And Her Name Was Pomponia Graecina

The following excerpt is taken from Elizabeth C. Hirschman and Donald N. Yates, The Early Jews and Muslims of England and Wales:  A Genetic and Genealogical History (forthcoming Summer 2013 from McFarland & Co. Publishers).

If Roman Britain had cities, and we know it did, there were Jews in them. In fact, we have a tantalizing record of what may be the first British Jew. Pomponia Graecina was the aristocratic wife of the conqueror of Britain, the commander Aulus Plautius, who defeated the sons of Cunobelinus (Shakespeare’s Cymbeline), seized the Celtic or Belgic capital of Camulodunum (Colchester) in Essex and secured the conquest of Britain for the emperor Claudius in 43 ce. Plautius became the first governor of the new colony. It is reasonable to think his wife lived with him during his governorship (43-47).

Ten years later, Pomponia Graecina was put on trial in Rome for a crime of character described as a “foreign superstition.” She was a member of the imperial Julio-Claudian family. The same charge was brought about the same time against Poppaea, the future wife of Nero. Poppaea was rumored to be privately a Jewish convert and to favor Jews.[i] Although many commentators and fiction writers believe Pomponia Graecina’s crime was the practice of Christianity, in the year 57 this would have been extremely unlikely. There were at that time very few Christians anywhere outside of Galilee. The apostles Peter and Paul were not yet dead. No Gospels had been set down in writing yet. In Rome Christians were a rarity far into the second century. They were so exotic even in the East that around 112 ce Pliny the Younger, then governor of Pontus and Bithynia, wrote the emperor Trajan for advice on how to identify and deal with them.[ii]

The Christian epigrapher Giovanni Battista de Rossi in 1879 associated Pomponia with family members buried in the catacombs of St. Callistus in the third century. She was gradually transformed into the apocryphal St. Lucina, even figuring in the historical novel by Henryk Sienkiewicz, Quo Vadis. But a gap of over a hundred and fifty years seriously weakens de Rossi’s theory. Sand identifies Pomponia Graecina as a Jewish convert, not a Christian.[iii]  She survived her husband by twenty years and died about 83 ce.

            Christianity struggled for several centuries to differentiate and distance itself from Judaism. Many of Britain’s Jews around 300 were undoubtedly “semi-converts—people who formed broad peripheries around the Jewish community, took part in its ceremonies, attended the synagogues, but did not keep all the commandments.”[iv] After the legalization of Christianity by Constantine in 313, some Jews and “semi-Jews” presented themselves publicly as Christian, while thinking of themselves and their ancestors as still wholly Jewish. Sometimes families were divided in their allegiances. Timothy of the New Testament had a Jewish grandmother, Lois, and Jewish mother, Eunice, but a Greek father. When Timothy converted to Christianity in his native Anatolia, the apostle Paul performed a ceremony of circumcision on him (Acts 16:1-3). Most of Christianity’s early converts came from Jews. Paul made a habit of preaching in synagogues.

As the Christianization of the Roman Empire accelerated during the fourth century, circumcision was forbidden to males who were not born Jews, the practice of converting one’s slaves to Judaism or of owning Christian slaves was proscribed, Jewish women who were not born Jewish were barred from ritual baths and Jewish men of all persuasions were outlawed from marrying Christian women.[v] Endogamy—marrying cousins and other close relations—became ingrained among Jews attempting to hold themselves apart from Christians. All these developments tended to make secret Jews out of people who defiantly regarded themselves as Jewish and honored the commandments of Judaism to varying degrees, often without benefit of a rabbi, community, synagogue or Torah. It was not until the eleventh century that the Hebrew language was introduced to Europe, and its dissemination was spotty. Moreover, that Hebrew was no product of an autochthonous linguistic development, but the artificial creation of Jewish scholars.[vi] In the rift, which covered most of the Middle Ages, the vast majority of European Jews were totally ignorant of Hebrew and were probably also not acquainted with rabbinical Judaism as it took shape in Judea and Western Asia.

Christianity’s final triumph put an end to all proselytizing by Jews “and perhaps also prompted the desire to erase it from Jewish history.”[vii] In the centuries that followed, especially after the rise of Islam, rabbis and other keepers of the collective memory were pained by the apostasy of the Jewish people on such a continuingly large scale. They sought to deny what was obvious, considering anyone who gave up their Jewishness “dead.” “Zionist historiography . . . [turned] its back on any meaningful discussion of the issue,” writes Sand. “Abandoning the Jewish religion was generally interpreted by modern sensibilities as betraying the ‘nation,’ and was best forgotten.”[viii]

Photo:  A Roman crypto-Jewish family. Copyright The Trustees of the British Museum.

Europe in the Year 3000 BCE

The archeogenetics of Europe and transition from hunter-gatherers to Neolithic agricultural societies made a quantum leap forward with the publication of an article investigating haplogroup H, the type carried by about half of Europeans today. But you may have trouble accessing the research in the new journal Nature Communications. I haven't found one ordinary mortal who has actually read the article, because few libraries and hardly any individuals can afford the crushingly expensive subscription to Nature Communications. 

So here is an abstract. 

CARLSBAD, Calif., April 1, 2013 /PRNewswire/ -- As the global market leader in human identification, Life Technologies Corporation (NASDAQ: LIFE) announced today it signed a global exclusive agreement with LGC Forensics for the right to distribute ParaDNA®, a portable rapid DNA system that determines the quality of human DNA faster and more economically than any existing method.  This announcement is the second in a series of new Rapid DNA products the company will introduce to expand the landscape beyond traditional Rapid DNA systems.


Watch video on how the ParaDNA works

http://paradna.lgcforensics.com/demonstration/

By MICHAEL SCHWARTZ


DNA is so tiny, only a few microns across, that we often don’t spend much time thinking about how much of our most personal and private information it contains. Yet each individual’s DNA also offers an 

While DNA may be small, it’s packed with information that has the potential to cause some pretty big problems. Uncontrolled access to this information, whether in a medical or law enforcement setting, could set individuals up for violations of privacy and discrimination, and as genetic testing becomes more common and inexpensive, the issues surrounding the protection of genetic information will become ever more pressing concerns in the larger public discourse.

