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Tags Australia cases , dna evidence , murder cases

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Old 26th May 2020, 12:43 AM   #81
Elaedith
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Originally Posted by Chris_Halkides View Post
Jane Taupin, the author of a number of books on DNA forensics and the coauthor of a book on the forensics of clothing, wrote, "The possibility of the crucial fingernail DNA evidence being contaminated has been raised by the defence at the start of the trial. Four other exhibits in the matter were shown to be contaminated with DNA from PathWest scientists. An intimate swab from the second deceased Jane Rimmer was analysed by PathWest in 1996 with no male DNA result, but later found in 2017 by Cellmark to have an almost complete profile of a male Pathwest scientist involved in preparing the evidence. An intimate swab from Ciara Glennon also yielded an almost complete profile of another PathWest scientist involved in testing the exhibit between 1997 and 2001. Fingernail samples from Jane Rimmer were found by Cellmark to have a DNA profile of another PathWest scientist who was not involved in testing but standing nearby. Two DNA results from branches at the crime scene of Jane Rimmer tested in 2003 years later yielded DNA of another PathWest scientist who examined them."

Ordinarily fingernail DNA evidence is highly useful, in part because so many studies have been done on it. Based on the case of Gregory Turner, I would say that when a sample is contaminated with a forensic worker's own DNA, it was by definition mishandled and should not be considered as evidence. The Australian cases of Farah Jama and Jaidyn Leskie should are cautionary tales with respect to DNA contamination. I am not offering an opinion on the overall innocence or guilt of the accused.

EDT
"Earlier, Mr Bagdonavicius was questioned about the role he played in selecting and preparing a series of "negative control blanks" to be sent to New Zealand, where additional forensic testing was being carried out on the evidence by an agency called ESR.

The "blanks" were supposed to be control samples that did not contain any traces of DNA, however, four out of the 21 samples tested at ESR were contaminated." abc

Here is an article that is skeptical of contamination in this case, although it lists one counterexample to its thesis.

From what I understand, none of the samples that were found to be contaminated with DNA from PathWest employees formed part of the prosecution evidence because they didn't contain DNA from Edwards. The only DNA that linked him to the murders was from fragments of Ciara Glennon's fingernails that were initially thought unsuitable for analysis in the 90s, and had been stored for many years in a sealed container marked 'debris'. Those samples didn't contain DNA other than from the victim and Edwards. The defence seems to be relying on an argument that all samples from PathWest should be considered suspect due to the number of other errors uncovered. The critical sample was analysed with a low copy number technique, which I understand increases the risk of detecting DNA resulting from contamination.

The proposed source of the contamination was the sample taken from the rape victim. The prosecution was emphasizing the point that no DNA from the rape victim was detected in the sample. I never saw any very clear sequence of the handling of the samples reported in the news so it's a little hard to follow, but I gather that there was no evidence of the samples being handled around the same time. The defence had been expected to call it's own DNA experts but didn't, and the case closed a few minutes after the prosecution wrapped up.

It will probably come down to whether the judge decides there is reasonable doubt about the sample. There is other evidence, but I don't think it's strong enough on it's own.

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Old 29th May 2020, 04:50 AM   #82
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more thoughts on the negative controls

The prosecution's...interpretion...of the DNA contamination is that because the most important samples were not contaminated, there is nothing to worry about. I have not seen enough reporting specifically on the question of the positive results from four negative controls to be confident in the proper interpretation of this result. A negative control is typically used to show the presence or absence of gross, as opposed to sporadic, contamination. When a negative control shows a positive result, one typically has to redo the entire batch. There is only one exception to this rule that I have found, and it is a very narrow one. We discussed negative controls in the Avery thread. I would like to know which batches were associated with the negative controls that were positive. Any experienced independent DNA consultant could have pointed problems like this out. I don't understand why the defense did not make a detailed presentation.

Perhaps the lab should be audited. Other cases might be found in which the work is questionable enough that an innocent person was convicted.
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Old 29th May 2020, 09:37 AM   #83
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I didn't see a lot of detail reported on the contaminated control blanks. Most of the news reports mentioned blanks being contaminated but didn't clearly explain their association with the crucial evidence. There is some discussion of the issue on this trial podcast site. I haven't listened to the full 37 min podcast yet so I don't know whether it provides any detailed information about the batches.

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Old 29th May 2020, 03:58 PM   #84
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two kinds of negative control experiments

On pages 76-77 in Advanced topics in forensic DNA typing: methodology John Butler wrote, "These controls typically include a "negative control," which is the entire PCR reaction mixture without any DNA template. The negative control usually contains water or buffer of the same volume as the DNA template and is useful to assess whether or not any of the PCR components have been contaminated by DNA (e.g., you or someone else in your lab). An extraction "blank" is also useful to verify that the reagents used for DNA extraction are free from any extraneous DNA templates."

It occurs to me that the controls in question might have been extraction blanks, but I am not sure.
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Old 29th May 2020, 04:42 PM   #85
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I found something referring to the control blanks on the WAtoday reporting of the trial, under 'State seeks to clarify impact of contamination on results'.

'Mr Hollingsworth is re-examining Dr Harbison and asking about which fingernail samples were impacted by the contaminated 'blank' or control samples.'

'She said AJM41 and AJM46 - which returned the presence of a female DNA profile - were in a batch with a contaminated blank. She said this means the SGM+ results become invalid, however the Y chromosome testing, which detected no male DNA, is still valid.

The critical exhibit AJM42's blank was blank. '

It's not the clearest wording, but I was wondering if this means the crucial sample was in a separate batch that did not have a contaminated blank.
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Old 1st June 2020, 12:02 AM   #86
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Originally Posted by Chris_Halkides View Post
Jane Taupin, the author of a number of books on DNA forensics and the coauthor of a book on the forensics of clothing, wrote, "The possibility of the crucial fingernail DNA evidence being contaminated has been raised by the defence at the start of the trial. Four other exhibits in the matter were shown to be contaminated with DNA from PathWest scientists. An intimate swab from the second deceased Jane Rimmer was analysed by PathWest in 1996 with no male DNA result, but later found in 2017 by Cellmark to have an almost complete profile of a male Pathwest scientist involved in preparing the evidence. An intimate swab from Ciara Glennon also yielded an almost complete profile of another PathWest scientist involved in testing the exhibit between 1997 and 2001. Fingernail samples from Jane Rimmer were found by Cellmark to have a DNA profile of another PathWest scientist who was not involved in testing but standing nearby. Two DNA results from branches at the crime scene of Jane Rimmer tested in 2003 years later yielded DNA of another PathWest scientist who examined them."

Ordinarily fingernail DNA evidence is highly useful, in part because so many studies have been done on it. Based on the case of Gregory Turner, I would say that when a sample is contaminated with a forensic worker's own DNA, it was by definition mishandled and should not be considered as evidence. The Australian cases of Farah Jama and Jaidyn Leskie should are cautionary tales with respect to DNA contamination. I am not offering an opinion on the overall innocence or guilt of the accused.

EDT
"Earlier, Mr Bagdonavicius was questioned about the role he played in selecting and preparing a series of "negative control blanks" to be sent to New Zealand, where additional forensic testing was being carried out on the evidence by an agency called ESR.

The "blanks" were supposed to be control samples that did not contain any traces of DNA, however, four out of the 21 samples tested at ESR were contaminated." abc

Here is an article that is skeptical of contamination in this case, although it lists one counterexample to its thesis.
That's a common defence strategy: any contamination whatsoever means the sample is unreliable and needs to be discarded.

Of course I fully understand why the defence wants to use that, if you eliminate the DNA evidence you don't need to explain how your clients' DNA came to be on the victims' fingernails, which is usually a problem that usually can't be solved outside of taking a plea deal.

The usual standard for laboratory contamination is to extract the samples from known donors (i.e. the swabs of suspects) in a separate room and when possible by different people (usually less qualified, students and techinicians) than the samples from the crime scene. Other steps may also be taken, using a different facility would be best but that's usually not possible, so the steps are to use different rooms, different people and different machines, in that order. That should make the transfer of DNA from the known sample outright impossible.

Controls help, but they only tell you there is no systemic contamination with DNA from a megadonor. If there is it should be widespread. German police for years searched in vain of a mystery murderer that was showing up in DNA samples from countless murder scenes. They knew nothing about the killer, just that it was a woman who was implicated in dozens of unconnected murders all over the country.

Then they figured out a fancy brand of swabs they were using in some investigations wasn't sterelized because they weren't intended for forensic use, "the mystery murderer" was a package line worker that left her DNA on the product. It wasn't a problem for the manufacturer because it never advertised their product as sterile or DNA free, but it was a huge issue for the (incompetent) police. Many cases had to be looked over and evidence discarded, thousands, perhaps millions of man-hours went to waste over improper and inadequate use of negative controls.

