A DNA expert will be available to answer your questions!

[questfortrue]

UKGuy, although you were framing your question for AK, I wanted to add some detail from what I've studied.

As we already know, both samples of the DNA tested were mixed with JonBenét’s. In the first sample tested in the mid 90’s by Cellmark, they were unable to tell with certainty if the contribution of foreign DNA was from only one or more than one person. They ended up saying that if it were from a single person, then the Rs were excluded. Because it was an inconclusive piece of evidence, one doesn’t hear much about it now.

It seems the second sample is attributed to a single male. But the second sample was also degraded (degradation meaning the process of DNA breaking down into smaller and smaller fragments.) As I’ve learned, the relevant fact in regards to the second Distal Stain 007-2 DNA is that in addition to it being from a mixed sample it also featured allele dropout. (That fact suggests legal concerns, which I won’t go into here.)

Apologies if this is a repeat, but the second sample was at the lower range of what is usually preferred in analysis – 500 pg (picograms) of DNA material, plus there was the possibility of masking of some of the unknown and degraded contributor’s alleles behind JonBenét’s rich sample. All this has been discussed at one time or another, and I know I’m not really adding anything new. From what I’ve understood as a non-expert, the reason it’s relevant to mention masking is that it brings special issues to bear in difficult sample scenarios, i.e., mistakes can and do happen.

Something else I read recently might be worth mentioning. It pertains to evidence of this type being virtually flaunted in cases. It comes from a recent European consortium of researchers in forensic genetics and its application in case work and was presented in 2013.
- Transfer of DNA is much ‘easier’ than previously believed
- Often these will be full profiles
- Therefore, much more caution is needed in reporting
- E.g. the association of an activity such as stabbing, with a DNA profile can never
be definitively inferred simply by the presence of a DNA profile on a knife handle
-The relevance of the evidence and the probative value of the DNA profile are two
separate issues to be dealt with.
-Unexpected ease of spread of DNA profiles means that scientists should be very
cautious in reporting – it is suggested that evidence should not be inadvertently
weighted to suggest that an activity is associated with a profile in the absence of other corroborating evidence**
-Collection of background controls makes a lot of sense (but currently it is unlikely that this procedure is ever followed in practice).

**It’s what we’ve all been saying, but not everyone listens.

 

[Annapurna]

andrewww you make a great point. We know the coroner was not the most rigorous about contamination as he used non-sterile nail clippers. Since its a tiny amount its feasible that someone was talking over the sample/ evidence. People had sticky fingers all over this case, wouldn't be the least surprised if some evidence clerk or the like invited a friend in to check it out.

 

[Anti-K]

Is it normal at all though to have a direct transfer of saliva from the perp to the victim with only 9 or 10 markers? If someone on the scene coughed or sneezed or whatever on the victim wouldn't there be a good amount of strong saliva DNA?

I mean especially with how rigorous they were with a lot of testing.


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I don’t think there is a normal. It could be anything from nothing to mere traces to as much as you’d like.

I think the number of markers identified was limited due to degradation. The DNA was breaking up. You can still get a full profile from a degraded sample, or no profile at all and anything in between. When they process a DNA sample they are essentially fragmenting it, they’re just fragmenting it in very exact locations.

The DNA in saliva is low per volume and the conditions – between legs, inside crotch, wet with urine, leggings on top, blanket on top – were near perfect for degradation to occur.
…

AK

 

[Anti-K]

Anti-K,
You have an extremely unattractive habit of not answering the question put to you and launching yourself off onto some theoretical tangent that may or may not have any relevance, patently you think this is a winning strategy.

I'll try again: Were the two samples of blood spots from two different people?

.

I answered your question as best and simply as I could.

Here is what Smit said in his deposition. Remember that these are Before CODIS samples.

…in the case of JonBenet, from what I recall from the reports, is that there are at least four markers under the fingernails of the left hand.

There are at least two markers, clear distinct markers under the fingernails of the right hand. And there is at least one marker in the panties of foreign DNA, a clear marker.

The markers in the panties, in the right hand, and in the left hand are the same foreign markers. They match in the same area as the markers under her fingernails and in the panties. And also the same thing with the other markers in the right hand comparing with the left hand.

Also what was found is that there are in the panties other markers which are foreign, but they are not as strong as the markers are under the fingernails, and they are not actually classified as a marker. But there are other indications that there is foreign DNA.

