DNA Revisited

Discussion in 'JonBenet Ramsey' started by cynic, Nov 1, 2009.

  1. cynic

    cynic Active Member

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    1. General DNA Background:

    DNA Polymorphism (“many forms”): Regions of DNA which differ from person to person.
    Locus (plural = loci) (Also referred to as a ”marker”): Site or location on a chromosome.
    Allele: Variations which can exist at a locus.
    DNA Profile: The combination of alleles for an individual.
    CODIS: Combined DNA Index System.
    CODIS uses two indexes to generate investigative leads in crimes for which biological evidence is recovered from a crime scene. The convicted offender index contains DNA profiles of individuals convicted of certain crimes ranging from certain misdemeanors to sexual assault and murder. Each State has different "qualifying offenses" for which persons convicted of them must submit a biological sample for inclusion in the DNA database.
    The forensic index contains DNA profiles obtained from crime scene evidence, such as semen, saliva, or blood. CODIS uses computer software to automatically search across these indexes for a potential match. 10 of 13 loci must yield identifiable results for a forensic profile to be included in CODIS.
    CODIS core loci: Thirteen STR sequences that have been selected for the Combined DNA Index System.
    Partial profile: DNA evidence that does not yield identifiable results in all 13 core loci.
    Amplification or PCR (Polymerase Chain Reaction): A technique for ‘replicating’ DNA in the laboratory (‘molecular Xeroxing’) Standard amplification is 28 cycles which produces nearly a billion copies. Ideal DNA test sample range is 0.5 – 2.0 nanograms.
    Electrophoresis: A technique for separating molecules according to their size.
    Electropherogram: A graph of results from an analysis done by electrophoresis.
    STR: Short tandem repeat Describes a type of DNA polymorphism in which: a DNA sequence repeats over and over again and has a short (usually 4 base pair) repeat unit.
    Testing introduced in ~1999
    4 repeats: AATG AATG AATG AATG etc.
    Y-STR: Short Tandem Repeats found on the male-specific Y chromosome. Testing introduced in ~2002.Performing Y-STR testing can help to identify all males who have contributed to a sample.
    Mini-STR: In cases where DNA evidence is limited, either in quantity or quality, such as highly degraded samples that are exposed to environmental insults or inhibitors, standard STR testing is often inadequate. Mini-STR primers “zoom in” on the STR locus so that the resulting DNA product is smaller, thereby increasing the chances of successful amplification.
    Commercially available for forensics labs in ~2007.
    LCN: Low copy number. DNA samples (typically skin cells) below ideal STR testing range, usually less than .25 nanograms (38 cells). (Tests can be run with as little as 5 to 20 cells.) To obtain a profile, special testing procedures must be used such increasing the the amplification cycles to greater than 28 – usually 34. There are a number of pitfalls, and it has not been well received in courts. Testing introduced in ~2001.
    Touch DNA: Touch DNA samples (typically skin cells) are processed/amplified exactly the same way as blood, semen, saliva etc, and can stand up to scrutiny in court much better than LCN DNA. Testing introduced in ~2005.
    Stutter: A testing artifact that appears as a peak, mimicking a true allele&#8217;s graph peak. Although they are generally <15% of a true allele peak and appear in predictable locations, stutters have been, and will continue to be, be interpreted as true peaks with the consequence of a false match or false exclusion.
    Allelic dropout: Failure to detect an allele within a sample or failure to amplify an allele during PCR. Causes include sample degradation and low sample quantity.

    Type of sample & Amount of DNA:

    Blood = 30,000 ng/mL
    stain 1 cm in area = 200 ng
    stain 1 mm in area = 2 ng

    Semen = 250,000 ng/mL
    Postcoital vaginal swab = 0 - 3,000 ng

    Plucked = 1 - 750 ng/hair
    shed = 1 - 12 ng/hair

    Saliva = 5,000 ng/mL

    Urine = 1 - 20 ng/mL

    Amount of DNA & Number of Cells:

    1ng = 152

    0.5ng = 76

    0.25ng = 38

    0.125ng = 19

    About 10,000 average-sized human cells can fit on the head of a pin.
    A pinhead has a diameter of about 1mm
    Grains of table salt vary slightly in size, a single grain is approximately 0.3 mm
    The width (diameter) of a human hair ranges from very fine (0.017 mm) to very coarse (0.181 mm)
    A human cheek cell is approximately 0.06mm
    A human red blood cell is approximately 0.0075mm
    Diameter of average human cell nucleus 0.0017mm

    Nuclear DNA
    Almost all cells in the body contain a nucleus (red blood cells are the exception). The genetic information coded for by nuclear DNA is carried in the chromosomes from one generation to the next, half of a person&#8217;s nuclear DNA being inherited from the mother and half from the father.
    The nuclear DNA of identical twins is expected to be the same. Other siblings inherit different combinations of nuclear DNA from the same parents and their DNA is therefore somewhat different from one another. The DNA from unrelated individuals is likely to be even more different. Each generation of people is a new and different combination of genetic material from the previous generation.

    From a forensic point of view, the interesting feature of an STR locus is that it consists of two alleles, one inherited from the mother and one from the father, and the number of repeats for each allele can vary independently of each other. Each allele has a name that reflects the number of repeats. &#8220;Allele 12&#8221; would indicate the presence of 12 repeats, &#8220;allele 14&#8221; would consist of 14 repeats, and so on.
    So, at one locus, a person may be designated (12,14) for example - indicating that he/she has one allele of 12 repeats at that locus and another of 14 repeats. It is, of course, possible for a person to inherit an allele with the same number of repeats for a given locus from both parents, so a person who has inherited, for example, the allele with 11 repeats from both parents would have a locus designated (11,11).If the number of STR&#8217;s is the same, the person is said to be homozygous at that locus/marker. If the number of STR&#8217;s is different, the person is classified as heterozygous at that locus/marker. The possible combinations for children, if the mother is (8,12) and father is (6,12) at a locus/marker are: (6,12), (8,12), (6,8) and (8,8).

    A full profile would be expected from items that are not degraded, such as reference blood samples, cheek scrapes and fresh samples from the scene of the crime. A partial DNA profile occurs when it has not been possible to obtain results for one or more of the STR loci or the gender marker. This can happen when the sample being analyzed has degraded after being exposed to the environment for a period of time, and/or when there is very little material available.

