Amanda Knox guilty - all because of a cartwheel

[Kestrel]

.
Part of the explanation of why Elizabeth Johnson sculpted her report the way she did could lay in the answer to how and why she was engaged to do this report, who engaged her, who gave her the material which she based her report on.

Maybe someone from FOA could give us some answers to those questions.

We see this argument far too often here on JREF.

When people don't understand the science behind an argument, they claim the scientist is part of a conspiracy.

 

[BobTheDonkey]

We see this argument far too often here on JREF.

When people don't understand the science behind an argument, they claim the scientist is part of a conspiracy.

So, now you're going to claim that the "List of 9" participants were not engaged by FoA specifically to add weight to the claim that the DNA evidence is not valid?

And to do that, you're going to claim that it's a conspiracy theory to point out that Dr Johnson has a vested interest (ties to the FoA) for her involvement in the letter?

Nice try to poison the well (at least, I think that's what this fallacy would be). There very much is a "conspiracy" to obfuscate the evidence and keep Amanda out of prison. Although, it's not really a conspiracy so much as an expensive PR campaign.

 

[Fulcanelli]

We see this argument far too often here on JREF.

When people don't understand the science behind an argument, they claim the scientist is part of a conspiracy.

What, a bit like how you people have been claiming Stefanoni and Biondo (and all the rest) are part of a conspiracy? And you say this without even the slightest hint of shame. Hypocrisy much?

And I find your comments pretty asinine considering the article I recently linked which shows that the main thrusts of your friends' 'scientific' arguments have been flat out bogus, the whole 'no blind controls' and 'none disclosure of protocols' and 'LCN DNA would never be admitted in a US court' rubbish.

 

[Kermit]

We see this argument far too often here on JREF.

When people don't understand the science behind an argument, they claim the scientist is part of a conspiracy.

.
I don't believe in conspiracy theories, I believe in common sense.

Part of common sense as regards Elizabeth Johnson's report is to understand why she did it, and who gave her the data she reviewed (did she pick it up from PMF? naw ...).

Also, if she got the material she reviewed from one side, did she actually make any effort to contact the other side and get further material.

I don't want to make it sound like I've a foregone conclusion here, but I think we can assume that the Knox/Mellas families or persons close to them supplied Elizabeth Johnson with the material she reviewed.

I also assume that Elizabeth Johnson, in spite of her long CV (and some curious professional incidents you come across if you google her name) did not attempt to contact Patrizia Stefanoni to go over the procedures followed, and which Johnson so harshly criticized from far off USA.

 

[quadraginta]

.
Part of the explanation of why Elizabeth Johnson sculpted her report the way she did could lay in the answer to how and why she was engaged to do this report, who engaged her, who gave her the material which she based her report on.

Maybe someone from FOA could give us some answers to those questions.

We see this argument far too often here on JREF.

You'd see it far less if the circumstances which merited it were not invoked so often.

The obsession of the Knox fan club to recycle the same tired, baseless canards incessantly, as if all past discussion somehow disappears and magically never existed, is the only reason you find yourselves faced with the same quite appropriate responses.

When people don't understand the science behind an argument, they claim the scientist is part of a conspiracy.

When people don't actually have science behind an argument, but only the tattered trappings of it, they still claim that the costume is the same as content.

There is something deliciously ironic about protestations deploring conspiracy allegations coming from such a source. The FOA effort began with dire intimations of conspiracy and has been flailing around with increasing desperation and rapidly diminishing success ever since.

 

[Chris_Halkides]

negative

BobTheDonkey,

In message #5358 you have the concept of something being too small for detection entirely wrong. To a chemist, saying that a test came up negative is identical in meaning to saying that the substance being tested for, if present, is present at lower than the threshold concentration of the test. You are making up an extra category that does not exist. BTW, Inconclusive means that one cannot say anything about the presence of the substance, one way or another.

Worse still is that you missed the point of Johnson and Hampikian’s argument. They make it that by the time blood drops below its limit of detection, DNA has already dropped below its limit of detection. This fact makes contamination the only plausible explanation for the knife profile.