Kolar doesn’t mention the one marker, from the first blood spot, panty sample that Smit talked about. Smit was speaking before the 10 marker, second blood spot panty (CODIS) sample that Kolar talks about. Kolar contradicts Smit on the fingernail DNA.

The first blood spot, the one Smit talked about, was later tested in 2001 using the CODIS Kits. One or two markers (out of 13) were found. At least, according to some sources. This finding has sort of vanished into the air and I can’t recall reading or hearing anything anywhere about whether the foreign samples from the two blood spots were from two people.
…

AK

 

[Anti-K]

UKGuy, although you were framing your question for AK, I wanted to add some detail from what I've studied.

As we already know, both samples of the DNA tested were mixed with JonBenét’s. In the first sample tested in the mid 90’s by Cellmark, they were unable to tell with certainty if the contribution of foreign DNA was from only one or more than one person. They ended up saying that if it were from a single person, then the Rs were excluded. Because it was an inconclusive piece of evidence, one doesn’t hear much about it now.

It seems the second sample is attributed to a single male. But the second sample was also degraded (degradation meaning the process of DNA breaking down into smaller and smaller fragments.) As I’ve learned, the relevant fact in regards to the second Distal Stain 007-2 DNA is that in addition to it being from a mixed sample it also featured allele dropout. (That fact suggests legal concerns, which I won’t go into here.)

Apologies if this is a repeat, but the second sample was at the lower range of what is usually preferred in analysis – 500 pg (picograms) of DNA material, plus there was the possibility of masking of some of the unknown and degraded contributor’s alleles behind JonBenét’s rich sample. All this has been discussed at one time or another, and I know I’m not really adding anything new. From what I’ve understood as a non-expert, the reason it’s relevant to mention masking is that it brings special issues to bear in difficult sample scenarios, i.e., mistakes can and do happen.

Something else I read recently might be worth mentioning. It pertains to evidence of this type being virtually flaunted in cases. It comes from a recent European consortium of researchers in forensic genetics and its application in case work and was presented in 2013.
- Transfer of DNA is much ‘easier’ than previously believed
- Often these will be full profiles
- Therefore, much more caution is needed in reporting
- E.g. the association of an activity such as stabbing, with a DNA profile can never
be definitively inferred simply by the presence of a DNA profile on a knife handle
-The relevance of the evidence and the probative value of the DNA profile are two
separate issues to be dealt with.
-Unexpected ease of spread of DNA profiles means that scientists should be very
cautious in reporting – it is suggested that evidence should not be inadvertently
weighted to suggest that an activity is associated with a profile in the absence of other corroborating evidence**
-Collection of background controls makes a lot of sense (but currently it is unlikely that this procedure is ever followed in practice).

**It’s what we’ve all been saying, but not everyone listens.

Nice post.

A couple things come to mind. The first thing is that tDNA found on the leggings confirms the results from the second blood spot foreign sample. Three different samples from three different locations on two articles of clothing, DNA analyzed in separate labs, in separate buildings by different entities (BODE, CellMark). Each one of these three samples brings confidence to the results of the other two.

The second thing that comes to mind is the most important and it is almost never mentioned, but the quoted post is a perfect example of it. The quoted post gives us various reasons why we might question the reliability of the DNA results (see first thing, above). If someone is identified and if investigation warrants an arrest and trial, this person can use the reasons in the quoted post to say, hey, that aint my DNA! and, it might not be. But, it is still someone’s DNA and that someone could be the killer.

There are two sides to this DNA. Inclusion and Exclusion. The quoted post goes to Inclusion and questions reliability but Exclusion is not questioned. Exclusion is absolute and certain. This DNA is located where the killer could have left his DNA, in areas of recent contact, and being able to say that this is not your DNA and it is not my DNA is something. It’s exculpatory for us. Just wanted to add that I’m in complete agreement with the bolded portion of the quoted post.
…

AK

 

[Ellie9]

That is the scary thing about DNA, you don't even need contact to transfer it. I was reading about another case where unidentified DNA was found on an item. Turns out it belonged to a lab worker who happened to have stopped by for a quick chat when the item was being processed. Now let's look at this case and look at what kind of media frenzy was going on. Is it not conceivable that somebody peaked in the evidence locker? We are not even talking about the days following the crime, but years later. Not one person peaked? Nobody?

