Amanda Knox guilty - all because of a cartwheel

[Kestrel]

How's about we take this over to the Science forum?

Already done, the new thread is here.

 

[Fulcanelli]

Already done, the new thread is here.

This is what you wrote in your knew thread:

In another thread, the assertion was made that dead skin cells don't contain DNA. Based on my knowledge, I can't see any support for this idea. Yet this fact was stated in court by a prosecution expert witness and accepted by the court as true. Rather than drag all the experts into a he said, she said argument about a crime, it seemed better to open a separate thread to discuss this.

Has anyone ever heard this before and is there a scientific basis for this claim?

Oh come on Kestrel! Be honest with your new audience and put the FULL question to them instead of just half the issue, you left out the 'dust' part. Don't you want to tell the new science friends your courting that your real end game is to attempt to establish an individual's full DNA profile, in high volume, appeared on an item of evidence in a murder case?

I also see you have completely ignored Kermit's post where he quotes the article halides1 posted that makes it absolutely clear, complete DNA profiles cannot yet be extracted be extracted from dust? Clearly, you are continuing your old habit of closing your eyes whenever proof is presented to show your arguments to be false.

You've lost the dust argument already. Move on.

 

[Fulcanelli]

Already done, the new thread is here.

This is what you wrote in your knew thread:

In another thread, the assertion was made that dead skin cells don't contain DNA. Based on my knowledge, I can't see any support for this idea. Yet this fact was stated in court by a prosecution expert witness and accepted by the court as true. Rather than drag all the experts into a he said, she said argument about a crime, it seemed better to open a separate thread to discuss this.

Has anyone ever heard this before and is there a scientific basis for this claim?

Oh come on Kestrel! Be honest with your new audience and put the FULL question to them instead of just half the issue, you left out the 'dust' part. Don't you want to tell the new science friends your courting that your real end game is to attempt to establish an individual's full DNA profile, in high volume, appeared on an item of evidence via 'dust' in a murder case?

I also see you have completely ignored Kermit's post where he quotes the article halides1 posted that makes it absolutely clear, complete DNA profiles cannot yet be extracted be extracted from dust? Clearly, you are continuing your old habit of closing your eyes whenever proof is presented to show your arguments to be false.

You've lost the dust argument already. Move on.

 

[Kermit]

Fiona was right

Oh come on Kestrel! Be honest with your new audience and put the FULL question to them instead of just half the issue, you left out the 'dust' part. .... I also see you have completely ignored Kermit's post where he quotes the article halides1 posted that makes it absolutely clear, complete DNA profiles cannot yet be extracted be extracted from dust? Clearly, you are continuing your old habit of closing your eyes whenever proof is presented to show your arguments to be false.

You've lost the dust argument already. Move on.

But this is typical behaviour on their part.

They lost the footprint argument, and changed in a millsecond to the Stefanoni-didn't-give-us-what-we-didn't-ask-for argument. Then the Raffaele's last alibi argument, now the legal-DNA-from-dust argument. Then around and around and around and around.

Fiona was right.

 

[shuttlt]

Fiona is always right

 

[lector]

The judge's report actually claims that there can be no DNA in dust, for instance, because dry skin cells do not contain DNA, so the only way DNA can be transferred is through direct contact (or presumably having gotten someone's saliva on your skin, or something!). Even as a non-scientist, this seems like a nonsense to me, since it would imply that transferring DNA from one source to another is a virtual impossibility. They use this argument repeatedly to deny the possibility of contamination.

I do remember remember reading that getting dried out damages the DNA. I'm going to try and get a good answer to this question. Given that the judges report is so arse achingly detailed, it will be good to read the fully fleshed out version of this argument.

I for one would like to see a good translation of this section of the judges' report.

We have begun with a paraphrase of an unknown translation of a detailed Italian document. Kestrel applied his usual idiosyncratic spin to that paraphrase & wound up starting a new thread based on a dubious interpretation, now four times removed from the original source. Amazingly, some good information has arisen on that thread, but what a tortuous tangent it is.

 

[shuttlt]

It'll be nice. The word on PMF is 1.5-2 weeks more for the fully edited, corrected and proof read translation.