    An example of a full 13 loci/marker profile that might be found in CODIS:
    Locus: D3S1358, Vwa, FGA, D8S1179, D21S11, D18S51, D5S818
    Genotype: (15, 18), (16, 16), (9, 24), (12, 13), (29, 31), (12, 13), (11, 13)

    Locus: D13S317, D7S820, D16S539, THO1, TPOX, CSF1PO, AMEL
    Genotype: (11, 11), (10, 10), (11, 11), (9, 9.3), (8,8), (11, 11), (X, Y)

    References and further reading:


    Continued below...
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  3. cynic

    cynic Active Member

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    2. DNA Fallibility:

    I am not a DNA &#8220;anarchist&#8221;, nor do I do I bow down at the altar of DNA infallibility.

    &#8220;The science of DNA profiling is sound.
    But, not all of DNA profiling is science.
    This is especially true in situations involving: small amounts of starting material, mixtures, relatives, and analyst judgment calls.&#8221;

    DNA has many uses and has proven its usefulness in many applications. In pristine clinical and medical applications such as paternity testing it is easy to work with and interpret.
    This changes as its record is analyzed in the forensic arena. In this setting DNA has had spectacular success as well as failure and scandal.
    While I am sure virtually everyone reading this is familiar with many success stories relating to forensic DNA testing, not all of you may be aware of its failings

    Although generally quite reliable (particularly in comparison with other forms of evidence often used in criminal trials), DNA tests are not now and never have never been infallible. Errors in DNA testing occur regularly. DNA evidence has caused false incriminations and false convictions.

    Here are a few examples:

    For the detective working the case, it looked like a sure thing. The 58-year-old suspect had confessed to raping his young niece. He had a prior sex-crime conviction.
    DNA evidence extracted from the 10-year-old girl&#8217;s underwear would be the clincher.
    Charged with child rape, the road-crew worker from the South King County town of Pacific faced up to 26 years in prison &#8211; until authorities learned of startling test results coming out of the Washington State Patrol&#8217;s Tacoma crime lab.
    The genetic evidence excluded the victim&#8217;s uncle and pointed to an unknown man. The airtight case suddenly had a gaping hole.
    Four months later, on Jan. 8, 2002, prosecutors offered a deal. The defendant pleaded guilty to a lesser charge of child molestation, shaving a decade off his sentence.
    A couple of weeks after that, the lab made an embarrassing discovery.
    Forensic scientist Mike Dornan had bungled the test, accidentally contaminating the child&#8217;s clothing with DNA from another case he&#8217;d been working on.
    DNA contamination and errors at the State Patrol crime labs are recurring problems, an investigation by the Seattle Post-Intelligencer has found.
    Forensic scientists contaminated tests or made other mistakes while handling DNA evidence in at least 23 cases involving major crimes over the last three years, according to State Patrol and court records.

    Crime lab forensic scientist Denise Olson called Seattle police with good news in December 2002. Her DNA testing revealed a match to the suspect in a case involving a brutal rape and attempted murder. The victim suffered a fractured skull, lacerated liver and other injuries.
    Detectives contacted a deputy prosecutor, who prepared to file charges against a former boyfriend of the military doctor attacked in the May 2002 assault. Police got ready to extradite the suspect from Denver.
    Eleven days after declaring the match, Olson called back.
    The test had actually ruled out the suspect. She&#8217;d misinterpreted the results, and so had a colleague who did a quick check. Another forensic scientist noticed the error during peer-review, a process in which workers double-check each other&#8217;s work.
    &#8220;I frankly had a brain fart,&#8221; Olson said in a recent interview.
    Her mistake was a &#8220;false-positive match&#8221; &#8211; one of the worst mistakes a forensic scientist can make, said Arvizu, the auditor. &#8220;That&#8217;s a classic error that reflects a bias on the part of the analyst wanting to make a match.&#8221;
    Olson, who has worked in the crime lab system since 1998, said she tried not to be swayed by detectives&#8217; belief that they had a strong suspect. &#8220;We&#8217;re all human,&#8221; she said. &#8220;I tried not to let it influence me. But I can&#8217;t say it never does.&#8221;
    Records show she didn&#8217;t keep notes on her calls to police, as required. She also threw out the erroneous draft report, a violation of lab policy.
    Police called lab officials to complain in January 2003.
    An investigation concluded that Olson had misread the test, which contained a mixture of DNA from at least two people &#8211; a complex sample that requires careful interpretation. She missed indications in the DNA that excluded the suspect.

    The case was one of the most puzzling in recent times. Hundreds of detectives in six specialist committees were set to work hunting the ominous female serial killer.
    The police were stumped. They eventually offered a 300,000 euro reward to find the killer. It&#8217;s no surprise the money was never claimed, however, because the so-called &#8216;phantom killer&#8217; was a complete myth!
    Detectives had apparently been tracking the DNA of a factory worker who packaged cotton buds used by the police to collect samples.
    Police linked the &#8216;killer&#8217; to seven murders.
    The most notorious case was in April 2007 in Heilbronn where a 22-year-old policewoman was shot dead and her colleague (25) seriously injured. On the back seat of the police car, detectives found what they thought was DNA from the mysterious killer.
    As part of the investigation, 800 previously convicted women were questioned &#8211; but there was no match to the sample.
    Her DNA was found over and over again: in bottles, tank lids, on bullets &#8211; and once even on a biscuit!
    Traces were found in southern Germany, Austria and France. Thousands of saliva tests were taken but there was still no answer.
    &#8230; In March, investigators announced the embarrassing fiasco to the general public: The DNA found at 39 different sites actually belongs to a worker at the cotton bud company!
    BILD found the respectable pensioner in a little village in Bavaria. Erika S. no longer works for the company. According to reports, she was not careful enough when she handled the swabs.
    and http://www.bild.de/BILD/news/bild-english/world-news/2009/05/14/phantom-killer-fiasco/police-found-dna-of-old-granny-at-crime-scenes-because-of-cotton-buds.html