Chris

 

[Chris_Halkides]

impasse

BobTheDonkey,

The only way around this impasse (#5348) that I see is to argue a hypothetical. Suppose (contrary to fact) that the knife yielded a strong, complete profile matching Meredith’s DNA, one without allele drop-ins, or peak height imbalance. Suppose also that (as was actually the case) the knife tested negative for blood with TMB. This argument is actually a more fundamental problem with the knife profile as evidence than the first one, that the profile is a weak, partial profile. Johnson and Hampikian were conservative in the limit of detection for blood, one part in 10,000. The actual limit is more like 1 part in 100,000. This fact makes their argument stronger: one would remove DNA to below its limit of detection before removing blood below its limit of detection. Note also that they do not specify whether the DNA is coming from blood or other cells in their letter; they just say DNA. Perhaps this is because, unlike Stefanoni, they know that skin cells, among other ones, do contain DNA.

Chris

 

[Chris_Halkides]

observation versus analysis

Kermit,

Watching the samples being run (#5329) tells one very little; the notion that doing so would make the cross examination unnecessary is nonsense. For one thing, the analysis of the data is probably more important that the running of the PCR machines. For another, contamination cannot be observed directly. Moreover, the defense asked repeatedly for the data and were stonewalled or given only a portion of what they requested.

Chris

 

[Chris_Halkides]

how the clasp was collected

Kermit,

It was your claim (#5338) that the DNA was abundant when in fact it was not, and this point is not insignificant. There was an argument given here to the effect that there was too much of Raffaele’s DNA present to be the result of secondary transfer, and that argument is nonsense, twice over. However, your claim that the crime scene was secure is contradicted by the documented movement of the bra clasp between when it was first observed and when it was collected. Who moved it, and were they wearing gloves?

One wishes that the errors in collection were limited to a single lack of a hairnet, but this is contradicted by video evidence of a dirty glove being used to retrieve the clasp and of technicians handling the clasp excessively, handling other objects at the same time, putting it on the ground, and not using disposable tweezers to handle it. Raffaele’s fingerprints were on the door and unless he magically told his skin cells not to shed, his DNA was in the girls’ flat.

Chris

 

[Chris_Halkides]

contamination references

Kermit,

In message #5341 you have several things wrong. True, most of the peaks have the same number of repeats as Meredith’s, but that is a necessary, not a sufficient condition to call it a good profile. First, there are eight loci where the lower peak is less than 70% of the height of the higher peak. In a strong profile this is taken to mean that one is dealing with a mixture, though I will allow that another explanation is more likely in this very weak profile. Second, you do not mention the two extra peaks in locus D3S1358. These problems and the abnormally low peak threshold make Johnson and Hampikian refer to it as a low level, partial profile. Again, I never said it isn’t Meredith’s profile, only that the profile fails to clear the bar for affirming that it is.

Yet, the issue is not whose DNA it is, but how it got there. And this leads to my third and most important point, namely that you fail to grasp the nature of DNA contamination. I have previously documented here that the exact cause of DNA contamination is seldom known. The best analogy of which I am aware is that we seldom know exactly how we picked up our last head cold, we only know that we did from the symptoms. However, one can learn some principles from previous contamination events. One of them is that coprocessing of samples raises the risk of contamination. I am including a couple of good links on contamination. The piece authored by Donald Riley treats contamination in two separate places within the essay.

http://www.scientific.org/tutorials/articles/riley/riley.html

http://www.nacdl.org/public.nsf/0/6285f6867724e1e685257124006f9177

Chris

 

[Chris_Halkides]

contamination and PCR

Kermit,

With reference to message #5346, the knife tested negative for blood and yet still yielded a DNA profile. That should have raised alarm bells in the lab in Rome about the possibility of contamination. Before getting to this case, let’s clarify something about the polymerase chain reaction (PCR) portion of DNA forensics. It typically amplifies the concentration of DNA by at least a million-fold. Therefore, one 1 part in 1,000,000 of the product of a completed PCR reaction is enough to contaminate the starting materials in a subsequent PCR reaction. First-generation DNA forensics did not use PCR, and contamination was less of a problem back then.

Let’s assume that it was Meredith’s DNA on the knife. There were hundreds of evidence samples processed, and many of them contained Meredith’s DNA. Any one post-PCR sample containing Meredith’s DNA has the potential to contaminate another reaction. In another comment today I have documented that contamination is especially a problem when samples are run close in time.