Just remember that JBRs morgue entry was stolen, photos were stolen, credit card records and phone records were stolen. Where there is money to be made, there are people who will peak in a box, and there will be DNA found


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\

If they ever happen to get a match on this mysterious DNA sample, and it's NOT completely obvious (a.k.a from a worker, a paparazzi person, etc. who could have contaminated after the death) would there be any possible way to link the crime to the person? I mean, if you ask me where I was on Dec. 25-26 1996 I'd have no idea. I don't even know what presents I got that year, and I was a teenager. If I said I was living in NJ at the time, would they even be able to look that up? And if an IDI then for sure the two (or three assuming her panties are gone) missing pieces of evidence are soooo long gone.

If the DNA is linked to an obvious source (someone who would have been known to steal stuff) would this take away the exoneration from the R's? And even if someone did a death bed confession (slim chance I think) how would we ever know if this one Ramsey still isn't covering for another Ramsey? (Such as John claiming he did it to protect BR, or even BR claiming he did it to protect both his parents' reputations because a child at the time of murder would get less harsh blame than an adult/parent).

In short, this open-endedness of this case drives me nuts.

 

[andreww]

I answered your question as best and simply as I could.

Here is what Smit said in his deposition. Remember that these are Before CODIS samples.

…in the case of JonBenet, from what I recall from the reports, is that there are at least four markers under the fingernails of the left hand.

There are at least two markers, clear distinct markers under the fingernails of the right hand. And there is at least one marker in the panties of foreign DNA, a clear marker.

The markers in the panties, in the right hand, and in the left hand are the same foreign markers. They match in the same area as the markers under her fingernails and in the panties. And also the same thing with the other markers in the right hand comparing with the left hand.

Also what was found is that there are in the panties other markers which are foreign, but they are not as strong as the markers are under the fingernails, and they are not actually classified as a marker. But there are other indications that there is foreign DNA.

Kolar doesn’t mention the one marker, from the first blood spot, panty sample that Smit talked about. Smit was speaking before the 10 marker, second blood spot panty (CODIS) sample that Kolar talks about. Kolar contradicts Smit on the fingernail DNA.

The first blood spot, the one Smit talked about, was later tested in 2001 using the CODIS Kits. One or two markers (out of 13) were found. At least, according to some sources. This finding has sort of vanished into the air and I can’t recall reading or hearing anything anywhere about whether the foreign samples from the two blood spots were from two people.
…

AK

I'll tell you what, I'll bet they are from two different people because the Ramsey's, Lin Wood, Mary Lacy, Lou Smit and all of team Ramsey would be bringing up that match at every given opportunity.


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[BBB167893]

Many, many posters have trouble understanding DNA. I explain things as simply as possible to help those people out. As someone who DOES understand the subject, it is very, very easy for me to recognize someone who does NOT, and you, SuperDave are clearly one of those who does not.

Don't tell me what I do and don't understand, Anti-K. I'm not some Johnny-Come-Lately--I remember when the CODIS to-do was fresh. I read the articles thoroughly, and I remember Larry Kobalinsky saying pretty much the same thing I said: that the tests have improved, not the DNA itself. Are you trying to claim now that DNA testing and detection methods have not improved over the last 20 years?

The post – your post http://tinyurl.com/om7jq3k - to which my explanation was addressed proves this point (as does virtually everything you post on the topic). So, I hope this explanation was able to help you out, too.

Maybe not the way you intended.

This DNA (CODIS and matching tDNA) represents a potential suspect who needs to be identified and investigated. This DNA is inculpatory for the donor, and it is exculpatory for everyone who is not the donor.

I reiterate: being excluded from being the DNA donor (if such a word can be applied) is a far cry from being excluded from being the killer.

 

[BBB167893]

SuperDave,
mmm, now I did think about referring to chromosomes as inherited from both parents and all that stuff.

But hey, we have a degraded evidence sample of touch-dna, but no reference sample to compare against.

So why do we need a lesson in the Product Rule as per probability, and whats the chance the Prosecutor's fallacy has been voiced here?

Are you suggesting someone could be excluded from being the DNA donor, yet still be the killer of JonBenet?


.