    And as a final example &#8211; here is some fine work by Bode Technology, yes the same lab that handled the Ramsey DNA found on the long johns:
    The Illinois State Police canceled its contract for DNA analysis with the Bode Technology Group after finding that it failed to recognize semen on evidence in 22 percent of cases that were checked again by forensic scientists who work for the police.
    Out of a random sample of 51 cases that were re-analyzed for quality assurance, the police said 11 tested positive for the existence of semen. They plan to test all 1,200 cases that Bode Technology said tested negative for semen and are asking the state attorney general for permission to sue the company.
    &#8216;&#8217;The work provided by Bode was imprecise and we can&#8217;t tolerate that type of work in this business,&#8217;&#8217; Larry Trent, the state police director, said at a news conference on Friday. &#8216;&#8217;I&#8217;m outraged that a company with their reputation would conduct business in this manner, and we&#8217;re not going to let them get away with it.&#8217;&#8217;

    Much more here: http://www.seattlepi.com/local/183018_crimelabboxesweb22.html
    and here: http://www.injusticebusters.com/04/forensic_labs.htm

    3. Causes of DNA fallibility:

    · The sample has become degraded due to exposure to heat, light, humidity, and microorganisms

    · The sample has been contaminated by human activity such as talking, sneezing, coughing or contact.

    &#8220;But the sensitivity of the test also means it detects even the slightest contamination.
    In January, the Seattle lab's DNA supervisor, George Chan, was chatting with a forensic scientist who was examining evidence in a child rape case. Although Chan had no other exposure to the case, a subsequent test found Chan's DNA, as well as that of the suspect, in the evidence -- a sample taken from a pair of boxer shorts. The likely culprit: saliva spewed during Chan's conversation.&#8221;
    Doubt was also cast on a number of convictions in Queensland when a forensic scientist who had previously worked for a state forensic laboratory publicly expressed concerns about the reliability of the lab&#8217;s work. He told The Australian newspaper that it was not uncommon for the lab to mix up DNA samples from different cases. For example, he said that analysts&#8217; own DNA, from blood samples used as analytical controls, often was mixed up with (or found its way into) casework samples, creating false matches: &#8220;Quite often my colleague would walk down the aisle and say, &#8216;I&#8217;ve just committed another rape on the Gold Coast.&#8217;&#8221;

    · The sample is a mixture of two or more donors and has been misinterpreted

    Three or more alleles at a locus indicate the presence of more than one contributor. It is often difficult to tell whether the sample originated from 2, 3 or 4 people. Statistical models can help analysts work out the probabilities of more than two contributors however a number of possible combinations could be consistent with the findings.
    Peak heights are often used in interpreting mixtures, but peak height imbalances occasionally occur. Peaks with the same height are presumed to be from the same person, but the reading of peak heights is far from an exact science. Even in a single person sample, peak heights may vary, so assumptions of regularity may be false.
    In mixed samples alleles may simply be undetectable or indistinguishable from background &#8216;noise&#8217;. Alternatively, alleles can simply &#8220;drop out&#8221; and not appear or stutters can be confused with alleles from a minor contributor.

    &#8220;Because so many different profiles may be consistent with a mixture, the probability that a non-contributor might, by coincidence, be "included" as a possible contributor to the mixture is far higher in a mixture case than a case with a single-source evidentiary sample&#8221;
    &#8220;In a separate mixture study, sponsored by the National Institute of Standards and Technology, forty-five local, state, federal and commercial forensic laboratories were requested to specify all contributors in each sample mixture, provided STR profiles, and estimate the amount of DNA in the samples as well as the amount of recoverable DNA per sample (5). No participant in the study mistyped the single contributor sample. However, many laboratories did not attempt to fully type the contributors profile or they provided incorrect genotype assignments. The inability to correctly assign the proper genotype to a contributor was attributed to multiple shared alleles. Further investigations will clarify these results.&#8221;
    See also: http://www.nfstc.org/pdi/Subject06/images/pdi_s06_m03_06.swf

    · The environment from which the sample has been collected has introduced inhibitors that interfere with replication during the STR process. (Examples of some sources of PCR inhibition can include: soil laden items, blue jeans or dyed clothing, and even items containing large amounts of blood. A few of the compounds that are indeed responsible for this inhibitory effect include hematin, humic acid and Indigo dye.)

    · The sample contains too little DNA and is analyzed using LCN procedures which can be very difficult to perform properly and interpret correctly.

    These LCN (low-copy number) procedures have a heightened risk of allelic drop-in and drop-out. LCN practitioners attempt to deal with the unreliability of the basic data by testing samples in duplicate, and sometimes in triplicate, and then inferring which results are reliable.However, the reliability of this method has been questioned. In one case I examined, the laboratory typed a sample three times and produced three different profiles http://www.councilforresponsiblegenetics.org/pageDocuments/H4T5EOYUZI.pdf

    · The sample contains a high ratio mix between a major and minor donor This can in some cases overwhelm the minor donor&#8217;s alleles and &#8220;hide&#8221; them.

    &#8220;Given information from sensitivity, stutter, and peak height ratio studies an evaluation of known mixtures was completed. Two samples were selected such that most loci contained non-overlapping alleles. The samples were mixed at ratios of 1:200 to 1:1 and then the series was reversed. The minor contributor could be detected at 1:20 but could fit the stutter model and was therefore not accepted as a true allele. At 1:10 and greater the minor component could be detected and defined.&#8221;
    &#8220;&#8230;beyond a ratio of 10:1, the minor component of a mixed sample is rarely detected.&#8221;

    · The evidence may have been contaminated or cross-contaminated. The long johns, panties and other items of evidence may have been handled in such a manner that DNA may have been transferred between items. This is especially an area for concern when dealing with items that are later scraped for skin cells.

    · The sample is analyzed by a biased or incompetent technician.

    The reviews found hundreds of cases where incompetence, inadequate training and resources, lack of guidance and even intentional bias on the part of a crime lab - which is not independent from the HPD - contributed to mistakes.
    A 2004 investigation by the Seattle Post-Intelligencer found 23 DNA testing errors in serious criminal cases handled in a Washington state lab. In North Carolina, the Winston-Salem Journal recently ran a series of articles about many DNA testing errors by the North Carolina State Bureau of Investigation. In Virginia, it took an outside investigation to clear Earl Washington Jr., who was falsely convicted of capital murder and nearly executed. An independent lab reused the same samples that led to his conviction but found contradicting results.
    That's not all. DNA testing errors are cropping up nationwide: California, Minnesota, Pennsylvania and Nevada have documented major problems recently.
    Munier agreed the troubles are widespread. These issues have prompted critics to call for greater independence among the nation's crime labs, which typically are run by law enforcement agencies.

