DNA revisited in light of James Kolar’s book

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

  1. SunnieRN

    SunnieRN Member

    :laffbig::rolling:

    I remember a year or two ago at Websleuths, when Cynic, OTG and UKGuy were talking about tDNA. I was scared then and still am now. I can't begin to tell you how many patients, family members, staff, I touch in one night at work. Let alone computer keyboards, copy machines, coffee pots, desk tops, etc, etc, etc....
     
  2. zoomama

    zoomama Active Member

    Thank you Cherokee for the great graphics. I was lost with your numbers during the radio show and this very old brain just couldn't keep up. These graphics are easier to follow along. Whoever was the DNA expert that told ML about the touch DNA should be brought forth and made to explain how much they knew and how much they carefully explained to her. The whole concept isn't an easy one to "get". ML needed an out for her friends and she got one with this touch DNA. Shame shame on her.
     
  3. Cherokee

    Cherokee FFJ Senior Member

    There is one more aspect of the DNA I mentioned on Tricia's show that I want to reiterate here:

    If scientists can get full y-DNA and mtDNA results from a 500-year-old skeleton that was dumped into a hasty dirt grave, then why is the alleged "intruder's" DNA (that was supposedly only 24-hours-old) partial and degraded enough that barely 10 markers could be found?

    Richard III's skeleton, particulary his femur and teeth, provided enough mitochondrial DNA (mtDNA) to match with two different living descendants of his sister, Anne of York. This provided conclusive proof the skeleton found under the Leicester parking lot was, indeed, Richard III.

    Mitochondrial DNA is passed down from a mother to her children. Only females can pass this DNA to males and females. The mother of Richard and Anne pased her mtDNA to both of them (and their other siblings), and it can survive unchanged for generations.

    Furthermore, scientiests are planning to use the y-DNA they were able to extract from Richard III's femur for matching with males from the line of York. Y-DNA is passed down only from a father to his sons. The reason why the scientists used mtDNA (first) for confirmation of the skeleton as Richard III, instead of y-DNA, is because mtDNA definitely shows maternal relationship.

    As we know, not all children are the offspring of their "fathers." In fact, it is estimated as much as 10% of the population has been sired by someone other than who they believe is their biological father. Therefore, y-DNA can have pitfalls if you are trying to match ancient remains. The fact that many "lords of the manor" insisted on sleeping with their peasant's brides is just one historical fact that has skewed many y-DNA lines.

    Be that as it may, the fact is ... scientists were able to extract viable and complete mtDNA and y-DNA from an unpreserved skeleton that was hastily buried in 1485! How much more so should the alleged "intruder DNA" have been viable and complete?!!!

    [Richard III DNA samples were extracted from the teeth and the right femur to compare with known descendants of Richard's family. Despite the potential for DNA to degrade, a match was found.]
     

    Attached Files:

  4. SunnieRN

    SunnieRN Member

    Cherokee, that is interesting! How amazing that they were able to get enough DNA from an unpreserved skeleton, dumped in a hole! Brings the whole intruder theory into even murkier waters!
     
  5. heymom

    heymom Member

    Great tie-in, Cherokee! I was stunned to hear how quickly and affirmatively this skeleton was identified as Richard III. The archeologists must be lining up and jockeying for a chance to analyze his bones!

    Unfortunately, most people cannot grasp even the basics of DNA, let alone any intricacies. I count myself as one who can "get" the basics, but I don't flatter myself that I know much beyond that. But even my limited brain can understand that degraded "touch" DNA does not implicate nor clear any suspect! However 5 separate individuals were NOT in that house on Christmas, as Kolar's introductory chapter illustrates.
     
  6. Elle

    Elle Member

    Cherokee,

    Congratulations on your knowledge of DNA. What an intelligent young woman you are to understand all this DNA information!:takeabow:I shall
    do my best to understand "some" of it!:doh:Thank you for posting the information of the DNA of Richard III. Wasn't that exciting!?
     
  7. BobC

    BobC Poster of the EON - Fabulous Inimitable Transcript

    Very fine posts, Cherokee, except that I'll go to my grave swearing I wasn't the donor!!

    All kidding aside, all I can add is that they didn't even have ten markers for years! As I recall, Didn't they start out with 3 or 4, and then have the strands regenerated with some crazy new scientific tech?

    It was also fascinating to hear Lacy claiming that two samples "matched," when the full strands were not there, and that in a court of law you can't call any DNA a "match"--you can only say it is "consistent with." In the 90's the FBI was trying to get legislation passed to change that--since in OJ Simpson's case, the DNA found at his crime scene was some crazy number like 10 billion to one that it belonged to somebody other than Simpson, but they couldn't call it a match in court. But Lacy called this garbage a match. Thus throwing away the ransom note and all the other staging that came from Pasty's personal effects!