BBM. This isn't a new idea, UKGuy. I've been pounding that drum for a while, now. To me, it works like this: let's say you get a suspect who looks good for this crime. Various other pieces of evidence array against him. And just when it looks like a lead-pipe cinch, the DNA doesn't match.

What do you do then? Say that the DNA is probably just an artifact and go ahead against him? Or let him go? Well, in this case, you'd HAVE to let him go, because the DNA's been sold to the public as the magic bullet.

I'm not "what-iffing" here, either! I firmly believe that the scenario I just expostulated is what happened with Mary Lacy when John Karr's DNA didn't match. If you read between the lines of her press conference, she actually DID try to backpedal on the DNA's importance briefly before letting him go. I can only guess that she realized (or more likely, was informed) that this would destroy her credibility (what she had left) because she'd made it the entire lynch-pin of her "investigation," and going back would only make it clear that she was okay with letting a phony confessor be punished for this crime.

 

[BBB167893]

I don’t think there is a normal. It could be anything from nothing to mere traces to as much as you’d like.

I think the number of markers identified was limited due to degradation. The DNA was breaking up. You can still get a full profile from a degraded sample, or no profile at all and anything in between. When they process a DNA sample they are essentially fragmenting it, they’re just fragmenting it in very exact locations.

The DNA in saliva is low per volume and the conditions – between legs, inside crotch, wet with urine, leggings on top, blanket on top – were near perfect for degradation to occur.
…

AK

Ah, but JB's DNA was not degraded.

 

[Anti-K]

DNA section copied from Ellie9's post, here: http://tinyurl.com/jpdzdtg Ellie9: "Actually, there is really only one part of the evidence that causes some guessing and wondering with RDI. I think the one thing is probably the trace DNA. Some people have no issue with this. They just explain it by saying there was a lot of trace DNA evidence on JBR's body and clothing. This is acceptable. Some say a factory worker sneezed/coughed on the clothing as he worked. This too is a reasonable explanation. This is the main thing they have to explain in debates, and in my opinion they do it pretty well."

i’m having problems with your use of the term “trace dna.” ‘m not sure what you mean. anyways…

i think it is not reasonable to equate the three matching samples with the other dna samples found.

the factory worker theory is destroyed by the matching – not saliva, not a sneeze, not a cough – dna on the leggings. this is no longer a reasonable explanation and never really was as tests on new panties could only find TRACES – no markers – of dna that were 1/10th to 1/12th the size found on jbr’s panties.

also, of the most reasonable explanations one of them includes the killer. and, investigators put effort into eliminating the rest.

it’s true that the DNA could have an innocent explanation, but it has not been shown that it has and investigators tried to show it.
…

AK

 

[UKGuy]

DNA section copied from Ellie9's post, here: http://tinyurl.com/jpdzdtg Ellie9: "Actually, there is really only one part of the evidence that causes some guessing and wondering with RDI. I think the one thing is probably the trace DNA. Some people have no issue with this. They just explain it by saying there was a lot of trace DNA evidence on JBR's body and clothing. This is acceptable. Some say a factory worker sneezed/coughed on the clothing as he worked. This too is a reasonable explanation. This is the main thing they have to explain in debates, and in my opinion they do it pretty well."

i’m having problems with your use of the term “trace dna.” ‘m not sure what you mean. anyways…

i think it is not reasonable to equate the three matching samples with the other dna samples found.

the factory worker theory is destroyed by the matching – not saliva, not a sneeze, not a cough – dna on the leggings. this is no longer a reasonable explanation and never really was as tests on new panties could only find TRACES – no markers – of dna that were 1/10th to 1/12th the size found on jbr’s panties.

also, of the most reasonable explanations one of them includes the killer. and, investigators put effort into eliminating the rest.

it’s true that the DNA could have an innocent explanation, but it has not been shown that it has and investigators tried to show it.
…

AK

Anti-K

it’s true that the DNA could have an innocent explanation, but it has not been shown that it has and investigators tried to show it.

With an absence of this degraded dna to be found elsewhere in the wine-cellar its more likely it has an innocent explanation.

.

 

[UKGuy]

BBM. This isn't a new idea, UKGuy. I've been pounding that drum for a while, now. To me, it works like this: let's say you get a suspect who looks good for this crime. Various other pieces of evidence array against him. And just when it looks like a lead-pipe cinch, the DNA doesn't match.

