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

Is There an Irony Gene?

Thursday, December 13, 2012
Richard Lewontin's Disappearing Act

The octogenarian bête noir of biological determinism reviews three new books about why we should be proud of our ancestry--or just be quiet about it. "There is a certain irony," he writes, "in claiming an undemonstrated biological superiority for a group, six million of whom were slaughtered for their claimed natural degeneracy." If your dynosaur feathers are not ruffled yet, read on. 

"Is There a Jewish Gene?"

by Richard Lewontin

December 6, 2012,

The New York Review of Books


Legacy:  A Genetic History of the Jewish People
by Harry Ostrer
Oxford University Press, 264 pp. $24.95


The Genealogical Science:  The Search for Jewish Origins and the Politics of Epistemology
by Nadia Abu El-Haj
University of Chicago Press, 311 pp., $35.00



Zionism and the Biology of the Jews (Zionut Vehabiologia Shel Hayehudim

by Raphael Falk
Resling, 2006 (not yet published in English)
Richard Lewontin.
Courtesy Istituto Veneto.

The question of ancestry has been of human concern in virtually all cultures and over all times of which we have any knowledge. Whether it be a story about the origin of a particular tribe or nation and its subsequent mixture with other groups, or curiosity about a family history, there is always the implication that we understand ourselves better if we know our ancestors and that we, within ourselves, reflect properties that have come to us by an unbroken line from past generations. As treasurer of the Marlboro Historical Society in Vermont, I am the recipient of requests for printed copies of the Reverend Ephraim Newton’s mid-eighteenth-century history of our town, 70 percent of whose pages consist of “Genealogical and Biographical Notes” and a “Catalog of Literary Men.” Over and over our correspondents write of the “pride” they have in descending from these early settlers.

Surely pride or shame are appropriate sentiments for actions for which we ourselves are in some way responsible. Why, then, do we feel pride (or shame) for the actions of others over whom we can have had no influence? Do we, in this way, achieve a false modesty or relieve ourselves of the burdens of our own behavior? As a descendant of late-nineteenth-century Eastern European immigrants I cannot depend on Reverend Newton’s pages to explain my frequent contributions to The New York Review, but neither have the extensive “begats” in Genesis 10 or Matthew 1 been more enlightening.  Read More...

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Fifteenth Anniversary of New Genome Sequencing

Monday, November 21, 2011

At a time when it seemed that American science had bitten off more than it could chew with the Human Genome Project, Craig Venter and his innovative company published "A New Strategy for Genome Sequencing." Appearing in the journal Nature in 1996, the Venter multi-center approach bypassed laborious gene mapping and allowed the HGP to meet its goal of full sequence information on the human genome in 2000.

"In the race to sequence the human genome," write the editors of Nature's DNA Technologies Milestones, "research groups had to choose between the random whole genome shotgun sequencing approach or the more ordered map-based sequencing approach." The choice of randomness versus order was present from 1982, but the Venter strategy was resisted for many years. Finally, in 1996 it was accepted and given an equal emphasis with the more orthodox approach.

After a standoff between the two groups of scientists, "a showdown ensued, with the biotechnology firm Celera Genomics wielding whole-genome shotgun sequencing and the International Human Genome Sequencing Consortium wielding map-based sequencing. Yet when the dust settled, it was a draw -- both groups published their initial drafts of the human genome concurrently in 2001."

The maverick technology helped make high throughput genomic sequencing at commercial labs an economy reality and gave birth to a range of new DNA tests within the reach of ordinary consumers like you and me. Today, fifteen years later, those interested in autosomal ancestry testing and personal genomics have biologist and entrepreneur Craig Venter and his irascible persistence as a scientific pioneer to thank.




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Are We Gazing into Crystal Ball or Navel?

Saturday, February 05, 2011
Science 4 February 2011:
Vol. 331 no. 6017 p. 547
DOI: 10.1126/science.1202571

Genome-Sequencing Anniversary

The Golden Age of Human Population Genetics 

By Molly Przeworski

Professor, University of Chicago, Chicago, IL, USA, Howard Hughes Medical Institute Early Career Scientist

Figure
N. KEVITIYAGALA/SCIENCE

The first draft of the genome provided the road map for the past decade of research in human genetics, allowing for the design of platforms that have been used to query variation in populations worldwide and helping to drive down the cost of sequencing by several orders of magnitude. Within years, tens of thousands of complete genome sequences will be available from humans and from extinct hominids, as well as from thousands of other species. Given the human mutation rate, we will soon know of variation among individuals at almost all sites in the genome. For population genetics, this ushers in a previously unimaginable opportunity to reconstruct the entire genealogical and mutational history of humans and pushes us against the limits of what we will be able to infer about the evolutionary and genetic forces that affected every region of the genome. Why are disease mutations present in human populations? What is the genetic basis of our cognitive and physiological adaptations? What was the sequence of demographic events that led to the colonization of the globe by modern humans? Stay tuned, and before long, we should know as much as genetic data alone can tell us.