 

[stilicho]

Oh come on Kestrel! Be honest with your new audience and put the FULL question to them instead of just half the issue, you left out the 'dust' part. Don't you want to tell the new science friends your courting that your real end game is to attempt to establish an individual's full DNA profile, in high volume, appeared on an item of evidence in a murder case?

I wish we could leave this case out of the other thread, though. The last one we tried over at Science & Medicine conked out because the OP didn't explain anything and didn't even ask a question.

To his credit, Kestrel has done so. And, to their credit, the science people are avoiding the problems we're having with sources and credibility.

The most common reply is what I expected: Not enough information to form a conclusion. This is what scientists will typically reply to simple statements or claims.

From what we know about the documentation now in translation, a great deal of time is spent on the forensics and both the claims and counterclaims. On this thread it's OK to argue about whether the prosecution had the technical people oversimplify things. But they haven't on our Science & Medicine thread and they apparently didn't in court or when putting together the motivations report either.

We're left here with incomplete information, too. There have been so many statements, by so many individuals, presented in cropped form or just plain unsourced. The real question is whether the court and the judges accepted a false scientific claim as factual. Was the claim false? Do we have the complete context of the claim? Was it clarified and/or cross-examined? If it was not false was it simplified or oversimplified? And on and on.

That should be covered in the motivations report.

 

[piktor]

Dead skin cells = Low Quality DNA

This is what you wrote in your knew thread:



Oh come on Kestrel! Be honest with your new audience and put the FULL question to them instead of just half the issue, you left out the 'dust' part. Don't you want to tell the new science friends your courting that your real end game is to attempt to establish an individual's full DNA profile, in high volume, appeared on an item of evidence in a murder case?

I also see you have completely ignored Kermit's post where he quotes the article halides1 posted that makes it absolutely clear, complete DNA profiles cannot yet be extracted be extracted from dust? Clearly, you are continuing your old habit of closing your eyes whenever proof is presented to show your arguments to be false.

You've lost the dust argument already. Move on.

It has already been established that dead skin cells contain low quality DNA. It is mostly unusable.

 

[stilicho]

It has already been established that dead skin cells contain low quality DNA. It is mostly unusable.

This is why it would be interesting to know exactly what the statement was and exactly what the defence questions were.

 

[Chris_Halkides]

Leskie case

Fulcanelli,

This is in response to message #5644, where you wrote, “Oh yes and just like a magic mop, that glove just soaked up every last trace of Raffaele's DNA off the handle so that when they tested the handle...guess what? Every last trace of his DNA was gone. Just like magic! According to halides1 anyway.

Raffaele's DNA on the clasp was in a ratio to Meredith's of 1:6...that's high! Our DNA experts on PMF (Greggy and Nicki - and Halides1, Greggy has a PhD in the field of genetics) tell us that in the case of contamination, one would reasonably expect a ratio of 1:100 or higher. Greggy actually designs the DNA detection kits for one of the two international companies that provide forensic science departments around the world with DNA kits. Nicki is a professor of micro biology at the University of Milan.”

To support my claims about secondary transfer versus direct vigorous handling, I cited the open letter, which was signed by nine forensic experts. I asked you to cite the literature, not to quote someone named “Greggy,” whose credentials cannot be evaluated. Nicki’s credentials are certainly no more impressive than Dr. Alexander Kekule’s, who wrote an article in Der Tagesspiegel last December which raised the possibility of secondary DNA transfer with respect to the clasp.

Your arguments about the relative size of contaminating DNA peaks are invalid on several grounds. First, if a profile had less than 1/100 the intensity of Meredith’s profile, the peaks would have intensities of less than 12 RFUs, which is at the level of noise. Second, if contamination always happened at a low ratio relative to other DNA, it would be trivial to differentiate legitimate DNA from contaminating DNA, and that is simply not true.

Third, your assertion is contrary to the facts of the Leskie case. Dan E. Krane. Victoria State Coroner's Inquest into the Death of Jaidyn Leskie. Supplemental DNA report. February 3, 2004. There are two electropherograms in this document, and both arise from contamination. Yet the peak heights in RFUs are almost entirely as high or higher than Raffaele’s DNA on the clasp. As an ancillary benefit, readers of the pdf file linked above can evaluate the benefits of allowing experts to reanalyze the electronic fsa files.