Genetic privacy may not yet be a concern for most Americans, but as technology develops and practices change, it’s critical to know what risks you face as well as your rights, the laws that protect you, and how you can ensure your DNA isn’t be accessed and analyzed without your knowledge and consent.

DNA Law and Policy

While the structure and makeup of DNA has been known since the late 1950s, it was not until the 1970s that DNA was sequenced. It would would be nearly two decades before an efficient method of sequencing DNA would be developed, allowing it to be used outside of the scientific setting. Because the use of DNA profiling has only recently became practical for use in medicine and law enforcement, there aren’t yet that many laws that address the privacy and discrimination risks posed by genetic information. Here are just a few that have passed or are on the docket for the coming year that play a major role, or have the potential to, in the security of your DNA.

• Genetic Information Nondiscrimination Act:Enacted in 2008, GINA prohibits the use of genetic information in health insurance and employment. This means that health insurers and group health plans cannot deny coverage or charge higher premiums to an individual based on a genetic predisposition for developing a particular illness. It also ensure that employers cannot make any decisions with regard to hiring, firing, promotion, or job placement based on genetic data.In light of the recent growth of genetic testing, however, many think GINA needs amending. Provisions have been proposed that will help protect genetic information from being used to discriminate in life or long-term care insurance coverage and will ensure that data from genetic testing is not disseminated in research studies or other ways without an individual’s consent.The state of California has already passed state-specific laws of this nature that will ensure DNA can’t be used to discriminate in the areas of housing, education, public accommodations, life insurance, mortgage lending, and elections, so it may only be a matter of time before federal laws follow suit.
• DNA Identification Act of 1994: The DNA Identification Act was among the first laws to address the establishment of federal databases of DNA information, passed into law in 1994. The act authorized the creation of CODIS, a national database of DNA identification records of persons convicted of crimes, the analysis of DNA samples recovered from crime scenes, and the analysis of DNA samples taken from identified human remains. The act was modified in 2004 by the Justice for All Act, which expanded the offenses for which DNA could be collected, created a new system of indexing, and required national accreditation for forensic laboratories.
• DNA Fingerprinting Act of 2005: The DNA Fingerprinting Act allowed the national CODIS database to include samples from any individual from whom collection was authorized under state law. It also made it permissible for DNA to be collected from federal arrestees and from non-U.S. detainees. As a result, criminal DNA databases have rapidly expanded, with nearly all states and the federal government maintaining their own systems today. It has not been legislation without criticism, however. Some argue that it has unjustly allowed for the cataloging not only of convicted individual’s DNA but also that of those accused or arrested for a crime.
• California Genetic Privacy Law: One state that is working hard to protect the genetic privacy of its constituents is California. Authored by state senator Alex Padilla, the law would help protect genetic information from being used without consent, requiring research and health organization to acquire consent to collect, share, and retain genetic material and information. In 2006, Minnesota passed a similar law and over the past year South Dakota, Alabama, Massachusetts, and Vermont have all proposed related bills that would define genetic materials as personal property. As of yet, none of those bills have become law.

Also important to note are state laws on when and why DNA information can be forcibly collected. In all 50 states, those who have been convicted of a felony of any kind must submit DNA to both the national CODIS database and state databases. Yet policies differ from state to state with regard to when DNA evidence can be collected from those who are accused or arrested for a crime and have not yet been convicted. In 28 states, arrestees can be subject to DNA collection. Thirteen of those states collect samples for anyone arrested for a felony while the rest limit collection to violent crimes, including sexual assaults. Seven states also collect DNA for certain misdemeanors.

While this might help in solving crimes, it also poses some privacy issues. Probable cause is only required in 11 states to obtain or analyze a sample from an individual who has been arrested for a crime. More troubling, perhaps, is that even if an individual is acquitted of the charges, DNA information remains in the system unless the accused requests for it to be expunged; the state does not take responsibility forremoving DNA evidence from those who have been judged innocent.

Court Cases on DNA

Laws regarding DNA and the collection of genetic materials have been hotly contested over the past decade. Many believe that current state laws infringe on the Fourth Amendment and are tantamount to unreasonable search and seizure. Others have argued that DNA laws violate the Fifth Amendment, with the obligation to provide DNA evidence acting as witness against the accused him or herself. To date, many major cases involving DNA are still being addressed by the Supreme Court. Here are just a few that may shape federal and state law over the coming years or that have already impacted DNA privacy, criminal law, and genetic policy nationwide.

• Maryland v. King: This case is currently under review by the Supreme Court after the justices agreed it to hear it late last year. Previously, Maryland’s top court ruled that taking DNA from individuals arrested, but not convicted, for a serious crime was a breach of the Fourth Amendment right against unreasonable search and seizure. If this decision is upheld, laws in 21 states and federal law enforcement practices could be impacted, and in the future, law enforcement officials would be required to procure a warrant prior to obtaining DNA evidence from suspects in a case.
• Bearder v. State of Minnesota: The Minnesota Supreme Court found the state’s own department of health in violation of the law for failing to dispose of blood samples routinely used to screen newborns for serious illnesses. In some cases, the samples were used to validate new genetic tests, a clear violation of the state’s Genetic Privacy Act.
• Washington University School of Medicine v. Catalona: In 2008, the Supreme Court ruled that tissue and serum samples donated to the school could continue to be used for cancer research and that donors could not require that the samples be transferred elsewhere, as former Washington University surgeon William Catalona had argued. This is significant for DNA privacy, as it acknowledges that once samples are donated that they become the property of the institution, not the donor.
• Kohler v. Englade: DNA dragnets faced a major legal challenge with this Louisiana case. In 2003, Shannon Kohler was asked to submit a DNA sample by Baton Rouge police. His refusal led to him being named as the primary suspect in a serial rape and murder case. Kohler eventually provided DNA and was cleared of the charges, but alleged that the police didn’t have probable cause to compel him to give up his DNA. The Circuit Court of Appeals agreed, saying that the probable cause provided by law enforcement was so broad that it would have encompassed thousands in the Baton Rouge area. This decision helped to toughen the circumstances under which a warrant for DNA evidence could be granted, at least in the state of Louisiana.
• District Attorney’s Office v. Osborne: Oddly enough, while the courts have largely upheld the right of law enforcement to compel those who have been arrested or convicted of a crime to give DNA, once individuals are convicted of a crime, they do not have a constitutional right to their own DNA evidence nor that collected from the crime scene. In older cases, this means that DNA evidence cannot be reanalyzed using better, more accurate methods; a practice that has already exonerated many behind bars. According to the Supreme Court ruling in 2009, individuals do not have the right to post-conviction access to State’s evidence for DNA testing, making it impossible to exonerate those who may have been convicted falsely. Luckily, while the federal government does not mandate this, many states do allow for post-conviction DNA analysis.

