Amanda Knox guilty - all because of a cartwheel

[BobTheDonkey]

Now you've veered into mindreading and lost me, I'm afraid.



If they only had one source of Sollecito DNA then what did they compare their readings to, in order to determine if it was his or someone else's? The obvious answer is that they must have had a sample of his DNA. I presume that sample would be a potential source of contamination in a lab.

My understanding is that in order to demonstrate that there hasn't been contamination you do control tests - you try to extract DNA from something you know has none and see what results you get. If you get Sollecito DNA from something that shouldn't have any DNA, then you can be fairly certain that contamination from his sample has taken place. I would presume such control tests must have been done, but we have also been told by Knox/Sollecito supporters that they weren't done. Do you have any further information about that?

Ok, so, if we are arguing over the clasp, we have 2 sources of contamination - the sample directly from Sollecito and the cig butt. The sample from Sollecito would have been processed at the beginning of the forensics testing, let's give a week and say around 40 days prior to the collection of the clasp. So, that rules the sample from Sollecito out pretty conclusively.

Next, we address the cigarette butt. Again, this piece was collected at the beginning of the investigation. We don't know which day it was tested, but I would suspect it was before the clasp was collected.

Again, what is the route of contamination in the lab? On the one hand, it's argued that there was 47 days before the clasp was collected. And then we're asked to believe that the clasp was contaminated in a lab that was likely done handling either of the other two samples of Sollecito's DNA.

Honestly, what is the likelihood that the lab said "hey, we didn't get the clasp. Let's wait till we have the clasp to test this cig butt and Sollecito's control sample".

Meanwhile, we still have 400+ other samples that weren't contaminated with Sollecito's DNA. So even if we allow that the butt or control were the source of contamination in the lab - it's again majic DNA that contaminates a single sample (in a substantial amount, mind you) and yet doesn't show up anywhere else.

 

[Fiona]

Neither has anybody else, which suggests that the information is not easy to come by for some reason.

The problem with that, Matthew Best, is burden of proof. It the same as Halides1's claim that the reports and evidence were not provided to the defence. Since the request was made and was not opposed; the court ordered delivery by a certain date and there is no report of the defence complaining it was not delivered the claim is extraordinary: but no extraordinary (or even plain mundane) evidence in support of it has been forthcoming. The assertion was made: challenged; and abandoned.

Similarly this assertion has been made that there were no controls. Controls are standard practice we are told. Dr Stefanoni is an experience forensic scientist: she has testified (for 15 hours, IIRC); she has said she uses standard protocols in her lab; independent sources (in particular the forensic scientist representing the victim's family) were there when the testing was done and were satisfied. It is therefore difficult to accept that control tests were not done and once again the onus is on Halides1.

I have no problem doing a lot of digging about in support of what I claim and none in being corrected; because it really is an enormous task to get to the sources and the facts. But I do not see why halides1 is not doing the same. All I see is doubts thrown out with nothing behind them and that just looks like smearing to me.

If there is evidence for what he claims let us see it from those who are in a position to know

 

[piktor]

All I see is doubts thrown out with nothing behind them...

If there is evidence for what he claims let us see it from those who are in a position to know

The Knox/Sollecito defense has not been able to acquit their clients, and they have all the documents.

Knox's lawyer Ghirga has called the process 'fair'.

Is this enough? Sounds, looks, quacks like a duck.

This blanket 'blame the prosecution, blame the forensics' tactic is used by Friends Of Amanda.

Nobody on the outside can back their claims because the 10,000 page investigation is still an open case. The documents are not public. Most of the evidence out has been collected in public media, by leaks, interviews and not much else.

The Micheli report is public, but redacted, and is in Italian-only. TrueJustice will not touch it.

Since all rounds have gone to the prosecution, they get to write history.

 

[Chris_Halkides]

loose ends

halides1 is a scientist and he posted a faulty link. What I did is search at the site's homepage www.istitutoaffarisociali.it "tagliabracci" and several PDF links were found. I clicked on the top link. One PDF has 7 pages and the other, the one I linked, has 18 pages. http://www.istitutoaffarisociali.it.../IT/ST/1?frmSearchText=tagliabracci&x=25&y=13

We have to ask halides1 if it is the correct PDF and "what it means" in plain English.

Piktor,

I made my desire to discontinue active participation in this discussion because of personal attacks clear in #1290. Nevertheless, I will make an exception for the sake of tying up several loose ends that have emerged in some recent comments.