Yes, we've heard exalted claims before, like 10 years ago, when the next phase of the Human Genome Project was to be devoted to the "conquest" of disease. How many diseases have been conquered in 10 years, after billions of research dollars? Guess. None. And as far as population genetics goes, the whole story of "classic" Darwinian evolution seems to be unraveling before our eyes with every passing month (except of course in textbooks and the creationist opposition, where it never changes). If we can't be sure about evolution, how can we decide what is true about early human migrations?

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DNA Was Invented by Watson and Crick in 1953, Right?

Wednesday, December 15, 2010

Wrong. According to a correction in Nature, it was discovered by Swiss physician Friedrich Miescher in 1869, nearly a hundred years before. James Watson, Francis Crick and the less often mentioned Rosalind Franklin were responsible for determining DNA's structure, a double helix shape.

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Is Evolution Still Occurring? In New York? London? Santa Monica?

Tuesday, December 14, 2010
What Happens When 'Pressure of Natural Selection' Ceases?

Maybe I do not understand "classic Darwinism," but I am puzzled by the claims of numerous articles in leading scientific journals that evolutionary change in human beings is "accelerating." Since when? One such article was published several years ago by the National Academy of Sciences, "Recent Acceleration of Human Adaptive Evolution." It claims an acceleration in evolution in the last 1000 years, on an inferred and theoretical, not observed basis, needless to say. Its projections are based on the 4 million SNP database called HapMap, a collection of mostly European and American gene irregularities. Several books and a slew of articles in journals like Nature and Science have jumped on the scientific bandwagon. But we have a few embarrassing questions.

If the "classic" model of Darwinism was based on primitive man, New Guinea orchids and Galapagos turtles, wouldn't we need to redefine what selection and survival of the fittest and its other tenets really mean for, say, a Harvard or Stanford white male Ph.D. who sits in front of his computer most of the time or the current population of the United States, few of whom qualify as hunter-gatherers or tribal or starved or threatened by predators?

Isn't there rather a disconnect today between surviving and your genetic composition? Pretty much anyone can marry and have children with pretty much anyone they want to, and few people are dying off without issue from bad genes or fatal decisions.

If genes are supposed to mutate and produce more "fit" and eligible marriage partners because of "pressure" from the environment like drought or low-protein diets or too much or too little sunshine, how does evolution operate on a level playing field where the environment is a shopping mall or suburbia?

World population has increased from 200 million in the year 1 to nearly 7 billion. Perhaps the presumed rise in SNPs is an effect of population growth? Evolution was supposed to operate on the basis of selection, not indiscriminate proliferation.

Evolution, it is claimed, has now sublimated beyond the physical realm. It is internal, or mental, or spiritual, or cultural, or social, or political, or even (God help us) scientific. This was the super-clever dodge favored by Teilhard du Chardin, a Catholic missionary to China who wrote The Phenomenon of Man. He called it the noosphere. Whatever else, this latest Big Science Fair project requires a new definition. There are no measures possible beyond our present lifetime. We have no way of judging a Neanderthal's consciousness.

I'm sorry but I just don't get it. I wish someone would please explain it to me so I do not need to feel guilty about not reading all those pat-me-on-the-back and pip-pip-don't-you-know-old-man Victorian recidivist articles that I find, somehow, very self-serving.

I am an avid follower of the Darwin Awards but the only thing I can see accelerating are modern American and European scientists' delusions of grandeur.

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Archeology from Non-Archeology

Wednesday, April 07, 2010

The explosion in commercial archaeology has brought a flood of information. The problem now is figuring out how to find and use this unpublished literature, reports Matt Ford in the current issue of Nature magazine.

"I became aware that what I was teaching would be out of date without looking at the grey literature (unpublished reports)," says one professor at the University of Reading in England.