This is hardly a complete list of all the major cases involving DNA testing and genetic privacy. For a great history on the subject, read a breif summary of major cases from Rhode Island College. For more information about major court cases on DNA around the world as well as some older cases here at home, check out the Electronic Privacy Information Center’s collection of important cases that have impacted genetic privacy all over the world.

When Your Genetic Privacy Is at Risk

While much of DNA law has to do with those who’ve committed a crime or been accused of committing a crime, the reality is that your genetic privacy can be at risk even if you’re a law abiding citizen. There are a number of cases when your DNA can be collected, analyzed, or retained without your consent.

• DNA dragnets:You don’t have to be accused of a crime in some cases to have your DNA requested by law enforcement. DNA dragnets occur when law enforcement officials as hundreds, sometimes thousands, of (presumably) innocent people to give samples of their blood or saliva in the hopes that one will be connected to a crime. While individuals can refuse to give DNA, in some cases the courts have forced compliance and most who refuse have faced increased scrutiny as a suspect in a crime, despite the fact that many see the request as an invasion of privacy.DNA dragnets aren’t especially common in the U.S., but in other places, like the U.K. and Germany, they have become common practice. In one case, DNA was collected from 16,000 individuals. While dragnets have been helpful in identifying the perpetrators of several high profiles cases, some who’ve been forced to partake say the dragnets have had unexpected consequences and have petitioned to have their DNA returned after being cleared.
• Discarded DNA: Directly giving a sample isn’t the only way for law enforcement officers to get a sample of your DNA. If your saliva is transferred onto another object, which you then discard, that object can be legally collected and used to analyze your DNA. While this practice has been challenged, it has held up in court because law enforcement officials state that there can be no reasonable expectation of privacy with regard to items that have been discarded. Not worried that the police will come after your DNA? Be aware that stray DNA could also be accessed by others looking for genetic information, like family members or those seeking to establish paternity.
• Family member searches: Another occasion when an innocent person may have their DNA requested by law enforcement is when a member of your family is suspected to be guilty of a crime, but no DNA can be gathered from that person because he or she can’t be found. In these cases, sometimes close family members are asked to submit their DNA to look for matching elements. If you wish to aid law enforcement, make sure that your DNA sample will be destroyed after it is analyzed, not stored.
• Participation in studies: Currently, few states have laws that protect genetic data once it has been collected and analyzed for research. This means that genetic material can be reused in future studies, transferred between institutions, or disseminated without the permission of the original donor. This doesn’t mean that individuals shouldn’t participate in research, but they should find out in writing before the study what will be done with their genetic information. Studies have shownthat DNA data alone can easily be used to figure out an individual’s actual identity, a fact that could influence insurance and employment opportunities.
• Elective genetic testing: Many worried about genetic condition opt to have their DNA sequenced by a private company. This can be beneficial, but it does come with risks. Not all DNA testing facilities have airtight privacy policies and some may do little to ensure your information stays confidential. If you submit to testing from a service, you may also be opening yourself up to these records being obtained by insurance companies or other outside sources. Once those records are out there, it’s very hard to get them back.

How to Protect Your DNA

While it’s useful to know what laws protect your genetic information and when it’s at risk, it is perhaps more important to know what you can do to ensure that your genetic information is kept safe and confidential, unless you choose to share it, that is.

• Always know the privacy policies of genetic testing companies. Getting genetic testing done through a private company is increasingly common, as prices have plummeted and access to these companies has increased. While these businesses do provide an opportunity to learn more about your health, they also pose a risk to your privacy if you’re not careful. Before submitting any samples to a company, carefully examine their privacy policy to see what it says and check out the business through the Better Business Bureau and TRUSTe.
• Know your rights under the law. We’ve outlined the major legislation that protects your genetic privacy above, but it doesn’t hurt to do additional research as well. The better you know what your rights are under state and federal laws, the better you can protect your personal and private health information. For additional information on privacy as a patient, learn more about HIPPA, which while not DNA specific does ensure that knowledge of your health issues can’t be shared.
• Don’t freely give out health information. Unless you are protected under law, do not share your personal family history or genetic information with others. In some cases, like when applying for life or long-term care insurance, this information can be used to discriminate against you. While GINA and other laws may protect you, there is no guarantee that sharing your genetic information won’t result in discrimination, so it’s best to always keep it to yourself unless absolutely necessary.
• Keep records about your DNA in a secure location. If you opt for DNA testing of any kind, especially that which looks at your risk for certain conditions, make sure to keep these records in a secure location that can’t be accessed by others. While you hardly need to worry about thieves, you do want to keep anyone who may be snooping around your home from finding out private information about you.
• Ensure that any research studies you participate in will keep data confidential. Sometimes, those suffering from certain diseases will choose to participate in research studies that collect genetic data. This can be an incredibly beneficial way to make strides in understanding and treating these conditions and others like them, but it does compromise DNA privacy. While not everyone will care about this, those who do will want to ensure that any studies requesting this kind of information will keep it confidential and, in some cases, you may even want to request that genetic material not be retained after the study is complete.
• Ask questions. You don’t have to agree to take part in a study for genetic information to be gathered on you. That’s why you should ask your doctor or health care professional if certain medical procedures will require genetic testing and find out in advance what his, her, or the medical facility’s policy is on personal genetic information.
• Seek legal recourse. If you believe your genetic information has been compromised in a way that violates your personal privacy and the law, contact a lawyer who can help you address these issues. You can also file a complaint with federal and state agencies for certain violations as well.

Much of the legislation and public policy regarding genetic privacy is still in its early stages, but as technology evolves and genetic testing becomes increasingly more common, how genetic data is handled, who has access to it, and the privacy rights of individuals will become increasingly more important. If you haven’t considered the risks posed by unsecured DNA information before, now is the time to look into protecting yourself and ensuring that your information isn’t being used, shared, or stored in ways that put your privacy at risk. While you may never face a serious issue with regard to your genetic privacy, it never hurts to be cautious and know your rights.

