DNA revisited in light of James Kolar’s book

Discussion in 'Justice for JonBenet Discussion - Public Forum' started by cynic, Jul 22, 2012.

  1. cynic

    cynic Member

    There are six unique and unidentified genetic profiles – five male profiles and one female profile.
    DNA testing involving fingernail scrapings from both hands revealed JonBenet’s genetic profile on both sides.
    In addition to JonBenet’s profile, scrapings from the left fingernails revealed unidentified male #1
    The right fingernails indicated that two further unique profiles were present, unidentified male #2, and a unique unknown female profile. (JonBenet could not be excluded as a contributor)
    The waistband, seams, and crotch of panties (Distal Stain 007-2) CODIS all matched and produced the profile that has been entered into the CODIS database, unidentified male #3 (Strength/weakness of profile: 10 markers)

    The above profiles were determined through typical STR DNA testing.
    Touch DNA (TDNA) testing, all presumably done at the Bode facility revealed one matching profile and a further two unique profiles, both male:
    TDNA on the waistband of leggings matching DS 007-2 male #3
    TDNA on the wrist bindings – male #4 (Strength/weakness of profile: 6 markers)
    TDNA on the “garrote” – male #5 (Strength/weakness of profile: 7 markers)

    (Also, TDNA on the pink Barbie nightgown found in the Wine Cellar with the body of JonBenét was identified as belonging to BR and PR.)

    A full CODIS profile has 13 markers; any profile with fewer markers is a partial profile. All DNA profiles in this case are partial profiles
    The highest quality DNA, and the only profile in this case that has been entered in the CODIS database, at 10 markers, is Distal Stain 007-2
    All other DNA is weaker, in other words, less markers.


    Kolar’s book confirmed the speculation that the profile from one of the blood spots that eventually ended up in CODIS originally had only 9 markers.
    The male DNA sample, subsequently identified as Distal Stain 007-2, only contained 9 genetic markers, and like the DNA collected from beneath JonBenét’s fingernails, was of insufficient strength to be entered into the state and national databases. Moreover, the sample was so small that technicians were not able to identify the biological origin of the exemplar.
    Foreign Faction, Who Really Kidnapped JonBenet, James Kolar, page 140

    Eventually a 10th marker was identified which then met the minimum standard for entry into CODIS:

    DNA replication technology was utilized in the Denver Police Department’s crime lab, and the 10th marker was eventually strengthened to the point that the unidentified male sample discovered in JonBenét’s underwear was able to be entered into the state and national databases. This laboratory success didn’t take place until 2002, nearly 6 years after the murder of JonBenét
    Foreign Faction, Who Really Kidnapped JonBenet, James Kolar, page 140

    I met with the man who had worked so diligently to enhance the DNA sample identified as Distal Stain 007-2. Denver Police Department crime lab supervisor Greg Laberge met me for lunch in early December 2005 and advised me that the forensic DNA sample collected from the underwear was microscopic, totally invisible to the naked eye. So small was it in quantity, consisting of only approximately 1/2 nanogram of genetic material, equivalent to about 100 – 150 cells, that it took him quite a bit of work to identify the 10th marker that eventually permitted its entry into the CODIS database.
    Foreign Faction, Who Really Kidnapped JonBenet, James Kolar, pages 303 - 304

    The profiles found from the fingernail clippings of JonBenet were presumably not from the non-sterile nail clippers that the coroner was in the habit of using.
    (However, to the best of my knowledge, clippers are not used in medical autopsies, only in autopsies performed for legal reasons. I don’t know the reasons for those eight prior autopsies. Therefore, as an example, if the last time the clippers were actually used was 10 autopsies ago it would have missed by this screening process.)
    Investigators were able to obtain the DNA samples from eight (8) of the autopsy examinations that preceded that of JonBenét. These samples were analyzed, but none of these matched the unknown male and female samples collected from JonBenét’s fingernails. Perhaps more disappointing, was the fact that the unknown samples lacked sufficient identifying markers that permitted their entry into the state and national DNA databases.
    Foreign Faction, Who Really Kidnapped JonBenet, James Kolar, pages 137 - 138

    Amylase or something else?
    Laberge indicated that the sample had flashed the color of blue during CBI’s initial testing of the sample, suggesting that amylase was present. Amylase is an enzyme that can be found in saliva, and it had been theorized by other investigators in the case that someone involved in the production phase of this clothing article could have been the source of this unknown DNA sample. It was thought that this could have been deposited there by coughing, sneezing, or spitting or through a simple transfer of saliva on the hands of a garment handler.
    Foreign Faction, Who Really Kidnapped JonBenet, James Kolar, pages 137 - 138

