and thus unaware of the identity of the killers), on the assumption that there was no evidence of a connection between Lumumba and Meredith, is thus clearly illogical"

3. As Bill points out, the Marasca CSC panel went beyond merely stating that the calunnia conviction was res judicata, but emphasized that even if the ECHR found that Knox had been the victim of an unfair trial, "the prospect for a revision of the verdict and sentence" would not be open to her because "the libelous accusations which the aforementioned defendant made against Lumumba owing to the impact of the alleged coercive acts were also confirmed by her before a public prosecutor ... and were also confirmed in a memorandum ["memoriale"] bearing her signature ... and were even repeated ... before the GIP [judge of preliminary investigation] ...." (Section 2.2, p. 23 of the English translation).

The Italian judiciary was so eager to support the calunnia conviction that the Marasca CSC panel resorts to a clearly false statement; Knox made no such statement before the GIP.

There is no mention in any of the calunnia trials of Memoriale 2 or of the most damaging statements in Memoriale 1 about Knox's allegations of mistreatment by the police during the interrogation. This failure of the prosecutors and judges to inquire into her allegations of mistreatment* is, based on my reading of ECHR case law, a clear violation of the procedural branch of Convention Article 3.

*which she testified to in the Massei court trial and was in each of the appeals on the calunnia provisional convictions.

[Numbers]

Originally Posted by Chris_Halkides

DNA can be degraded by bleach (NaClO) or hydrogen peroxide, which is also an oxidant. I have discussed this study previously, but I will try to attach a file of an electropherogram that shows this effect. See how the peak heights slope downward from left to right, which is from shorter to longer DNA fragments. When DNA degradation is random, one expects this sort of downward slope. This is a figure from "An Investigation of the Effect of DNA Degradation and Inhibition on PCR Amplification of Single Source and Mixed Forensic Samples." The authors of this study are Bruce McCord, Kerry Opel, Maribel Funes, Silvia Zoppis, and Lee Meadows Jantz. I cannot detect such a slope in profile 36B (the knife profile). There is a great deal of variation in peak height in 36B, but this is to be expected when the amount of DNA is very small. Therefore I strongly doubt that 36B arose from a bloody knife cleaned with bleach or hydrogen peroxide.

PM: She said there is a complete profile, did I not hear correctly?
President: … it’s futile that…
GB: That’s not what she said.
President: … that we speak of contamination of Meredith.
PM: Did I not hear correctly? Is there a complete profile?
Vecchiotti: There is an unreliable profile. Absolutely not interpretable.
PM: Is it complete or is it not complete? How many loci are there?
Vecchiotti: Well it’s a complete profile, not reliable and not repeated…
PM: Is it incompatible with Meredith’s profile?
Vecchiotti: Well, according to the standards that are followed, it is necessary to examine all of the alleles that are above 50 RFU, there is not one or maybe there are two that are above 50 RFU, and I can show you and there is a complete imbalance of the alleles. If we then evaluate also those that are of height 15 and not 50 well then we can make it all come out but it absolutely should not be evaluated this way. This is what was done.

Source: http://www.amandaknoxcase.com/raffaeles-kitchen-knife/

[Stacyhs]

Originally Posted by Numbers

PM: She said there is a complete profile, did I not hear correctly?
President: … it’s futile that…
GB: That’s not what she said.
President: … that we speak of contamination of Meredith.
PM: Did I not hear correctly? Is there a complete profile?
Vecchiotti: There is an unreliable profile. Absolutely not interpretable
PM: Is it complete or is it not complete? How many loci are there?
Vecchiotti: Well it’s a complete profile, not reliable and not repeated…
PM: Is it incompatible with Meredith’s profile?
Vecchiotti: Well, according to the standards that are followed, it is necessary to examine all of the alleles that are above 50 RFU, there is not one or maybe there are two that are above 50 RFU, and I can show you and there is a complete imbalance of the alleles. If we then evaluate also those that are of height 15 and not 50 well then we can make it all come out but it absolutely should not be evaluated this way. This is what was done.

Source: http://www.amandaknoxcase.com/raffaeles-kitchen-knife/

It's only the highlighted parts that are usually quoted by the PGP. They just ignore the rest.

[Chris_Halkides]

Numbers,

The imbalance of peak heights of alleles is something that happens because of stochastic effects when dealing with very small amounts of DNA (link to Promega). Suppose that you only have (for example) five cells and for one allele all five are copied in the first round of PCR and for the other allele, four of the five cells are copied. This will lead to an imbalance of peak heights. The peak heights differences don't have any relationship of which I am aware, to the length of the DNA. "Advanced Topics in Forensic DNA Typing" by John Butler has a nice discussion of the stochastic threshold on pp. 93-96.

On the other hand any process that leads to random degradation is more likely to affect longer strands of DNA than shorter ones.* That is why degraded DNA gives electropherograms that slope down, going left to right. Jason Gilder's Ph.D. thesis (Chapter 3) is as good a discussion as I have seen, although he may have written a review article or chapter on the subject since then.

I agree that using a reasonable RFU cutoff, profile 36B would also be incomplete. If we do away with a cutoff, then there are still at least two problems. At one locus one of the alleles has almost completely dropped out (there is a tiny stub of a peak). There are also two extra peaks that are not in Meredith's profile that have a height of about 15 RFU. I am sorry but I have forgotten which locus this is. This information is probably posted in the very first thread.

*Strictly speaking, the DNA strand of one allele is very slightly longer than the other, and the peak associated with the shorter DNA should give a peak with greater height. However, the effect from one locus to the next should be easier to see than the effect between two alleles within the same locus.