There are several problems with Stefanoni’s claim of no contamination in seven years. One is that we do not know how her lab defines contamination (unfortunately, agreement on this is not universal). Another is that we do not know whether her lab keeps a log of contamination events (not all do). But a third is that Stefanoni is implying her lab is far better than anyone else’s (http://www.seattlepi.com/local/183007_crimelab22.html). “The occasional ‘contamination event’ is inevitable, said [Ed] Blake, the California scientist, but crime labs aren't routinely disclosing those miscues.” This entire article is well worth one’s time.

Chris

 

[Fulcanelli]

BobTheDonkey,

In message #5358 you have the concept of something being too small for detection entirely wrong. To a chemist, saying that a test came up negative is identical in meaning to saying that the substance being tested for, if present, is present at lower than the threshold concentration of the test. You are making up an extra category that does not exist. BTW, Inconclusive means that one cannot say anything about the presence of the substance, one way or another.

Worse still is that you missed the point of Johnson and Hampikian’s argument. They make it that by the time blood drops below its limit of detection, DNA has already dropped below its limit of detection. This fact makes contamination the only plausible explanation for the knife profile.

Chris

Or, a test showing negative simply means the test isn't sensitive to detect what's there. All tests will only detect something down to a minimum level. If I test an object for forensic information with a magnifying glass and that test comes oyp negative, does that mean for a fact that there is no forensic information on the object? Or does it only mean there is none above a certain minimum, in this case a macro level? All tests have their limits.

Inconclusive means you can't rule it out either. And that has been the main argument hitherto from the FOA...that because the test didn't indicate blood that completely rules blood out when it does not. THAT is the only point we are making...not that there IS blood on the knife, only that you cannot rule it out as being the material, or part of the material that provided the DNA. You are deliberately shifting the goal posts.

Contamination the only plausible explanation? When you have not offered a single piece of evidence that contamination occured, except to demand we simply assume it? When you have not offered a single plausible explanation of how it got contaminated with Meredith's DNA and ONLY Meredith's DNA? Were poor protocols or a break in the chain of evidence a factor, we should be seeing multiple profiles on that blade not only one and one that just HAPPENS to be the murder victim's!

 

[Fulcanelli]

kermit,

watching the samples being run (#5329) tells one very little; the notion that doing so would make the cross examination unnecessary is nonsense. For one thing, the analysis of the data is probably more important that the running of the pcr machines. For another, contamination cannot be observed directly. Moreover, the defense asked repeatedly for the data and were stonewalled or given only a portion of what they requested.

Chris

cite?

 

[Fulcanelli]

One wishes that the errors in collection were limited to a single lack of a hairnet, but this is contradicted by video evidence of a dirty glove being used to retrieve the clasp and of technicians handling the clasp excessively, handling other objects at the same time, putting it on the ground, and not using disposable tweezers to handle it. Raffaele’s fingerprints were on the door and unless he magically told his skin cells not to shed, his DNA was in the girls’ flat.

Are you attempting to argue this 'supposed' dirt was a handful of Raffaele's DNA???

 

[Fulcanelli]

Second, you do not mention the two extra peaks in locus D3S1358. These problems and the abnormally low peak threshold make Johnson and Hampikian refer to it as a low level, partial profile. Again, I never said it isn’t Meredith’s profile, only that the profile fails to clear the bar for affirming that it is.

Two extra peaks, as much as that? Oh the shock, the horror. I take it you've never looked at a noisy sample have you...do you have any idea how many extra peaks there are in those? Potentially hundreds. Two extra peaks (apparently) and that suddenly means that isn't Meredith's DNA? Funny, since the defence believe it's Meredith's DNA, all their forensic experts believe it'#s Meredith's DNA, the victim's genetics experts believe it's Meredith's DNA, the prosecution experts believe it's Meredith's DNA, the genetics experts on PMF believe it's Meredith's DNA, the judges in the trial believed it was Meredith's DNA. The only person arguing that it isn't Meredith's DNA is 'you'. My, aren't all these genetics experts fortunate that a chemist came along to set them all straight from his armchair!