But anyway, contamination with DNA from laboratory personnel happens from time to time, even though every step is taken to minimize the incidence. That doesn't mean there was transfer of DNA from two samples that were handled in different rooms (that's mandatory, if you want to be accredited), probably by different people and on different days. Any such contamination would have to be found by the negative control.

Defence going the contamination route because a lab worker showed up in some of the samples is akin to "Collusion is not a crime!". It works sometimes too.

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Old 1st June 2020, 05:50 AM   #87
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The persistence of DNA in an office

Fonnelop et al., Forensic Science International: Genetics 29 (2017) 48–60. http://dx.doi.org/10.1016/j.fsigen.2017.03.019

“The [20] participants were all handed T-shirts, one for each of the experiments they would participate in. They were instructed to wear each T-shirt for 3 h. This gave an opportunity to both deposit their own normal background DNA but also to collect “foreign” background DNA from their immediate environment. Participants were instructed not to have any direct physical contact with others during the period."

“In addition we observed one occasion of secondary transfer from a co-worker who had been on leave for two months. This means that sufficient amount of DNA for transfer could persist in the office environment for two months or more.”

The period of 14 months is relevant to this case. One could argue that DNA might persist longer in an office than a lab, but it would be better to be able to demonstrate that point.

There is another aspect of the contamination issue that is worrying. "But Mr Egan said the laboratory would have been cleaned hundreds if not thousands of times in the 14-month period from February 1996 to April 1997 and PathWest had not identified any possible way for the fingernail samples to have been accidentally contaminated by the rape samples." link

Yet it is often not possible to specify the mechanism of transfer: "He [Mr. Egan] said PathWest had been unable to pinpoint the exact way her DNA had been transferred to the twig, but had concluded it must have been through equipment used during the processing of the samples."
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Old 2nd June 2020, 12:32 AM   #88
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Originally Posted by Chris_Halkides View Post
Fonnelop et al., Forensic Science International: Genetics 29 (2017) 48–60. http://dx.doi.org/10.1016/j.fsigen.2017.03.019

“The [20] participants were all handed T-shirts, one for each of the experiments they would participate in. They were instructed to wear each T-shirt for 3 h. This gave an opportunity to both deposit their own normal background DNA but also to collect “foreign” background DNA from their immediate environment. Participants were instructed not to have any direct physical contact with others during the period."

“In addition we observed one occasion of secondary transfer from a co-worker who had been on leave for two months. This means that sufficient amount of DNA for transfer could persist in the office environment for two months or more.”

The period of 14 months is relevant to this case. One could argue that DNA might persist longer in an office than a lab, but it would be better to be able to demonstrate that point.

There is another aspect of the contamination issue that is worrying. "But Mr Egan said the laboratory would have been cleaned hundreds if not thousands of times in the 14-month period from February 1996 to April 1997 and PathWest had not identified any possible way for the fingernail samples to have been accidentally contaminated by the rape samples." link

Yet it is often not possible to specify the mechanism of transfer: "He [Mr. Egan] said PathWest had been unable to pinpoint the exact way her DNA had been transferred to the twig, but had concluded it must have been through equipment used during the processing of the samples."
This is why the contamination defence works sometimes, you confound the jury with a theoretical possibility and leave the obvious questions unasked.

Here's one: How come the fingernail samples, the ones that would contain assailant's DNA, were contaminated, but not other samples?

If his DNA persisted in the lab then you'd expect it to be picked up by many samplings. Yet somehow it only contaminated the samples that would implicate him in the crime, but not any others. Conveniently there was no other DNA in the sample either, because any such contamination would be truly minimal (though possible). If there was a different perpetrator and there was his DNA, there is no way such a minimal contaminant could overwhelm the assailant's DNA. At worst you'd get a mixture of two DNA profiles, that you'd be able to deduce come from your suspect and someone else.

Personally I'd rather go with "police set me up". It's less likely to work, but also less embarassing to listen through. Setting someone up is trivially easy if amplified DNA samples are stored (as is common). You just need to find the tube, thaw it and take out half a microliter or so. You're in and out in ten minutes, no one will ever know. I mean sure, "there was a persistent contamination in the laboratory" is more likely to work on the jury that never knows to ask the follow-up question, or at least isn't able to deduce the defence's argument "it's up to the prosecution to prove the negative" doesn't hold water. But it's embarassing to listen through nonetheless.

By way of comparison, that defence is equivalent to "no sir, it wasn't me in the photo and the video, but someone who looks just like me and wears the same clothes and speaks in my voice and has the same accent, but the prosecution must prove it's actually me, not just someone who looks, dresses and talks just like me". That defence isn't going to work, but it's a pretty good equivalent to the persistent DNA contamination in the laboratory.

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Old 2nd June 2020, 05:39 AM   #89
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Jane Mixer and Gary Letterman

McHrozni,

You wrote, "How come the fingernail samples, the ones that would contain assailant's DNA, were contaminated, but not other samples?" I am not sure that we know about all samples from this lab, as opposed to the samples pertaining to this case. A good deal stands or falls on what is released during a discovery process.

The laboratory of van Oorschot has been studying DNA transfer for many years. They wrote, Our forensic biology laboratory has had an EDM programme in place for a number of years in which various surfaces and tools from within the laboratory are sampled on a peri- odic basis. The items sampled vary each cycle and include those that are deemed high risk (i.e. items that may come in direct contact with exhibits), medium risk (i.e. items that may be touched just prior or during examination of an exhibit) and low risk." If Dr. van Oorschot had testified for the prosecution, I would take it very seriously. I am less inclined to take the lab's own testimony seriously. For one thing, at least one person was fired for not following laboratory procedures.

Do you think that laboratory contamination happened in the Letterman/Mixer case? If so, what do you see as the difference here?
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Old 2nd June 2020, 08:10 AM   #90
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Originally Posted by Chris_Halkides View Post

Perhaps the lab should be audited. Other cases might be found in which the work is questionable enough that an innocent person was convicted.

Laurence Webb, a senior forensic biologist at PathWest was sacked in 2016 for breaching protocols between 2008 and 2014. He was involved in processing the fingernail samples from Ciara Glennon in 2008..

Following this a review concluded no evidence was compromised. I'm not sure how thorough the review was.
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Old 2nd June 2020, 08:15 AM   #91
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The prosecution's expert witness

I have now briefly reviewed Jonathan Whitaker's credentials and they look sound, although I still think that Dr. van Oorschot would have been as good or better. Andrea Mays reported on some of his testimony. "Dr Whitaker said the DNA found on the fingernails was mixed-profile DNA, matching both Ms Glennon's profile and that of Edwards, and both components of the DNA had degraded in the same way, suggesting they had been exposed to the same environmental conditions." This is true, but my understanding of the defense's hypothesis is that the putative contamination happened a long time ago.
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Old 2nd June 2020, 11:46 AM   #92
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Leiterman, not Letterman

Originally Posted by Chris_Halkides View Post
Do you think that laboratory contamination happened in the Letterman/Mixer case? If so, what do you see as the difference here?
This should be the Gary Leiterman/Jane Mixer case. The best summary of this case can be found in Erin Murphy's book.
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Old 2nd June 2020, 12:21 PM   #93
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Originally Posted by Chris_Halkides View Post
I have now briefly reviewed Jonathan Whitaker's credentials and they look sound, although I still think that Dr. van Oorschot would have been as good or better. Andrea Mays reported on some of his testimony. "Dr Whitaker said the DNA found on the fingernails was mixed-profile DNA, matching both Ms Glennon's profile and that of Edwards, and both components of the DNA had degraded in the same way, suggesting they had been exposed to the same environmental conditions." This is true, but my understanding of the defense's hypothesis is that the putative contamination happened a long time ago.
Ciara Glennon's body was discovered three weeks after her murder and had been semi-buried in bushland during what would have been fairly hot weather. The sample from the rape was taken immediately after the offence. Would DNA degrade more from a few weeks out of doors under those conditions than a couple of years stored in a lab? I remember reading this evidence before, but I thought it was referring to degradation that would have occurred prior to the samples coming to the lab, which would not have happened to Edwards' DNA if it had been transferred later. Is that plausible?

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Old 2nd June 2020, 01:43 PM   #94
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A study on fingernail DNA and environmental conditions

Originally Posted by Elaedith View Post
Ciara Glennon's body was discovered three weeks after her murder and had been semi-buried in bushland during what would have been fairly hot weather. The sample from the rape was taken immediately after the offence. Would DNA degrade more from a few weeks out of doors under those conditions than a couple of years stored in a lab? I remember reading this evidence before, but I thought it was referring to degradation that would have occurred prior to the samples coming to the lab, which would not have happened to Edwards' DNA if it had been transferred later. Is that plausible?
There is a paper by Nakanishi and colleagues that studied degradation of DNA underneath fingernails: DOI: 10.1016/s1344-6223(02)00109-8. "Then thumbnails of five volunteers were left in dried soil, wet soil, river water, sea water, distilled water or air for 3 months. Each nail sample was tested monthly for sex chromosome-specific repeats, ABO genotype, STRs (TH01, TPOX, CSF1PO, FES and vWA loci), and D1S80 locus. These markers were correctly detected from nails after 1 month, irrespective of environmental conditions. Thereafter, the detection rates were decreased to various degrees, except for nails left in air. The detection of longer DNA markers tended to be more difficult than the detection of shorter markers. Nails were more fragile in wet soil than in any other condition."