[Numbers]

Originally Posted by Chris_Halkides

Numbers,

The imbalance of peak heights of alleles is something that happens because of stochastic effects when dealing with very small amounts of DNA (link to Promega). Suppose that you only have (for example) five cells and for one allele all five are copied in the first round of PCR and for the other allele, four of the five cells are copied. This will lead to an imbalance of peak heights. The peak heights differences don't have any relationship of which I am aware, to the length of the DNA. "Advanced Topics in Forensic DNA Typing" by John Butler has a nice discussion of the stochastic threshold on pp. 93-96.

On the other hand any process that leads to random degradation is more likely to affect longer strands of DNA than shorter ones.* That is why degraded DNA gives electropherograms that slope down, going left to right. Jason Gilder's Ph.D. thesis (Chapter 3) is as good a discussion as I have seen, although he may have written a review article or chapter on the subject since then.

I agree that using a reasonable RFU cutoff, profile 36B would also be incomplete. If we do away with a cutoff, then there are still at least two problems. At one locus one of the alleles has almost completely dropped out (there is a tiny stub of a peak). There are also two extra peaks that are not in Meredith's profile that have a height of about 15 RFU. I am sorry but I have forgotten which locus this is. This information is probably posted in the very first thread.

*Strictly speaking, the DNA strand of one allele is very slightly longer than the other, and the peak associated with the shorter DNA should give a peak with greater height. However, the effect from one locus to the next should be easier to see than the effect between two alleles within the same locus.

Thanks for providing this additional information.

Is it correct that a minimum profile height for validity of a peak, generally set at 50 RFU, is set to avoid mistaking or misinterpreting signals from low-level contaminant DNA or other "noise" (such as clumps of dye) as part of a valid DNA profile?

If one chooses, for the knife blade DNA, to set the DNA peak minimum valid height as 15 RFU (or less), and applies this (unvalidated) standard consistently, what interpretation must be given to the additional peaks in the profile?

Did Stefanoni discuss what minimum peak height she had adopted for her interpretation? Did she discuss the additional peaks and incorporate their presence in her explanation of how she assigned the knife blade DNA profile to Meredith Kercher? Did Stefanoni explain how she validated her methodology, including any standard she used for minimum peak height for a peak call?

[Numbers]

Originally Posted by Numbers

Thanks for providing this additional information.

Is it correct that a minimum profile height for validity of a peak, generally set at 50 RFU, is set to avoid mistaking or misinterpreting signals from low-level contaminant DNA or other "noise" (such as clumps of dye) as part of a valid DNA profile?

If one chooses, for the knife blade DNA, to set the DNA peak minimum valid height as 15 RFU, and applies this (unvalidated) standard consistently, what interpretation must be given to the additional peaks in the profile?

Did Stefanoni discuss what minimum peak height she had adopted for her interpretation? Did she discuss the additional peaks and incorporate their presence in her explanation of how she assigned the knife blade DNA profile to Meredith Kercher? Did Stefanoni explain how she validated her methodology, including any standard she used for minimum peak height for a peak call?

From https://www.promega.com/resources/pr...mounts-of-dna/
(the link provided by Chris)

Quote:

Stochastic (random) variation is a fundamental physical law of the PCR amplification process when examining low amounts of DNA. Stochastic effects are manifest as a fluctuation of results between replicate analyses. In other words, amplifying the same DNA extract twice can result in different alleles being detected at a locus.

Since stochastic effects cannot be avoided when testing small quantities of DNA, there are essentially two schools of thought on how to handle these types of samples: 1) stop testing or interpreting data before you go low enough to be in the stochastic realm, or 2) try to limit the impact of the stochastic variation by additional testing and careful interpretation guidelines based on validation studies. Those who advocate the second approach usually enhance their method sensitivity, such as increasing the number of PCR cycles, to get as much out of the limited sample as possible. The “enhanced interrogation” approach typically involves replicate testing and the development of consensus profiles.

[Numbers]

"In practice, the risk of contaminated-matching is much greater than matching a distant relative, such as contamination of a sample from nearby objects, or from left-over cells transferred from a prior test. The risk is greater for matching the most common person in the samples: Everything collected from, or in contact with, a victim is a major source of contamination for any other samples brought into a lab. For that reason, multiple control-samples are typically tested in order to ensure that they stayed clean, when prepared during the same period as the actual test samples. Unexpected matches (or variations) in several control-samples indicates a high probability of contamination for the actual test samples."

Source: https://en.wikipedia.org/wiki/DNA_profiling

Apparently Italian lab tech Stefanoni and some Italian judges aren't aware of the above information.

[Ergon]

Deleted post

[Ergon]

Originally Posted by Chris_Halkides

DNA can be degraded by bleach (NaClO) or hydrogen peroxide, which is also an oxidant. I have discussed this study previously, but I will try to attach a file of an electropherogram that shows this effect. See how the peak heights slope downward from left to right, which is from shorter to longer DNA fragments. When DNA degradation is random, one expects this sort of downward slope. This is a figure from "An Investigation of the Effect of DNA Degradation and Inhibition on PCR Amplification of Single Source and Mixed Forensic Samples." The authors of this are Bruce McCord, Kerry Opel, Maribel Funes, Silvia Zoppis, and Lee Meadows Jantz. I cannot detect such a slope in profile 36B (the knife profile). There is a great deal of variation in peak height in 36B, but this is to be expected when the amount of DNA is very small. Therefore I strongly doubt that 36B arose from a bloody knife cleaned with bleach or hydrogen peroxide.

