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review of scientific and news articles on dna testing and popular genetics

The Sins of Science

Saturday, April 21, 2012

Science, it seems, has been "the new religion" for a long time. And by the same token, it has always had its apostates and heretics, even its unremarkable and quotidian sinners. In an article titled "Disgrace," Charles Gross, a professor of psychology and neuroscience at Princeton University, reviews the whole subject of contemporary and historical scientific misconduct (The Nation, Jan. 9/16, 2012, pp. 25-32). He finds nothing new in the shocking case of Harvard's Marc Hauser, who was exposed two years ago for scientific misconduct, in of all fields, the biological basis of morality and genetic inheritance of doing evil.

Hauser apparently was guilty of the very venial sin of fudging facts. The three ways to do that, all frowned upon, are by fabrication (making data up), falsification (altering or selecting data, cherry picking) and sheer plagiarism (which all but entering Freshmen understand).

In 1830, computer science pioneer Charles Babbage published a book in which he distinguished "several species of impositions that have been practised in science...hoaxing, forging, trimming, and cooking."

Gross classifies the Piltdown man as an example of hoaxing. This fossil combining parts of an ape and human skull was discovered in 1911 and not discredited until the 1950s. Most hoaxes are intended to poke fun at the public's credulousness, but the Piltdown hoax was undertaken by well-meaning British imperialists who hoped their construction would fill an awkward gap in the record. Like God, if the missing link did not exist, we should have to invent one. Pip pip for the Royal Society!

Babbage believed that forging was uncommon. Rarely are results completely counterfeited and pulled out of thin air.

"Trimming" is probably a form of scientific misconduct that few scientists confess to their most exacting monitors such as the National Science Foundation but rather quietly cover up in bland hypocrisy. It consists of "eliminating outliers to make results look more accurate, while keeping the average the same." Who has not committed that little white sin? Let him who is without self-assurance cast the first chad.

"Cooking," on the other hand, the purposive selection and distortion of data, might be a real concern for all of us.

Gross goes on to inspect the career of Harvard's "war crimes professor" Richard Herrnstein, who became a co-author after his death of the book The Bell Curve about racial differences in intelligence. It is not a very pretty kettle of fish.

Charles Darwin essentially stole the idea of natural selection from Alfred Russel Wallace, the father of biogeography, did he not, and if he didn't, certainly failed to credit some of his predecessors in his rush to fame and self-glorification.

In genetics, we are reminded that the saintly Gregor Mendel probably falsified the suspiciously exact 1:3 ratio he "observed" in comparing pure dominant with hybrid peas (p. 26).

Alarmingly, we learn that "the modal scientific miscreant is a bright and ambitious young man at an elite institution," just the sort of role model worshiped by the popular press.

Maybe our society should be examining a few of science's feet of clay rather than pompously setting more laurels on the heads of its exalted heroes.

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How Good Is Direct-to-Consumer Genetic Screening? Not Very, According to Study

Thursday, April 19, 2012

It is clear that consumers, and many geneticists and medical professionals, underestimate the complexity of genetically determined diseases and their risk levels as measured by genomic testing. The question is whether it is ethically sound to sell consumers packaged DNA tests that could exaggerate their risk for say, heart disease, or render a false negative result. In one study, DTC testing on average handed out very slight risk factors across the board, lower than those known to be in the general population. Another study, the first of its kind, performs an experiment comparing traditional genetic screening by counselors to "insta-testing" by Navigenics. It looks like the technology of DTC has a long way to go, while our understanding itself of genetically inherited disorders is still in a rudimentary stage of development. Rather than exploring new sites and new tests the emphasis needs to be on interpreting the studies and data we already have.

Direct-to-consumer genetic testing services: what are the medical benefits?

Thierry Frebourg

Eur J Hum Genet 2012 20: 483; advance online publication, January 4, 2012; 10.1038/ejhg.2011.229

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Arcpoint Labs of Des Moines commented on 19-Apr-2012 01:05 PM

Very interesting! Thank you for sharing!


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What is a Megapopulation?

