Dead skin cells don't contain DNA?

[Chris_Halkides]

conservative threshold

Thanks for proving the point halides1. Partial profiles only can be extracted from dust and only then with amplification.

It's settled then.

You need to reread what I wrote, or better yet read the paper itself. Identifying a single person's profile was not the point of the study. Moreover, they used a conservative threshold of 200 RFUs. All modern DNA forensics involves amplification via the polymerase chain reaction.

 

[Fulcanelli]

You need to reread what I wrote, or better yet read the paper itself. Identifying a single person's profile was not the point of the study. Moreover, they used a conservative threshold of 200 RFUs. All modern DNA forensics involves amplification via the polymerase chain reaction.

Your article is redundant in this case. Raffaele's FULL profile was on that clasp. Ergo, it did not come from dust.

 

[Chris_Halkides]

strong peaks shown in the paper

To all,

Here is Figure 3 from the 2008 paper by Toothman et al I cited before. Note how strong the peaks are. They are several hundred to several thousand RFUs.

 

[Chris_Halkides]

with respect to the previous message

The profiles recovered in this paper were partial, whereas Raffaele's was complete. However, the peaks that were seen n this paper were up to tenfold more intense in RFUs than Raffaele's profile.

 

[shuttlt]

Are we still arguing about dust? Why is there more dust from Raffaele in the appartment, let alone the room where the murder took place, than from Amanda, or any of the other housemates. In any case, in the study wasn't it the total dust from a 576 cm(2) area. Are we assuming the bra clasp acted like the swab and absorbed the dust from a significant area of the room?

What percentage of the dust in the room do we think were Meredith's skin cells, as opposed to Raffaele's? I'd have thought the bra clasp would have had to have been dragged through a significant and surprising concentration of Raffaele's dust to achieve this.

 

[Fulcanelli]

The profiles recovered in this paper were partial, whereas Raffaele's was complete. However, the peaks that were seen n this paper were up to tenfold more intense in RFUs than Raffaele's profile.

What does that have to do with dust?

 

[Chris_Halkides]

this is what DNA from dust looks like

What does that have to do with dust?

These are DNA profiles from dust, and some of the peaks are intense.

 

[shuttlt]

Halides,

the thing about the dust for me is that:

1. They swabbed a decent area, 500+ square centimetres.
2. Wouldn't most of the dust in the room be Merredith's?

I wonder if you could address these two points to put the papers you quote in context of the situation we have in the room where the clasp was found.

 

[Chris_Halkides]

dust from classrooms and hallways

Are we still arguing about dust? Why is there more dust from Raffaele in the appartment, let alone the room where the murder took place, than from Amanda, or any of the other housemates. In any case, in the study wasn't it the total dust from a 576 cm(2) area. Are we assuming the bra clasp acted like the swab and absorbed the dust from a significant area of the room?

What percentage of the dust in the room do we think were Meredith's skin cells, as opposed to Raffaele's? I'd have thought the bra clasp would have had to have been dragged through a significant and surprising concentration of Raffaele's dust to achieve this.

Some of the samples that were studied in this paper were from classrooms, so they were likely to contain mixtures, which is borne out by the evidence. I contacted the lead author, and she said that this was one of the factors that complicated the analysis. We don't know how heavy the dust was in the 576 cm^2 area, but the bra clasp looks dusty in the photos. Presumably Raffaele would not have contributed much dust, but it would have been recent and therefore less degraded.

I don't happen to think that dust is the most likely reason for Raffaele's DNA profile on the clasp. However, I think it is quite an extrapolation to say that just because this study did not observe a complete profile, that one cannot yet observe a complete profile (that was not the goal of this study, anyway). Had the authors sampled dust from someone's home, not a classroom or a hallway, they might have seen a complete profile.

I will have to leave it at that. Professional responsibilities are calling.

 

[Fulcanelli]

These are DNA profiles from dust, and some of the peaks are intense.