For more information visit BackgroundCheck.org. 

Researchers at the Max Planck Institute in Leipzig, Germany last week announced they have completed the first high-quality sequencing of a Neanderthal genome based on a hundredth of a gram of DNA extracted from a 100,000 year-old toe bone in a Russian cave and are making it freely available online for other scientists to study. Advantageously, Neanderthal and Denisovan remains were found in the same cave, making for breakthrough comparisons in hominid history. 

Read more: http://www.foxnews.com/science/2013/03/19/researchers-publish-full-neanderthal-genome

In a press release on March 19, 2013, Dr. Svante Pääbo, the head of the team that released the draft genome of Neanderthal man three years ago, said:  “We are in the process of comparing this Neandertal genome to the Denisovan genome as well as to the draft genomes of other Neandertals. We will gain insights into many aspects of the history of both Neandertals and Denisovans and refine our knowledge about the genetic changes that occurred in the genomes of modern humans after they parted ways with the ancestors of Neandertals and Denisovans.” 

The group plans to publish a major paper later this year. 

Maybe If It's First Generation Sex-Linked Testing, Not Autosomal 

Dust off the crystal ball. Scientists consider DNA ancestry services “genetic astrology,” according to a recent BBC article by Pallab Ghosh. In “Some DNA Ancestry Services Akin to ‘Genetic Astrology’,” Ghosh quotes Professor David Balding as maintaining that ‘“such histories are either so general as to be personally meaningless or they are just speculation from thin evidence.’” One article, “Don’t Believe the Guy Who Claims He’s Descended From Vikings,” quotes evolutionary geneticist Mark Thomas, as saying “these tests have so little rigor that they are better thought of as genetic astrology.”  That may be right about some tests. But the key word is “some.”

Not all DNA ancestry tests or companies are created equal.  It is as much an oversimplification to suggest they are as it would be to claim that all lab tests are the same or all pharmaceutical drugs are the same. Do you get a shot for epilepsy when you have diabetes? Hardly. There are DNA tests and there are DNA tests. Customers are generally careful to get  the right medicine from a reputable doctor. A customer needs to be just as careful choosing a DNA test and a DNA ancestry company. Not all DNA ancestry companies, even some of the larger companies, have an ISO certified lab, for instance. This not only guarantees the reliability of results, it is also the highest standard in the genomics industry. A few have this laboratory benchmark, but it is, unfortunately, not required, in direct- to-the-consumer DNA testing. Would you want to entrust your genetic identity with anything less? The buyer needs to be aware that with non-certified labs there is a stronger possibility of contamination or lost or swapped samples. I know someone who was the unknown victim of a sample swapped. He thought he was someone else for two years.

Secondly, there are a variety of tests to choose from. There are sex-linked tests (Y chromosome, X chromosome- mitochondrial) and non-sex linked tests called autosomal. The sex-linked tests are haplotype tests based on genetic markers handed down by the male (Y chromosome, received only by other males) or female (mitochondrial). The industry started out with sex-linked testing, but its limitations dictated a move increasingly to autosomal or non-sex linked testing. There are weaknesses with sex-linked tests.

The mitochondrial genome is small compared with the nuclear genome according to the article “Mitochondrial Genome Analysis with Haplotyping” which means there cannot be that much variation with mitochondrial DNA analysis. For instance, some have expressed doubts that the recently found Leicester skeleton could be Richard III because of the mitochondrial DNA analysis that was done. Live Science writer, Stephanie Pappas, quoted Maria Avila, a computational biologist at the Center for GeoGenetics at the [British] Natural History Museum as saying “people could share mitochondrial DNA even if they don’t share a family tree” (Pappas).  

How is this possible? Mitochondrial DNA is ancient DNA and mutates slowly.  In the article, “Doubts Remain that the Leicester Body is Richard III,” a Mark Thomas at University College London is quoted as saying that “people can have matching mitochondrial DNA by chance and not be related.” So, it might not be Richard III after all. Male line haplotype testing has different limitations. “The Male Y- linked tests have very rapid mutation rates and are very fragile, so you can get a lot of errors with that type of testing,” according to Dr. Donald N.Yates, head of Research and Development for DNA Spectrum.

According to a recent New Scientist article by Colin Baras, “The Father of All Men Is 340,000 Years Old,” the Y chromosome seems more ancient than previously thought. If so, it is also less stable than we thought. Brian Sykes, Professor of Genetics at Oxford University and the author of The Seven Daughters of Eve, makes a strong argument that the Y chromosome is weakening and in trouble in his book, Adam’s Curse. He says it is “doomed to a slow and humiliating decline” (279) because of its instability and rapid genetic mutation and is thus headed toward extinction. Before the 1990’s paternity testing was based on Y chromosome comparisons and limited to fathers and sons. Sometimes, an uncle would be mistaken as the father. Today, it relies on autosomal DNA comparisons, can be applied to females, and is 99.99% accurate.

But then there are non-sex-linked Autosomal DNA tests which are based on a different science altogether. Anyone can take this traditional type of Autosomal DNA test because it does not rely on X or Y chromosomes (women are unable to take the Male Y- linked test and must entice a male in her line, if one is available, to take this test). This test is not testing ancient DNA but  goes back only some four or five generations, so it does not have these limitations. And it provides a complete analysis of all ancestral lines. Not just one line at a time as in haplotype testing. This is next generation ancestry DNA testing and the wave of the future. Moreover, this type of testing is more stable and has more scientific validity as it uses the same science that is used in the legal court system, by the government, and on CSI comparing loci markers to population databases. And two research teams independently reached the same groundbreaking results that the DNA mutation rate is slower than previously thought:  James X Sun et al., in the article, "A Direct Characterization of Human Mutation Based on Microsatellites," in Nature Genetics 44/10 (October 2012):1161-65, and A. Kong et al., in the article "Rate of de novoMutations and the importance of Father's Age to Disease Risk," in Nature 488 (2012):471-75. All done by the magic of math and laws of large numbers.