    The only test that “flashes blue,” in the presence of amylase is the Phadebas test. Take note of some of the things which can produce a false positive:
    What is the Phadebas Press Test? How specific is it and what can cause a false positive result?
    The Phadebas Press Test uses a filterpaper “test sheet” impregnated with an insoluble starch-dye complex. The test sheets are moistened with sterile water and then laid on an article of evidence. Saliva present on the item being examined will contain α-amylase that will hydrolyze the starch in the overlying area of the test sheet. This process releases a blue dye to form a blue stain that co-localizes with the position of the saliva stain. Areas of the evidence that do not contain α-amylase should not show the presence of a blue stain. Phadebas Press Test provides only a presumptive indication of saliva and is not human specific. This test is known to yield false positive results with fecal samples and some investigators have reported positive results with vaginal swabs, human milk, some plant materials and the saliva of animals including dogs and cats. Positive results have also been reported as very likely resulting from secondary transfer of saliva (e.g., from the hands to an article of clothing).

    http://forsci-associates.com/serologysaliva.html

    Pro and con for the “sweatshop” theory
    Pro:
    The male sample identified in Distal Stain 007-2 was weak, and degraded to begin with, and weaker samples of the same genetic material were found in the waistband and leg bands of the underwear. It was observed that these were areas of the clothing that would have been handled more strenuously during the production phase of the clothing article.
    Foreign Faction, Who Really Kidnapped JonBenet, James Kolar, page 304
    Con:
    Laberge advised, confirming what Tom Bennett had previously shared with me, that some random DNA tests had been conducted in ‘off-the-shelf’ children’s underwear
    [SNIP]
    He indicated that DNA samples had been located on the articles of new clothing, but that they had been approximately 1/10 the strength of the unknown sample found in JonBenét’s underwear.
    Foreign Faction, Who Really Kidnapped JonBenet, James Kolar, pages 304 - 305

    Conclusions (from the book.)

    Laberge indicated that it was his opinion that the male sample of DNA could have been deposited there by a perpetrator, or that there could have been some other explanation for its presence, totally unrelated to the crime. I would learn that many other scientists held the same opinion.
    Foreign Faction, Who Really Kidnapped JonBenet, James Kolar, page 305

    The same theoretical principles of transfer thought to be involved in the DNA collected from beneath JonBenét’s nails could be applied to the transfer of genetic material from her underwear to the leggings. “Cloth to cloth” transfer could be responsible for this new evidence.
    Foreign Faction, Who Really Kidnapped JonBenet, James Kolar, page 427

    I believed, as did many of the other investigators working the case, that that there may have been a plausible explanation for the DNA found in the underwear and that its presence may have had nothing whatsoever to do with the death of JonBenét. The presence of this DNA is a question that remains to be resolved, but it continues to be my opinion that this single piece of DNA evidence has to be considered in light of all of the other physical, behavioral, and statement evidence that has been collected over the course of the investigation.
    Foreign Faction, Who Really Kidnapped JonBenet, James Kolar, page 305
     
    Last edited: Jul 22, 2012
  2. Karen

    Karen Member

    Thank you cynic for all this info from the book. There is so much to digest I'll have to re-read it and then I'll be able to discuss.
     
  3. Elle

    Elle Member

    Truthfully, cynic, I am at a loss with all this technique and find it very confusing!
     
  4. cynic

    cynic Member

    It can be, Elle. I suppose if I had to summarize things, it would go something like this.
    Lacy exonerated the Ramseys because she said one DNA profile equals one intruder.
    What she kept from the public, which Kolar reveals, is that there were six unique DNA profiles. Therefore, based on Lacy’s way of thinking, six profiles must equal six intruders, which is, of course, preposterous.
     
  5. koldkase

    koldkase FFJ Senior Member

    Awesome, cynic! I was so hoping you'd do the heavy lifting for us on this.

    Here's the gist of it, Elle: if the "touch" DNA proves there was an intruder, then the rest of the six unidentified DNA profiles found on the body/clothing mean there were six intruders.

    Or no proof of any intruders, just artifact DNA we all have contact with in our daily interactions in life.

    Edited to add: Oops. Cynic explained it well while I was typing.
     
  6. koldkase

    koldkase FFJ Senior Member




    Now think about the stronger samples of DNA on JB's panties compared to off-the-shelf samples tested: how much were THOSE random panties handled in doing the DNA testing? What year was this control testing done? Were the technicians/scientists using newer, more stringent handling procedures, considering the advancements in the field of DNA and "touch" DNA?