Hi, Chris, the data from the study you cite shows on p.59 the sample was soaked for 18 hours in bleach. I doubt Knox soaked the knife for 18 hours. Perhaps that might explain why you did not observe the same downward slope?
Table 2: Percentage of Alleles recovered from DNA samples that were both naturally and chemically degraded, using STR Powerplex 16 amplification.
Samples / Treatment Exposure Time/∗Storage Time†/% Alleles recovered
Blood DNA + 0.6% NaClO/ 18 hours/ 1 day/ 60 ± 1.0

[Numbers]

"It can be concluded that complete decontamination of equipment and surfaces from DNA and DNA containing biological material is important in forensic DNA laboratories in order to avoid secondary transfer of this contaminating DNA to evidence samples. Therefore, it is recommended to regularly perform a stringent decontamination of laboratory surfaces and equipment and to check surfaces after decontamination to guarantee the effectiveness of the decontamination procedure. Also, prevention of secondary transfer from potentially contaminated objects and surfaces is of particular importance, e.g. by frequent renewal of gloves. The emphasis of contamination prevention procedures should not lie on filtering laboratory air, as air is unlikely to be the source of DNA contamination, but on proper decontamination procedures and appropriate laboratory operating procedures aiming at avoiding secondary transfer."

Source: Vandewoestyne M, Van Hoofstat D, De Groote S, Van Thuyne N, Haerinck S, et al. (2011) Sources of DNA Contamination and Decontamination Procedures in the Forensic Laboratory. J Forensic Res S2:001. doi:10.4172/2157-7145.S2-001

https://www.omicsonline.org/sources-...1.php?aid=1614

How often did Stefanoni and her team change their gloves? Foreign material (dirt) was evident on the gloves they used to handle the bra clasp, as seen in the police video of its recovery.

What was Stefanoni's procedure to decontaminate laboratory and equipment surfaces?

The study quoted above, by Vandewoestyne et al., looked for relatively gross DNA contamination (resulting in peaks in the range 50 to 100 RFU) and found little of such contamination in the lab air.

But the potential for smaller contaminants transferring through the air would likely be greater for LT (LCN) DNA. What was Stefanoni's procedure for assuring there was no airborne contamination, since she was conducting LT (LCN) DNA analysis in this case?

[bagels]

The DNA analysis is interesting and was probably vital for convincing the Hellmann court, but I still find it a red herring to the broader discussion.

Vixen bringing up the Ashley Olsen case gets to the root of this case. Amanda Knox is not guilty of murdering Meredith Kercher for the same reason Ashley's friend Amy isn't - because in both murder cases the murderer is known, identified by the considerable evidence against them, and their name is neither Amanda Knox nor Amy. If we found out Ashley's friend Amy couldn't remember the precise time she had dinner, if we found her DNA in her own sink, if the police were able to coerce a few vague incoherent statements out of her in an unrecorded all night aggressive interrogation, it wouldn't change the fact whatsoever that Ashley Olsen was murdered by Cheik Diaw, just as Meredith Kercher was murdered by Rudy Guede.

The PGP seem incapable of realizing that Rudy Guede changed the case against Amanda Knox. Completely nullified it.

If there was a bloody handprint found next to Laci Peterson's bed, and it was matched to a serial killer who was found to have a history of dumping women he killed into the same area of the San Francisco Bay where Laci's body was recovered, Scott Peterson would instantly become the unluckiest innocent person ever.

This is the core truth of this case and always has been.

[Numbers]

"DETECTING DNA CONTAMINATION

Appropriate control reactions are helpful in determining whether DNA contamination has occurred. A “reagent blank” control consists of all reagents used during sample processing but contains no sample. This control is used to detect DNA contamination of the analytical reagents used to prepare the sample for analysis. In a separate negative control reaction, water is used instead of extracted sample or reagent blank. This negative control reaction is often referred to as the “no-template” control and allows identification of contamination in the amplification reagents themselves. The reagent blank and no-template controls are effective in detecting contamination because there is no added DNA template to compete with minute amounts of contaminating DNA for amplification. However, contamination can also be detected based on the results from a positive control template The presence of unexpected peaks in the negative or positive control reactions can indicate DNA contamination."

Source: Identifying and Preventing DNA Contamination in a DNA-Typing Laboratory
By Terri Sundquist and Joseph Bessetti
Promega Corporation

Contamination was detected in the limited number of control results provided by Stefanoni. See: http://www.amandaknoxcase.com/contam...bwork-coverup/

Many of the control results were not provided. Electronic copies of the raw DNA data, which could show the profiles of the DNA contamination in the controls and samples, were withheld by Stefanoni. See: http://www.amandaknoxcase.com/lab-data-suppression/

[Numbers]

"Recent environmental monitoring studies have highlighted a need to confirm cleaning procedures are performing to suitable levels for highly sensitive STR kits such as PowerPlex 21. To ensure that DNA contamination minimisation procedures are adequate, we have investigated the efficacy of sodium hypochlorite and a commercial, non-corrosive alternative, Virkon, at a range of concentrations for their DNA decontamination ability. Cleaning solutions were trialled across a range of body fluids and surface types, to cover the variety of potential contamination circumstances encountered within typical forensic laboratories. Given all factors tested, it was concluded that a 1% solution of sodium hypochlorite, sprayed on the surface and left for 5 min before drying and wiping with 70% ethanol, was able to remove DNA, saliva, blood, semen and skin cells from both smooth and pitted surfaces. However, safety testing revealed that the combination of hypochlorite and ethanol produced levels of gaseous chlorine at or above the recommended exposure limits. Subsequently, a cleaning protocol of 1% hypochlorite followed by distilled water was tested for efficacy, and subsequently introduced throughout the laboratory."

Source: DNA contamination minimisation – finding an effective cleaning method
Kaye N. Ballantyne et al. Australian Journal of Forensic Sciences
Volume 47 2015 - Issue 4:428-439

http://www.tandfonline.com/doi/figur...eedAccess=true

[bagels]

This case is kind of like having perfect pitch and instantly identifying musical notes, some people just can't "get it" and never will while everyone else can look at the case for 5 minutes on wikipedia and figure it out.