No doubt you have misinterpreted what Greggy and Nicki said (go back and ask them). It is time to admit that the signers of the open letter had it right: There is no way to discern how the bra clasp DNA was deposited from the profile itself. One final correction: Raffaele left prints on the door, which is not the same as leaving them on the handle.

Chris

 

[Chris_Halkides]

Krane and Nature

Fulcanelli,

This is in response to messages #5356 (p. 134) and #5640 (p. 141).

In message #5640 you wrote, “As for Krane, the article in Nature says the opposite about what is the 'norm'. Now, who should I put more stock in...this Krane guy, or one of the most prestigious journals in the world...hmm, that's a tough one.”

In message #5356, you quote Michael at PMF who said, “This has been a recent favourite complaint by certain sections of the FOA who have claimed (without supporting it with evidence I would add) that blind controls were not used in testing the knife.”

From Nature, 464, 18 March 2010:

“Common forensics practices can also lead to biasing errors, says Dan Krane, a molecular evolutionist at Wright State University in Dayton, Ohio. “Forensic scientists tell me that it is easier for them to distinguish between noise and what is really coming from the DNA if they have a reference sample to work with,” he says. Low copy number or not, that reference sample is often the suspect’s DNA — and faint peaks in a crime-scene sample might seem more convincing when viewed side by side with a strong peak from the suspect. Only
a couple of labs in the United States, he says, require blind testing in their protocols.
Critics’ fears are confounded by an unwillingness of the labs that use the technique to reveal their guidelines for interpreting results. Labs should be forced to disclose details, says Budowle. Given the technique’s reproducibility problems, he argues it is imperative that these protocols are robust and reliable. But “none of the labs disclose what they do. They say it is proprietary information,” he says.
[end quote]

First, protocols are not the same thing as fsa files, and nothing in this article suggests that not releasing fsa files is standard practice. Therefore your statement to the effect that the Nature article contradicts Dr. Krane is completely false. Second, Dr. Krane’s comments to Nature about bias are pertinent to the knife DNA profile. Third, you put confidence in Nature as a journal. Then the fact that Nature sought him out as an expert gives even more weight to Dr. Krane’s credentials and comments about the near universal release of the fsa files. It is the same Dr. Krane.

From the same article, “In low-copy-number profiling, forensic scientists generally split their limited amount of DNA into two or three samples and run analyses on two of them. The third, if available, is reserved for the defence. The results of analyses aren’t completely reproducible, profiles often won’t match and the scientists generally accept as true those STR signals that show up in both runs. The practice is worrying, says Budowle: ‘The logic of this approach makes some sense, but the confidence in it has not been assessed.’” (emphasis added) Thus, the knife profile failed to conform to the standards discussed in the Nature article, there being only a single test, not two or three.

Finally, you are confusing blind controls with all controls, but blind controls are only one type of control. Laboratories typically perform negative controls. Dr. Donald Riley wrote, “Alternatively, the blank may show no profile, consistent with, but not proving that contamination didn't occur. Unfortunately, a few forensic DNA laboratories omit their controls…Good PCR technique is no guarantee that contamination didn't influence the results. Steps must be taken to try and detect contamination. Negative controls are blank PCRs that have all the components of the evidentiary PCRs but have no other DNA added intentionally. Fortunately, there are often two negative controls used, one when the DNA is extracted, and another when the PCR is set up. Any PCR signal in the negative control would warn that contamination has occurred. Unfortunately, the negative controls are virtually the only warning of PCR contamination. Negative controls may alert the analyst to general contamination occurring within the lab or the lab reagents.” http://www.scientific.org/tutorials/articles/riley/riley.html

In summary neither your comments about release of fsa files nor your comments about controls are supported by the article you cited.

Chris

 

[Chris_Halkides]

open letter

Kermit and Fulcanelli,

This is in response to message #5659 and message #5679. I don’t know the answers to these questions. If you think that it is worth your time to do so, ask the signers of the letter. Your questions are unimportant tangents at best, smokescreens at worst, to the most critical questions, which are the forensic issues that Johnson and Hampikian raised. No one on this thread has provided substantive arguments supported by the primary literature to rebut theirs.