    I wonder if the panties in the JB case were handled differently in 1996/97 than those tested as control samples? Dr. Meyer tried to "match" the blood spots in the crotch of the Bloomies to the genital area of the victim. That had to involve lots of handling, after all.

    I venture that when the JB samples were collected for testing, standard procedures were much less stringent than now, when the possibility of transfer is realized as much more possible than they knew when the JB clothing was processed.

    I venture that Dr. Meyer handled them with much less caution than is standard today, as well as the CBI and other labs. Think about this: only one person had to handle the Bloomies and longjohns with contaminated hands to spread DNA to other parts of the clothing, right?
     
  7. Cherokee

    Cherokee FFJ Senior Member

    I want to add that the "six unique DNA profiles" were not COMPLETE DNA profiles! Not ONE of them had the 13 markers considered a full DNA complement, but were partial DNA profiles!

    For a comparison, when a cheek swab is done for DNA genealogy purposes, there are enough markers to make a detailed DNA analysis going back thousands of years in time.

    Paternal Y-DNA tests can be taken as far as 111 markers. Full sequencing of maternal mtDNA is possible from a check swab. How is it that allegedly fresh, crime-scene DNA is so miniscule and degraded, there isn't even a full 10 markers present?!!!

    It's absolutely preposterous! If the DNA found on JonBenet's underwear and clothing was anything more than pieces of old contaminent, THERE WOULD BE AT THE VERY LEAST 13 MARKERS FULL OF USEABLE DNA!
     
    Last edited: Feb 6, 2013
  8. cynic

    cynic Member

    Remember this?
    Augustin and Gray are convinced that the DNA sample belongs to JonBenet's killer, because of a small amount of matching DNA that also was found under the 6-year-old murder victim's fingernails. http://www.cbsnews.com/2100-18559_162-661569.html

    First a little historical perspective:

    1997 — DNA collected from a blood spot on JonBenet Ramsey's underwear described as contaminated.
    1999 — FBI releases new technology called Short Tandem Repeat to profile DNA.
    2001 — The new testing (by Cellmark Diagnostics) is allowed after a legal battle in Colorado's courts, and JonBenet's underwear is analyzed again resulting in between one and two markers out of 13 being defined.
    2002 — The Boulder County District Attorney's Office, now led by Mary Lacy, formerly Mary Keenan, takes over the investigation from Boulder police.
    2003 — Second blood spot on JonBenet's underwear tested resulting in between nine and 10 markers on the spot to be defined. That genetic fingerprint meets the threshold to be placed into a national database, Combined DNA Indexing System or CODIS, which holds DNA profiles of those convicted in most states of certain crimes. No match has been made.
    http://www.dailycamera.com/archivesearch/ci_13062285

    The first PCR based DNA Typing system was the AmpliType PM & DQA1 system from Applied Biosystems
    The discriminatory power was quite limited, approximately 1:2000
    This was used in the early tests in the JonBenet case.

    The AmpliType PM & DQA1 system tests at 6 loci:
    Low Density Lipoprotein Receptor (LDLR)
    Glycophorin A (GLYPA)
    Hemoglobin G Gamma Globulin (HBGG)
    D7S8
    Group-Specific Component (GC)
    HLA-DQA1

    This system was quite different from the tests used today and, as a matter of fact, it did not test for markers that are used in CODIS.
    The CODIS markers, by comparison are:
    D3S1358, Vwa, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, THO1, TPOX, CSF1PO, and the sex marker, AMEL
    It’s clear from Kolar’s book that the fingernail samples were retested using STR analysis and although he informs us that they are weak mixed DNA samples that do not meet CODIS standards he does not give us a count of the markers present.
    What we have known previously with respect to the fingernail DNA is no longer relevant, such as Lou Smit’s comments in his deposition relating to the primitive PM & DQA1 testing.
    What’s interesting is that Ramsey’s stooges (Ollie Grey and John San Agustin) were running around comparing 2-4 marker DNA from the incompatible PM & DQA1 to the 10 marker STR based CODIS sample.
    I had thought that maybe they were referencing new DNA testing so I couldn't be certain that they were lying, until now.

    Kolar’s book has revealed so much deception from the RST that it is simply a must-have, must-read book.
     
  9. koldkase

    koldkase FFJ Senior Member

    If y'all listen to Tricia's podcast tonight, after the segment on the Colorado theater murders at about 15 minutes, she talks with Carol McKinley about Kolar's book. It's really good stuff Carol shares with us.

    She says that when she interviewed Mary Lacy for the Daily Beast article, she asked Lacy about the multiple profiles of DNA found. Astonishingly, Lacy said she didn't know anything about those other samples. The story is they were the result of work done by an ADA who worked for Lacy, a man whose name I never quite caught, but he was the expert in the Office on DNA.