I'm being a hypocrite with 1000+ posts on this case here (and elsewhere) cause I made sparring about it and observing PGP a pointless side hobby, but if you can't look at a crime scene covered in the traces of a burglar with an obvious break-in and immediately go "well, unless they've got like phone logs or witnesses connecting the burglar to the students, direct testimony, or a literal smoking gun, I don't see how they were accomplices..." all the DNA experts in the world wont convince you Amanda didn't plan an impromptu sex murder on 20 minutes notice and spontaneously added in a random burglar she couldn't speak the same language as when they happened to run into him unplanned on the 3 minute walk to the murder (and then incidentally staged his precise break-in technique they couldn't know a thing about). The latter scenario is literally a non sequitur, it's not even a scenario, but it's unquestioned by the PGP and I've never been able to crack the formula as to why. Is it a disbelief that a coercive interrogation could ever produce false statements? Is it a disbelief the police would so enthusiastically pursue innocent people? What is the secret to being able to ignore the obvious and indulge in an indecipherable blur of vague imagery of Amanda slashing a giant kitchen knife about (that didn't match the 4 forensic knife profiles at the scene) while the random burglar ingratiates himself with his new psycho stranger friends and makes sure to rape the victim and get her blood all over him so as to be the only one leaving definitive traces.

I want to know but I never will.

[Planigale]

Originally Posted by Numbers

"It can be concluded that complete decontamination of equipment and surfaces from DNA and DNA containing biological material is important in forensic DNA laboratories in order to avoid secondary transfer of this contaminating DNA to evidence samples. Therefore, it is recommended to regularly perform a stringent decontamination of laboratory surfaces and equipment and to check surfaces after decontamination to guarantee the effectiveness of the decontamination procedure. Also, prevention of secondary transfer from potentially contaminated objects and surfaces is of particular importance, e.g. by frequent renewal of gloves. The emphasis of contamination prevention procedures should not lie on filtering laboratory air, as air is unlikely to be the source of DNA contamination, but on proper decontamination procedures and appropriate laboratory operating procedures aiming at avoiding secondary transfer."

Source: Vandewoestyne M, Van Hoofstat D, De Groote S, Van Thuyne N, Haerinck S, et al. (2011) Sources of DNA Contamination and Decontamination Procedures in the Forensic Laboratory. J Forensic Res S2:001. doi:10.4172/2157-7145.S2-001

https://www.omicsonline.org/sources-...1.php?aid=1614

How often did Stefanoni and her team change their gloves? Foreign material (dirt) was evident on the gloves they used to handle the bra clasp, as seen in the police video of its recovery.

What was Stefanoni's procedure to decontaminate laboratory and equipment surfaces?

The study quoted above, by Vandewoestyne et al., looked for relatively gross DNA contamination (resulting in peaks in the range 50 to 100 RFU) and found little of such contamination in the lab air.

But the potential for smaller contaminants transferring through the air would likely be greater for LT (LCN) DNA. What was Stefanoni's procedure for assuring there was no airborne contamination, since she was conducting LT (LCN) DNA analysis in this case?

That is why I keep on saying there should be the SOP for laboratory decontamination, the records to show that this actually happened, and the environmental samples for the laboratory to show the decontamination process is effective, and since samples were analysed to a level below 50 RFU probably at a level below 50pg then we need to know that the environmental sampling would have detected contamination below this level.

Steffanoni said she was aware of no contamination. The best way of not being aware is not to look for it. My guess is there were no routine environmental samples taken, if there were Steffanoni would have said when asked that they had a flawless record and she would be happy to provide a copy of the records to the court.

[Chris_Halkides]

From the paper by McCord and collaborators: "To verify the ability of the HPLC-EC system to detect oxidative damage, a series of reactions were performed on DNA extracted from human blood and buccal swabs as well as from bovine tissue using either H2O2 or NaClO. The reactions were performed at 37 °C with 0.3% H2O2 using 100 μg of total DNA and incubated for 1 hour. To increase the rate of oxidation, DNA samples were also treated with 0.3% H2O2 in a solution containing 0.05 M Fe(NH4)2(SO4)2.6H2O, 0.1 M HEPES for both 1 h and 3 h at 37 °C. All experiments were performed in triplicate. In order to obtain a tissue control, 500mg of bovine tissue was also treated with 1% H2O2 or 2% NaClO at 37 °C for 18 h. DNA from these samples was then extracted using the above organic extraction method." The authors performed other experiments for three hours. See also Figures 3 and 4, which used three hours.

Clearly the authors were not trying to destroy all biological matter (they wanted to show the effects of partial degradation). It is possible that the ratio of the amount of oxidant to the amount of biological matter was small enough not to lead to complete degradation. However in a quick skim of the paper, I did not find the volume of bleach or the volume of hydrogen peroxide. Oxidants will attack other biomolecules such as carbohydrates and proteins. There are a number of protocols available for how to decontaminate with bleach. One from Promega called for a 33-fold dilution of commercial bleach and noted that if this dilute bleach were not thoroughly washed out of the pipets being decontaminated, the residual bleach would destroy the desired DNA as well. A paper that I have cited in these threads from the journal Biotechniques (coauthored by Andrus and Prinz IIRC) called for using a tenfold dilution of bleach to decontaminate prior to PCR.