Some years ago I conversed with someone who had studied DNA degradation as part of his thesis. He cautioned me against over interpreting the degree of DNA decay. The problem is that there are so many factors that can lead to degradation.
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Old 2nd June 2020, 01:46 PM   #95
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His DNA got around

Originally Posted by Elaedith View Post
Laurence Webb, a senior forensic biologist at PathWest was sacked in 2016 for breaching protocols between 2008 and 2014. He was involved in processing the fingernail samples from Ciara Glennon in 2008..

Following this a review concluded no evidence was compromised. I'm not sure how thorough the review was.
I think that one of the intimate samples I mentioned in a comment above also had Mr. Webb's DNA, but I don't have a citation handy.
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Old 2nd June 2020, 11:12 PM   #96
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Originally Posted by Chris_Halkides View Post
McHrozni,

You wrote, "How come the fingernail samples, the ones that would contain assailant's DNA, were contaminated, but not other samples?" I am not sure that we know about all samples from this lab, as opposed to the samples pertaining to this case.
Actually there's a pretty good chance we do know that.

Every sample that returns a positive will be matched against the database of known profiles. It's called a cold hit, the police have been doing it for decades now. Every time you profile someone it goes on file, sometimes for a few years, sometimes for a few decades, sometimes permanently, it depends on the jurdistiction. Positive results with no known matches are stored permanently, every new profile is matched against the database.

If there was a persistent contamination in the laboratory he would be implicated in a whole range of otherwise unconnected cases, with zero evidence of the suspect ever being there and at least a few where he definitely wasn't there (i.e. a bank robbery while serving 30 days for drunk and disorderly conduct).

Quote:
The laboratory of van Oorschot has been studying DNA transfer for many years. They wrote, Our forensic biology laboratory has had an EDM programme in place for a number of years in which various surfaces and tools from within the laboratory are sampled on a peri- odic basis. The items sampled vary each cycle and include those that are deemed high risk (i.e. items that may come in direct contact with exhibits), medium risk (i.e. items that may be touched just prior or during examination of an exhibit) and low risk." If Dr. van Oorschot had testified for the prosecution, I would take it very seriously. I am less inclined to take the lab's own testimony seriously. For one thing, at least one person was fired for not following laboratory procedures.

Do you think that laboratory contamination happened in the Letterman/Mixer case? If so, what do you see as the difference here?
A bit of lingo first: known sample is the cheek swab you'll use for DNA matching, an unknown sample is stuff that should contain DNA from a person of interest.

There's a significant disconnect between following procedures in order not to contaminate a critical sample and following procedures in order to deny the defence the ability to scream "contamination" on top of their lungs to secure acquittal. All of these studies, procedures, protocols and whatnot are about the second point, to prove beyond any reasonable doubt there was no contamination. This is nearly impossible to do because you're proving the negative, hence the hassle.

The first point, actually preventing contamination from implicating an innocent person, is non-issue. Extremely basic protocols, followed by every lab that deals with human samples (not just forensics), do that for you. Forensic laboratories do at least one better and process known and unknown samples in separate rooms. However that's to prevent widespread false alarms, not to prevent an innocent person being framed as a result of contamination. You see, it would be an incredible coincidence for a laboratory that might process 1000 known samples (swabs for matching) and 500 unknown samples every week to have a contamination from a known sample from several months ago to specific sample that was relevant to the case from exactly that individual, but not have it contaminate any other sample. That's what negative controls tell you, there is no omnipresent, systemic contamination in the laboratory or equipment or reagents or anywhere else.

Odds of a specific known sample contaminating one and only one unknown sample that is also relevant to that suspect are on the order of one in several billion or less. If it just contaminated a sample it wouldn't be a problem for the suspect, no prosecution is followed on DNA sample alone. At a minimum you also examine the alibi and in most cases people who didn't do the deed have a rock-solid alibi, plus motive, means and everything else. If you find a DNA sample that just doesn't fit anywhere, when the implicated person was obviously nowhere near the victim, ever (i.e. locked up), then you suspect contamination. The samples aren't separated because it would cause a spike in false convictions or unnecessary prosecutions, they're separated to eliminated pointless police work in chasing down leads caused by laboratory contamination.

The overwhelming majority of contaminations would look like that, they would imply random people who literarily couldn't have had anything to do with the crime. This happens just about never, which means the laboratory contamination with a known sample also doesn't happen all that often either.

But explaining that to a jury is often impossible, plus you can't prove this wasn't a unique one type event that. That's still possible, the odds are femtoscopic but nonzero and the court is supposed to interpret everything in favor of the defendant, so you do everything that is humanely possible to prove it didn't happen, then do another three steps further for good measure (thanks, CSI).

As to why you have these studies that show this is indeed possible, the answer is mundane. You see, expert witnesses aren't exactly community service, you expect to be well fed and well paid for your testimony. Having a study of some sort to back up whatever claims you make means you're more valuable as an expert witness. Rule of thumb, if defence claims laboratory contaminiation without very credible and specific evidence it really did happen - someone in the laboratory not following the proper procedure once in the past five years is not it - then the result is fine and defence is just unable to explain it. A credible claim of contamination would be the same DNA profile being found in a completely unrelated case, with zero explanation, or at least a number of false cold hits coming from the laboratory. This will be on the DNA profile and there will be a police report regarding the hit, if you can find that you can claim contamination and remain credible. If you don't have that or something as good as that you're grasping at straws.

That is not to say laboratories shouldn't do everything in their power to prevent contamination from arising in the first place, they should. I'm just saying this is a solved issue, it's not much harder that keeping the workplace cool in summer and warm in winter.

Also, don't think police framing doesn't happen. It's very easy for the police to take one of the swabs and contaminate evidence before it ever reaches the laboratory. I know of some cases when this was basically the only explanation for the quantity and quality of DNA evidence provided. It was either that or the suspect repeatedly licked the bags he used to store drugs.

But that's not a laboratory contamination or something the forensic lab can solve. The official explanation was a superdonor, which is also possible - some people just normally shed way more DNA than others.

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Old 17th June 2020, 12:36 PM   #97
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Originally Posted by Chris_Halkides View Post
This should be the Gary Leiterman/Jane Mixer case. The best summary of this case can be found in Erin Murphy's book.
If I understand this case correctly, I would think the main difference between the Leiterman case and the current one concerns the time interval between processing the critical sample and the potential source of contamination. I understand that in the Leiterman case the samples can into the lab around the same time and were processed within a few weeks of each other. The time interval is much longer in the Claremont case. I suppose in theory the DNA sample from the Claremont rape could have survived that long somewhere where it escaped cleaning, and if a sample escapes cleaning for a few weeks it could continue to do so for longer. It's also possible that the trace could have contaminated more than one sample in the lab, but that this was only detected in the fingernail sample due to the use of low copy number methods for that sample. I would say overall the probability of contamination could be lower in the current case based on the length of time and that there was another unexplained incidence of contamination from Ruleas on the actual critical sample in the Leiterman case.

As for the probability of inferring guilt based on DNA evidence, what struck me about the Leiterman case is that there was apparently no reason to suspect him until the DNA match was made. That means that even if the prior probability of the DNA getting into the sample by contamination was low, the prior probability that he left the DNA at the crime scene would be even lower (given no more reason to suspect him over any other male who might potentially have done so). In the Claremont case, the Karrakatta Cemetery rape had already been linked to the murders on the basis of similarity in the location and characteristics of the offences and fibres found on the rape and murder victims. That means that even had no DNA been recovered from the murder victims, being identified as responsible for the rape would still have meant Edwards would be under suspicion for the murders (although harder to prove without the DNA).