What does this mean concerning autosomal DNA ancestry tests? They have even more scientific validity. This second-generation type of DNA ancestry testing is based on these same genetic markers, and that is confirmation that the alleles on your DNA that are examined using a statistical basis have been relatively unchanged for the past 20,000 years. That’s about twice the length of what we call world history, hence a meaningful enough time frame for valid inferences about population patterns and ancestry of individuals. These are markers that everyone has (and why anyone can take an autosomal ancestry test).  These genetic markers change at a much slower rate than the Y chromosome which seems to be highly changeable, depending on the father’s age (Kong 201). (The Y chromosome is a marker only males have. It is used for other types of tests: male, haplotype, sex-linked DNA tests. Only males can take these tests, and it only provides information about that one male line).

Of course, anything can be over-interpreted. DNA testing is not magic. Maybe you should put that crystal ball up after all.

You've heard of Gaius Flavius Antoninus, the assassin of Julius Caesar. You are probably familiar with crocodile shears, a notorious torture device. If you are an aficionado of the annals of rock and roll, you know about the band named Tilly that perished in an airplane crash on December 12, 1956 en route to a "Lester Concert Hall." And if you are really into military trivia, you probably could name the Bicholim Conflict as a little known Dutch war of the seventeenth century, right? 

The trouble is none of these persons, places or things ever existed, happened or lived. They are all fictions, examples of hoaxes on Wikipedia. The Gaius Flavius Antoninus hoax lasted for eight years and a month, from 2001 to 2008. During that time, probably many high school or college papers mentioned Gaius Flavius Antoninus' name without realizing that he never existed, that he was one of the jokey little displays of sophomoric humor in a cheap online information source whose content anyone can alter.  

You may think it is a harmless prank to invent a spurious entry like the Adyhaffe people (whose civilization lasted for five years on Wikipedia's list of ethnic groups, until last October when they were wiped out with a single click of a mouse), but depending on your motives and your practice of deceit such juvenile behavior may easily cross the line into cyber-bullying. 

Here's Not Looking at You, Kid
On a personal note, we were recently a bit bent out of joint when an article about our Principal Investigator Donald N. Yates in Wikipedia was vandalized (for the second time in a year) and attempts to remove offensive and defamatory material about him, the company and others were frustrated by the Wikipedia team of super-editors. 

To summarize, an article begun on Living Authors by ClaudeReigns (remember the actor in the 40s . . . cute, right?) in December 2010, survived until February 24, when two "users" began to blow it up and replace it, word for word. We became curious about the identities and motives of the two users. Both have been active in the upper echelons of Wikipedia for six to eight years, but are not identifiable by name. One hides behind a picture of himself or herself with a ski mask that makes himself or herself look like a terrorist. We were sufficiently scared to stay away from further research or poking around, especially after a Wiki official stepped in by the name of Red Pen of Doom (also unidentifiable). 

The M.O. of these losers, excuse me, users is similar. They become puffed up by power after volunteering content and help in no recognizable pattern of interests for year after year. Some are in the top 25% of contributors in terms of sheer mass of megabytes they have edited for Wikipedia. Like vultures, they often descend on controversial, especially racially charged subjects. Insecure as Walter Mittys going to Toastmaster sessions, they display "awards" and Thank You certificates on their home user pages. It is doubtful from their wide interests and anonymity and mechanical citation of administrivia that they actually correspond to real people you might be able to reach on the phone. 

Well, as said, we felt pretty bad about our experience being featured in Wikipedia, fairly abused and manhandled by malicious people you could never expose. Creepy? Yes. Wrong? Yes. Anything you can do about it? No. At least, however, nothing ended in tragedy, like the suicide victim in Maryland. 

One of the insidious things is you cannot combat libel or other abuses "within" Wikipedia. You will be banned for insisting on correcting the record or threatening legal action. This actually happened to one of the well-wishers who wrote to us. 

Read on in the comments. Unfortunately, you cannot edit or censor them. This is not Wikipedia. It is reality. 

To get to the crux of the cyber-bullying, read "A Personal Message from Donald N. Yates" in the February DNA Consultants Newsletter. 

PHOTO:  Bloviators, anarchists and agents provocateurs can hide behind anonymity on Wikipedia. 

Behind the Numbers:  Jim Bentley

Jim Bentley, DNA Frontiersman

(Part Three of a Series)

We interviewed  one of Chromosomal Labs Bode Technology’s senior staff members, Director of Sales and Marketing Jim Bentley, to get his perspective on industry changes over the past thirty-five-plus years.

Jim Bentley.

When did you first get interested in DNA?

JB: I’ll have to preface my answer with a few remarks on “the early days.” When I graduated from Arizona State University in the 1970s, DNA testing as we know it, was not really a field that was in existence. There was not a lot going on. The little work I did with chromosomes was using electron microscopy. I worked in the biochemistry department, however and performed hundreds of assays using poly-acrylamide gel electrophoresis, mainly for separation of proteins. This technique, although improved and streamlined remains in use today for DNA-STR separation. The field we’re in today where we can determine a person’s profile and compare it with others for forensics  for relationships, ancestry, missing persons, adoptions and the like, that technology hadn’t been developed yet. It wasn’t quite as easy as it is today.

Tell us more about the evolution of DNA testing.

JB: It basically began with blood groups and types. The first paternity test was done in a court case with Charlie Chaplin in the 1940s. He was excluded as the father, but the court said he could go ahead and pay child support anyway—probably, because he could afford it. Since that time, scientists started moving past groups and types into some other techniques. Human Leukocyte Testing (HLA), DQ-Alpha, and Restriction Enzyme STR testing (RFLP) are examples of the evolution of DNA testing.

The big breakthrough came when Dr. Alec Jeffreys at the University of Leicester discovered STR testing in England the late 1980s. He used STR profiling on the Colin Pitchfork case. Colin Pitchfork became the first criminal convicted on the basis of DNA evidence and as a result of a mass DNA screening operation. He was charged with raping and murdering two teenage girls. Since that time the forensic community has really refined the techniques to perform STR testing. They’ve made it simpler and more accurate. It’s really moved exponentially in the last twenty years. Today competent biologists and chemists can produce excellent results, every time.  Dr. Jeffreys has been knighted for his contributions.

So what got you involved?

JB:  I came out of college as a chemist, one interested in the medical field. I started out working in clinical chemistry and toxicology. The work we did with DNA was extremely limited and very costly. But I did stick with a career in clinical chemistry. Within four years after graduating from school I was managing a clinical laboratory in Houston, Texas called National Health Laboratories. It was a laboratory of about one hundred scientists and support staff. After mergers, acquisitions and such, that company remains as Lab Corp. (It performs more than 1 million tests on more than 370,000 specimens each day.)