I am still waiting for anyone to answer to my question about the knife profile. Do you think it was perfectly OK for Patrizia Stefanoni to ignore the appearance of two extra peaks in locus D3S1358, both of which have a peak height of about 20 RFUs? They have fifteen and sixteen repeats, respectively, and neither of which is part of Meredith’s profile, which has fourteen and eighteen repeats at this locus. There is one peak in locus D7S820 with an intensity of only 15 RFU, which is interpreted to be part of Meredith’s profile. Why should this latter peak be treated as part of Meredith’s profile and the two other peaks ignored?

Chris

 

[Chris_Halkides]

DNA and dust

Fulcanelli and Kermit,

This is in response to message #5674 and #5676 about skin cells and DNA. Kermit wrote, “So it seems that the technique isn't quite there yet for useful forensic purposes, to the contrary of what you write.” Fulcanelli wrote, “You've yet to provide an explanation as to why it is Raffaele alone that possesses it.”

I am happy to see the DNA discussion move to a new thread; therefore, I will focus on rebutting only a few points. Here is the primary article on which the New Scientist article is based:
http://www.ncbi.nlm.nih.gov/pubmed/18420364
Forensic Sci Int. 2008 Jun 10;178(1):7-15. Epub 2008 Apr 16.
Characterization of human DNA in environmental samples.
Toothman MH, Kester KM, Champagne J, Cruz TD, Street WS 4th, Brown BL.

In the abstract to this article the authors wrote, “Environmental samples from indoor surfaces can be confounded by dust, which is composed largely of human skin cells and has been documented to contain roughly tens of micrograms of total DNA per gram of dust…Overall, human DNA was detected in 97% of 36 dust samples and 61% of samples yielded allele distributions of varying degrees of complexity when subjected to STR analysis. The implications of this study are twofold. First, the presence of dust in evidence can be a significant contamination source in forensic investigations because the human DNA component is of sufficient quality and quantity to produce allele calls in STR analysis. This can be effectively managed by implementing stringent protocols for collection and analysis of potential biological samples.”
(emphasis added)

Andy Coughlin in the New Scientist (http://www.newscientist.com/article/mg19826584.200-telltale-dna-sucked-out-of-household-dust.html) wrote, “The amount of DNA in dust is tiny and from so many people that singling out any individual could be tricky.” (emphasis added) The key point is that if the dust has contributions from many individuals, the resulting DNA profile will likewise have multiple contributions.

Kermit, this article in the New Scientist does not say what you think it says. It implies that a mixed sample is hard to analyze, a well-known problem in DNA forensics. Moreover, the amount of dust on the bra clasp may have been greater than the amounts analyzed in this paper. Fucanelli, Raffaele’s DNA was not alone on the bra clasp. Instead of your unsubstantiated community laundry theory, the possibility that dust contributed several profiles is supported in the literature and is parsimonious.

Katy_did (message #5657) wrote, “The judge's report actually claims that there can be no DNA in dust.” Thus, Stefanoni put forth and the judges accepted a scientifically invalid argument.

Chris

 

[Chris_Halkides]

Professsor Thompson on electronic file release

Here is more information on the release of electronic files.

William C. Thompson. Victoria State Coroner's Inquest into Death of Jaidyn Leskie. DNA report. December 3, 2003.

William Thompson said, “When I review the casework of forensic DNA laboratories in the United States, I typically ask for and receive copies of the electronic data collected by laboratory instruments during DNA testing. These data show the actual results of the DNA tests. By examining these data, an independent expert can check whether the forensic laboratory interpreted its results correctly and can detect a host of potential problems that would not be apparent from examining the laboratory notes.”

William C. Thompson. Tarnish on the 'gold standard:' Understanding recent problems in forensic DNA testing. The Champion. 30(1):10-16, January/February 2006.

“A key aspect of discovery in DNA cases is the electronic data produced by the computer-controlled genetic analyzers that are currently used to “type”
DNA samples. Analysis of the computer files can not only reveal undisclosed
problems and support alternative interpretations of the findings, but also, as discussed above, these files can be crucial for detecting instances of scientific fraud, such as that committed by Jacqueline Blake and Sarah Blair.”