    So Lacy exonerated the Ramseys based on foreign DNA BEFORE the ligature was tested and never learned of other DNA found later, if I heard this right.

    Now something else strikes me about what McKinley said about her interview with Lin Wood. Wood had sued her and Fox News on behalf of the Ramseys, you remember, but the case was thrown out. Carol said when she called Wood for a response to Kolar's book, Wood was nice to her and answered her questions politely, no hard feelings, apparently. Then she said something I blew off, but it's come back to me now in yet another question.

    Carol said Wood pointed out even though there were other unknown DNA profiles, still none of them belonged to the Ramsey's.

    So here's the question I now have: why is that?

    I get that the DNA on the ligature would have been damning if it belonged to a Ramsey, because they said they knew nothing about that cord, it was the intruder's. But who really expected NO DNA from her parents on the body or clothing? This seems odd, doesn't it?

    Patsy dressed her in those very same longjohn bottoms, did she not? She would have pulled them onto the child, after pulling her pants off JB wore to the Whites' party.

    Patsy claimed JB was "zonked" and never awoke while being undressed and put into the longjohns. So the child is lying on her bed, dead weight, and those pants had to be tugged off. Add in the huge Bloomies Patsy said JB already had on, and surely Patsy would have to have pulled them back up--though I can't believe the child was wearing them they were so huge (see my avatar for a model comparison).

    John had to lift a sleeping JB out of the car, carry her upstairs in his arms. He said he put her into her bed and took her boots and coat off, though the coat was found in the car in later pictures, if memory serves.

    So why was there no DNA from these parents on this child or her clothing?

    I don't know. It just seemed weird when I thought about it.

    The Bode tech Williamson said she "discarded" DNA that wasn't...what was the word she used? Relevant? I wondered then how she determined what was important DNA vs not relevant?

    Oh well, it's just a question that came into my mind because I would expect DNA to be on the child from the family who obviously touched her and her clothing that night.

    Good job on the interview with Carol, Tricia! You got some great info from her.
     
  10. brenk

    brenk Member

    Did I miss it or did Kolar say the last time the DNA samples were tested?
    Forgive me if I'm asking questions that has already been explained.
    Sometimes I have to go back over what I have read.
    The touch or skin DNA they found on the longjohns was it the same DNA found on the waist band of her under pants? Or were there any?
    Seems if someone redressed her there would the same DNA there also.

    I wish there were a list of everyones DNA that was tested.
    brenk
     
  11. cynic

    cynic Member

    It was a very good interview.
    I'm sorry, I'm not buying that. The only way I would believe that would be if I saw date stamped lab reports proving that she was out of office at the time.
    The person that Carol mentioned is Andy Horita, a DA's office investigator. He is the one that Kolar mentions as addressing the Task Force with the TDNA information that he relates to us in his book.
    Knowing the history of Mary Lacy’s announcements, I should not have been surprised when D. A. Investigator Andy Horita shed further light on the Touch DNA test results during the Cold Case Task Force meeting held in February 2009. I had supervised Horita during my stint as chief investigator at the D.A.’s office, and it was my opinion that he had a promising future ahead of him. He had no experience as a police officer, but he was an extremely intelligent young man. He looked decidedly dejected as he delivered the news about the additional DNA test results.
    Foreign Faction, Who Really Kidnapped JonBenet, James Kolar, pages 412 - 413

    We've seen his name before:
    In October of 2007, we decided to pursue the possibility of submitting additional items from the JonBenet Ramsey homicide to be examined using this methodology. We checked with a number of Colorado sources regarding which private laboratory to use for this work. Based upon multiple recommendations, including that of the Boulder Police Department, we contacted the Bode Technology Group located near Washington, D.C., and initiated discussions with the professionals at that laboratory. First Assistant District Attorney Peter Maguire and Investigator Andy Horita spent a full day with staff members at the Bode facility in early December of 2007.
    http://www.thedenverchannel.com/news/16834938/detail.html
    Note that it says ITEMS.

    Kolar is clear in his book that we still don't have all the details. For example, he was never able to find out the amount of markers from the TDNA on the leggings, other than it did not meet CODIS requirements. WHY?
    Furthermore, I'm not buying that Patsy's DNA at the very least was not found on the leggings especially since her DNA and Burke's DNA was found on the Barbie nightgown through TDNA.
    Horita indicated that Touch DNA testing had discovered traces of genetic material on the pink Barbie nightgown found in the Wine Cellar with the body of JonBenét. This Touch DNA belonged to Patsy and Burke Ramsey.
    Foreign Faction, Who Really Kidnapped JonBenet, James Kolar, page 414
     
  12. cynic

    cynic Member

    He doesn't mention the last time evidence was subject to DNA testing. 2008 is a good bet, though.
    The TDNA found on the leggings/long johns matched the waistband of the Bloomies. (All partial DNA profiles.)
     