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Old 17th June 2020, 06:28 PM   #98
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Rex and Pad and Profile N; Leiterman

I found an old blog post of mine which mentioned both the Leiterman case and Profile N in New Zealand. I will quote only a small portion here:

Michael Strutt reported, “One caught up in the testing was a mild mannered Christchurch man who had been assaulted outside his local, the Hagley Arms Hotel, on 23 April 1998. Police had taken blood in order to eliminate his DNA from samples taken from the scene of the assault and sent it to ESR for testing. The result of this test came to be dubbed 'Profile N' by the inquiries which were to follow… The Christchurch assault victim was subjected to 'extensive police inquiries' for more than three months and his financial records were seized. This established what he had claimed all along, that he had not left Christchurch around the time of the murders. In fact he hardly left Christchurch at all… Although they never discovered exactly how the mistakes had happened they did determine that the 'Rex' and 'Pad' samples had been accidentally contaminated with DNA from Profile N at an early stage of processing at ESR's Mt Albert laboratories. Extracts from them sent to other laboratories for testing also returned Profile N. Numerous recommendations for improving oversight, record keeping and even laboratory ventilation were made....The fact that the lab in question met the audit requirements is evidence that simply following accepted protocols does not guarantee that contamination will never happen. The lack of the determination of an exact mechanism of contamination is consistent with Dr. Kessis’s caution in the Mixer case above. People who argue that Amanda Knox and Raffaele Sollecito are guilty sometimes demand a mechanism of contamination; unfortunately, this cannot always be determined.”

I was surprised by certain aspects of the Letterman case; for example, that Ruelas's sample was sent to another lab. Erin Murphy wrote, "Leiterman's sample came into the laboratory on February 22, 2002; the evidence in Ruelas's case was processed the day before. Leiterman's sample was first analyzed between July 17 and July 23; Ruelas's reference sample was submitted on July 19 then sent to an outside lab for testing. The Mixer evidence was processed at the lab between March 26, 2002, and April 9, 2002." p. 57, Inside the Cell: The Dark Side of DNA.

So it seems as though there were some time gaps between various samples entering the lab or being processed. The link that I used for Michael Strutt's reporting on Profile N may be dead.
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Old 21st June 2020, 11:12 PM   #99
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Originally Posted by Elaedith View Post
If I understand this case correctly, I would think the main difference between the Leiterman case and the current one concerns the time interval between processing the critical sample and the potential source of contamination. I understand that in the Leiterman case the samples can into the lab around the same time and were processed within a few weeks of each other. The time interval is much longer in the Claremont case. I suppose in theory the DNA sample from the Claremont rape could have survived that long somewhere where it escaped cleaning, and if a sample escapes cleaning for a few weeks it could continue to do so for longer. It's also possible that the trace could have contaminated more than one sample in the lab, but that this was only detected in the fingernail sample due to the use of low copy number methods for that sample. I would say overall the probability of contamination could be lower in the current case based on the length of time and that there was another unexplained incidence of contamination from Ruleas on the actual critical sample in the Leiterman case.
You run at least one sample in each batch to clear up such questions. It only contains the reagents and no human DNA, so if there is any persistent contamination this will pick it up. It did not do so, I wager. Furthermore, I reckon at least some of the proper samples the lab ran came up as wholly negative too. This is incompatible with a contamination within the laboratory.

I'd say a contamination by a sample that was present in the laboratory within weeks of the crime sample being ran is less likely than deliberate framing.

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Old 21st June 2020, 11:25 PM   #100
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Originally Posted by Chris_Halkides View Post
I found an old blog post of mine which mentioned both the Leiterman case and Profile N in New Zealand. I will quote only a small portion here:

Michael Strutt reported, “One caught up in the testing was a mild mannered Christchurch man who had been assaulted outside his local, the Hagley Arms Hotel, on 23 April 1998. Police had taken blood in order to eliminate his DNA from samples taken from the scene of the assault and sent it to ESR for testing. The result of this test came to be dubbed 'Profile N' by the inquiries which were to follow… The Christchurch assault victim was subjected to 'extensive police inquiries' for more than three months and his financial records were seized. This established what he had claimed all along, that he had not left Christchurch around the time of the murders. In fact he hardly left Christchurch at all… Although they never discovered exactly how the mistakes had happened they did determine that the 'Rex' and 'Pad' samples had been accidentally contaminated with DNA from Profile N at an early stage of processing at ESR's Mt Albert laboratories. Extracts from them sent to other laboratories for testing also returned Profile N. Numerous recommendations for improving oversight, record keeping and even laboratory ventilation were made....The fact that the lab in question met the audit requirements is evidence that simply following accepted protocols does not guarantee that contamination will never happen. The lack of the determination of an exact mechanism of contamination is consistent with Dr. Kessis’s caution in the Mixer case above. People who argue that Amanda Knox and Raffaele Sollecito are guilty sometimes demand a mechanism of contamination; unfortunately, this cannot always be determined.”

I was surprised by certain aspects of the Letterman case; for example, that Ruelas's sample was sent to another lab. Erin Murphy wrote, "Leiterman's sample came into the laboratory on February 22, 2002; the evidence in Ruelas's case was processed the day before. Leiterman's sample was first analyzed between July 17 and July 23; Ruelas's reference sample was submitted on July 19 then sent to an outside lab for testing. The Mixer evidence was processed at the lab between March 26, 2002, and April 9, 2002." p. 57, Inside the Cell: The Dark Side of DNA.

So it seems as though there were some time gaps between various samples entering the lab or being processed. The link that I used for Michael Strutt's reporting on Profile N may be dead.
The DNA evidence in Knox/Sollecito case should be thrown out entirely. Not because of any laboratory or collection contamination, but because if you collect samples of a place someone lives in, there is a built-in explanation for their DNA being whereever: they lived there.

DNA may be used to establish the presence of person X on the scene. If that scene is his or her home then DNA is nearly useless to proving that yes, they indeed lived there. If all you find is their DNA, even if it's in a room they claim they never went to, there is an explanation for that - they left their DNA somewhere (perhaps from a sneeze) and someone else transported it to the room. If all you have is DNA that is useless as evidence.

Police investigation is always personal, first and foremost. You question the suspect and try to have them establish a story. Then you look at all the evidence, including forensic evidence, to see if it matches the story or if there is some bit or piece that cannot be explained by the story. I can explain the presence my own DNA in my home, thank you very much. My DNA on the handle of a knife that was used to kill the victim? It's entirely possible that someone held it with a glove, or else had very dry hands, and my own DNA remained there as the main donor.

This is far more likely than some mysterious "laboratory contamination" that only affected one sample - crucially the one that made the difference in the case.

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Old 21st June 2020, 11:39 PM   #101
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Originally Posted by Chris_Halkides View Post
I found an old blog post of mine which mentioned both the Leiterman case and Profile N in New Zealand.
I'll comment on this part:

The main issue in this case is a disagreement among experts over the correct statistical calculation to use in cold hit cases. Another key element in this case is that it made use of a partial, not full, DNA profile. In the United States a full DNA profile has thirteen separate markers (loci). A profile must have seven markers for it to be searched in California’s database. However, only 5 and a half markers were clearly found in the Sylvester murder. The jury was told that the chances of a random person’s matching the DNA found at the crime scene were 1.1 million to one. Yet when the odds were calculated with a different set of statistical assumptions the odds were only one in three, a statistic that the jury was barred from hearing. This is why the odds were only 1.1 million to one, and not substantially higher. However, when one uses a model that takes into account that there were 338,000 profiles in the database, one arrives at the 1-in-3 odds. The question of which model is better is a difficult one, yet it is odd that California courts have taken it upon themselves to decide which model is more appropriate. And the difference between one in 1.1 million and 1 in 3 is huge. It would have probably been enough to move at least one juror from guilty to not guilty beyond a reasonable doubt.

The way you calculate odds of a random person matching is by looking at the frequency of each locus in a given population. Each locus is a simple number, ranging from something like 4 all the way up to 17 and sometimes more. This is the number of short, four nucleotide repeats in non-coding DNA that appears in specific places, you count the number of repeats the person has on that alele.

Anyway, if you have five loci to work with, you'll have something like:
D3S1358 14, 17
vWA 14,14 (homozygote)
D16S539 10,11
D2S1338 19,25
D8S1179 14,15

This is a realistic example, taken from a kit that would be used in 2002, page 94:
https://assets.thermofisher.com/TFS-...cms_041049.pdf

You then look up for frequency of each alele, either in racial information or take the whole thing, and come up with a number that 1 in 1.1 million people would have a profile like that. This is the approximate odds of this sample above that I made up.

So the match is not 1:3, because the database is 380,000 people strong. That's just the odds of having one person with that DNA profile in the database. The DNA could still be deposited there by only one person in an entire city worth of people. If you had a database of 33 million people you'd expect about 30 people to be possible donors and if you did so the police could check those people one by one to exclude them as suspects. Most would have rock-solid alibis (innocent people usually do) and the rest could be excluded by other basic measures, such as not matching the description or whatever other evidence is used to convict. DNA evidence alone is useless.

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Old 30th June 2020, 05:41 PM   #102
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random match probability versus source probability

My lone paragraph about the Puckett case could not do justice to the interest in it that has been shown by academics. I will try to return to it over the next few weeks, because I think that some of the issues in the Pockett case illuminate the present one. For example, I was not questioning the calculation of the random match probability (RMP) in the former; instead, I was implying that giving only one statistic to the jury, particularly without context, might have been misleading.