Monday, April 09, 2012

The dictionary defines "megapopulation" as a very large one, from the Greek suffix mega, the same element as in "megabyte." In statistics, a population is the whole field from which you choose a sample or representative segment. Thus, to test American Hispanic/Latinos you might draw a sample of 400 people from a predefined population of everyone with a Hispanic surname in a telephone book.

How reliable and valid your sample is depends on methodology. By combining populations you can study a metapopulation (all related populations, for instance North and South American Latin or Iberian populations) or megapopulation (all populations with Iberian ancestry in the world).

Going from the small to the large, we  have then:

Individual

Sample
Population
Metapopulation
Megapopulation
Universe

In a census, the sample and population coincide; everyone is counted.

In population statistics, this hierarchy might look like this:

John Doe
Arizona Hispanic study (n=104, that is 104 persons in the sample)
U.S. Hispanics
North American Hispanic
Iberian American
Iberian or Part-Iberians in the World

At DNA Consultants, megapopulations are the broadest ethnic category calculated and reported to you. (We look at metapopulations, too, but only as a control measure.) Our database coverage is described below.

Megapopulation Names

and number of populations included

 

African 17

African American 28

American Indian 24

Australoid 3

Austronesian 6

Central Asian 39

Central European 13

East Asian 39

East European 8

European American 24

Iberian 32

Iberian American 61

Jewish 3

Mediterranean European 20

Melungeon 1

Middle Eastern 36

North Asian 3

Northern European 15

Romani 4

South Asian 35

Southeast Asian 12

 

 

Beyond Megapopulations (and percentage of total populations) These categories correspond roughly to what people used to think of as "race," a now-discredited notion. They are continent-specific, with African and Caucasian extended to North and South American African and European populations.

 

African   45     11%  

 

Amerind   24    6%

 

Austral 9    2%

 

Asian  67    17%

 

Caucasian  255    64%

 

 

 

Another Calculation We created these totals to see what kind of white versus non-white coverage the database has.

 

White  255  64%

Non-White  145   36%

Total 400 Populations

And that's all you need to know about megapopulations! But in case you're still confused here are some useful links:

Metapopulation in Wikipedia

Autosomal DNA Based Populations in atDNA 4.0 (DNA Consultants)
405 Populations with links to further information in many cases

What Everyone Always Wanted: Our New Megapopulations Report

30-Nov-2011
After a lot of hard work, DNA Consultants has introduced "bottom l... (more)

New Megapopulations: The Bottom Line
17-Nov-2011
Work by our head of statistics over the summer has made it possible to... (more)

Population Pages Are Coming!
09-Apr-2012
Have you ever wanted to know more about the populations you match? May... (more)



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Charlene commented on 13-Apr-2012 01:03 PM

Glad to see the DNA Newsletter is still coming out. Have been missing it and looking for it to appear. Always some interesting things in it. Was pleased with the items I ordered from you a few months ago. Many thanks. Charlene

Arcpoint Labs of Overland Park commented on 16-Apr-2012 03:12 PM

Great site! Bookmarking it now!


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When Wales Was Jewish

Monday, April 02, 2012

Short answer: pre-Roman times.

As is well known, Haplogroup E1b1b1 accounts for approximately 18% to 20% of Ashkenazi and 8.6% to 30% of Sephardic Y-chromosomes. This North African type appears to be one of the major founding lineages of the Jewish population.[i]

In Britain, this quintessential Jewish type (together with J, another telltale sign of Middle Eastern roots) is absent or negligible in many towns and regions but reported in elevated frequencies in Wales (Llanidloes 7%, Llangefni 5%), the Midlands (Southwell, Nottinghamshire 12%, Uttoxeter 8%), Faversham in Kent (9%), Dorchester in the West Country with historic harbors (7%), Midhurst in West Sussex commanding ancient sea-ports (5%)  and the Channel Islands, always an important crossroads of influences (5%).[ii] Bryan Sykes’ survey of paternal clans in England and Wales confirms significant traces of the E haplogroup which he dubs Eshu in southern England (4.9%) and Wales (3.1%).[iii] It reaches its highest point in Britain in Abergele, Wales (nearly 40%), an anomaly that has been attributed to Roman soldiers of Balkan origin but may have alternative and more complex explanations.