  13. heymom

    heymom Member

    I don't know this for a fact, but I just have a feeling that the family's DNA was not considered relevant when it came to things they might have had normal contact with. And that wipe down JonBenet got after she was dead, I guess that managed to get rid of at least some of what may have been incriminating. In this case, the DNA evidence will NOT ever convict the killer.
     
  14. koldkase

    koldkase FFJ Senior Member

    :spit:
    DOUBLE TAKE HERE!

    So the Ramsey's DNA WAS at the crime scene. AND IT WAS PATSY'S AND BURKE'S?

    Oh. My.

    Where oh where have we seen that combo show up at the crime scene before?

    Bowl of pineapple and glass of tea?

    I am reading, I swear! I'm up to Part II of the book. But trying to keep up with the forums and Tricia's great podcasts and the Fam...I'm starting to fray a little around the edges myself.

    So does Kolar tell us what the biological sample on the gown is from? I know there was some blood found on it.

    Don't just drop that bomb on us, cynic! I'm trying not to jump ahead, as Tricia told us not to...which I hate, because I'm one of those people who peeks at the ending as soon as questions are laid out in mystery novels. :blush:

    Okay, you listed the page. I'm going to look it up.
     
  15. BobC

    BobC Poster of the EON - Fabulous Inimitable Transcript

    The Ramsey's DNA would be all over the place in that home so it is inconsequential. Since all family members spent the entire day with JBR it would be virtually impossible for their DNA not to be there.


    The fact that there are multiple DNA matches on the clothing, including a female's, tells me that you either had half a dozen intruders stomping around the house, or the samples came from multiple people who weren't related to the crime.

    Remember, JBR's body was not found in a river six months after the fact. The body was fresh, the crime scene was fresh--so where was the hair evidence? Footprints?

    You know I am not even going to feed in to this red herring anymore. That's what John Ramsey wants.
     
  16. koldkase

    koldkase FFJ Senior Member

    Here is an excerpt from Kolar's book on the DNA as presented to the Cold Case panel in 2009, pages 413-16:

     
    Last edited by a moderator: Aug 1, 2012
  17. BobC

    BobC Poster of the EON - Fabulous Inimitable Transcript

    I agree completely. Remember--it was Christmas. JBR got new clothes, a new bike, new toys. That stuff was probably covered in stray DNA and secondary transfers probably happened all day long.
     
  18. koldkase

    koldkase FFJ Senior Member

    Reading on, after recounting a crime he'd been involved in investigating where an unidentified fingerprint at a crime scene turned out to be artifact, Kolar writes more on the DNA markers of these partial samples which led him to ask further questions about the significance of the profiles:

    Page 417:

     
  19. koldkase

    koldkase FFJ Senior Member

    Not to mention, JonBenet had been to a party at the White's with other children and adults present, plus she'd been to the Stine's and the Walker's homes on the way home.

    Patsy said in her '98 LE interview she didn't know if JB had bathed or washed her hands that day. She didn't seem to know when JB had last had a bath, though I may have a memory gap there. Anyone else remember this line of questioning?

    There were also neighborhood children in and out of the Ramsey home that Christmas Day playing with Burke and JonBenet.

    Really, this is just mind-numbing.

    Kolar repeats throughout his book that it's always "possible" that a foreign faction of ninja-like intruders committed this crime...but not very likely.

    Since I believe Patsy wrote the note, and I think that's clear to anyone with two eyes and a modicum of intelligence, unless Patsy belonged to the foreign faction, I don't think it is possible, IMO.

    Plus there's that bugaboo, the pineapple in the intestinal tract. Kolar mentions early in the book the medical experts gave the timeline of that pineapple being digested and moving through to her intestine as approx. 2 hours. The head blow injuries were given 90 minutes from the blow to the strangulation, according to Kolar, so that timeline works like this: JonBenet ate the pineapple; half an hour later she was bludgeoned; 90 minutes later she was asphyxiated with the ligature.
     
  20. heymom

    heymom Member

    I think we (I mean the LE community) really are going all CSI now, getting into areas that are useless to crime investigations and will allow many perpetrators to get off scot-free. This is ridiculous, finding this kind of trace DNA and trying to figure out who it's from! Have all murders been committed by this crowd of anonymous DNA contributors? For God's sake!

    Wild goose-chasing? Or chasing unicorns?
     
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