What opportunities for professional growth did you have over the years?

JB: Through taking a lot of continuing education coursework, I became proficient and qualified as a general supervisor in clinical chemistry, toxicology, hematology, parasitology, microbiology, serology—everything except for tissue work like histology and cytology, which was done by certified medical experts in those specialties. My interests kept me in touch with the staff pathologists, however, as well as all the rest of the laboratory. Though my present-day field did not exist at the time I graduated, by staying current I was able to benefit from the changes and be part of an emerging valuable service provided not only to the medical community but also to the forensic one, and the general population at large.

What are some famous cases you’ve been involved with . . . that you can talk about?

JB:  Actually, that’s my problem. We’ve been involved in a number of high-profile cases, but we’re not allowed to talk about any of them. Most have been on the forensic side, serial killer trials in Arizona, also in California, some that made the news in Florida . . Texas . . .Georgia.

Were you involved in catching the Grim Sleeper?

JB:  Actually, that’s an ongoing case in Los Angeles we are familiar with, but we didn’t do the work on it, so we can talk about that one. The importance of the Grim Sleeper case has to do with familial testing and autosomal DNA. It was termed the Grim Sleeper case because there were a number of homicides that took place beginning in the mid-1980s, all with the same basic MO [modus operandi], and then the murderer went underground for fourteen years. The victims were typically prostitutes shot with a firearm. In 2010, a suspect, Lonnie David Franklin Jr., 57, was arrested and charged with multiple counts of murder. He has not yet been convicted, nor the evidence against him tested in court.

How was DNA used to catch him?

JB: So here were a number of cold cases, but they were being tracked, and the law enforcement authorities in Los Angeles continued to monitor progress. The sole survivor of one of the Grim Sleeper’s attacks furnished a description of him as a black man in his 30s, along with other details. According to her story in the press, he lured her into an orange Ford Pinto, shot her in the chest with a pistol, took Polaroid’s and raped her, leaving her for dead. In 2008, the body count was thirteen, and a $500,000 reward was put out for “America’s Most Wanted.”

It became the first use in California, and one of the first three cases in the United States, of the use of familial DNA searching, that is, using the FBI’s CODIS database to match one family member’s profile with a suspect’s profile. The LA police were able to provide a close partial match to  Franklin’s crime scene profile with that of his son, whose CODIS markers were on file for a minor crime. They then set up a kind of mini-sting operation at a pizza parlor in Buena Park, where they knew the family liked to eat. Undercover detectives masqueraded as waiters and busboys. When the family left, they whisked away an unfinished pizza slice. The crust yielded DNA which police linked on a more solid basis to Lonnie Franklin. It was the first high-profile case in which a family member’s DNA had been used to catch a criminal. The ACLU and others had been critical of familial searching on grounds of privacy, and there is still a lot of debate over familiar searching because it might open up the search and include those who hadn’t committed any crime.

Did this help produce new commercial products like the “cousin finders”?

Only a few states are doing familial searching, and they are pretty guarded about it. It’s hard for me to make a connection. Certainly, these developments have been concentrated in the past three or four years, but the use of this technique is spreading.

Are people legitimately suspicious about DNA databases?

JB: Fears surface from time to time. There have been claims that keep popping up that someone’s going to take everything that’s in the database and use it to determine genetic deficiencies that could lead to medical issues down the road. Once it was speculated that if such  information was released, insurance companies would begin denying people coverage based on their profiles.

This is the mother of conspiracy theories, isn’t it?

JB:  It really is. For the most part—not for everyone—the vast majority of the markers we are using are in the “junk DNA” area. That is, they don’t by themselves “do” anything or give you genetic information on the face of things. There may be one or two markers that possibly could be construed as yielding some medical information—such as a trisomy at vWA or TPOX [a CODIS locus]. But by and large, you are not going to be able to do any medical diagnostics with the markers we run. Usually trisomies such as Down’s syndrome would be physically expressed and not hidden. It’s a little different with SNP panels [single nucleotide polymorphisms] such as those run by 23&me. With a high number of those, it’s entirely possible to predict medical predisposition. That’s what they base their business on.

Let’s talk some more about the CODIS database.

JB:  It’s important to realize that even law enforcement doesn’t provide much access to the CODIS [Combined DNA Identification System] databank. That’s something I have to give the FBI credit for. They have developed a system that is secure. It’s the DNA administrator at each facility who has undergone FBI training and uploads the data under very strict rules, and they are notified of any “hits” that involve them, but otherwise there is very little access, and the use of the database is very even across the country. There are not a large number of portals that can be used to access the CODIS database. There are several hundred law enforcement laboratories that are running profiles across the country, and the database is best thought about on three different levels:  LDIS, SDIS and NDIS, local, state and national versions. Between our labs in Phoenix and Virginia, we’ve tested over a million profiles for entry into CODIS. That’s about one-tenth of the entire number. I can tell you there is tight security. Hundreds of thousands of investigations have been aided by a DNA hit (we don’t like to say “match” so much, because statistically nothing is 100%) generating a lead.

How did you get bitten by the genealogy bug?

JB: I’ve always been fascinated with ancestry. I think it came about because my father took an interest in discovering our family’s roots and had to do so at the time by traveling to Salt Lake City, Utah, and poring over whatever records he could find there about our fathers, and great-grandfathers, and great-great-grandfathers, and so forth. He had tintypes of some of the relatives. We had various pieces of the puzzle. My father pretty much consolidated everything back to William Bentley, who settled in Rhode Island in the early 1700s and had come from Bedfordshire, England. He put together a book for family use. He glorified a few of them and left a few out that weren’t ready for glorification. For the sensitivity of some of the relatives, he left a few details out, but it was a pretty solid piece of work. For me, it kind of fostered this interest in ancestry and its importance. Certainly, when I started at Chromosomal Labs • Bode Technology, we started looking at the various tools that could be used. Our history, to be sure, is passed down from generation to generation. Initially, we were using mitochondrial DNA, Y-SNP’s and Y-STRs and then autosomal STRs to determine how we’re connected to general and specific individuals back to the Revolutionary War days and how you are linked with the world population, what your roots were. I have a particular Y haplogroup of G2a, which is not one of the more common ones.