A policy shift in 1990 required all construction projects to document archaeological remains in Britain and generated an avalanche of findings that cannot be absorbed by the official academic field. The result is that our picture of the past is very much outdated. Academia is not likely ever to get caught up. Nor are academicians ever likely to warm to new theories of population genetics like diffusionism and trans-Oceanic contact and colonization, since few of those theories ever received a hearing in the halls of academe in the first place.

Read the full story in Nature, "Archaeology:  Hidden Treasure."

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Officious or Official Regulation?

Thursday, October 22, 2009
Council of Europe adopts protocol on genetic testing for health purposes

In a report so-titled by Laurence Lwoff in the European Journal of Human Genetics (2009) 17, 1374–1377, first published online in July, it was noted that the Council of Europe has weighed in on one of the most controversial areas of DNA testing, whole-genome sequencing and SNP testing to find genetic predisposition to disease for individual customers. Recent editorials in Nature have called for similar measures in the United States, which is home to 23&me and other companies offering such services.

So far, no regulatory proposals have been aimed at genetic ancestry testing, only medical and health-related screening. One of the warnings often raised in the public discussion on genetic testing for health purposes, however, is that results may confuse and unnecessarily alarm consumers--a criticism that could apply equally to ancestry services.  Another is that commercial research scientists and business operators may jump the gun with findings and peddle bad science, although critics admit that the state of knowledge on nearly every topic of interest to geneticists and medical researchers is in a constant state of flux. A finding about a gene for Alzheimer's will be trumpeted in the pages of a major journal one week only to be updated or withdrawn in the next. 
 
This being the case, one wonders when discoveries will ever be fit to be commercialized or made available to the public. Should science only serve scientists?

We have always maintained that the would-be regulators underestimate moderately educated people's ability to understand emerging science. They overestimate commercial companies' disregard for professional practices and responsible communications. Most of the measures under discussion will have the effect of denying people access to valuable information. Regulation will also hamper growth in a direct-to-the-consumer business with unimaginable promise for society at large. A home paternity test purchased at the corner drugstore may make all the difference in the life of a family. Discovery of varied ancestry through a DNA test can be an important factor in furthering a consumer's interest in other peoples and countries, in history, and ultimately in tolerance of others. DNA testing can help bring peace of mind but it can also help bring peace in the world. 

Many, if not most, of the innovative contributions to society by science have come from non-specialists. The scientific establishment is not oriented toward practical applications of knowledge. The Croatian inventor and engineer Nikola Tesla dropped out of college and never received any formal training. Driven entirely by his natural aptitude for learning, he patented some of the most important contributions to the birth of commercial electricity, including alternating  current (AC) electric power systems and the AC motor. His inventions helped usher in the Second Industrial Revolution. So far from being overpowered by the profit motive, he died penniless at the age of 86 in 1943. No government program or university gave him any support or assistance. Whatever else the Council of Europe deliberated about, we hope they were not cynical or self-important enough to discount the possibility there may be many more popular scientists like Tesla in Europe's future. Science and technology are increasingly becoming a way of life for millions of people around the world who do not happen to have an advanced degree. It is a positive sign that consumers are so eager to take responsibility for their own health they will use the latest innovations from genomics to gain knowledge and control. Scientists should be glad they have such an impact. They should not squander the respect they enjoy in our eyes with pedantic discussions about fixing something that is not broken.  

Isolated populations as treasure troves in genetic epidemiology:  the case of the Basques

Paolo Garagnani et al. (2009) in European Journal of Human Genetics 17: 1490-1494.

The Basques living on the western border between Spain and France are a unique population. "Basques" often comes up as a match in people's DNA Fingerprint results, often because (as is widely believed, at least) a people resembling Basques helped repopulate the British Isles after the last Ice Age. But Basques are not an isolate. This article proves they blend gradually into their closest neighboring populations in Spain and France so they are not a candidate population, as say the Finns are, for the study of disease associations. "Basques do not show the genetic properties expected in population isolates," according to the authors. On the contrary, as many previous studies suggest, the Basques have so much diversity among themselves they were probably the source of population diffusions in prehistory, not a backwater trap for inbreeding.
  
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Anonymous commented on 22-Oct-2009 11:28 PM

This is most perplexing and sounds medieval. Does the Council of Europe think we are all children? Are they truly concerned that their citizens may become confused and alarmed? What planet are they living on currently? I suppose they are unaware (or have forgotten) that Darwin had a background in religion (how alarming). This is 2009 and the world is an alarming place. One gets rather used to it though after a number of years. There must be some other reason than this for their suggested protocol. Something truly alarming.


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