Recently I found an article that dealt with both the Puckett case and which also addressed an issue that applies to a number of cases. Among other things, it distinguishes the RMP from the source probability. The article is "Safety in numbers-Deciding when DNA alone is enough to convict," by Andrea Roth link. Here is a paragraph that may whet one's appetite for the whole article:

"In sum, there appear to be three critical shortcomings in how courts-both in the United States and in the United Kingdom-have dealt with the issue of legal sufficiency in pure cold hit cases. First, while courts appear to understand that the sufficiency of a DNA pro- file match is a function of how high the source probability is, courts do not understand how to calculate the source probability, typically con- flating it with the RMP and failing to consider the size of the suspect population. Second, although courts appear to have found some match statistics sufficient and others insufficient, no court has explained how it made this determination-that is, whether there is some numerical threshold that the source probability must meet to render the DNA match alone legally sufficient evidence of guilt. Finally, neither courts nor litigants appear to have explored the more fundamental question of whether numerical evidence alone, even a very high source probability, should ever be deemed sufficient evidence of guilt by itself."
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Old 30th June 2020, 11:17 PM   #103
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Originally Posted by Chris_Halkides View Post
My lone paragraph about the Puckett case could not do justice to the interest in it that has been shown by academics. I will try to return to it over the next few weeks, because I think that some of the issues in the Pockett case illuminate the present one. For example, I was not questioning the calculation of the random match probability (RMP) in the former; instead, I was implying that giving only one statistic to the jury, particularly without context, might have been misleading.

Recently I found an article that dealt with both the Puckett case and which also addressed an issue that applies to a number of cases. Among other things, it distinguishes the RMP from the source probability. The article is "Safety in numbers-Deciding when DNA alone is enough to convict," by Andrea Roth link. Here is a paragraph that may whet one's appetite for the whole article:

"In sum, there appear to be three critical shortcomings in how courts-both in the United States and in the United Kingdom-have dealt with the issue of legal sufficiency in pure cold hit cases. First, while courts appear to understand that the sufficiency of a DNA pro- file match is a function of how high the source probability is, courts do not understand how to calculate the source probability, typically con- flating it with the RMP and failing to consider the size of the suspect population. Second, although courts appear to have found some match statistics sufficient and others insufficient, no court has explained how it made this determination-that is, whether there is some numerical threshold that the source probability must meet to render the DNA match alone legally sufficient evidence of guilt. Finally, neither courts nor litigants appear to have explored the more fundamental question of whether numerical evidence alone, even a very high source probability, should ever be deemed sufficient evidence of guilt by itself."
Ooh, good one. I can answer why no universal standard for a DNA match was ever made: it's impossible to make one.

Suppose you have 11 people stranded on an island, 10 males and one female. Just before the rescue, the female is raped but can't identify which of the 10 males was it. A rape kit is done and you get a partial DNA profile, with only one locus.

The male profile is a very common variant, shared by over 30% of the population, so the match is a measly 1 in 3. Yet, by coincidence, none of the other 9 males nor the female has that variant on the locus and could be the donor of the DNA in her vagina.

The DNA sample in this case is good enough to be the key bit of evidence (alongside corroborating pieces) to secure a conviction. Yet the match is a mere 1:3, which is basically useless in a less extreme scenario.

Most cases are like that. Yes, the match is a mere 1 in 100 million. But there were only about 500 thousand people who could possibly be anywhere near the crime scene, the rest of the world's population were all too far away to drive there and back and not be noticed. That means the odds are none of them could've been the donor of the DNA.

You can't get a universal, transparent standard of when the match is "good enough" that would be better than an expert opinion on each individual case. If there are many possible donors you need a far better match, especially if they're related to one another or even inbred. Gypsies can be a major problem for DNA profiling for precisely that reason.

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Old 8th July 2020, 01:07 PM   #104
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Originally Posted by Chris_Halkides View Post
My lone paragraph about the Puckett case could not do justice to the interest in it that has been shown by academics. I will try to return to it over the next few weeks, because I think that some of the issues in the Pockett case illuminate the present one. For example, I was not questioning the calculation of the random match probability (RMP) in the former; instead, I was implying that giving only one statistic to the jury, particularly without context, might have been misleading.

Recently I found an article that dealt with both the Puckett case and which also addressed an issue that applies to a number of cases. Among other things, it distinguishes the RMP from the source probability. The article is "Safety in numbers-Deciding when DNA alone is enough to convict," by Andrea Roth link. Here is a paragraph that may whet one's appetite for the whole article:

"In sum, there appear to be three critical shortcomings in how courts-both in the United States and in the United Kingdom-have dealt with the issue of legal sufficiency in pure cold hit cases. First, while courts appear to understand that the sufficiency of a DNA pro- file match is a function of how high the source probability is, courts do not understand how to calculate the source probability, typically con- flating it with the RMP and failing to consider the size of the suspect population. Second, although courts appear to have found some match statistics sufficient and others insufficient, no court has explained how it made this determination-that is, whether there is some numerical threshold that the source probability must meet to render the DNA match alone legally sufficient evidence of guilt. Finally, neither courts nor litigants appear to have explored the more fundamental question of whether numerical evidence alone, even a very high source probability, should ever be deemed sufficient evidence of guilt by itself."

If I understand this correctly, the conflation of RMP with source probability described in the article as due to the 'fallacy of the transposed conditional' is the same as 'confusion of the inverse' where the probability of a match, given innocence, is conflated with the probability of innocence, given a match. I find this interesting as it seems to be a ubiquitous error (the same as conflating the probability of getting an outcome when the null is true with the probability that the null is true that seems to explain so much confusion over p values). I'm not sure why the RMP would be given to a jury at all given that this is likely to be misleading. I could see that a likelihood ratio alone is somewhat imprecise given that the 'size of the suspect population' is not really the actual number of potential suspects in reality (since some will in reality not be plausible suspects), but the LR is easier to understand and less likely to bias perception than a tiny RMP.

I am personally very interested in this issue of how probability is understood by juries. I have seen some interesting research on the effect of using different ways of presenting probabilistic evidence. It's probably getting away from the Claremont case since there is is no jury and there is other evidence. In cases where is nothing but the source probability of DNA evidence it seems the main difficulty is having no reliable way to estimate the possible impact of other unknown factors on probability of guilt. In the Claremont case, the difficulty would be how much weight to give the other factors.
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Old 8th July 2020, 02:42 PM   #105
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Originally Posted by McHrozni View Post
I'll comment on this part:



So the match is not 1:3, because the database is 380,000 people strong. That's just the odds of having one person with that DNA profile in the database. The DNA could still be deposited there by only one person in an entire city worth of people. If you had a database of 33 million people you'd expect about 30 people to be possible donors and if you did so the police could check those people one by one to exclude them as suspects. Most would have rock-solid alibis (innocent people usually do) and the rest could be excluded by other basic measures, such as not matching the description or whatever other evidence is used to convict. DNA evidence alone is useless.

McHrozni
I'm assuming the 1:3 was referring to the distinction between RMP match and database match (where the sample is compared against every entry in the database, so any chance match is bound to be detected). Although obviously that still does not provide probability of guilt which is also based on other factors that affect likelihood that the culprit will or won't be in the database.

You have mentioned DNA evidence alone being useless in the context of excluding suspects. I think the question is what happens when somebody has no alibi and can't be excluded, but the DNA is the only evidence against them (or other evidence is weak and only discovered as a result of the DNA match). It may not happen often but has happened in some of the cases discussed.
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Old 10th July 2020, 03:39 AM   #106
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Some background information on negative controls

I have collected a few quotes to explain what negative controls are, although more could be said on this subject. All three articles are worth reading in their entirety.

“Identifying and Preventing DNA Contamination in a DNA-Typing Laboratory,” by Terri Sundquist and Joseph Bessetti (Promega Corporation) link
“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.”

“DNA Testing: An Introduction for Non-Scientists,” by Dr. Donald E. Riley link
“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. These controls don't offer protection against contamination occurring before the samples arrived at the PCR lab. Negative controls also can't rule out contamination of individual samples. The individual samples lack individual signs of contamination if it occurs. Unlike a human patient, a PCR is incapable of showing signs of infection (contamination) such as fever or undue pain. PCRs also have no immune system to ward off contaminants.”

"Tarnish on the Gold Standard,” by Professor William Thompson (University of California at Irvine) link to a number of articles
“While most of the problems are due to inadvertent mistakes, a number of cases involving dishonesty have also come to light…In all of these cases, the analysts were caught faking the results of control samples designed to detect instances in which cross-contamination of DNA samples has occurred.”

“In most instances, these errors produced unexpected results that flagged the problem, such as positive results in a control sample that was supposed to contain no DNA or a second DNA profile in a sample that was supposed to be from a single person. Upon noticing such problems, labs typically throw out the results of that test and start over.”