    Continued below...
  4. cynic

    cynic Active Member

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    4. The problem of &#8220;cold hit&#8221; DNA profile searches:

    (A cold hit refers to an instance where one or more connections are made between a crime victim, a perpetrator, and/or a crime scene in the absence of a current investigative lead (i.e., a cold case)).
    Indeed, the British Home Office has reported that between 2001 and 2006, 27.6% of the matches reported from searches of the UK National DNA Database (NDNAD) were to more than one person in the database. According to the report, the multiple-match cases arose &#8220;largely due to the significant proportion of crime scene sample profiles that are partial.&#8221;

    False incriminations arising from such coincidental matches have occurred in both the UK and the US. In 1999 the DNA profile of a sample from a burglary in Bolton, UK was matched in a database search to the profile of a man from Swindon, UK. The frequency of the six-locus profile was reported to be 1 in 37 million. Although the Swindon man was arrested, doubts arose about the identification because he was disabled and apparently lacked the physical ability to have committed the Bolton crime. Testing of additional genetic loci excluded him as the source of the sample, proving that the initial 1-in-37 million match was simply a coincidence.

    People sometimes mistakenly assume that if the frequency of the matching profile is 1 in 10 million, that there is only one chance in 10 million that the suspect is not the source of that profile. This is a logical error that has been labeled the prosecutor&#8217;s fallacy. As a matter of simple logic, the DNA evidence cannot distinguish any particular suspect who has the 1-in-10 million profile from the other 600 or so people in the world who have it; hence, without considering other evidence for or against a particular suspect, it is impossible to draw any conclusion. If the other evidence against a particular suspect is weak or entirely lacking, or if the suspect has a good alibi, then the odds may be very strongly against his being the source of the evidence, notwithstanding the 1-in-10 million match (and this is why the prosecutor&#8217;s fallacy is fallacious).

    Accidental cross-contamination of DNA samples has caused a number of false &#8220;cold hits.&#8221; For example, the Washington State Patrol laboratory accidentally contaminated samples from a rape case with DNA from the reference sample of a juvenile felon. The juvenile was identified through a database search but could not have been involved in the rape because he was only a child when the rape occurred. According to the lab&#8217;s contamination/Extraneous DNA Log, &#8220;it was determined that the felon&#8217;s sample was being used as a training sample by another analyst&#8221; when the rape case was being analyzed.

    One of the best-known false cold hits occurred in a high-profile Australian case involving the murder of a toddler named Jaidyn Leskie. The toddler disappeared in 1997 under bizarre and mysterious circumstances while in the care of the boyfriend of the toddler&#8217;s mother. The toddler&#8217;s body was found in a reservoir six months later, with a crushed skull, and the boyfriend was charged with murder. But the case was clouded by the discovery of DNA from an unknown woman in what appeared to be bloodstains on the toddler&#8217;s clothing. In late 1998, the boyfriend was acquitted.
    In 2003, the unknown DNA was matched, via a database cold hit, to a young &#8220;mentally challenged&#8221; woman who lived hundreds of miles away and who, by all accounts, had never left her own village. Police could find no way to link the young woman to the toddler&#8217;s murder and at first dismissed the cold hit as an &#8220;adventitious&#8221; (coincidental) match. It was a seven-locus match and the estimated frequency of the matching profile was 1 in 227 million.
    The young woman had allegedly been the victim of a sexual assault involving a condom. Her DNA, which was extracted from the outside of the condom, had been in close proximity in the laboratory to extracts from the toddler&#8217;s clothing. Although laboratory personnel maintained that accidental transfer of samples between cases is impossible, I was able to document dozens of cases in which cross-contamination of samples had occurred under similar circumstances in other laboratories, and therefore suspected that accidental contamination explained the match with the young woman.
    &#8230;additional testing showed that the woman also matched at six additional loci. Furthermore, re-examination of the data produced in the first test revealed low-level matching alleles at two additional loci. Altogether there were fifteen matching loci with an estimated frequency of less than 1 in 100 trillion, which made the theory of a coincidental match seem far less plausible than the alternative theory of cross-contamination. The Victorian State Coroner issued a formal finding in 2006 that the evidence linking the young woman to the toddler was a false match caused by cross- contamination in the laboratory.

    The facts of some recent cases in the United States have also raised suspicions about false cold hits due to contamination across cases. For example, in 2002, while investigating the 1969 murder of University of Michigan law student Jane Mixer, the Michigan State Police Crime Laboratory in Lansing found DNA of two men on her clothing. The profiles were searched through a database and matched two Michigan men, Gary Leiterman and John Ruelas. Police immediately suspected that Leiterman and Ruelas had been involved in the murder, but there was a problem&#8212;Ruelas was only four years old when Mixer was killed and had been living with his parents in another city.
    According to news account, police could find no link between young Ruelas and Mixer. That did not deter Washtenaw County Assistant Prosecutor Steven Hiller who charged Leiterman with the murder. Hiller &#8220;created a scenario placing a young Ruelas at the [murder] scene as a chronic noise-bleeder whose blood dropped on Mixer.&#8221; Although creative, this explanation seems rather farfetched. There was no evidence that Leiterman had ever had contact with young Ruelas or his family and they lived in different parts of the state. A more likely scenario is that this &#8220;cold hit&#8221; occurred through the same type of laboratory error as in the Leskie case. Examination of laboratory records revealed that known samples of DNA from both Leiterman and Ruelas were being processed in the Michigan State lab on the same day as the old samples from the Mixer murder. Both men were being tested in connection with other cases unrelated to the Mixer murder. Although the Michigan State laboratory maintains that cross-contamination of samples across cases was impossible, it seems a very strange and unlikely coincidence that two men who, according to the prosecutor, were present when Mixer was murdered in 1969 just happened to have their DNA tested (for other cases) on the very same day as samples from the Mixer case were tested. Leiterman was nevertheless convicted of Mixer&#8217;s murder in 2005.