[Numbers]

Originally Posted by Chris_Halkides

From the paper by McCord and collaborators: "To verify the ability of the HPLC-EC system to detect oxidative damage, a series of reactions were performed on DNA extracted from human blood and buccal swabs as well as from bovine tissue using either H2O2 or NaClO. The reactions were performed at 37 °C with 0.3% H2O2 using 100 μg of total DNA and incubated for 1 hour. To increase the rate of oxidation, DNA samples were also treated with 0.3% H2O2 in a solution containing 0.05 M Fe(NH4)2(SO4)2.6H2O, 0.1 M HEPES for both 1 h and 3 h at 37 °C. All experiments were performed in triplicate. In order to obtain a tissue control, 500mg of bovine tissue was also treated with 1% H2O2 or 2% NaClO at 37 °C for 18 h. DNA from these samples was then extracted using the above organic extraction method." The authors performed other experiments for three hours. See also Figures 3 and 4, which used three hours.

Clearly the authors were not trying to destroy all biological matter (they wanted to show the effects of partial degradation). It is possible that the ratio of the amount of oxidant to the amount of biological matter was small enough not to lead to complete degradation. However in a quick skim of the paper, I did not find the volume of bleach or the volume of hydrogen peroxide. Oxidants will attack other biomolecules such as carbohydrates and proteins. There are a number of protocols available for how to decontaminate with bleach. One from Promega called for a 33-fold dilution of commercial bleach and noted that if this dilute bleach were not thoroughly washed out of the pipets being decontaminated, the residual bleach would destroy the desired DNA as well. A paper that I have cited in these threads from the journal Biotechniques (coauthored by Andrus and Prinz IIRC) called for using a tenfold dilution of bleach to decontaminate prior to PCR.

McCord et al. do not describe an experiment where they try to clean off blood DNA or other DNA from a surface such as a knife blade. They are comparing how much degradation may be observed in DNA in tissue over a length of time to that resulting from a treatment with H2O2 (hydrogen peroxide) or NaClO (bleach); they include blood DNA treated with both chemicals.

In cleaning a knife of blood and tissue, with the aim of removing DNA, one would probably treat the knife with bleach, followed by a water rinse and drying with, for example, a towel (a disposable, perhaps paper if available). The possibility of any tissue or blood DNA surviving a thorough enough cleaning of the knife blade seems remote. The area where the blade enters the handle would be difficult to clean, and there could be blood that enters the space where the blade tang is attached to the handle by capillary action, and might thus remain after a thorough cleaning.

In this case, as I understand, the prosecution and the courts refused to do DNA testing on the disassembled knife. They were satisfied with the anomalous DNA trace material allegedly found on the knife blade by Stefanoni. This suggests that the level of "truth" that they sought was limited to these DNA traces, one which maybe matched Kercher (but not reliably) and another that matched Knox. The blade had no blood on it when tested by the police or by the court-appointed experts.

The prosecution and courts were, IMO, well aware that these traces were contaminants and that there would be no additional relevant DNA found on the tang-handle surfaces by disassembly the knife, because it clearly was not the murder weapon. The murder weapon, based upon the blood-soaked pattern left on a bed and the wounds, was clearly a much smaller knife that, as far as is known, was never recovered by the police.

It should be added that there is no credible evidence to suggest that Knox and Sollecito were not together at his apartment at the relevant time. There is considerable irrefutable evidence that shows that not only was Guede at the cottage at the relevant time, but significant amounts (not traces) of his DNA were recovered from Kercher's body, clothing, and purse. A palm print in blood, stated by police to match him, was found in the murder room. Shoe sole patterns attributable to his shoes - which he had discarded - in blood and a substance that appears to be semen - were found on a pillow that had been under Kercher's body. It is noteworthy that the police and prosecution have either never tested the presumed semen for identity of material or source, or not made public the result of any such tests.

The only reasonable conclusion that can be derived from the pattern of police and prosecution behavior in the way testing has been done in this case is that there was an effort to fabricate a case against Knox and Sollecito even at the cost of minimizing the case against Guede.

[Chris_Halkides]

From Prince AM and Andrus L "PCR: How to Kill Unwanted DNA" Biotechniques 1992 12(3) 358-360, here is their abstract: "Avoidance of contamination in the PCR laboratory requires the use of strict precautions. Among these, chemical decontamination of surfaces and equipment is desirable to prevent inadvertent contamination of samples by the gloved hand and by pipettors. We have investigated the use of sodium hypochloride (Clorox), in comparison to concentrated HCl, for PCR sterilization. Ten percent Clorox was found to eliminate all ethidium bromide-stainable DNA and to prevent PCR amplification of a 600-bp DNA segment within one minute of template treatment. RNA was similarly destroyed. By contrast, even 2.0 N HCl did not destroy DNA detectable by PCR within five minutes. Because of its high efficacy, low cost and relatively low corrosiveness, we recommend the use of ten percent Clorox as a decontaminant for elimination of DNA templates in the PCR laboratory."

In the body of the paper they state, "Figure 2 shows that treatment of template DNA with 10% v/v Clorox for 30 s eliminated PCR amplification of the 3.5 kip segment (Figure 2A) and greatly reduced amplification of the 600-bp PCR product (Figure 2B)." Note that the larger of the two pieces of DNA was the one which was completely destroyed with respect to its ability to support the polymerase chain reaction. It was Prince and Andrus' observation that led me to suggest the results of an experiment in these threads similar to the one the McCord and collaborators did.

[Chris_Halkides]

Originally Posted by Planigale

That is why I keep on saying there should be the SOP for laboratory decontamination, the records to show that this actually happened, and the environmental samples for the laboratory to show the decontamination process is effective, and since samples were analysed to a level below 50 RFU probably at a level below 50pg then we need to know that the environmental sampling would have detected contamination below this level.

Steffanoni said she was aware of no contamination. The best way of not being aware is not to look for it. My guess is there were no routine environmental samples taken, if there were Steffanoni would have said when asked that they had a flawless record and she would be happy to provide a copy of the records to the court.