Hmm . . . you and Joseph Stalin.

JB:  [Laughs]. Is that what his haplogroup was? Uh-oh! He was one of the worst. Well, I got interested in G2a and hooked up with about 50 other Bentleys and we identified our founder  patriarch haplotype. I get emails from them on a regular basis. The other thing we tried to find out was what in the world were all these G2a’s doing in England. I don’t know. But one of the things I find in the literature most often was that the Sarmatians were horsemen that gave the Romans a pretty rough time. Eventually, they were decimated. The Romans took their remaining cavalry and pressed them into service for 12 to 13 years or longer. Some were dispatched to Hadrian’s Wall. Now do I know for a hundred percent certainty that’s where I came from? No, but its fun to regard that as a hypothetical personal history.

You have a Scythian gene, don’t you?

JB:  Yes, I do according to the analysis DNA Consultants did for my autosomal ancestry. The work Dr. Yates has done on the rare alleles supports a lot of the stuff the family has been putting together for years and years.  I was very pleased to get my Rare Genes from History report back showing I had the Scythian gene. That seems to go along with the Sarmatian theory about the Bentleys.

How do you see the industry changing over the next few years?

JB:  I can speak best about changes I am seeing in the field. They’re getting closer to having rapid DNA testing on a chip. This gives flexibility to those who want to use DNA as “point of use” testing. The FBI this past year came out at the Promega conference and said that within the next two years they would like to see wide adoption of “point of use” testing. The IntegenX prototype allows you to put your swab into a cartridge, insert it into the instrument on the fly and get your STR results in a few hours. Previously, Rapid DNA testing was not only time-consuming and lab-bound but it was very expensive. It cost several hundred dollars in reagents alone. As the technology improves to allow 2 hour testing in our lab or on a chip, reagent and personnel time continue to drop,  Now, the FBI would like to see point of use testing in every booking station in the country. At the last show, I also saw an instrument from Illumina that would run Y-STRs, mtDNA and autosomal DNA profiles simultaneously on one sample. Another change that is coming is we will see an expanded profile becoming the standard, perhaps something similar to the GlobalFiler kit from Life Technologies with its 24 loci. With the new technology you can increase the speed for amplifying the specimen by five times and achieve nine times the discriminating power or resolution.

Any final remarks?

JB: The DNA testing field is on the threshold of even greater accolades of appreciation both from the scientific community and the public. If DNA wasn’t even in anyone’s mind twenty years ago, soon it will be part of everyone’s daily lives.

 
























Sir Alec Jeffreys, inventor of DNA fingerprinting, and Jim Bentley at forensics meeting.

We are our DNA. It was not a surprise to find that our entire DNA is Functional (“Junk DNA Isn’t Junk, and That Isn’t Really News”). The surprise is in the discovery of what we can do with what we once thought was junk. According to that recent NPR article, “It is a massive control panel that regulates the activity of our genes.” Our genes “would not work” without it. So instead of being junk- they are critical and “control how cells, organs, and other tissues behave.” But we can also now read the markers and mutations on this “panel” and discover much more information than knowing it is just working efficiently for our body. This knowledge is considered a “major medical and scientific breakthrough” (Ibid.). We just have to read it well.

But first, what is DNA exactly? John Wilwol, in his recent NPR article, “A ‘Thumb’ on the Pulse of What Makes Us Human,” quotes Sam Kean, author of the book, The Violinist’s Thumb And Other Lost Tales of Love, War, and Genius, As Written by Our Genetic Code, as saying that DNA is what makes us who we are. Wilwol further quotes Kean to help us understand what DNA is and how it differentiates from genes: “ ‘While DNA is a thing- a chemical that sticks to your fingers, he writes, genes are more conceptual in nature, …“‘like a story with DNA as the language the story is written in.”

So if DNA is a language how are we able to read it? All parts of our genetic code are now readable and meaningful. Marker locations (loci) are spread across one’s entire genome, not confined to one’s male (Y chromosome) or female (mitochondrial) DNA. (This is how sex-linked, haplotype tests that follow one line at a time are analyzed). Different mutations are handed down genetically – different according to the region where one’s ancestors lived.

Because of this new ability to read markers, consumers are now able to buy Autosomal DNA tests that provide a complete analysis of where all one’s ancestors’ ethno-geographic origins – reflecting the entire spectrum of all ancestral lines. Not just one line at a time as in haplotype testing. This is next generation ancestry DNA testing and the wave of the future. Anyone can take an Autosomal DNA test because it does not rely on X or Y chromosomes (women are unable to take the Male Y- linked test and must entice a male in her line, if one is available, to take this test). The future is now in many ways.

What else can you learn from Autosomal DNA testing? Anne Tergesen, in a recent article in the Wall Street Journal,” quotes Megan Molenyak, author of, Hey America, Your Roots Are Showing, as saying that this relatively new test deciphers the amount of DNA shared between those whose common ancestors lived within the last half-dozen or so generations. Tergersen explains it like this, “Y-DNA and mitochondrial DNA can connect people whose common ancestors lived recently or hundreds of years ago. But to find out how closely you are related—and to locate relatives besides those on your direct maternal or paternal lines—you will need an autosomal DNA test.” (Of course, you would both need one to compare) and “in general, the more DNA two people share, the closer their connection”.

But there are even more things on the horizon with Autosomal DNA for the future. Personalized Medicine. According to a recent Smithsonian article, “Fetal Genome Sequenced Without Help From Daddy,” “A fetus’ entire genome can now be sequenced” from the mother alone with a “99.8% accuracy.” How is that possible? It was just “last month clinicians announced that they could sequence a fetus’ entire genome by taking samples from the pregnant mother’s blood and that of the father to be” (“Fetal Genome”). Now they have a “more difficult, but more complete method [that] uses DNA from the pregnant woman and the fetus to map out every last letter of the fetal genome…with the advantage that it can pick up mutations that a fetus has but its parents do not” (Ibid.).  Rob Stein quotes Dr. Alan Guttmacher, director of the National Institute for the Child Health and Human Development in a recent NPR article, “Genome Sequencing For Babies Brings Knowledge and Conflicts,” as saying, “Instead of screening for currently something like 30 conditions, it would allow you to screen for hundreds if not thousands, [of conditions] at birth.  He goes on to say that, “One could imagine a day where knowing someone’s entire genome sequence at birth, you could really begin to think about structuring health care, their dietary choices, their exercise choices…early in life, in a way that would have an impact on truly lifelong health.” Stein says that this gene sequencing could “spot babies that are prone to conditions such as obesity, diabetes, heart attacks or cancer” and that we may soon be “sequencing all babies when they’re born.”  It could be a wonderful tool. But we are not there yet.