What do you do then? Say that the DNA is probably just an artifact and go ahead against him? Or let him go? Well, in this case, you'd HAVE to let him go, because the DNA's been sold to the public as the magic bullet.

I'm not "what-iffing" here, either! I firmly believe that the scenario I just expostulated is what happened with Mary Lacy when John Karr's DNA didn't match. If you read between the lines of her press conference, she actually DID try to backpedal on the DNA's importance briefly before letting him go. I can only guess that she realized (or more likely, was informed) that this would destroy her credibility (what she had left) because she'd made it the entire lynch-pin of her "investigation," and going back would only make it clear that she was okay with letting a phony confessor be punished for this crime.

SuperDave,
That was neatly outlined, its mostly what I think too. Also I reckon the days of dna as a magic bullet are over since people now recognize how easy it is to transfer dna from person to person.

An example is the Max Planck Institute where they arrived at erroneous statistics for particular genes in the human genome, until they realized that palaeontologists excavating ancient sites had simply transferred human dna, by various means, e.g. touching, coughing, etc thereby inflating particular gene counts.

Even after telling the palaeontologists to wear surgical gloves and place artifacts, i.e. bone etc into sterile plastic containers, the Max Planck Institute whilst operating in clean room conditions still found modern genes making their way into the test samples!

The scientists at the Max Planck Institute, even while clothed in the white cotton boiler-suits, plastic masks, and wearing surgical gloves still transferred dna onto ancient specimens!

.

 

[Anti-K]

Anti-K

With an absence of this degraded dna to be found elsewhere in the wine-cellar its more likely it has an innocent explanation.

.

two matching samples were found on the leggings.

the degradation was probably caused by environment: minor component, saliva, urine, between legs, under layers of clothing and blanket. wet samples degrade more readily than dry samples. jbr’s sample – the major component – may or may not have been degraded, the sample may have been of sufficient size to overcome any degradation. this is an unknown (to us).
.

if people want to argue that the tDNA found on the ligatures was from innocent transfer – i’ll go along with that. that makes sense, to me. under the fingernails? sure; maybe (i am skeptical about Kolar’s DNA description). but, these three matching samples? that’s a hard sell. three locations, two articles of clothing, one on the inside commingle din victims blood, two on the outside where her leggings would have been grabbed to pull down, one probably saliva, two probably skin cells. a hard sell, indeed. keep trying.
…

AK

 

[UKGuy]

two matching samples were found on the leggings.

the degradation was probably caused by environment: minor component, saliva, urine, between legs, under layers of clothing and blanket. wet samples degrade more readily than dry samples. jbr’s sample – the major component – may or may not have been degraded, the sample may have been of sufficient size to overcome any degradation. this is an unknown (to us).
.

if people want to argue that the tDNA found on the ligatures was from innocent transfer – i’ll go along with that. that makes sense, to me. under the fingernails? sure; maybe (i am skeptical about Kolar’s DNA description). but, these three matching samples? that’s a hard sell. three locations, two articles of clothing, one on the inside commingle din victims blood, two on the outside where her leggings would have been grabbed to pull down, one probably saliva, two probably skin cells. a hard sell, indeed. keep trying.
…

AK

Anti-K,

two matching samples were found on the leggings.

So maybe events went like this: JonBenet's stager opened up the pack of size-12's transferring foreign dna onto their hands, from there onto the sides of longjohns, which then fell by gravity into JonBenet's underwear?

The foreign dna might be coincidental artifact originating from the person who either packed the size-12's or delivered them to the R's house?

Thats a neat innocent explanation which also offers a reason for an absence of the same dna elsewhere at the crime-scene, which an IDI scenario does not!

I've yet to see a reference to the saliva test.

 

[Ellie9]

It also could have gone like this...

Paintbrush handle had small amounts of DNA from sale, art instructor, or painting friend of PR. The handle is used inside jbr to stage sexual assault after death. The injury resulted in bleeding. The paintbrush handle wss held by a gloved hand, and some DNA from handle gets attached to gloves.

Person puts it away, wipes JBR down, and then pulls size 16 panties on her. Injury from brush causes small amount of blood to drop down, mixed with DNA from brush. Long johns are pulled up next and contaminated with DNA from handle transferred to gloves.