See our blog post "Right Church, Wrong Pew," arguing that the footprint of E in Britain is attributable to North African influence, not the descendants of Roman legionnaires from the Balkans.

In 2011, Llangefni  and Wrexham in North Wales became the focus of a call for local men to provide samples of their unusual DNA. A team of scientists lead by Andy Grierson and Robert Johnston from the University of Sheffield hoped to link the migration of men from the Mediterranean to the copper mined at Parys Mountain on Anglesey and on the Great Orme promontory nearby. A preliminary analysis of 500 participants showed 30% of the men carried E1b1b, compared to 1% of men elsewhere in the United Kingdom.[iv]

Significantly, Welsh tradition associates the Iron Age hilltop town on Conwy Mountain known as Castell Caer Seion with a settlement of ancient Jews. This site overlooks Conwy Bay on the north coast of Wales and lies on the ancient road between Prestatyn in Denbighshire and Bangor in Gwynedd opposite Angelsey.  In the Black Book of Caermarthen, the Welsh national bard Taliesin casually remarks in the persona of the battling hero,

When I return from Caer Seon,

From contending with Jews,

I will come to the city of Lleu and Gwidion.[v]

Lleu and Gwidion are the names of two other legendary figures; they are believed to be historical and to have lived in the early centuries of the Common Era or anterior to it.

It is hard to avoid the thought that the hilly area to the west of the town of Conwy, in North Wales was once inhabited by Jews.


[i] A. Nebel et al, "The Y Chromosome Pool of Jews as Part of the Genetic Landscape of the Middle East", American Journal of Human Genetics69.5(2001) 1095–1112. [ii] C. Capelli et al, “A Y Chromosome Census of the British Isles,”  Current Biology 13 (2003) 979–984. [iii] Bryan Sykes, Saxons, Vikings and Celts (Norton:  2007) 206, 290. [iv] “’Extraordinary’ Genetic Make-up of North-east Wales Men,” BBC News North East Wales, article retrieved Jan. 2012 at http://www.bbc.co.uk/news/uk-wales-north-east-wales-14173910. On Dienekes’ Anthropology Blog there is speculation about whether the main sub-clade involved is Balkan or North African E; posts and comments retrieved Jan. 2012 at http://dienekes.blogspot.com/2011/07/eastern-mediterranean-marker-in.html. [v] William F. Skene, The Four Ancient Books of Wales (Edinburgh, 1868, republished 2007 by Forgotten Books) 206.
Comments

Stephen Blevins commented on 03-Apr-2012 05:02 AM

My DNA is E1b1b1, my most distant ancestor is William Blevins (Longhunter) from the area you mentioned. My autosomal DNA places my ancestors in the orkney islands of Scotland. I'm convinced that a tribe of Jews migrated from Israel to north to Scandinavia
or Denmark and may have been apart of the invasion by Vikings to Scotland before they were found in Wales as Poweys in the Northern Mountains. Blevins comes from Blethyn meaning little wolf or (Hero) look up Ap Blethyn of Gwynedd.

Belvins Descendant commented on 12-Apr-2012 02:05 PM

I was always told the Blevins came from Wales, but in checking this story out I was unable to verify it, nor could I find any substantiation of the etymology from Bleddyn ("son of wolf"). There is not a single Blevins in the Welsh census records, although
the name is found sparsely in Cheshire, Lancashire and other northern English counties. "Formby, Wales" is actually Formby in Merseyside in Lancashaire. The -dd- element in the Welsh name Bleddyn cannot be twisted into a -v-. So go figure.

Paul commented on 28-Apr-2012 08:46 PM

My mother is a descendant of Henry Cook I of Devon. His ascendants were among the first settlers of Massachusetts and Connecticut. A great Uncle, Lemuel Cook, was the oldest surviving Revolutionary War veteran when he died at 106 years of age. We recently
had my mother's autosomal dna analyzed and found strong population matches from the Balkans (Croatia, Bosnia, Macedonia, Serbia, etc.) - which was very unexpected. There was also prominent representation form Spain and Portugal - not so unexpected. In my own
18 marker test, I had one Jewish III marker, though I can't say from whom. There is no known Judaism on either side. Sounds like your article might be describing the early Cooks. Interesting...


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