    And worse, she didn't just throw everything else away, she cleared them. Disgusting.
     
  8. BOESP

    BOESP Member

    Cherokee, Didn't the lab have to amplify the DNA sample to even come up with 10 markers so the sample would qualify for entry into CODIS or am in a state of confusion. :doh:
     
  9. BOESP

    BOESP Member

    Awww, Bob, we must quit meeting like this. Just cross-posting in the night in passing under the stars and the moon (see my post made right after yours). :bateye:
     
  10. DeeDee

    DeeDee Member

    HIYA, Sunnie!:beats::welcome:
     
  11. DeeDee

    DeeDee Member

    They have extracted DNA that can still be identified from some Egyptian mummies from the 18th Dynasty or even older!

    One day....Jurassic Park will be a reality!
     
  12. Cherokee

    Cherokee FFJ Senior Member

    Ha ha, I didn't think about THAT when I included you in the DNA profile! I was trying to make the DNA graphic more interesting than just using John Doe-type names. :)

    It's good thing pea-brained Mary Lacy isn't the Boulder DA now because she'd have all of us in the chart graphic arrested on suspicion of being her partial and degraded intruder!

    Seriously, that made-up graphic I posted is more valid than the "touch" DNA results she used to "exonerate" the Ramseys! At least it has real numbers and is based on real people. I also posted my graphic PUBLICLY, which is more than Mary Lacy was willing to do! And now we know why!!!
     
  13. Cherokee

    Cherokee FFJ Senior Member

    Ha ha, and here I thought you'd be honored to be the "ten-marker man"! :D

    Yes, according to a "JonBenet Ramsey DNA Timeline" published August 29, 2006 in the Boulder Daily Camera:

    In 1997, DNA collected from a blood spot on JonBenet Ramsey's underwear was described as contaminated.

    In 1999, the FBI released new technology called Short Tandem Repeat to profile DNA. It used 13 markers to raise the probability that a randomly selected individual would match it is one in 1 quintillion.

    In 2001, the new testing was allowed after a legal battle in Colorado's courts, and JonBenet's underwear was analyzed again, resulting in between only one and two markers out of 13 being defined.

    In 2003, a second blood spot on JonBenet's underwear was tested, resulting in between nine and 10 markers on the spot to be defined.

    Initially, there were only nine very weak markers found, but later, a 10th marker was added by using enhancement tecniques. James Kolar describes this in his book Foreign Faction: Who Really Kidnapped JonBenet?

    p.140

    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. Regrettably, they could not tell police investigators if the biological source of the male DNA was derived from blood, semen, epithelial skin cells, or some other genetic material.


    The challenge to technicians was enhancing the DNA sample so that it could be entered into the state and national DNA databases, and it took a while for this technology to develop. As noted above, the FBI requires that 10 out of 13 genetic markers be identified in order for a sample to be entered into the Forensic Index database.

    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.

    p. 303-304

    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.

    DNA samples generally consist of 13 Core loci markers, so it is important to note that Distal Stain 007-2 is not a full sample of DNA, and the FBI requires at least 10 markers be identified before an unknown sample can be entered into the national CODIS data base.

    The male sample identified in Distal Stain 007-2 was weak, and degraded to begin with ....


    My thoughts exactly!
     
  14. Cherokee

    Cherokee FFJ Senior Member

    No, you are not confused! Bob asked the same question right before you, so I answered both of you in that post. :)
     
  15. Cherokee

    Cherokee FFJ Senior Member

    Yes, and 10,000-year-old Native Americans buried in Florida, the ones I mentioned on Tricia's show last Monday. Unfortunately, one set of bones were found to be contaminated when the DNA result showed a European ancestry, and it was traced to one of the research team members!

    That's why it is important to suit up and glove up when recovering remains, performing autopsies and testing DNA in labs. Contamination has recently been discovered as a huge issue in many forensic labs.

    Dr. Jo Appleby, an osteoarchaeologist from Leicester University, followed correct procedure when she went to examine and remove the bones of Richard III from it's small burial pit.
     

    Attached Files:

  16. BobC

    BobC Poster of the EON - Fabulous Inimitable Transcript

    Not to mention 40.000 YO wooly mammoths.
     
  17. cynic

    cynic Member

    Ditto, nice to see you over here :sunny:RN!
     