 

[Kermit]

Andy Coughlin in the New Scientist (http://www.newscientist.com/article/mg19826584.200-telltale-dna-sucked-out-of-household-dust.html) wrote, “The amount of DNA in dust is tiny and from so many people that singling out any individual could be tricky.” (emphasis added) The key point is that if the dust has contributions from many individuals, the resulting DNA profile will likewise have multiple contributions.

- Your comment may be of interest it you erroneously believe that Raffaele's clearly and distinctly identified profile on the bra clasp came from dust.

- Comments on the other thread point out that getting a strong DNA profile from dust for legal purposes is not yet a ripe science.

- Comments on the other thread point out that any "contribution" of partial DNA information from dust would be simply a contribution to a low level of noise.

- You seem to be suggesting that by some statistical coincidence, a bunch of bits and pieces of other peoples profiles, in an extremely weak quantity in dust, somehow come together a sum up to a clear profile which (what bad luck!) looks exactly like Raffaele's.

I'm not convinced, and - more importantly - I don't think the judges or jury would be very convinced. Keep trying.

Kermit, this article in the New Scientist does not say what you think it says. It implies that a mixed sample is hard to analyze, a well-known problem in DNA forensics.

- This is irrelevant. We've already discussed here and on the other thread (backup up by references to technical journals) that a strong DNA profile such as Raffaele's could not have been detected with current techniques in dust contanimation.

the possibility that dust contributed several profiles is supported in the literature and is parsimonious.

- Maybe there could have been some contamination from minute, partial DNA profiles in dust, but - as pointed out already several times - Raffaele's profile was strong and could not have come dust.

Katy_did (message #5657) wrote, “The judge's report actually claims that there can be no DNA in dust.” Thus, Stefanoni put forth and the judges accepted a scientifically invalid argument.

You derive a legal conclusion from a blog poster's paraphrasing of a legal document which is being translated.

I think it's quite clear that if the judges' report said something to that effect (I'm still waiting to see the translation), the judges are writing from a legal perspective, and the usability of evidence. The judges weren't writing about the next generation of forensic techniques which will be available in 10 years.

From there you make a negative conclusion and comment about the judges and Stefanoni. Take it easy. I'm surprised that you can't admit what your own initial link on the magical DNA dust said (from a rhetorical point of view, you should have read it before posting it): that DNA testing on dust is not yet at a stage of development which is useful for legal purposes.

 

[Fulcanelli]

Fulcanelli,

This is in response to messages #5356 (p. 134) and #5640 (p. 141).

In message #5640 you wrote, “As for Krane, the article in Nature says the opposite about what is the 'norm'. Now, who should I put more stock in...this Krane guy, or one of the most prestigious journals in the world...hmm, that's a tough one.”

In message #5356, you quote Michael at PMF who said, “This has been a recent favourite complaint by certain sections of the FOA who have claimed (without supporting it with evidence I would add) that blind controls were not used in testing the knife.”

From Nature, 464, 18 March 2010:

“Common forensics practices can also lead to biasing errors, says Dan Krane, a molecular evolutionist at Wright State University in Dayton, Ohio. “Forensic scientists tell me that it is easier for them to distinguish between noise and what is really coming from the DNA if they have a reference sample to work with,” he says. Low copy number or not, that reference sample is often the suspect’s DNA — and faint peaks in a crime-scene sample might seem more convincing when viewed side by side with a strong peak from the suspect. Only
a couple of labs in the United States, he says, require blind testing in their protocols.
Critics’ fears are confounded by an unwillingness of the labs that use the technique to reveal their guidelines for interpreting results. Labs should be forced to disclose details, says Budowle. Given the technique’s reproducibility problems, he argues it is imperative that these protocols are robust and reliable. But “none of the labs disclose what they do. They say it is proprietary information,” he says.
[end quote]

First, protocols are not the same thing as fsa files, and nothing in this article suggests that not releasing fsa files is standard practice. Therefore your statement to the effect that the Nature article contradicts Dr. Krane is completely false. Second, Dr. Krane’s comments to Nature about bias are pertinent to the knife DNA profile. Third, you put confidence in Nature as a journal. Then the fact that Nature sought him out as an expert gives even more weight to Dr. Krane’s credentials and comments about the near universal release of the fsa files. It is the same Dr. Krane.