    A similar incident in New Jersey led to a different outcome. During a cold case investigation of the 1968 rape/murder of a 13-year-old girl named Jane Durrua, a laboratory discovered male DNA on the girl&#8217;s underwear. In early 2004, a database search revealed that the male profile matched a man named Jerry Lee Belamy. Belamy was charged with the 1968 murder. Fortunately for him, however, the forensic scientists who had made this &#8220;cold hit&#8221; were invited, in late 2004, to appear on a television program about the case. While preparing for their TV appearance, they went back over their laboratory notes and made a disturbing discovery. The analyst who extracted the male DNA from the victim&#8217;s underwear had, on the same day, been working on another case that included samples from several individuals&#8212;including Jerry Lee Belamy. There was no direct evidence that cross-contamination of samples had occurred, but it seemed a very unlikely coincidence that Bellamy just happened to be involved in two different criminal cases, years apart, that were processed by the same analyst at the same time. The theory that the &#8220;cold hit&#8221; had been produced by cross-contamination of samples between the two cases was sufficiently plausible to persuade the district attorney 29 to dismiss the murder charges against Bellamy. One can only wonder what would have happened to Bellamy had the forensic scientists not been invited to make the television appearance.

    5. Future DNA problems:

    Kary Mullis, who invented PCR, anticipated this potential misuse of the technique. In a conversation I had with him in 1995, Mullis jokingly discussed creating a company called &#8220;DN-Anonymous&#8221; that would sell highly amplified solutions of DNA from celebrities, or from large groups of people, that criminals could use to cover their tracks. Although Mullis was not serious about doing it himself, he predicted that someone would do so within the next ten years. As far as I know, Mullis&#8217; prediction has yet to come true, but it may only be a matter of time before materials designed to stymie DNA tests (by planting other people&#8217;s DNA at crime scenes) become available for sale on the internet along with kits designed to thwart drug tests.

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  5. cynic

    cynic Active Member

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    6. DNA in the Ramsey case:


    1997 &#8212; DNA collected from a blood spot on JonBenet Ramsey's underwear described as contaminated.

    1999 &#8212; FBI releases new technology called Short Tandem Repeat to profile DNA. It uses 13 markers to raise the probability that a randomly selected individual would match it is one in 1 quintillion.

    2001 &#8212; 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 &#8212; The Boulder County District Attorney's Office, now led by Mary Lacy, formerly Mary Keenan, takes over the investigation from Boulder police.

    2003 &#8212; 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.

    2008 &#8212; Bode Technologies uses Touch DNA procedures on both sides of the waist area of JonBenet&#8217;s long johns. The male profile previously identified from the inside crotch area of the underwear matched this DNA.

    DNA sampled from JBR&#8217;s panties.

    Initial testing of two very small blood stains in the crotch area of JBR&#8217;s panties revealed a weak low marker partial profile from one stain, and after retesting, a 9 ½ marker profile from the second stain.
    (&#8220;The underwear is urine stained and in the inner aspect of the crotch are several red areas of staining measuring up to 0.5 inch in maximum dimension.&#8221; (Autopsy Report))
    There was no sperm present in the sample.
    "There is always a possibility that it got there through human handling," said former prosecutor Michael Kane, who ran the 13-month grand jury investigation&#8221; (2002)
    "The DNA on the underwear may be from the killer, but it may not be," Bennett said. "It`s minute DNA, like from a cough or sneeze. ... You can`t just jump to the conclusion it`s positive proof that will trace back to the killer."
    &#8220;So we don't know whether that's saliva or what, whether that's skin cells, you know, there was -- it could be DNA from the original manufacturer of the underwear. I know Dr. Henry Lee went out and bought underwear of the same kind and took it out of the plastic wrapper and took a cutting and extracted DNA and got some profiles from it. So, I mean, it's a little unclear&#8230;&#8221;
    There has been no mention of any presumptive test or alternate light source forensic testing in this case indicating that saliva was present. (Vaginal and other swabs were taken during JBR&#8217;s autopsy)
    There are very sensitive presumptive tests available for the presence of saliva:
    &#8220;Saliva could be detected with RSID-Saliva on swabs from the skin of a normal active individual 72 hours post saliva deposition. After DNA analysis of the swabs, mixed DNA profiles were obtained that could be accounted for by the donor of the saliva and the individual that the saliva was swabbed from. Note: the DNA originating from the saliva may not necessarily be in the majority of a mixed DNA profile when both saliva and skin cells are present&#8221;
    A &#8220;Y&#8221; marker was found indicating a male donor contributed to the sample.
    Allelic dropout or other mixture issues relating to problems with the sample (degradation or probably low sample quantity) resulted in missing markers.
    The most probable components of the sample are blood cells from JBR mixed with skin cells from an undetermined donor.

    DNA sampled from under JBR&#8217;s fingernails.
    The weakest DNA in this case that has received some press is the DNA from under JBR&#8217;s fingernails. The samples were contaminated by the nail clippers that were used and only &#8220;matched&#8221; (and I use the word loosely) the panty DNA at 2 &#8211; 3 markers (by most accounts).

    "When Meyer (the coroner) clipped the nails of each finger, no blood or tissue was found that would indicate a struggle. He used the same clippers for all the fingers, although doing so created an issue of cross-contamination. For optimal DNA purposes, separate and sterile clippers should have been used for each finger. Furthermore, we later learned that the coroner's office sometimes used the same clippers on different autopsy subjects." - Steve Thomas

    Then there is also the mysterious DNA-X mentioned in Beckner's deposition.

    &#8220;Q Obviously you're telling me there was DNA
    20 that was not on JonBenet or on her clothing; is that
    21 correct?
    22 A Correct.
    23 Q Where was that?
    24 A We're getting into areas where I feel like
    25 we can't go.
    Q -- to the fact that you took the DNA from
    12 Chris Wolf, you obtained it in February or March of
    13 1998.
    14 A And we did not have DNAX at that time.
    15 Q So DNAX came along subsequent in time?
    16 A Yes.&#8221;

    Since very little has been made of this, it is difficult to comment on.
    There has never been a claim that it matched any other DNA in this case.
    No information has ever been released relating to the strength of the profile (number of markers).
    For all we know it may the same &#8220;quality&#8221; as the fingernail DNA

    DNA found on JBR&#8217;s long johns.