Tagliabracci report

The link to the Tagliabracci DNA report sometimes gives an error message but then the document appears. The report is in Italian and is 18 pages.

http://www.istitutoaffarisociali.it...0a4daa67d625c63/indagini_genetico_forensi.pdf

The last bullet on page 13 deals with the minimum acceptable signal-to-noise ratio in DNA profiling:

“adottare come valore soglia per l'interpretazione dei picchi valori di RFU

solidi, che possono variare da laboratorio a laboratorio, comunque non

inferiori a 50 RFU”

English translation
adopted as the threshold value for the interpretation of peak values RFU
solids, which may vary from lab to lab, but not below 50 RFU

My comment (#1136) discusses the knife DNA on the assumption of a slightly lower standard of acceptable signal-to-noise, 40 RFU. “The signal-to-noise ratios for all 29 peaks fall below about 100 RFU in the electropherogram of the knife. Of the 29 peaks, 16 fall below 40 RFU. The more stringent the standard, the lower the chance of mistaking signal for random noise.” Other pertinent comments exist elsewhere in the thread.

Bleach link

Link to Bleach and DNA (this link works OK, AFAIK)
http://www.bio.net/bionet/mm/methods/1998-June/067669.html
text of this link found upthread #1289

Control experiments

I am not sure that I understand Fiona’s recent mention of her own comment #572. If the question is whether or not control experiments were done, I would say that this is disputed. The only information I have comes from Dr. Waterbury, whose posts are checked by an anonymous molecular biologist for accuracy (http://www.sciencespheres.com/2009/10/lcn-dna-profiling-part-ii-watch-where.html). With respect to the knife, “Stefanoni apparently did not perform any negative controls with same system parameters as that used for the kitchen knife DNA. That's another deficiency.” Elsewhere (http://www.sciencespheres.com/2009/10/methods-of-polizia-pseudoscientificaa.html), he states, “These negative controls are essential to performance of LCN work, as shown in Part II of this series. They were either not performed, or not reported by Stefanoni. Perhaps even more important for the knife DNA, no control experiments were run to follow the handling of the item from the field through to the laboratory. That is, to see if other, random objects retrieved from the same drawer and handled in the same, unprofessional way [the knife apparently sat on a desk for a day], might also appear to have DNA on them.” I have offered information from this site in the past only to be told by Fiona that the site is “disgraceful,” with no further explanation. I urge everyone to read these two posts and come to his or her own conclusions.

I have discussed one of the correct controls for the bra clasp in #1136, “The DNA-critics respond that the best control experiment would have been to collect items in similar location [and just as dusty] to the clasp on the same day as it was collected, and this was apparently not done.”

Chris

 

[Fiona]

And I urge everyone to read the first link from halides1 to that site: I urge them to remember that Dr Waterbury is an engineer: I urge them to find out where he got his information as to what Dr Stefanoni reported since Halides1 has not chosen to link to her report or anything else in support of these statements about her procedure.

Then I urge them to visit PMF and search the archive for Dr Stefanoni's testimony and the subesequent comments from Greggy in particular since he is a person who works in this field and check out his comments from then in relation to the evidence given: and from the last few days when he commented again. His remarks seem balanced and informed to me.

ETA: oh and read the Tagliabracci report in english (Piktor's link) and see if you can see any relevance: and if you can see if you can work out why this same person, in court, did not manage to persuade them to his point of view on the basis of all the evidence supplied

 

[BobTheDonkey]

And, yet, Chris, you fail to acknowledge that Sollecito admits that Meredith's blood/DNA was likely to be found on the murder weapon.

But, who's counting. Right?

This is why I maintain that you are being disingenuous. You have an agenda to push, and anytime that agenda hits a snag - you simply ignore the snag.

It doesn't matter about the procedure used to identify the DNA on the knife - the defense admitted that it was likely to be Meredith's.

I know, I know. That doesn't matter because the DNA evidence is wrong. Except for 2 things:

You have yet to produce a plausible contamination scenario - only claiming that it happened without anything else being contaminated

You have yet to recognize that the DNA found on the knife is irrelevant because the defendant has provided a non-plausible excuse for why it would be there - he expected it to be there, even if it wasn't.