But we've already established complete profiles cannot be extracted from dust and Raffaele's profile is complete, as you freely admit. Ergo, his profile on the clasp is not as a result of dust. Moreover, I think it's just plain silly to even argue that 'part' of Raffaele's profile may have come from dust. He had only been in the cottage for 'hours', nowhere near enough time to generate enough dust to give any kind of reading. Otherwise, we would expect the DNA of every man and his dog to be on that clasp via dust, including the boyfriends of the other housemates who had accrued 'days' if not weeks of time spent in that cottage.

You are trying to argue a case based on weak science and logic at best, at worst, junk science. It smacks of desperation.

 

[Fulcanelli]

Some of the samples that were studied in this paper were from classrooms, so they were likely to contain mixtures, which is borne out by the evidence.

Right...classrooms that pupils and staff would have spent days, weeks, months of total time in order to deposit enough dust to generate a reading. And even then, only partial profiles were obtained. How does that compare to this case?

 

[Chris_Halkides]

But we've already established complete profiles cannot be extracted from dust and Raffaele's profile is complete, as you freely admit. Ergo, his profile on the clasp is not as a result of dust. Moreover, I think it's just plain silly to even argue that 'part' of Raffaele's profile may have come from dust. He had only been in the cottage for 'hours', nowhere near enough time to generate enough dust to give any kind of reading. Otherwise, we would expect the DNA of every man and his dog to be on that clasp via dust, including the boyfriends of the other housemates who had accrued 'days' if not weeks of time spent in that cottage.

You are trying to argue a case based on weak science and logic at best, at worst, junk science. It smacks of desperation.

You are putting words into my mouth, and it is your logic that is faulty. A study done on dust in classrooms and hallways will yield peaks from many individuals. If the same amount of DNA came from only a few, each of the peaks would be stronger AND it would be easier to in deconvolute. I asked the lead author about the factors that led to the lack of a complete proflle, and she described my questions as "salient." Who should I trust, you or the author of the study?

 

[Fulcanelli]

But these people spent many months in that environment in order to deposit the volume required, often in closed rooms. Raffaele had been in the cottage for a total of only 'hours' in his whole life, nowhere near enough time to deposit any volume and certainly not enough volume to end up in a room he claimed to have never entered in his life, a room that was sealed and to arrive on the tiny metal clasp portion of the bra clasp in an abundant quantity and as a full profile. It also does not explain how his dust landed nowhere 'else' that was tested, such as the main part of the bra or any of the other items. Moreover, those that had spent enough time in the cottage to do so had their DNA absent from the clasp...how is this possible in your dust theory? How is it possible only one Y haplotype, Raffaele's, is on that clasp? What of all the other men that had entered the cottage over the previous days, weeks and months? Do they have a 'special' kind of 'dust'?

What you are arguing here is not scientific, it is not logical and it isn't plausible.

The most plausible explanation and Iccam would agree, is that Raffaele handled the clasp.

 

[Fulcanelli]

"The most plausible explanation and Iccam would agree, is that Raffaele handled the clasp."

Typo - Should read 'Occam'.

 

[shuttlt]

Thanks for your reply Chris,

Some of the samples that were studied in this paper were from classrooms, so they were likely to contain mixtures, which is borne out by the evidence. I contacted the lead author, and she said that this was one of the factors that complicated the analysis. We don't know how heavy the dust was in the 576 cm^2 area, but the bra clasp looks dusty in the photos. Presumably Raffaele would not have contributed much dust, but it would have been recent and therefore less degraded.

More recent than who? Merredith? Surely not significantly less degraded than the killer dust, who presumably actually set foot in the room. It seems to me this is a very different kind of space that we are talking about. One in which there is a pretty even amount of dust from a large number of people, from which we see random fragments in the analysis. The other is a room where the vast majority of the dust will come from a single individual. One might then expect some dust from anybody who had been in the room recently and then perhaps background dust circulating around the flat. Unlike the paper you quote we have the second strongest (and in this case complete) reading from someone who had never been in the room.

I don't happen to think that dust is the most likely reason for Raffaele's DNA profile on the clasp.