    Finally, there is the DNA found by using a blade to scrape two areas along the waistband of the long johns that JBR was found to be wearing when her body was &#8220;discovered&#8221;.

    &#8220;ANGELA WILLIAMSON, BODE TECHNOLOGY: OK, Nancy. Touch DNA is left behind every time that you touch somebody. It`s essentially shed skin cells. If you touch somebody on the shoulder, you`re leaving behind DNA. However, it`s very hard to find this touch DNA. It`s invisible. We can`t see it. So the way we have to try and sample it is to have a good idea where a person may have been touched and where these shed skin cells may be.
    &#8230;The area that we sampled from, there was no visible staining. We believe it to be touch DNA, most likely skin cells from maybe someone`s hand.&#8221;

    &#8220;While the amount of DNA they found was much less than would appear in a stain, there was enough to be processed in the routine way DNA is analyzed, Williamson said. (In other cases, so-called "low copy number DNA" has to be processed in a different way).&#8221;

    This almost certainly would reveal a mixed profile DNA sample. (JBR and PR, JR at least, in addition to the &#8220;unknown&#8221; donor). The number of markers found in the &#8220;intruder&#8221; DNA profile has never been released to the public.
    We have been told that the profile matched that of the panty DNA, so it is relatively safe to assume that the profile also has at least 9 ½ markers. It is also an equally safe assumption that had they found a full 13 loci profile, that an announcement to that effect would have been made. I believe that the Bode lab was simply given the CODIS &#8220;intruder&#8221; profile to look for and they found it. They quite probably didn&#8217;t attempt any sort of further analysis.

    Continued below...
  6. cynic

    cynic Active Member

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    7. How do people transfer/deposit skin cell DNA?

    Primary and Secondary Transfer

    (Skin cells continually flake off at rate of ~35,000 dead skin cells per minute)

    A group of 29 people were tested for their ability to deposit their DNA profile onto touched objects. It was found that a typical good shedder leaves a complete profile on the surface of a plastic tube after contact of only 10 seconds, whereas at the other end of the scale a poor shedder will leave only a few alleles, possibly with several loci dropping out completely.

    Work was carried out to determine whether DNA profiles could be obtained from clothing; specifically, plain white T-shirts. After 8 hours wear, more of the wearer’s DNA was recovered from the front of the Tshirt than the back. Targeting the neck area maximized the chance of obtaining a useful result. In a series of simulated assaults, where one person grabbed the shoulder of another for a period of 30 seconds, mixed profiles were obtained from the grabbed area of the T-shirts. The “assailant” always contributed the major component to this mixture, regardless of his/her shedder type.

    Experiments were carried out to determine whether it was possible for individual A to transfer his DNA to individual B through contact, who could in turn transfer A’s DNA onto an object. We began with a scenario which was most likely to yield a result: a good DNA shedder (A) shook hands with a poor shedder (B), who then gripped a plastic tube for 10 seconds. The results from swabs of the tubes showed that on five separate occasions all of the good shedder’s profile was recovered, with none of the poor shedder’s alleles appearing. The experiment was then repeated, but with the introduction of a delay of 30 minutes between the time of the handshake and the tube-holding. The results indicated that although the poor shedder deposited some alleles, secondary transfer of the good shedder’s DNA still occurred.

    Many factors may affect the persistence of low level DNA; time, temperature, humidity, etc. While it is unreasonable to test every combination of variables, some generic experiments have been undertaken and certain scenarios addressed. A time-study of the persistence of DNA is currently underway, where touched items have been stored at room temperature and tested to find out how much DNA can be recovered after certain periods of time. full profiles were still recovered from surfaces touched by a good shedder even after 4 months, whereas a marked decrease in the recovery of the poor shedder’s DNA was observed.
    An exchange of identical wrist-watches between certain shedder types was carried out to ascertain the period of time needed for the original wearer’s DNA profile to be replaced by that of the new wearer. Generally we found that a good shedder completely replaced the original wearer’s profile in 2-3 weeks, and after only a few days had become the major component of a mixture. An example of this is shown in In contrast, a poor shedder typically took around 2 weeks just to comprise the major component.

    We have shown that there is a difference between individuals in their tendency to deposit DNA on an item when it is touched. While a good DNA shedder may leave behind a full DNA profile immediately after hand washing, poor DNA shedders may only do so when their hands have not been washed for a period of 6 h. We have also demonstrated that transfer of DNA from one individual (A) to another (B) and subsequently to an object is possible under specific laboratory conditions using the AMPFISTR®SGM Plus™ multiplex at both 28 and 34 PCR cycles. This is a form of secondary transfer. If a 30 min or 1 h delay was introduced before contact of individual B with the object then at 34 cycles a mixture of profiles from both individuals was recovered. We have also determined that the quantity and quality of DNA profiles recovered is dependent upon the particular individuals involved in the transfer process. The findings reported here are preliminary and further investigations are underway in order to further add to understanding of the issues of DNA transfer and persistence.

    Objects handled by many individuals all produced profiles with multiple alleles of varying intensity. To determine the effect of multiple handlers, we exchanged polypropylene tubes between individuals (2 or 3, 10 min each) with different genotypes. Although the material left by the last holder was usually present on the tube, that of previous holders was also retrieved to varying extents. The strongest profile obtained was not always that of the person who last held the object, but was dependent on the individual. We regularly observed profiles of previous holders of a tube from swabs of hands involved in these exchanges, showing that in some cases material from which DNA can be retrieved is transferred from object to hand (secondary transfer).