I agree with the need for the laboratory to release its SOPs. In addition examination of the DNA quantitation runs indicate that there was contamination on one occasion at the very least, as Diocletus has discussed.

[Chris_Halkides]

Originally Posted by Numbers

Thanks for providing this additional information.

Is it correct that a minimum profile height for validity of a peak, generally set at 50 RFU, is set to avoid mistaking or misinterpreting signals from low-level contaminant DNA or other "noise" (such as clumps of dye) as part of a valid DNA profile?

If one chooses, for the knife blade DNA, to set the DNA peak minimum valid height as 15 RFU (or less), and applies this (unvalidated) standard consistently, what interpretation must be given to the additional peaks in the profile?

Did Stefanoni discuss what minimum peak height she had adopted for her interpretation? Did she discuss the additional peaks and incorporate their presence in her explanation of how she assigned the knife blade DNA profile to Meredith Kercher? Did Stefanoni explain how she validated her methodology, including any standard she used for minimum peak height for a peak call?

Numbers,

Suppose that a low template sample is heterozygous for 5 and 8 repeats for locus G. Suppose further that the 5-repeat allele drops out. The 8-repeat peak would then mislead the person interpreting the electropherogram. He or she would think that this profile was homozygous at locus G when in fact it is heterozygous. There is a graph (I think I saw it in John Butler's textbook that I mentioned yesterday) which indicates that as peak heights get smaller, the chance of having a drop-out increases. This is one reason for a minimum threshold (to minimize the chances of an erroneous interpretation, but it may not be the only one.

There are two peaks in D3S1358 (at 15 and 16 repeat units, I believe) that are not marked on the copy of the electropherogram I have. The look to be 15-20 RFU in height. In D7S820 there is a peak at 11 repeats that is 15 RFU high that is marked ("called"). IIRC the marked peaks correspond to Meredith's profile. If one had used a consensus method and not found these two peaks in all of the electropherograms, one would have grounds to ignore them. Yet Stefanoni did not run the sample twice; therefore, I see no rational basis for ignoring the two unmarked peaks. To the best of my knowledge, the answers to your last two questions are no and no.

[js202]

Originally Posted by bagels

This case is kind of like having perfect pitch and instantly identifying musical notes, some people just can't "get it" and never will while everyone else can look at the case for 5 minutes on wikipedia and figure it out.

I'm being a hypocrite with 1000+ posts on this case here (and elsewhere) cause I made sparring about it and observing PGP a pointless side hobby, but if you can't look at a crime scene covered in the traces of a burglar with an obvious break-in and immediately go "well, unless they've got like phone logs or witnesses connecting the burglar to the students, direct testimony, or a literal smoking gun, I don't see how they were accomplices..." all the DNA experts in the world wont convince you Amanda didn't plan an impromptu sex murder on 20 minutes notice and spontaneously added in a random burglar she couldn't speak the same language as when they happened to run into him unplanned on the 3 minute walk to the murder (and then incidentally staged his precise break-in technique they couldn't know a thing about). The latter scenario is literally a non sequitur, it's not even a scenario, but it's unquestioned by the PGP and I've never been able to crack the formula as to why. Is it a disbelief that a coercive interrogation could ever produce false statements? Is it a disbelief the police would so enthusiastically pursue innocent people? What is the secret to being able to ignore the obvious and indulge in an indecipherable blur of vague imagery of Amanda slashing a giant kitchen knife about (that didn't match the 4 forensic knife profiles at the scene) while the random burglar ingratiates himself with his new psycho stranger friends and makes sure to rape the victim and get her blood all over him so as to be the only one leaving definitive traces.

I want to know but I never will.

This is spot on, but it's even worse.

PGP refuse to interrogate Guede's preposterous story that he'd been invited by Kercher the previous night to come have sex that fated evening, and that they only stopped because they had no condoms, though Kercher knew about the bathroom stash.

Broken window, burglar with no excuse to be in the building other than his transparent lies, burglar's DNA in the victim's vagina. But let's not dig too deeply into this, other than to create a kind of fallen saint out of the lying scumbag Guede, since, after all there are bigger fish to make material out of thin air in the project of making a Salem witch out of Ms. Knox.

Like Mignini, PGP use Guede as a pawn for their diaphanous fantasy of Amanda as the true instigator and knife-wielder. Guede exists in some liminal space, where his lies must not be fully vetted any more than what Mignini and PGP perceive to be his truths.

[Bill Williams]

Originally Posted by bagels

This case is kind of like having perfect pitch and instantly identifying musical notes, some people just can't "get it" and never will while everyone else can look at the case for 5 minutes on wikipedia and figure it out.

I'm being a hypocrite with 1000+ posts on this case here (and elsewhere) cause I made sparring about it and observing PGP a pointless side hobby, but if you can't look at a crime scene covered in the traces of a burglar with an obvious break-in and immediately go "well, unless they've got like phone logs or witnesses connecting the burglar to the students, direct testimony, or a literal smoking gun, I don't see how they were accomplices..." all the DNA experts in the world wont convince you Amanda didn't plan an impromptu sex murder on 20 minutes notice and spontaneously added in a random burglar she couldn't speak the same language as when they happened to run into him unplanned on the 3 minute walk to the murder (and then incidentally staged his precise break-in technique they couldn't know a thing about). The latter scenario is literally a non sequitur, it's not even a scenario, but it's unquestioned by the PGP and I've never been able to crack the formula as to why. Is it a disbelief that a coercive interrogation could ever produce false statements? Is it a disbelief the police would so enthusiastically pursue innocent people? What is the secret to being able to ignore the obvious and indulge in an indecipherable blur of vague imagery of Amanda slashing a giant kitchen knife about (that didn't match the 4 forensic knife profiles at the scene) while the random burglar ingratiates himself with his new psycho stranger friends and makes sure to rape the victim and get her blood all over him so as to be the only one leaving definitive traces.