“Given the unexpectedly high frequency of contamination in DNA testing we have just discussed, it is interesting, and not at all surprising, that the major form of fakery discovered to date involves control samples known as extraction blanks that are designed to detect contamination. These samples are supposed to contain no DNA. When they produce positive results, it indicates there was a problem — DNA somehow ended up in a sample where it did not belong. If that happened to a control sample, it could also have happened to other samples, so the analyst must throw out the whole test and start over.”
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Old 15th July 2020, 02:37 AM   #107
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Originally Posted by Elaedith View Post
You have mentioned DNA evidence alone being useless in the context of excluding suspects.
Well, no. DNA evidence alone is useless for conviction, you need to at least show the person didn't have an alibi and is a possible culprit. It can be used to exclude a suspect, in a trivial example you'd be dealing with a rape case and have semen available (a very good donor, for obvious reasons), but the suspect you're investigating wouldn't have the same DNA profile as the semen. The victim survived and identified a possible culprit from a photo line-up, that's the only reason why you investigated him as the suspect.

Any sensible investigator would conclude this man is not the culprit and that you're dealing with a case of mistaken identity. The culprit probably looks like him. If you want to be extra careful you'll ask for a semen sample to exclude chimerism (where one person is actually a cojoined, assimilated twin), but that's extraordinarily rare, with about six known cases in 70 years.

Quote:
I think the question is what happens when somebody has no alibi and can't be excluded, but the DNA is the only evidence against them (or other evidence is weak and only discovered as a result of the DNA match). It may not happen often but has happened in some of the cases discussed.
Wait, evidence discovered as a result of DNA match, if the match was attained lawfully (that's ... not always the case), can be used against the suspect without issue.

DNA alone can't be used to convict. DNA plus a lack of alibi plus weak other evidence, even if the DNA match led to it, can.

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Old 15th July 2020, 02:50 AM   #108
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Originally Posted by Chris_Halkides View Post
I have collected a few quotes to explain what negative controls are, although more could be said on this subject. All three articles are worth reading in their entirety.
Reagent blank is a sample in which you do not add a compound to be detected. It works the same if you're working with DNA or looking for pesticides in drinking water. It's used to detect an ongoing, persistent contamination of the apparatus. There's also a sample blank, which is the sample without reagents, but that's not useful in DNA.

I'm pointing it out because it's a good thing to keep in mind when reading the articles. It's an ubiquitous concept throught the relevant sciences, DNA is a tad special because a PCR based method will readily detect a single molecule of contaminant. The articles are well worth the read, but do keep in mind this is not something unique that only DNA guys need to worry about.

Again, you do not prevent contamination via negative control. You detect an ongoing contamination with it. What prevents contamination with a known sample is competent handling of the samples - separate rooms for known and unknown samples, handling both in separate batches, making sure those paths do not cross, having different people do them, daily or more frequent decontamination and so on.

These protocols are multiple redundant, you need to make several major errors to theoretically introduce a contamination. Even if all of them fail, even if you deliberately pippete the crime scene sample right next to a known sample of a suspect to be investigated (that's a "you're fired!" on the spot), you're still unlikely to produce a contamination, because you won't pipette it with the same tip. If you do s o the transfer of DNA can be considered deliberate, it's a reflex ingrained in everyone to change the pipette tip after each action (and in between, just in case). This is not limited to DNA but it is most critical when working with small samples of DNA.

That's why it is my opinion contamination with a known sample in a laboratory is only possible if it was deliberate, or else if the laboratory has a history of such results. Deliberate contamination cannot be excluded, but a single case of contamination with a known sample occuring by chance or incompetence can. Unless the laboratory had several instances of false positive results of DNA tests the incidental cross-contamination is excluded as a possibility.

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Old 15th July 2020, 05:52 AM   #109
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John Puckett, Raymond Easton, and Stephen Myers

Offhand I can think of at least three ways in which an innocent person might be seemingly inculpated by DNA evidence: a coincidental match of a partial profile, contamination in the narrow sense of a laboratory event, and sample mix-ups. All three have happened. Chapter 7 in Erin Murphy's indispensable book Inside the Cell is called dangers of the database, and she gives several illustrative examples, going into the greatest depth on the John Puckett case (which may deserve its own thread). She also discusses the Arizona database search that surprised some. The following are quick summaries.

Raymond Easton was identified and arrested on the basis of a six-locus match. He had late state Parkinson's and could not have committed the crime (I mentioned this case at my blog). He was eventually exonerated by further testing. Along with the Easton case, the Stephen Myers case also illustrated the problem that investigators are slow to conclude that DNA has pointed to the wrong person. The Newark, Ohio burglar was short, stout, and balding whereas Mr. Myers was tall, slender, and was fifteen years old at the time of the offense. From what I can gather, he lived in a neighboring state, West Virginia. Professor Murphy wrote, "Investigators waved away the physical discrepancy by noting the tappearanced change."

In the John Puckett case, there was a drop of blood from another suspect, but when his attorney asked that it be tested, it had gone missing from the case file. On the basis of the available evidence, Mr. Puckett was not obviously innocent, but neither was he guilty beyond a shadow of a doubt. The Puckett case has attracted the interest of at least one other academician besides Professor Murphy, but that will have to wait for another time.

With respect to laboratory contamination, the Farah Jama and Jaidyn Leskie cases are good examples that it does occur. IIRC Mr. Jama spent time in pretrial detention, although I am certain that he was cleared eventually. IIUC, Ms. P (the unknown person whose DNA ended up on items of evidence in the Leskie case and herself a possible crime victim) was quickly cleared of involvement. The previously mentioned Rex and Pad murder investigations in New Zealand were also instances of laboratory contamination.

Whenever there is a cold case hit, the question should arise as to whether or not the police investigation will clear an innocent person. This quick survey suggests a mixed record.
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Old 15th July 2020, 01:53 PM   #110
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false cold hits and cross-contamination

In a book chapter called "Forensic DNA Evidence," William Thompson wrote, "Cross-contamination is also known to have caused a number of false cold hits. For example, while the Washington State Patrol Crime Laboratory was conducting a “cold-case” investigation of a long-unsolved rape, it found a DNA match to a refer- ence sample in an offender database, but it was a sample from a juvenile offender who would have been a toddler at the time the rape occurred. This prompted an internal investigation at the laboratory that concluded that DNA from the offender’s sample, which had been used in the labo- ratory for training purposes, had accidentally contaminated samples from the rape case, producing a false match.12 Similar errors leading to false database matches have been reported at forensic DNA laboratories in California, Florida, and New Jersey, as well as in New Zealand and Australia.13 Three separate cases have come to light in which cross- contamination of samples at the Victoria Police Forensic Services Centre in Melbourne caused false cold hits. Two of those cases led to false convictions.14"

In "The Potential for Error in Forensic DNA Testing (and How That Complicates the Use of DNA Databases for Criminal Identification)," Professor Thompson wrote, "He [a forensic scientist who had previously worked in a public forensic laboratory] told The Australian newspaper that it was not uncommon for the lab to mix up DNA samples from different cases.[62] For example, he said that analysts’ own DNA, from blood samples used as analytical controls, often was mixed up with (or found its way into) casework samples, creating false matches: “[Q]uite often my (colleague) would walk down the aisle and say, ‘I’ve just committed another rape on the Gold Coast.’”[62]" This paper was written in 2008 as part of a conference, Forensic DNA Databases and Race: Issues, Abuses and Actions held June 19-20, 2008, at New York University.
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Old 17th July 2020, 03:11 AM   #111
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Originally Posted by Chris_Halkides View Post
Offhand I can think of at least three ways in which an innocent person might be seemingly inculpated by DNA evidence: a coincidental match of a partial profile, contamination in the narrow sense of a laboratory event, and sample mix-ups. All three have happened.
"Have happened" and "do happen nowadays" are two different things. Planes have fallen out of the sky due to metal fatigue, that doesn't mean it's a plausible explanation for what happened to MH17.

Quote:
With respect to laboratory contamination, the Farah Jama and Jaidyn Leskie cases are good examples that it does occur. IIRC Mr. Jama spent time in pretrial detention, although I am certain that he was cleared eventually. IIUC, Ms. P (the unknown person whose DNA ended up on items of evidence in the Leskie case and herself a possible crime victim) was quickly cleared of involvement. The previously mentioned Rex and Pad murder investigations in New Zealand were also instances of laboratory contamination.
The two events where DNA contamination within the laboratory is suspected (though not proven) happened 20 and 24 years ago, respectively. It is entirely plausible extraction and amplification protocols were inadequate and contamination did occur. It is not hard to do so, IF the protocols leave enough to be desired.

No later than 2010, and probably years prior, adequate protocols were in place for accidental laboratory contamination to be non-issue. Deliberate contamination is possible, crime scene accidental contamination (i.e. Knox case) is possible, but accidental laboratory contamination is not plausible.