    The presence of DNA with a profile matching that found on an item does not necessarily show that the person ever had direct contact with the item. “It has also been shown that a full profile can be recovered from secondary transfer of epithelial cells (from one individual to another and subsequently to an object) at 28 cycles [the standard method].”
    “The full DNA profile of one individual was recovered from an item that they had not touched while the profile of the person having contact with that item was not observed. This profile was also detected using standard 28-cycle amplification

    Secondary transfer refers to the fact that, through physical contact with other people, individuals can inadvertently carry and deposit other people’s DNA onto objects of evidence. For example, two people shaking hands will transfer their own DNA to each others’ hands. If each then goes on to touch another object such as a coffee mug, baseball bat, knife etc., they could transfer the other’s skin cells to the object. If that object is a murder weapon, the identification of DNA through LCN could prove problematic and misleading.
    • Variable shedding refers to the extent to which different people shed their skin cells in different quantities under different circumstances. Some people are more likely than others to leave behind their DNA in the form of skin cells. Through research at the FSS, it has been found that there are, for example, “heavy shedders,” “medium shedders,” and “light shedders.” Thus, the last person to touch a particular object may not leave the most DNA or strongest profile.
    • The amount of DNA deposited can also be affected by certain actions taken by the individual. Washing of one’s hands will, for a period of time, decrease the amount of skin cells a person deposits on other objects. Additionally, the amount of perspiration exerted at the time the object is being held may also affect the amount of skin cells that are deposited. Both of these scenarios could adversely affect results upon LCN-DNA analysis.
    • Given the nature of variable shedding and secondary transfer, the risk of obtaining a mixture is increased when applying a technology with increased sensitivity such as LCN. It is impossible to amplify the “right” DNA profile because all of the DNA that is contained in a biological evidence sample will be amplified.

    “It has also been demonstrated that DNA containing material can be deposited onto surfaces that without physical contact being made. In 2003, Rutty carried out a series of experiments to determine the extent to which a crime scene could be contaminated by crime scene investigators (Rutty et al. 2003). A series of experiments were carried out to investigate the level of DNA deposition after 15 minutes of silence or talking, with and without physical activity. The level of DNA deposition after 10 seconds coughing was also tested. The results of these experiments showed that high levels of DNA could be detected after 15 minutes of talking, whilst kneeling, even when a face mask was worn. It was hypothesized that the detected DNA could have arisen from orally projected saliva particles or could be due to the sloughing of epithelial cells around the area that the face mask was in contact with the face (Rutty et al. 2003). In order to distinguish the contribution of orally projected biological material from shed epithelial cells a second set of experiments were conducted by Rutty&#8223;s group (Port et al. 2006). These follow-up experiments greatly simplified the model used in Rutty&#8223;s original work to investigate orally projected biological material only. The results of these experiments showed that DNA-containing biological material could be detected up to 184cm (72 inches) away from the donor and a full DNA profile could be detected in the area immediately in front of the donor after only 30 seconds of talking (Port et al. 2006).”

    Secondary Transfer and Scene Technicians
    The body of an adolescent female was found on a couch in her home where she lived with her mother and younger brother. She was wearing only a shirt and bra at the time of discovery. She was determined to have died of "asphyxia secondary to manual strangulation." She had a history of sexual abuse, suggested by the absence of her hymen and numerous anal scars, as well as a history of promiscuity. The DNA of one of her mother's lovers was found on her perineum, in the form of sperm.
    Given the location and circumstances of the crime, the precise conditions of this exchange could not be reliably established. One possibility is that the suspect was engaged in some form of sexual activity with the victim, and that sperm transferred to her perineum as a result. However, the suspect and the victim's mother had sexual relations in the mother's bed, where the victim had been playing previously with her brother. There were also reports that the suspect and the victim's mother may have had sexual relations on the couch, were the victim would have been sitting. Additionally, a review of the crime scene video shows several evidence technicians moving evidence around on the couch and other locations, and then touching the victim's body in multiple locations, examining her body as it is being photographed, with and without gloves.

    Given these circumstances, and the victim's history, the following are potential evidence transfer relationships in this case:
    From the suspect to the victim during a forced sexual assault;
    From the suspect to the victim during a consensual (but unlawful) sexual encounter;
    From the couch to the victim's perineum;
    From the mother's bed to the victim's perineum;
    From the scene technician's fingers to the victim's perineum

    Secondary and Tertiary Transfer

    Transfer of DNA is seen with variable degrees of efficiency in each of the two types of transfer experiments conducted. In most cases the transferred DNA was a lower concentration than the DNA of the individual to whom it was transferred, however, this was not observed in all instances.
    In the experiments involving a kiss to the face, DNA or cells containing DNA were transferred b a kiss to an individual’s face and then to a glove in all of the experiments fun in this study.
    In the experiments involving transfer of DNA via a towel, DNA or cells containing DNA were transferred to a towel, then to an individual’s face and then to a glove in all experiments with one of the towels and in none of the experiments with the other towel. In each of these sets of experiments the towel was exposed to the individuals DNA from only one face washing and drying. Larger quantities of DNA would be expected to be deposited on the towel from multiple uses of the towel.

    I believe that secondary transfer of foreign DNA may account for the DNA found on the panties and long johns. The transfer may have been a result of contact with these articles of clothing by JBR herself, or perhaps by JR and/or PR as well. Another possibility may also be transfer via a DNA-laden wash cloth or towel that may have been previously used by someone untested/cleared by LE.
    These are only some of the possibilities, and I don’t dismiss that perhaps the long johns and panties may have been contaminated at some point after they were collected and taken into evidence. (Especially in light of the way the fingernails were handled.)
    (The later DNA findings could well have been the result of contamination during the autopsy of JonBenet.)
    The theory that I presently believe is the most likely explanation of the early PM and DQ Alpha DNA evidence in this case is below.

    8. The Mixture Theory:

    “Full siblings born to unrelated parents have identical STR profiles at an average of four of the thirteen CODIS core loci, compared to, on average, identity at less than a single locus among unrelated individuals. My data set included a sibling pair with identity at nine of the thirteen CODIS core loci, and another colleague has informed us of an eleven locus match in a brother and sister.”
    DNA and the criminal justice system: the technology of justice –by David Lazer

    Despite having seen this bit of information before relating to the panty bloodstain, which ultimately was also found to contain a 9 ½ marker “intruder” DNA profile, its full significance never occurred to me.