 

[odeed]

Just out of interest, how much DNA does a person shed through dead skin cells and hair?

I was under the impression much of the "dead skin" and hair was keratin and contained no DNA, which is why forensics need hair roots or mouth swabs from people.

 

[Fulcanelli]

Just out of interest, how much DNA does a person shed through dead skin cells and hair?

I was under the impression much of the "dead skin" and hair was keratin and contained no DNA, which is why forensics need hair roots or mouth swabs from people.

Yes, this is true. However, recent cutting edge breakthroughs now enable scientists to extract DNA from actual hair (now being used in archaeology and palaeontology, though still in its infancy). Hair contains mitochondrial DNA which they can now extract and amplify with newly developed specialised techniques. It has several advantages. Primarily, the keratin protects the DNA from the environment and therefore preserves it indefinitely. Secondly, it protects the DNA from contamination from other DNA sources. However, it's use has not transferred over to forensics yet. Forensic science still uses the old tried and tested sources for DNA (those you list).

 

[BobTheDonkey]

BobTheDonkey,

The only way around this impasse (#5348) that I see is to argue a hypothetical. Suppose (contrary to fact) that the knife yielded a strong, complete profile matching Meredith’s DNA, one without allele drop-ins, or peak height imbalance. Suppose also that (as was actually the case) the knife tested negative for blood with TMB. This argument is actually a more fundamental problem with the knife profile as evidence than the first one, that the profile is a weak, partial profile. Johnson and Hampikian were conservative in the limit of detection for blood, one part in 10,000. The actual limit is more like 1 part in 100,000. This fact makes their argument stronger: one would remove DNA to below its limit of detection before removing blood below its limit of detection. Note also that they do not specify whether the DNA is coming from blood or other cells in their letter; they just say DNA. Perhaps this is because, unlike Stefanoni, they know that skin cells, among other ones, do contain DNA.

Chris

This is not an Impasse, Chris.

Is blood the only source of DNA?

 

[Dan O.]

Unfortunately, I don't have time for the online course, but I'll assume you've done it, so I ask you: do you think that the DNA profile on the knife matches Meredith's DNA? (or, on the contrary, is the profile too unreliable to be said that it matches her?)

Here's the next point in the decision tree: if the profile can be ascribed to Meredith, do you think it was due to contamination? Which of the online course's causes of contamination do you think caused this contamination? Or are you only able to say in generic terms that "contamination can happen"?

Dr. Patrizia Stefanoni has stated that there has never been a case of contamination of DNA samples in the history of her lab. To the supporters of the contaminated Double DNA Knife Theory, was it just bad luck (for Amanda) that it occurred this time?

Patrizia Stefanoni must be blind because for proof of contamination I ask you to look again at the reference chart of Meredith's DNA that you yourself used to make the comparison to the knife DNA. See those peaks down around 50 RFU? That is foreign DNA contaminating what is supposed to be a clean reference of DNA from a single person. That contamination is the same level as the signal we see from the knife. From the evidence of these two charts, Patrizia Stefanoni's lab conditions produce contamination of 50 RFU at least 50% of the time.

Given that the profile from the knife is in the same range as the known contamination, it is highly likely that the knife profile is also the result of contamination. Whether this is a contamination from a whole genome of Meridith's DNA or a stochastic sampling of post amplification fragments is unclear to me but one might be able to determine this statistically given more data to analyze.

 

[Fulcanelli]

Patrizia Stefanoni must be blind because for proof of contamination I ask you to look again at the reference chart of Meredith's DNA that you yourself used to make the comparison to the knife DNA. See those peaks down around 50 RFU? That is foreign DNA contaminating what is supposed to be a clean reference of DNA from a single person. That contamination is the same level as the signal we see from the knife. From the evidence of these two charts, Patrizia Stefanoni's lab conditions produce contamination of 50 RFU at least 50% of the time.

Given that the profile from the knife is in the same range as the known contamination, it is highly likely that the knife profile is also the result of contamination. Whether this is a contamination from a whole genome of Meridith's DNA or a stochastic sampling of post amplification fragments is unclear to me but one might be able to determine this statistically given more data to analyze.

Point it out to us, I don't see it. Thanks.