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Old 17th July 2020, 04:43 AM   #112
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Originally Posted by Chris_Halkides View Post
In a book chapter called "Forensic DNA Evidence," William Thompson wrote, "Cross-contamination is also known to have caused a number of false cold hits. For example, while the Washington State Patrol Crime Laboratory was conducting a “cold-case” investigation of a long-unsolved rape, it found a DNA match to a refer- ence sample in an offender database, but it was a sample from a juvenile offender who would have been a toddler at the time the rape occurred. This prompted an internal investigation at the laboratory that concluded that DNA from the offender’s sample, which had been used in the labo- ratory for training purposes, had accidentally contaminated samples from the rape case, producing a false match.12 Similar errors leading to false database matches have been reported at forensic DNA laboratories in California, Florida, and New Jersey, as well as in New Zealand and Australia.13 Three separate cases have come to light in which cross- contamination of samples at the Victoria Police Forensic Services Centre in Melbourne caused false cold hits. Two of those cases led to false convictions.14"
It would be helpful if you could link to these cases. The cross-contamination did happen before it was sufficiently understood. It also explains how it looks like, laboratory either has contamination in several random cases (cold hits), or else none at all.

Quote:
In "The Potential for Error in Forensic DNA Testing (and How That Complicates the Use of DNA Databases for Criminal Identification)," Professor Thompson wrote, "He [a forensic scientist who had previously worked in a public forensic laboratory] told The Australian newspaper that it was not uncommon for the lab to mix up DNA samples from different cases.[62] For example, he said that analysts’ own DNA, from blood samples used as analytical controls, often was mixed up with (or found its way into) casework samples, creating false matches: “[Q]uite often my (colleague) would walk down the aisle and say, ‘I’ve just committed another rape on the Gold Coast.’”[62]" This paper was written in 2008 as part of a conference, Forensic DNA Databases and Race: Issues, Abuses and Actions held June 19-20, 2008, at New York University.
This is another question entirely, sample contamination by a laboratory worker or a crime scene technician is a common problem that does happen from time to time. Laboratories keep DNA profiles of all employees at hand for that eventuality.

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Old 17th July 2020, 02:32 PM   #113
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some links to Professor Thompson's works

William Thompson's 2008 article "The Potential for Error in DNA testing..." can be found here. It can also be obtained through Research Gate.

Professor Thompson's 2012 chapter "Forensic DNA Evidence: The Myth of Infallibility" is available at Research Gate and through SSRN.

A number of articles by Professor Thompson and others are available at the Forensic Bioinformatics Resources page.
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Old 21st July 2020, 12:08 AM   #114
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Originally Posted by Chris_Halkides View Post
William Thompson's 2008 article "The Potential for Error in DNA testing..." can be found here. It can also be obtained through Research Gate.
This ... isn't a scientific article. I don't know what it is, but given the content within it's a general interest article that wants to give the impression of being a scientific article. It leaves a whole lot out, laboratories don't just feed the kit into a machine and read out the numbers, yet that's the impression I got within the first few pages. You get the elecropherogram and are expected to figure out whether the sample is degraded or not (NOT difficult) and whether or not you should run the sample again, with a kit specialized for degraded samples (yeah, those exist ... and were common already in 2008).

The next issue is mixtures. Yes, mixtures can be a problem, but he leaves out the two ways used to solve them. The first is that it often happens the quantities of the two DNA profiles differ and it's possible to entirely separate the two profiles. If the samples are present in, say, a ratio of 10:1 you can separate the taller peaks from smaller ones with ease. The second solution is that we do know how often do certain allelles appear in the population. A 1:1 mixture of two DNA samples, where one person could be the donor, is still attributable to that person as a one in a million match or so. That's because the number of people that could give that exact same mixture is so low. That's why we use 13 (now often 16) loci in the first place.

These are known solutions to the problems that have been routine by 2008, when the article was produces.

The next up is the probability of two people sharing the same 13-loci profile that the author considers worthy to mention, because there are so many people to compare them to. I think the greatest known match is about 7-8 loci, and even that was in an inbred population of European gypsies (Roma). I use inbred as a description of their marriage patterns, not as some form of insult. They do that and it's a problem for forensics. Birthday paradox is mentioned, but that's just the odds of ANY two people in a room sharing the same birthday. This is the odds of THIS person sharing a genome with someone else, a completely separate statistical question. This is neither explained, nor discussed in any depth.

Furthermore, the author claims it is possible for two siblings to have the same STR profile. This is true, odds of a match to a sibling are significantly greater than those with a random population. However this was a solved issue long before 2008: you don't convict based on DNA alone. At a minimum you have to show the alledged culprit had no alibi and some other ancilliary evidence, motive and such (it depends a bit on the crime, a bulgrary comes with a built-in motive, a murder does not). The author mentions several times when such methods worked, they resulted in an unnecessary arrest at worst. That is annoying, but there's usually a rather good reason why your DNA profile is in the database anyway.

Or this one:
"Clothing the person wore, a cigarette the person smoked, a glass the person drank from could all, if placed at a crime scene, create a false DNA link between an innocent person and a crime."

It was routine in 2008 for criminals to claim this exact thing happened to them and the police had to figure it out. That's one of the reasons why DNA isn't a miracle silver bullet, merely a tool in the database. The usual standard is for the suspect to exclude the possibility their DNA has been there in the first place, then present them with evidence they're lying. The sought after result is a confession and a plea deal, not a jury trial.

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Old 22nd July 2020, 04:09 AM   #115
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Cases of Gregory Turner and Kevin Brown

Originally Posted by McHrozni View Post

This is another question entirely, sample contamination by a laboratory worker or a crime scene technician is a common problem that does happen from time to time. Laboratories keep DNA profiles of all employees at hand for that eventuality.

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It would be a mistake to draw a bright line between laboratory workers contaminating a sample with their own DNA with contaminating it with a suspect's DNA. For one thing, consider the Gregory Turner case. The victim's DNA was found was found on his wedding ring. However,

"A lucky hunch by Mr. Kennedy - now Newfoundland's Minister of Health - saved Mr. Turner from a life behind bars. He sought the name and DNA profile of every technician who had worked at the RCMP lab. It turned out that the technician who had tested the ring had also been working on the victim's fingernails a few inches away, creating a strong possibility of contamination.
The technician conceded at Mr. Turner's 2001 trial that she had also contaminated evidence in two previous cases. In another disturbing twist, it emerged that she had mistakenly contaminated Mr. Turner's ring with her own DNA, causing police to waste considerable time on a futile search for a presumed accomplice.

Mr. Turner still has nightmares. "I remember the judge saying that he was denying me bail based on the likelihood I'd be convicted based on a DNA match," he said. "I think DNA can be good, but its only as good as the people who perform it. I spent 27 months in jail for a crime I didn't do."
In just 20 years, DNA has become a staple of crime-lab analysis, capturing the imagination of scriptwriters and anchoring thousands of criminal convictions. Its record of accuracy is superb - at least, when samples are collected and analyzed under reliable conditions by experts."

For another, consider the sad case of laboratory worker Kevin Brown, who probably contaminated a sample and yet became a suspect. IIUC he later committed suicide.

Why the defense in this case did not call an expert to walk the jury through instances of laboratory contamination like Mr. Turner's is puzzling.
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Old 22nd July 2020, 04:29 AM   #116
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Russell Gesah, Farah Jama, and Gary Leiterman

Originally Posted by McHrozni View Post
The two events where DNA contamination within the laboratory is suspected (though not proven) happened 20 and 24 years ago, respectively. It is entirely plausible extraction and amplification protocols were inadequate and contamination did occur. It is not hard to do so, IF the protocols leave enough to be desired.

No later than 2010, and probably years prior, adequate protocols were in place for accidental laboratory contamination to be non-issue. Deliberate contamination is possible, crime scene accidental contamination (i.e. Knox case) is possible, but accidental laboratory contamination is not plausible.

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Some labs have instituted "more stringent cleaning processes," according to the Sydney Morning Herald. However, beyond that I see no reason for optimism. If anything, low template DNA work makes laboratory contamination more likely than it would otherwise be. In the Knox Sollecito case, the bra clasp may have been contaminated during its collection, but the kitchen knife was almost certainly an instance of laboratory contamination, of which there have been many examples. In the Leskie case work by Professor Thompson's associate, Professor Dan Krane, was one of the things that made laboratory contamination a more plausible explanation than a coincidental match. Reports on the Leskie case by both professors are worth reading and can be found at a link previously given. Even the coroner conceded that this was laboratory contamination

The case of Russell Gesah is also instructive. "Weeks after crediting DNA technology with a breakthrough in the 24-year-old case, police yesterday announced they had withdrawn the charges against Russell John Gesah because the evidence they were relying may have been contaminated." link

The case of Farah Jama, which I also covered at my blog, is another instance of laboratory contamination. "This chapter is concerned with an emerging third strand of the narrative: DNA’s potential to conceal truths and create falsehoods. Recently this dark side of DNA has become prominent in the Australian state of Victoria, where it is now associated with one name. Farah Jama was convicted solely on the basis of a matching DNA profile, with tragic repercussions."