 

[Fiona]

I am confused by the bleach. Halides1's link still does not work for me but I have found it (I think) or something like it.

http://docs.google.com/viewer?a=v&q...&gl=uk&sig=AHIEtbQUFD63tRF3flv0hb6FqIidZyUEiQ

It is interesting to note that physically removing the surface of the bone (treatment c) did not remove the contamination, suggesting that contaminant DNA can penetrate more deeply than can be redressed by its removal by abrasion or excision. Therefore, we strongly suggest the use of bleach as the most cost-effective means for decontaminating bone surfaces,

<snip>
The elimination of surface contamination from bone requires immersion in at least 3.0% (w/v) sodium hypochlorite (approximately equal parts of commercial bleach and water) for at least 15 min.

Maybe it is me but this does not seem to support what halides1 claims. It seems that a small amount of DNA trapped in groove of a knife could easily survive "scrubbing" or vigorous cleaning with bleach because it is quite hard for me to imagine someone doing that for a full 15 minutes on the basis of a google search about how to remove dna (I am assuming that none of the convicted would know this already but I could be wrong)

First hit is this (for me)

http://www.sciforums.com/showthread.php?t=45471

The second is the one halides1 cites but it is a bit of a dense read though they could easily have read the abstract if it comes up in the same order in Italy and is available in Italian (assuming again that they used Sollecito's computer)

The third one doesn't work for me

The fourth

http://www.exploreforensics.co.uk/detecting-evidence-after-bleaching.html

says this

With oxygen bleach, the bleach has an oxidising agent, which could be a substance such as hydrogen peroxide. In these instances, haemoglobin is completely removed and can't later be detected.

Since it talks about ways round this with clothing (look in the seams etc) this may well have looked quite promising if you were doing a clean up of a knife

 

[Matthew Best]

Did someone (i.e either Knox or Sollecito) do a google search on "how to remove DNA"?

 

[Fiona]

No idea. As I said it was based on my assumption that they would not know that bleach was effective in this way: that they used bleach in Dr Stefanoni's opinion: and that google is the first place most young people go when they want to know something

Pure speculation

 

[Matthew Best]

I would presume that any such search would have shown up when the police examined the computers of the suspects.

 

[Fiona]

Yep. Doesn't fly

 

[Chris_Halkides]

It takes less than one minute to destroy DNA with bleach

Did someone (i.e either Knox or Sollecito) do a google search on "how to remove DNA"?

Matthew,

Medline is a better way to search for this kind of thing. Polymerase chain reaction (PCR) is an essential step in DNA profiling. The bleach they used was 10% of full strength.

http://www.ncbi.nlm.nih.gov/pubmed/1571142

Biotechniques. 1992 Mar;12(3):358-60.
PCR: how to kill unwanted DNA.

Prince AM, Andrus L.

Laboratory of Virology and Parasitology, Lindsley F. Kimball Research Institute, New York Blood Center, NY 10021.

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

Chris

 

[Fiona]

More likely they got it off the tv than from medline, I suspect: I always forget about the telly

 

[piktor]

Fiona, this is a beauty

and read the Tagliabracci report in english (Piktor's link) and see if you can see any relevance: and if you can see if you can work out why this same person, in court, did not manage to persuade them to his point of view on the basis of all the evidence supplied

My General Theory Of Common Sense, used by the 19 judges on this case, makes clear that they are not scientists, they are lawyers by training and six of them are lay civilians. Do they have any truly informed scientific background to really understand what Tagliabracci is saying?

No?

Well, yes, no. The people in Court have a reasonable understanding of the DNA science but is is superficial and as Micheli wrote on the Guede Report, acquired in a "crash course", Micheli's words.

halides1 is making a case here but it falls on deaf ears. We are not scientists but we make judgements on topics we really have no business pretending to comprehend. halides1 knows what he is talking about but it as well might be Greek. Habla Ingles, halides1?

The defence will bump into the same wall of deep scientific ignorance on appeal. It is a case of too much good science for the defendant's benefit.

halides1 has not convinced anyone here because his narrative is obscure to us ignorant rabble. Tagliabracci has not developed a believable narrative because he is talking over his audience, not to his audience.

 

[Fiona]

I don't agree. It is absolutely true that I am not a scientist. But that is not the reason I am not persuaded by Halides1. I am not persuaded by Halides1 because he relies on just the kind of reaction you display. He makes no attempt to make a case or to tie his observations into a sensible narrative: and so far he has not said one thing which I am not aware of about the importance of care in handling samples etc. Nor has he said anything about the limits of LCN testing I have not read elsewhere.