According to Rob Stein in another recent NPR article, “Perfection is Skin Deep: Everyone has Flawed Genes,” Scientists have determined we are all more flawed than they thought. “Researchers discovered that normal, healthy people are walking around with a surprisingly large number of mutations in their genes.” Chris Tyler-Smith of the Wellcome Trust Sanger Institute in Cambridge, England and his colleagues analyzed the DNA of 179 people from several countries who volunteered their genetic information to the 1,000 Genomes Project.

In a published paper in the American Journal of Human Genetics, the researchers reported that though none of the people whose DNA was studied were sick, the average person has about 400 minor flaws and one or two that could contribute to disease. Tyler-Smith says, “It’s a bit surprising that people should be walking around apparently healthy yet we’re seeing known disease-causing mutations in their genomes,” he says. “But the answer was that these tended to be for mild and very often late-onset conditions. Things like heart disease, an increased risk of disease or developing cancer. On its website, the American Diabetes Association highlights the interaction of genetic and environmental factors: “You inherit a predisposition to the disease then something in your environment triggers it. Genes alone are not enough.”

So the problem is not so much with the analytical tool but rather the possibility of over- interpretation. Again, we just have to read it well, with the same critical eye for what is written in us as that which is written by us. And who knows what else we will soon be able to discover from reading our DNA?

DNA, not Gothic literature, has all the best stories and tales of murder and intrigue. According to Sam Kean, author of The Violinist’s Thumb: And other Lost Tales of Love, War, and Genius as Told by Our Genetic Code, “ …Somewhere in the tangle of strands are the answers to many historical mysteries about human beings that were once thought lost forever.”  Kean says each one of us has”… enough DNA to stretch from Pluto to the sun and back,” and “…every human activity leaves a forensic trace in our DNA” and the story that DNA tells, Keans says, “…is a larger and more intricate tale of the rise of human beings on Earth: why we’re one of nature’s most absurd creatures, as well as its crowning glory.” We just have to know how to read the story and solve the mystery. Like the one about the French Revolution and King Louis XVI.

Victor Hugo’s classic novel about the French Revolution, Les Miserables, has been given a facelift for a modern audience to ponder over popcorn in the theater.  Or discuss at a local café or bookstore over cappuccino. But few of us would imagine that scientists have had any interest in the French Revolution. We would be wrong if we did, and it is a gruesome tale of the intersection of science and history in this case.

Phillipe Charlier, a forensic scientist, dubbed the “’ Indiana Jones of the Graveyards, ‘“according to the recent Abroad in the Yard article, “DNA Analysis Links Blood of Louis XVI, Beheaded in French Revolution, and Mummified Head of His Ancestor Henri IV,” by Tom Martin Scroft, has linked blood stains in a decorated squash gourd to the mummified head of King Henry IV. There was once a handkerchief, according to the article, that had been “in the possession of an Italian family for over a century” in an “ornate calabash gourd” that had been “dipped in the [beheaded] blood of King Louis XVI” by a Maximilien Bourdalou.mAccording to an earlier Discovery News article by Jennifer Viegas, “Royal Blood May Be Hidden inside Decorated Gourd,” the handkerchief “is now missing.” Most certainly it has “decomposed” by now as David Blair suggests in his recent article, “Louis XVI Blood Mystery Solved.”  Viegas also says the ornately decorated gourd was “dated to 1793” and that the dried squash reads, “Maximilien  Bourdaloue on January 21^st, dipped his handkerchief in the blood of Louis XVI after his beheading.” Why he would have done such a thing?  For a bloody relic no doubt.  What  a coffee table conversation piece. Viegas quotes Carles Lalueza Fox, “lead author of the study and a researcher at Spain’s Institute of Evolutionary Biology,” as saying that the act was common: “In fact, many people went there to dip their handkerchiefs in the blood.” How gruesome. But linking blood found in the Italian family’s gourd to King Louis XVI?  It took DNA analysis to validate that tale.

How was that done? In careful steps. First, according to Fox (qtd by Viegas) her team had to identify the “brownish substance” inside the squash as “dried blood.” Later, Fox remembered that the King had “blue eyes” and he identified the genetic marker for the “blue eyes mutation.” But that is a long way off from identifying it as the blood of King Louis XVI. The researchers also analyzed its mitochondrial profile and its Y-Chromosome profile and they found the “’DNA profile [before they had a match]…was rare among Eurasians’” which “suggest[ed] that it [might] derive from a royal bloodline.” But Fox knew that they had to have “ ‘someone’” for comparison. They first thought of the “[pickled]heart located in a royal French crypt thought to belong to the King’s son, Louis XVII.”  It is beginning to sound like a tale from Edgar Allen Poe.

But they didn’t use the heart after all. They discovered the mummified head of King Henri IV, who ruled France from 1589 until 1610, which had been “shuffled between private collections ever since it disappeared during the French Revolution,” according to Marie Cheng’s AP article, “Scientists ID Head of France’s King Henry IV.” (According to the article, “Henry IV was buried in the Basilica of Saint Denis near Paris, but during the frenzy of the French Revolution, the royal graves were dug up and revolutionaries chopped off Henry’s head which was then snatched.”) I don’t suppose the head was in such great condition after all this shuffling about, but it still turned out to be useful. 

With that mummified head, DNA analysis has “solved a mystery that has lasted for almost 220 years,” according to Blair. He quotes a new study in the current issue of Forensic Science International as saying that the comparative analysis with the mummified head of King Henri IV confirms the connection by “…establish[ing] that Henri possessed a rare partial “’Y’” chromosome” and Louis, a “direct male-line descendant, separated by seven generations,” [had] this same Y chromosome. Along with “other [genetic] matches,” the study concluded that “…historically speaking, this forensic DNA data would confirm the identity of the previous Louis XVI sample.”

And you thought scientists were boring. Another DNA mystery solved.