We are in agreement on that at least. I really don't see the dust issue resolving itself any time soon. There's been a debate on whether the DNA on the knife is Merredith's, even though you think it probably is, and a debate on whether the DNA on the clasp came from dust, even though you think it probably didn't. I can't see the point of debates like this where, at the very least, both sides agree that the mechanism under discussion is probably not what happened.

However, I think it is quite an extrapolation to say that just because this study did not observe a complete profile, that one cannot yet observe a complete profile (that was not the goal of this study, anyway). Had the authors sampled dust from someone's home, not a classroom or a hallway, they might have seen a complete profile.

But we are talking about getting a profile from a hallway from someone who had never been in the hallway and had only ever spent a few hours in the house (46 days before the profile was discovered). For me there is a rather large leap between the study and this case at this point.

I will have to leave it at that. Professional responsibilities are calling.

OK. By the way, since I'm asking everybody, do you have access to any of the information that Charlie has access to, or Dr Waterbury, or Bruce....? Dr Waterbury seems to have a vast cache of information that would be exactly your kind of thing. I'm assuming he didn't spend tens of thousands of dollars getting hold of it himself, so there is presumably a source out there willing to share.

 

[Fulcanelli]

Dr Waterbury seems* to have a vast cache of information that would be exactly your kind of thing.

*claims

 

[little grey rabbit]

Contamination can enter in a number of areas
1. At the lab (unlikely)
2. During sample collection (possible)
3. Naturally, through communal living (getting more probable).

The trouble of extending PCR sensitivity is it becomes difficult to rule out non-incriminating cross-contamination if the accused has a good reason for being in the victim's living space.
The 2nd problem is you begin to amplify every allele in existence. Then you over lay your reference sample and low and behold you have a match. But since there are now so many little bumps that COULD be a peak, you have widened the pool of people who would return positive enormously.

My "favorite" DNA fingerprinting story is one from New Zealand where a yachtie was supposed to have killed a young couple in the Marlbrough sounds. He had a hair covered blanket. 11 hairs were selected from the blanket and subjected to DNA profiling, they were all negative for either victim. Then a hair brush of the victim was found with lots of positive control hairs on it. After this two more hairs were selected from the blanket, and would you believe it they were positive!
The court was presented were a photo of evidence sampling bag where the hairs for testing had been stored and someone had clearly (inappropriately) cut away a corner. On cross-examination no one could explain why or who.

Just for fun I worked out the probability of having only 13 hairs, 11 negative and 2 positive, they would appear in such an order: the 11 negative first and the 2 positive at the end. It is a simple enough binomial, IIRC it was around 1.67%

The yachtie is still serving a life sentence.

 

[Chris_Halkides]

evidence of degradation in the electropherogram

To all,

Here is Figure 3 from the 2008 paper by Toothman et al I cited before. Note how strong the peaks are. They are several hundred to several thousand RFUs.

The reason why some peaks are strong and some are weak has to do with the length of the DNA fragments that are subjected to capillary electrophoresis. In an electropherogram, the smaller fragments are to the left of the larger fragments, which are more toward the right. Notice how the tall peaks are at the left portion and the short peaks are at the right portion of the figure in the previous message.

If the degradation events are not sequence-specific, then a long piece of DNA is more likely to be subjected to a degradation event than a short one. Once a degradation event such as a nicking of the backbone occurs, the DNA cannot be properly replicated in the PCR reaction. This is the reason why finding a complete profile was difficult in this study: it is just partial degradation of the DNA.

 

[Chris_Halkides]

There was a smaller amount than you think

I've no idea where you heard that. There was 1.4 ng of Raffaele's DNA on the clasp. This was offered in the trial during cross examination. That figure was never given to indicate the total amount of DNA on the clasp, but one individual's.

The appeals documents give 1.14 ng as the total amount of DNA present, and Raffaele's DNA was 1/6 to 1/10 of the total. This is borderline to the low copy number region of DNA profiling.