I want to know but I never will.

It's hard to tell if he believes it himself or is simply reporting what even the convicting courts believed, but in his memoirs.....

Francesco Maresca himself relates the unplanned, unpremeditated nature of even believing that AK and RS had something to do with this. Maresca reiterates Judge Massei's opinion (in 2010 from the 2009 trial) that all was hunky dory until Rudy, alone with the victim, started molesting her. And then, inexplicably, RS and AK made a "choice for evil".

But why even go there? The unplanned/unpremeditated nature of the crime (as accepted by even the convicting courts) means that a lot had to have been accomplished between an Italian, and American, and an Ivorian in the minutes after Amanda had been sighted at Raffaele's. Even them, the only thing needing accomplishing acc. to Massei is a momentary "choice for evil", with no evil intent anywhere prior to that!

None of that makes any sense, so it is no wonder that remaining PGP need to buttress this case with phony armchair-psychology, and attacking even the relatives of AK and RS. The fanciful buttressing into all that stuff is the PGP's tacit admission that the Italian courts got all this wrong - it was far far worse!!

Maresca acknowledges that Conti & Vecchiotti were independent DNA experts appointed by the court, and as soon as their own findings came into the Hellmann court that the prosecution fell apart. There is no mention in M's memoirs that C&V are crooked or particularly wrong; just that the main difference between the first two trials was that Massei denied a request for an independent analysis and Hellmann granted it.

I hope someone does a competent English translation of his 12 to 14 pages of memoirs; Google translate certainly gives some funny results.

[Bill Williams]

Originally Posted by js202

This is spot on, but it's even worse.

PGP refuse to interrogate Guede's preposterous story that he'd been invited by Kercher the previous night to come have sex that fated evening, and that they only stopped because they had no condoms, though Kercher knew about the bathroom stash.

Broken window, burglar with no excuse to be in the building other than his transparent lies, burglar's DNA in the victim's vagina. But let's not dig too deeply into this, other than to create a kind of fallen saint out of the lying scumbag Guede, since, after all there are bigger fish to make material out of thin air in the project of making a Salem witch out of Ms. Knox.

Like Mignini, PGP use Guede as a pawn for their diaphanous fantasy of Amanda as the true instigator and knife-wielder. Guede exists in some liminal space, where his lies must not be fully vetted any more than what Mignini and PGP perceive to be his truths.

And above all, do not - repeat, do not! - test the presumed semen stain found on the pillow below the victim's hips.

[TruthCalls]

Originally Posted by Chris_Halkides

I agree with the need for the laboratory to release its SOPs. In addition examination of the DNA quantitation runs indicate that there was contamination on one occasion at the very least, as Diocletus has discussed.

IIRC, it was observed during amplification of sample 36B that after numerous cycles (13-15?) there was no DNA detected. Then suddenly, following a cycle, DNA was detected and then gradually increased with additional cycles. As I understood it, typically one would expect to see a minimal amount of DNA (as noted in the quantification, which in this case was "Too Low") and that it would increase exponentially with each cycle. The implication of a sudden appearance of DNA instead of the exponential increase across all cycles suggested contamination.

What I can't remember is where/when I read/heard this and I am not able to find corroborating evidence so would like to know if anyone else can confirm this. And if so, could anyone explain how contamination could be introduced once amplification is underway? I'm afraid I am not familiar with mechanics of amplification other than it's a cycling of heating/cooling.

While I always felt the blood/human species/DNA quantification results all proved DNA was not present in 36B prior to amplification, if true, this would be the strongest direct evidence of contamination.

[TruthCalls]

Originally Posted by js202

This is spot on, but it's even worse.

PGP refuse to interrogate Guede's preposterous story that he'd been invited by Kercher the previous night to come have sex that fated evening, and that they only stopped because they had no condoms, though Kercher knew about the bathroom stash.

Broken window, burglar with no excuse to be in the building other than his transparent lies, burglar's DNA in the victim's vagina. But let's not dig too deeply into this, other than to create a kind of fallen saint out of the lying scumbag Guede, since, after all there are bigger fish to make material out of thin air in the project of making a Salem witch out of Ms. Knox.

Like Mignini, PGP use Guede as a pawn for their diaphanous fantasy of Amanda as the true instigator and knife-wielder. Guede exists in some liminal space, where his lies must not be fully vetted any more than what Mignini and PGP perceive to be his truths.

The police also disregard Guede's original claim of the attacker being an unknown male, smaller than himself (i.e., NOT Raffaele), and that Amanda wasn't there. Guede tells of fighting with this intruder and explains this is where the cuts on his hand came from. But in his later story this attacker, and the fight with him, disappear. Did Guede ever therefore explain the cuts on his hand? Did the police ask him? I'm pretty sure the cuts on his hands never came up in court. How can that be? Perhaps this is what investigative amnesia means? It certainly isn't being objective and unbiased.

[Planigale]

Originally Posted by TruthCalls

IIRC, it was observed during amplification of sample 36B that after numerous cycles (13-15?) there was no DNA detected. Then suddenly, following a cycle, DNA was detected and then gradually increased with additional cycles. As I understood it, typically one would expect to see a minimal amount of DNA (as noted in the quantification, which in this case was "Too Low") and that it would increase exponentially with each cycle. The implication of a sudden appearance of DNA instead of the exponential increase across all cycles suggested contamination.