From the same article, “In low-copy-number profiling, forensic scientists generally split their limited amount of DNA into two or three samples and run analyses on two of them. The third, if available, is reserved for the defence. The results of analyses aren’t completely reproducible, profiles often won’t match and the scientists generally accept as true those STR signals that show up in both runs. The practice is worrying, says Budowle: ‘The logic of this approach makes some sense, but the confidence in it has not been assessed.’” (emphasis added) Thus, the knife profile failed to conform to the standards discussed in the Nature article, there being only a single test, not two or three.

Finally, you are confusing blind controls with all controls, but blind controls are only one type of control. Laboratories typically perform negative controls. Dr. Donald Riley wrote, “Alternatively, the blank may show no profile, consistent with, but not proving that contamination didn't occur. Unfortunately, a few forensic DNA laboratories omit their controls…Good PCR technique is no guarantee that contamination didn't influence the results. Steps must be taken to try and detect contamination. Negative controls are blank PCRs that have all the components of the evidentiary PCRs but have no other DNA added intentionally. Fortunately, there are often two negative controls used, one when the DNA is extracted, and another when the PCR is set up. Any PCR signal in the negative control would warn that contamination has occurred. Unfortunately, the negative controls are virtually the only warning of PCR contamination. Negative controls may alert the analyst to general contamination occurring within the lab or the lab reagents.” http://www.scientific.org/tutorials/articles/riley/riley.html

In summary neither your comments about release of fsa files nor your comments about controls are supported by the article you cited.

Chris

First, you still have not demonstrated that it is standard practice for labs to release .fsa files.

Second, you've yet to establish the .fsa files weren't released to the defence anyway.

Third, it is clear nobody asked the Italian defence lawyers for any .fsa files.

Fourth, you've yet to provide any proof as has been requested from you numerous times. It seems in your world, the police and police scientists have to prove EVERYTHING, but YOU don't, your say so is merely enough.

 

[Fulcanelli]

Now on the matter of the phones and the Postal Police...since for a period of time in this thread there was intense 'interest' in the subject. This is from the translated part of the Judges' Report.

1. It was argued here by some that the Postal Police went to the cottage with both of Meredith's phones. I argued they went with no more then one, the first phone that was found. We were all wrong...from the report, they didn't go with any, the phones were retained at the police station together.

2. The first phone (Filomena's) was handed in at 10:15 am.

3. The second phone was found at 11:45 - 12:00. At about 12:15 to 12:20 this phone was brought into the station.

4. Filomena's phone was traced to Filomena by Bartalozzi at 11:38 and he dispatched two officers to the cottage at 12:00. They didn't take Filomena's phone and the second phone had not been handed in at this point.

5. Bartolozzi tried to trace the second phone, handed in at 12:15 to 12:20 but was unable. It was placed in the offices with Filomena's phone.

6. Meanwhile the Postal Police were en route to the cottage, having been dispatched at 12:00, but had difficulty finding it. having gone up and down the same road several times in an attempt to find it. They then dismounted and went to find the house on foot, finally arriving a little after 12:30.

7. Shortly after their arrival at the house, the Postal Police were informed by Bartolozzi that a second phone had been found and that this one could not be traced. However, it was judged that the phones were connected since they'd been found in the same place.

 

[shuttlt]

Fulcanelli,

The other translation "could easily take another 4 weeks" according to Bruce. It looks like PMF is out in front by quite a way.

 

[stilicho]

Here is more information on the release of electronic files.

William C. Thompson. Victoria State Coroner's Inquest into Death of Jaidyn Leskie. DNA report. December 3, 2003.

Isn't this another in a seemingly endless stream of unrelated cases?

The argument here is that the forensics laboratory initially matched the DNA on the victim's possessions to an individual who was hundreds of kilometres from the crimescene. Were RS and AK hundreds of kilometres from Perugia on the night of Meredith's murder?

Moreover, the individual who was identified had also been a crime victim and her own clothing was being tested at the same time by the same lab team. Were RS/AK's belongings being investigated by Stefanoni's team for an unrelated crime against each of them?

Does the same apply to RG and Patrick?

Can you tell me exactly what your point is?