I have written about the Gary Leiterman case here and elsewhere on several occasions. Let me focus on one issue right now. John Ruelas was four years old and did not live in Ann Arbor, MI. His DNA could not have appeared in the Jane Mixer case in any reasonable except laboratory contamination

These cases illustrate that in a cold case the suspect usually does not have an alibi, that DNA alone is enough to convict, and that juries will convict in spite of evidence of laboratory contamination; these points may be relevant to the present case.
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Old 22nd July 2020, 04:50 AM   #117
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Originally Posted by Chris_Halkides View Post
Some labs have instituted "more stringent cleaning processes," according to the Sydney Morning Herald. However, beyond that I see no reason for optimism. If anything, low template DNA work makes laboratory contamination more likely than it would otherwise be. In the Knox Sollecito case, the bra clasp may have been contaminated during its collection, but the kitchen knife was almost certainly an instance of laboratory contamination, of which there have been many examples. In the Leskie case work by Professor Thompson's associate, Professor Dan Krane, was one of the things that made laboratory contamination a more plausible explanation than a coincidental match. Reports on the Leskie case by both professors are worth reading and can be found at a link previously given. Even the coroner conceded that this was laboratory contamination

The case of Russell Gesah is also instructive. "Weeks after crediting DNA technology with a breakthrough in the 24-year-old case, police yesterday announced they had withdrawn the charges against Russell John Gesah because the evidence they were relying may have been contaminated." link

The case of Farah Jama, which I also covered at my blog, is another instance of laboratory contamination. "This chapter is concerned with an emerging third strand of the narrative: DNA’s potential to conceal truths and create falsehoods. Recently this dark side of DNA has become prominent in the Australian state of Victoria, where it is now associated with one name. Farah Jama was convicted solely on the basis of a matching DNA profile, with tragic repercussions."

These two case illustrate respectively, that in a cold case one usually does not have an alibi and that DNA alone is enough to convict; the former may be relevant to the present case.
I thought in the Farah Jama case there was even exculpatory evidence (including alibi evidence) that was ignored.

In the current case, I was wondering how the use of a LCN method could contribute to the risk of a match being the result of contamination. An argument was that it is unlikely contamination of just one critical sample would occur (assuming all cases of contamination are in fact recorded). Is it possible that contamination of other samples could be undetected if they weren't analysed with the same methods?
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Old 22nd July 2020, 07:31 AM   #118
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Farah Jama; low template samples and the increased risk of contamination

Originally Posted by Elaedith View Post
I thought in the Farah Jama case there was even exculpatory evidence (including alibi evidence) that was ignored.

In the current case, I was wondering how the use of a LCN method could contribute to the risk of a match being the result of contamination. An argument was that it is unlikely contamination of just one critical sample would occur (assuming all cases of contamination are in fact recorded). Is it possible that contamination of other samples could be undetected if they weren't analysed with the same methods?
Justice Frank Vincent wrote a report on the Farah Jama case that deserves to be re-read and quoted frequently. There were various kinds of exculpatory evidence: IIUC e was praying with his father at the time of the incident. However, his father was very sick and may have passed away not long after. I discussed his case here and here. The following two paragraphs come from the second link:

The discussion of low copy number (LCN) testing from the Crown Prosecution Service noted, “This increased sensitivity means ultra-clean laboratories are needed for the testing to minimise contamination of the sample by DNA from any other source.” The New Zealand Institute of Environmental Science and Research has spent $1 million building anticontamination areas for low copy number (LCN) DNA forensics. The New Zealand Herald wrote, “The bogey is contamination. The very sensitivity of the technique which enables it to extract a DNA profile from the tiniest sample also makes it extremely vulnerable to contamination. Stringent measures are needed to minimise that risk… We live in a ‘soup’ of DNA, explains ESR forensic programme manager Keith Bedford. ‘If I were to shed dandruff, massive amounts of dna could fall ... hair could carry DNA. The way I am speaking at the moment, we could probably detect DNA on this pad in front of me.’”

Sara Gino testified for the defense in the trial of the first instance, and some of what she had to say is pertinent to this issue. From the Massei report (p. 258, English translation): “She reaffirmed that [the risk of] contamination exists, and emphasised that in minimal quantities of DNA there is not necessarily a greater risk of contamination but it was easier to notice the effects of the contamination and be misled (‘...It's not that the risk of contamination is greater; but it is easier to see the contamination...’ page 92).” In response to a question on this subject, Professor Dan Krane responded, “There is absolutely no question but that contamination is a much greater problem in LCN cases than conventional DNA testing. The reasons that it is a greater problem are both because it is easier to detect contaminants ([Sara] Gino's point) and because it is easier to transfer (and to transfer without knowing) smaller amounts of DNA than larger amounts of DNA.”

As for the size of a sample, low-template profiling works on a dozen cells or less. Let me offer a simple analogy. If I go to the beach on a windy day, I don't expect to be hit with pebbles, but I do expect to feel sand hit me.
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Old 22nd July 2020, 10:32 AM   #119
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Who watches the technicians?

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Old 22nd July 2020, 10:36 AM   #120
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Who watches the technicians?

Originally Posted by McHrozni View Post

The next issue is mixtures. Yes, mixtures can be a problem, but he leaves out the two ways used to solve them. The first is that it often happens the quantities of the two DNA profiles differ and it's possible to entirely separate the two profiles. If the samples are present in, say, a ratio of 10:1 you can separate the taller peaks from smaller ones with ease. The second solution is that we do know how often do certain allelles appear in the population. A 1:1 mixture of two DNA samples, where one person could be the donor, is still attributable to that person as a one in a million match or so. That's because the number of people that could give that exact same mixture is so low. That's why we use 13 (now often 16) loci in the first place.

These are known solutions to the problems that have been routine by 2008, when the article was produces.

McHrozni
Let me begin with mixtures then move on. Once you get to a 10:1 mixture or so, it becomes more difficult to differentiate stutter peaks from real peaks. More generally, analysis of mixtures is prone to subjectivity and bias. A good example of a suspect-centered analysis in the work that Stefanoni did with respect to the bra clasp profile in the Knox/Sollecito case. She found Sollecito's profile, yet other peaks she called stutter, even though some would have had to have been backwards stutter peaks (which is quite uncommon).

That Professor Thompson knows about these sorts of problems is suggested by the fact that he is a coauthor on a paper (see this link for a page of downloads) that advocates sequential unmasking as a way to minimize bias in the interpretation of mixtures, a well known problem. With respect to Professor Thompson's qualifications more generally, see this link. Until his retirement, my understanding is that his area of specialty was probability and decision making. He was not a practicing DNA forensic technician, as his report in the Leskie case made clear. However his expertise complemented Professor Krane's expertise.

Now I would like to address more generally the need to have lawyers oversee forensics. IIRC Professor Thompson and Professor Paul Giannelli were members of the committee that drafted the ABA's model rules on DNA evidence, a thoughtfully written statement from which I often quote. Professor Giannelli's book chapter on the Duke lacrosse case provides a pedagogically clear description of DNA forensics, one that I consulted as I was preparing lectures on the subject of DNA forensics. A draft of this chapter was available on the web some time ago. Professor Erin Murphy's book, which I previously called indispensable, goes into many issues relevant to the present case, as well as others.

Why does forensics need oversight from lawyers such as Professor Thompson and others? First, because it blends law and science. Such a statement may seem banal, but this overlap is more complex than it first appears. In addition, the technicians do not always come out looking good. See for example the article "Painting the target around the matching profile: The Texas sharpshooter fallacy," by William Thompson. Second, because some labs have shown themselves to be error-prone or dishonest and because the reports from lab or the testimony from lab personnel is incomplete or false.

Let me provide just a few examples of the second reason. As Professor Thompson documented in "Tarnish on the Gold Standard," the negative controls have been shown to have been faked (Many of Professor Thompson's articles are available through the Forensic Bioinformatics page on resources, for which I have previously given the link). Others documented that forensic reports in the Duke lacrosse and Steven Avery cases were shown to have been incomplete and highly misleading. The Gary Letterman case shows that lab personnel claim no contamination even when audits of their documents show otherwise. The Theodore Kessis Report on this case might be consulted for more information.

These behaviors are object lessons in how not do forensic science or any other science. The defense in the present case should have asked Professor Murphy or any of the other people whom I have mentioned to testify to such problems.
__________________
It is possible both to be right about an issue and to take oneself a little too seriously, but I would rather be reminded of that by a friend than a foe. (a tip of the hat to Foolmewunz)

Last edited by Chris_Halkides; 22nd July 2020 at 11:07 AM.
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