Is that possible maybe? Not sure because I'm not sure they found the instrument used to assault JBR. If they had they would have DNA tested it.


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[Anti-K]

Anti-K,

So maybe events went like this: JonBenet's stager opened up the pack of size-12's transferring foreign dna onto their hands, from there onto the sides of longjohns, which then fell by gravity into JonBenet's underwear?

The foreign dna might be coincidental artifact originating from the person who either packed the size-12's or delivered them to the R's house?

Thats a neat innocent explanation which also offers a reason for an absence of the same dna elsewhere at the crime-scene, which an IDI scenario does not!

I've yet to see a reference to the saliva test.

This opens up a can of worms for me because imo the evidence does not support the believe that jbr’s panties were changed. So, i reject the premise right from the start.

On the other hand, why not consider it? Maybe i’m wrong about the panties.

If the panty sample is saliva and the leggings samples are not, then one did not transfer from the other.
I don’t think that dna is going to fall through the side hip area of the leggings and through the panties and then somehow make their way to the crotch of the panties, transforming into saliva along the way.

If three matching samples don’t tell you something, neither will four, or five, or… regardless, your expectation that, if idi, even more dna would have been found is merely your opinion and has no factual basis.

You’ve asked this about the saliva a few times, and you’ve always been answered. The last time you asked, aussiesheila answered you, here: http://tinyurl.com/h2qwwox you thanked her for, in your words, “her post and detailed information,” here: http://tinyurl.com/h37fvl imo, when coming from you, this is now a troll question.
...

AK

 

[Anti-K]

It also could have gone like this...

Paintbrush handle had small amounts of DNA from sale, art instructor, or painting friend of PR. The handle is used inside jbr to stage sexual assault after death. The injury resulted in bleeding. The paintbrush handle wss held by a gloved hand, and some DNA from handle gets attached to gloves.

Person puts it away, wipes JBR down, and then pulls size 16 panties on her. Injury from brush causes small amount of blood to drop down, mixed with DNA from brush. Long johns are pulled up next and contaminated with DNA from handle transferred to gloves.

Is that possible maybe? Not sure because I'm not sure they found the instrument used to assault JBR. If they had they would have DNA tested it.


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And, what kind of coincidence would that be? They just happen to grab the one paintbrush that some other person had been last to touch.

And, i don’t understand how it transforms into saliva inside the panties while it remains not saliva for the leggings. And, how it gets onto both sides of the leggings – or are you saying they held the paintbrush with both hands?
Etc.

Oh. A cpl things you got wrong: the sexual assault occurred at or near point of death, not after death.
And, it was not staged. It was real. The sexual aspect of this crime, which occurred at or near point of death, and was very, very real, was covered up.

Also, weren’t the panties size 12?

And, I think it is most widely believed that the missing end of the paint brush was used for the assault.
…

AK

 

[Ellie9]

And, what kind of coincidence would that be? They just happen to grab the one paintbrush that some other person had been last to touch.

At least it would be the only coincidence.

And, i don’t understand how it transforms into saliva inside the panties while it remains not saliva for the leggings. And, how it gets onto both sides of the leggings – or are you saying they held the paintbrush with both hands?
Etc.

Yes I think paintbrush was in both gloves hands because it was broken in half - you need both hands to snap it. I'm not sure the saliva test is accurate and it has been shown to give false positives. Also that enzyme is found in blood and urine. Because both blood and urine were present, it could have more easily given a false positive.

Oh. A cpl things you got wrong: the sexual assault occurred at or near point of death, not after death.

Okay

And, it was not staged. It was real.

erm, agree to disagree then. The loose binds, the unnecessary duct tape... that's staging.

The sexual aspect of this crime, which occurred at or near point of death, and was very, very real, was covered up.

Yes the sexual assault was real. In my opinion it was part of staging.

Also, weren’t the panties size 12?

Yes, that's right. I must have mistyped, thanks.

And, I think it is most widely believed that the missing end of the paint brush was used for the assault.

That's what I heard, too, which is why I went with this as my theory.

 

[andreww]

What exactly did JB wear to the White's? Dress or pants? I am wondering because if she wore a dress or skirt, and she wore the size 12s, I have a hard time believing they would have stayed on. Especially if the kids we amped up and running and playing as kids do. Could she have actually taken them off? Maybe they were in a pocket or a purse?


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