What I can't remember is where/when I read/heard this and I am not able to find corroborating evidence so would like to know if anyone else can confirm this. And if so, could anyone explain how contamination could be introduced once amplification is underway? I'm afraid I am not familiar with mechanics of amplification other than it's a cycling of heating/cooling.

While I always felt the blood/human species/DNA quantification results all proved DNA was not present in 36B prior to amplification, if true, this would be the strongest direct evidence of contamination.

I think you are getting confused with the RTPCR quantification process not used on 36B which was quantified using QUBIT. During the amplification process the DNA goes through fixed number of cycles with primers for the tandem repeats of interest. Then is typed. there is no quantification during this phase.

[Vixen]

Originally Posted by Stacyhs

Vixen, I am still waiting for you to provide evidence that "the woman" sent anything regarding "Brazilians" to the Kerchers. Should I expect a long wait?

Since my comment with the photo of the claimed "naked torso" has been moved, I'll include it here.

http://www.internationalskeptics.com...295fa142e2.jpg

Not sure why you are sticking up for this person. Her behaviour is notorious. Before she was banned on twitter (and who then set up yet another twitter account, against twitter rules for banned posters).

Here attached are her direct attacks on the Kercher family, including one which is still up on Bruce Fischer's site, IIP, apparently. It is a reflection of that site and the supporters of FOA that they see nothing wrong with it.

That various members here state that the Kerchers deserve the abuse (some of this person's 'tweets' are too obscene for me to reproduce here) shows how twisted is the logic that the Kerchers have anything at all to do with the prosecution (rightful in the eyes of the first and second instance courts [trial/appeal]).

I should add, Amanda Knox herself was a follower of this person on twitter and no doubt this encouraged this disturbed person to be ever more daring, obscene and aggressive towards the Kerchers.

[Vixen]

Here's another.

[Vixen]

And another:

[Vixen]

Here's another:

[Vixen]

And another. Perhaps Stacy would like to withdraw her claim it is all untrue.

Perhaps LoJo, acbytesla, Samson et al would like to comment on why they consider the Kerchers fair game, as they have stated.

[Vixen]

Here's another addressed directly to Mez' brother.

[Vixen]

Originally Posted by Bill Williams

IIRC there is a practise in Italy of denying lawyers (until the last minute) to mafioso types, as their lawyers can be a conduit of information back to the outside world - naming those who need to be rubbed out so that the pending charges can go nowhere.

In that sense, the withholding of lawyers is justifies as public safety. I'm not sure anyone can point to a similar-fact murder (to the Kercher case) where suspects were denied counsel using mafia-busting techniques.

But we now may know where the "mafia conspiracy thinking" comes from.

True it was instigated to deal with witness intimidation by mafia dons. However, as it is written into the Italian Penal Code, it is within the law. This was to police eyes, drug-fuelled and some kind of a 'party', and had every reason to suspect serious organised crime, given Perugia's reputation as a druggie haven.

[Bill Williams]

Originally Posted by Vixen

True it was instigated to deal with witness intimidation by mafia dons. However, as it is written into the Italian Penal Code, it is within the law. This was to police eyes, drug-fuelled and some kind of a 'party', and had every reason to suspect serious organised crime, given Perugia's reputation as a druggie haven.

Lol!

Of all the ludicrous theories that Mignini put forward, THIS is NOT one of them.

This is a post consisting of a word salad, which has no connection to anything the Perugians ever claimed about this murder.

It's proof that some will say or post anything regardless of its relationship to anything.

[Stacyhs]

Originally Posted by Vixen

Not sure why you are sticking up for this person. Her behaviour is notorious. Before she was banned on twitter (and who then set up yet another twitter account, against twitter rules for banned posters).

Here attached are her direct attacks on the Kercher family, including one which is still up on Bruce Fischer's site, IIP, apparently. It is a reflection of that site and the supporters of FOA that they see nothing wrong with it.

That various members here state that the Kerchers deserve the abuse (some of this person's 'tweets' are too obscene for me to reproduce here) shows how twisted is the logic that the Kerchers have anything at all to do with the prosecution (rightful in the eyes of the first and second instance courts [trial/appeal]).

I should add, Amanda Knox herself was a follower of this person on twitter and no doubt this encouraged this disturbed person to be ever more daring, obscene and aggressive towards the Kerchers.

I am not "sticking up" for this person. I am exposing your lies that she sent "pictures of Mez' naked torso in exchange for his following her on twitter. She adds hatefully, 'I'm sure Mez wouldn't mind'.

This is someone who has regularly attacked the Kerchers and sent the family pictures of vaseline jars and salacious references to 'brazilians'. "

In my post to you, I specifically highlighted the above and spoke of nothing else. As for the rest of your post and the tweets, they have nothing to do with anything I said. I never mentioned the Vaseline, attacks on the Kerchers, nor any other tweets concerning/to the Kerchers.

Therefore, I see no reason to withdraw my statement that the four claims I specifically addressed are lies.


1) I presented the picture that was sent and it does not, in fact, show a "naked torso". So that is a lie.

2) She did not add "hatefully" that "I'm sure Mez wouldn't mind". I presented the actual tweet that shows what she did say. So that is a lie.

3. She did not send the picture "in exchange for her following him on Twitter". It was not technically possible for her to PM him unless he did follow her. So that is a lie.

4. She did not send "salacious references to 'brazilians'". You have not provided any evidence of this. You would if you could. So this is a lie.

Perhaps you would now like to withdraw those four claims since you have failed to provide any evidence they are true?

[Vixen]

Here is the one posted just a few days ago, that we were talking about and Stacyhs tried to play it down.

If Stacyhs is still trying to argue that this person was 'only going to send a very limited shot' - given the track record - well, we can all see that claim for the shabby facsimile of a bluff it is.