But no matter what he may or may not know he still comes up against the fact that people who know as much as him do not agree: so he has a case to make and "I am a scientist" isn't it.

No matter what he knows he still has to show one of the basic things:

1. That there is a route for contamination of this sample in this lab
2. That there is evidence of incompetence which other experts, who actually looked at the testing, did not see: and why they did not see it.
3. That his assertions about the protocols are true
4. That his assertion that the evidence was not released is true
5. That a sample size of 1.4 ng cannot be described as abundant

What he is doing is arguing from authority. There are times when that is all that can be done because the subject is too arcane to convey easily: this is not one of those times. Most of those things and the other things he has raised are quite easy to understand but what we do not have is any evidence from him at all. And that is also true of his famous letter: it is a general statement and I do not think respectable scientists should pronounce in the terms they did till they have seen the evidence

I am not competent to judge dna testing etc: but I am able to judge an argument and he hasn't taken the trouble to make one.

 

[stilicho]

The defence will bump into the same wall of deep scientific ignorance on appeal. It is a case of too much good science for the defendant's benefit.

halides1 has not convinced anyone here because his narrative is obscure to us ignorant rabble. Tagliabracci has not developed a believable narrative because he is talking over his audience, not to his audience.

This is exactly why I suggested that the defence appeal to something none of us really understand doesn't belong in this thread. I have few doubts that the appeals of RS and AK will focus on this contamination idea rather than creating a believable alternative narrative.

As you do, I think this is an error but not a significant one.

From what I understand about this case, nobody is getting a big bonus for "turning state's evidence" here. The prosecution has made it clear that (as Italian law allows) all of them are equally guilty if only because they did nothing to help Meredith as she was dying.

Even in the unlikely event that the defence teams manage to prove DNA contamination they will still have done nothing to damage the case against AK and RS. That's the real issue that is the scope of this thread and not whether amateur observers really know anything about DNA contamination.

I can only add that none of the cases, where laboratories or investigators have been proved to have been neglecting or outright lying, were even close to this one in its details. All them, on the contrary, were systemic and very obvious from the evidence. I agree with you that articulating obscure stuff is not going to convince anyone. If you read those cases of contamination carefully enough you will see that they didn't depend on obscure data but upon very clear testimony and very clear evidence.

Can we agree to put the validity of obscure DNA contamination arguments into a science or medicine forum where they belong and will attract the attention of experts in the field?

 

[piktor]

I am not competent to judge dna testing etc: but I am able to judge an argument and he hasn't taken the trouble to make one.

Exactly my point.

Trials are about competing narratives.

The prosecution has made a thorough investigation. The defence has failed time and again to defeat it. It is beginning to look like the appeal will not be pretty for the accused.

 

[stilicho]

IWhat he is doing is arguing from authority. There are times when that is all that can be done because the subject is too arcane to convey easily: this is not one of those times.

See, I disagree that it isn't arcane.

The argument is that there is a brand new form of DNA contamination not included in any of the examples. Of course, I might have missed those, but supplying links (about half that I have had time to read) that don't truly mimic the defence teams' claims is at least misleading.

The example of the Washington State DNA laboratory contaminations, for example, is fairly familiar to me since I have seen it widely reported here. But in this case it affected about a dozen cases and not just one. It wasn't a "one-off" as the RS team has challenged. When something goes wrong with a forensics team it seems to be widely influential on results rather than simply popping up once in a decade.

I hope that helps explain why I think the halides1 defence is arcane!

 

[stilicho]

No matter what he knows he still has to show one of the basic things:

5. That a sample size of 1.4 ng cannot be described as abundant

What? Did he say this? Can you cite the post? I have had to do some catching up but I didn't see that.

I had used the term "abundant" because that's what the prosecution team used. And that word did not seem to be challenged by the defence teams when the amount was revealed.

Did I miss something in the trial evidence too?

 

[stilicho]

Stilicho,

One of the most memorable things my PhD advisor said to me was that there is no clear line between sloppy science and fraudulent science. Based on my present understanding of the evidence, I am not sure that evidence tampering (if that is what you mean by dishonest analysis) can be excluded here, nor do I see a reason to conclude that it must have happened. That is why I have not discussed it. I am still waiting for an answer to my question.

Chris

Your question which was what?

What I bolded wasn't in any way relevant to the links you posted. They provided clear examples of false positives contrasted with faked evidence. They distinguished one from the other.

Why do you include evidence tampering as a possibility when the defence teams didn't?