  18. cynic

    cynic Member

    US court rooms have been very reluctant to accept TDNA but it is, unfortunately, starting to make some inroads. With respect to admissibility, TDNA has been in the court room but, of course, has been challenged in both of the cases that I’m aware of.
    It won the challenge once, and lost once, so it will continue to be challenged until such time as a more definitive ruling can be obtained.

    A controversial new technique in DNA Testing and Criminal Evidence is being challenged in a Murder case in Supreme Court, Queens County…[SNIP]
    "Trace" DNA or "Touch" DNA, also known as "low copy number" DNA, a technique with serious limitations, developed and used in the United Kingdom, is key evidence in the case of People v. Hemant Megnath…
    [SNIP]
    Mr. Greenberg, Defense Counsel for Mr. Megnath, petitioned the Supreme Court, Queens County, Judge Robert Hanophy, for a "Frye" Hearing, wherein the Prosecution must establish that scientific evidence, before admission as evidence at trial, be "sufficiently established to have gained general acceptance in the particular field in which it belongs". As examples, the results of Breathalyzer tests in DWI cases, "conventional" DNA results and fingerprint results, have met the Frye standard and such evidence is admissible in a criminal trial. Conversely, the results of a "lie Detector" test are inadmissible in that the science has not fully been accepted in the relevant scientific community.
    Judge Hanophy's Decision has important ramifications for the admissibility of "Touch" DNA evidence in future cases in New York and the United States: If the Judge finds scientific acceptance, such evidence will be admitted routinely in criminal cases.

    http://www.addabboandgreenberg.com/...-Or-Touch-Dna-On-Trial-In-Queens-County.shtml
    The decision was in favor of allowing the testing:
    A Queens judge has become the first in the nation to approve a controversial DNA-tracking technique that can nail criminals with a speck of blood or the mere touch of a finger.
    Wednesday's precedent-setting decision by Supreme Court Justice Robert Hanophy came in the case of Hemant Megnath, a man prosecutors say slashed a young woman's throat just before she was about to testify against him in a rape case.

    http://www.nydailynews.com/news/cri...rsial-dna-test-article-1.197478#ixzz2KI8KBbZj


    Low Copy Number DNA Fryed in California
    Another recent development is the Frye hearing victory by a team of Los Angeles public defenders headed by Jennifer Friedman that resulted n low copy number analysis. This kind of test is performed when only very small samples are available for testing, and is not uncommon. With such small samples, all sorts of confounding artifacts can interfere with the reliability of the test. The defense team convinced the trial judge in People v. Hector Espino (March 18, 2009) that there has been insufficient validation research done on the methods used to produce and interpret the results of low copy number cases.
    http://www.state.il.us/defender/ctnewsletter/illinois_lifeline_volume1_issue1.pdf

    Though it takes some uncovering, the debate within the forensic community over the use and reliability of LTDNA still rages, especially in the USA. There, the admissibility of LTDNA (sometimes referred to as “touch DNAâ€, “low copy DNA†or “low-level DNAâ€) in criminal cases has been far more controversial than in the UK.
    Eminent experts including Dr Bruce Budowle (Department of Forensic and Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA and ex head of the FBI’s DNA laboratory) have spoken out against the forensic use of LTDNA as evidence in criminal trials.
    Professors Krane and Mueller continue to be skeptics, and broadly take the view that “fit for purpose†should mean limiting that purpose to the generating of intelligence leads. US courts have recently taken differing and contradictory approaches to admissibility.
    The decisions known to the authors have been from courts equivalent to our Crown Court, not appellate decisions, and they arise from litigation within the state, as opposed to federal, court system. In a case before a New York court, LCN evidence was ruled admissible, while in California the court was concerned with the dangers inherent in LTDNA–stating that “based on the evidence before the court, that there is no general acceptance in the scientific community as to the procedures to be used once you’re dealing with a LCN sample, there’s no general acceptance as to how to interpret the results that you would get when you begin with a LCN sample, and there’s no general acceptance as to the statistics that can be applied to those results.†The court went on to rule the test results in that case inadmissible. In this jurisdiction, challenges to admissibility will now be relatively rare, given the guidance from the Court of Appeal in Reed. But if LTDNA evidence is to be properly understood by juries and not given undue weight in a particular case, then lawyers will need to understand the limitations and shortcomings of this type of evidence. Indeed not all DNA evidence is equal.

    http://www.doughtystreet.co.uk/files/110215 - Low Template DNA .pdf
     
  19. BOESP

    BOESP Member

    Was this Touch DNA compared to samples in this case other than the Ramseys?
     
  20. cynic

    cynic Member

    The full extent to which the TDNA was compared has not been stated anywhere, at least not that I’m aware of.
     
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