    The DNA profiles developed from exhibits #7, 14L and 14M revealed a mixture of which the major component matched JonBenet Ramsey.
    If the minor components from exhibits #7, 14L and 14 M were contributed by a single individual then John Andrew Ramsey, Melinda Ramsey, John B. Ramsey, Patricia Ramsey, Burke Ramsey, Jeff Ramsey, XXXXXXXXXXXXXXX and XXXXXXXXX, would be excluded as a source of the DNA analyzed on those exhibits. (By way of explanation: #7 refers to bloodstains from panties. #14L,#14M are right and left hand fingernails from JonBenet Ramsey.) (From a lab report held up by Erin Moriarty on "48 Hours Mystery”)

    I always looked at this as saying that there was a mix of JonBenet’s blood and an unknown male DNA minor profile, in other words the mystery “intruder” profile.
    While true, I overlooked the other possibility which is clearly spelt out:
    If it is not a single contributor then a DNA mix involving two of the following people: John Andrew Ramsey, Melinda Ramsey, John B. Ramsey, Patricia Ramsey, Burke Ramsey, and Jeff Ramsey may be what produced the minor profile and not an intruder after all.
    (At least one of the two people would have to be a male, as there is a Y marker present) This means that the DNA found in the panty blood stain could simply be a mixture of JonBenet’s blood cells and skin cells from JR and PR as one example.

    9. Conclusions:

    · This is not a DNA case.

    · Secondary transfer, contamination or a DNA mixture may have led to an imaginary “intruder” profile.

    · Other items of evidence that would be difficult to explain by an intruder theory should also be tested using Touch DNA analysis. These items should include at least the ligature and paint brush handle.

    · At the very least, the current DA should repeal the Ramsey exoneration and apologize to the public that someone as utterly incompetent as Mary Lacy was ever allowed to hold a position of authority whereby she was able misdirect an important investigation for so long.

    · The science of DNA profiling is sound.
    But, not all of DNA profiling is science.

    10. Closing Argument:

    “I can understand people get excited about the presence of DNA. It`s always important to talk about it. But you know something? There is no way that just because they might want to include some other unknown male that that by definition destroys the significance of the mountain of other evidence. And it is that very point that I think makes me crazy when I hear people say this proves that a stranger did it. You`d have to actually abandon the millions of pages of other evidence that points away from the stranger theory.” - Wendy Murphy
  7. Holdontoyourhat

    Holdontoyourhat Former Member

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    "2008 &#8212; Bode Technologies uses Touch DNA procedures on both sides of the waist area of JonBenet&#8217;s long johns. The male profile previously identified from the inside crotch area of the underwear matched this DNA."

    Better slow down and read this, because this was a MAJOR BREAKTHROUGH in JBR's murder.

    Need some headlines?


    DNA clears JonBenet's family, points to mystery killer -CNN


    DNA evidence clears entire family in death of JonBenet Ramsey 12 years ago -the insider


    The JonBenet Ramsey saga has been a longtime popular topic on Internet news sites, and the trend continued Wednesday.
    Web sites from China to Ireland featured the news that no member of the Ramsey family is under suspicion in the 1996 death of JonBenet. In the U.S., the story was prominent on sites such as CNN, MSNBC and FOXNews.
    Among the worldwide Web sites:
    * Inside China Today
    * Cambodia Post
    * The Star (Malaysia)
    * New Zealand Herald
    * Irish Times
    * Central Europe Online (Czech Republic)
    * The Independent (London)
    * London Daily Mirror
    * BBC
    One country where the story apparently has not appeared is Thailand, where John Mark Karr was arrested in 2006 after he sent e-mails about the Ramsey case to University of Colorado journalism professor Michael Tracey. Karr confessed that he was with JonBenet when she died, but his DNA was not a match - Rocky Mountain News
  8. cynic

    cynic Active Member

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    HOTYH, I agree that with respect to DNA in this case, Bode is at the top (of a house of cards, on sinking sand)
  9. Holdontoyourhat

    Holdontoyourhat Former Member

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    I, for one, try to stay up on the news on these things, so I don't wind up with an antiquated POV.

    Have you read even one single RDI-favoring news story lately that wasn't just an opinion. Something that contained new information that points toward RDI.

    I don't know if you've noticed but it seems like RDI is suffering from a new information drought that has lasted for at least five years.

    What new information has been uncovered in the last five years that points to RDI?
  10. madeleine

    madeleine New Member

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    Thank you cynic! :clap:
  11. SuperDave

    SuperDave Well-Known Member

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    I second that notion! Always a good idea to look behind the "headlines." (Wink wink, nudge nudge say no more!)
  12. SuperDave

    SuperDave Well-Known Member

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    I'm hoping to change that. Let the people decide for themselves, and all that.
  13. DeeDee249

    DeeDee249 New Member

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    Wouldn't be the first time CNN reported things that were not accurate.

    This isn't a DNA case. Like they said.
  14. Holdontoyourhat

    Holdontoyourhat Former Member

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    Looking behind the headlines is very close to making stuff up. Or seeing things that just aren't there. Maybe ask yourself why you have to do that?

    Is it because the headlines don't say what you want them to?

    If the headlines were RDI instead, would you still look behind them? I doubt it, because RDI seems most willing to accept a confession from the R's without looking behind that.
  15. SuperDave

    SuperDave Well-Known Member

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    I KNOW why! And it wouldn't do me any good to remind you of it.

    It's likely.

    Apples and handgrenades, HOTYH, on a lot of different levels.
  16. cynic

    cynic Active Member

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    The “latest” headlines are certainly not always the latest truth.
    The latest headline in the O.J. Simpson murder trial was “O.J. – Not Guilty”
    The truth behind the headline is, of course, that he brutally massacred two human beings and got away with it.
    Is there a similar parallel to the Ramsey case?
  17. Roy23

    Roy23 New Member

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    The problem cynic is that all new relevant information is not in the hands of us Websleuther's but we still like to be critical and not trust the professionals in this case. I mean we all act like it is 1997 but in reality we are too naive to think out of the box.
  18. cynic

    cynic Active Member

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    I agree.
    In an “ideal Websleuth world”, we would have unrestricted access to the official case file, sadly, that is but a dream.
  19. Holdontoyourhat

    Holdontoyourhat Former Member

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    Just come up with some blood in the bedroom, a mess on the inside of a car, and a freeway chase and then there's a 'similar parallel'.

    These two cases are apples and oranges, I'm afraid. :laugh:
  20. cynic

    cynic Active Member

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    The parallel is “Ramseys exonerated” and getting away with murder.
  21. Holdontoyourhat

    Holdontoyourhat Former Member

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    I can certainly see the parallel when guilt is presumed.

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