Quotulatiousness

September 12, 2012

Richard III’s remains may have been found in Leicester

Filed under: Britain, History — Tags: , , , , — Nicholas @ 09:17

Fascinating announcement today from the dig site:

11.12: He says one skeleton and other human remains have been found and a barbed metal arrowhead was found between vertebrae of the skeleton’s upper back. The arrow was near the spine, but not embedded in the bones.

11.15: Mr Taylor says that an articulated skeleton has been found that is of significant interest to us. Scientists have also found a set of “disarticulated human remains” but because they are female and therefore not Richard III.

The skeleton shows signs of “near death trauma” that “appears to be consistent with injury from battle”. Scientists now hope to extract DNA from the bones.

He added:

“It also has spinal abnormalities and an individual form of spinal curvature, which makes his right shoulder visibly higher than his left shoulder. We believe the individual would have had severe scoliosis. The skeleton was not a hunchback.”

It is consistent with other accounts of Richard III.”

It is now at an undisclosed laboratory where it is going through “rigorous” testing.

September 6, 2012

It’s time to retire the pop-sci term “Junk DNA”

Filed under: Health, Science — Tags: , , — Nicholas @ 08:42

In the Wall Street Journal, Gautam Naik and Robert Lee Hotz report on the most recent discoveries about the human genome:

The new insight is the product of Encode, or Encyclopedia of DNA Elements, a vast, multiyear project that aims to pin down the workings of the human genome in unprecedented detail.

Encode succeeded the Human Genome Project, which identified the 20,000 genes that underpin the blueprint of human biology. But scientists discovered that those 20,000 genes constituted less than 2% of the human genome. The task of Encode was to explore the remaining 98% — the so-called junk DNA — that lies between those genes and was thought to be a biological desert.

That desert, it turns out, is teeming with action. Almost 80% of the genome is biochemically active, a finding that surprised scientists.

In addition, large stretches of DNA that appeared to serve no functional purpose in fact contain about 400,000 regulators, known as enhancers, that help activate or silence genes, even though they sit far from the genes themselves.

The discovery “is like a huge set of floodlights being switched on” to illuminate the darkest reaches of the genetic code, said Ewan Birney of the European Bioinformatics Institute in the U.K., lead analysis coordinator for the Encode results.

August 31, 2012

The search for the burial place of Richard III

Filed under: Britain, Cancon, History — Tags: , , , , , — Nicholas @ 07:40

Elizabeth sent me another link on the ongoing archaeological search for the burial place of King Richard III:

A high-profile search for the gravesite of the 15th-century monarch King Richard III — begun Saturday beneath a parking lot in the English city of Leicester — has a remarkable connection to a Canadian family whose members hold the genetic key to solving one of British history’s most enduring mysteries: Where is Richard III’s body?

The London, Ont.-based Ibsen family, recently proven to be descended from King Richard’s maternal line, has provided DNA samples aimed at confirming the regal identity of any human remains found during the unprecedented dig, which continues this week at the former site of a medieval church where — 527 years ago — the violently overthrown monarch was buried.

The University of Leicester-led archeological project was launched after the discovery that the maternal bloodline of the last Plantagenet king — killed in 1485 in the climactic battle of the War of the Roses — survived into the 21st century through Joy Ibsen, a British-born woman who immigrated to Canada after the Second World War and raised a family in southwestern Ontario.

If nothing else, the media coverage of this dig may generate lots of new members for the Richard III Society (Canadian branch, American branch).

June 27, 2012

California primed to make bad decision for “good” reasons

Filed under: Environment, Food, Government, Health, Science, USA — Tags: , , , , — Nicholas @ 00:05

California’s already bad economic situation could be made even worse by mandating that genetically modified foods be labelled to call attention to themselves:

The American Medical Association resolved this week that “there is no scientific justification for special labeling of bioengineered foods.”

The association has long-held that nothing about the process of recombinant DNA makes genetically engineered (GE) crop plants inherently more dangerous to the environment or to human health than the traditional crop plants that have been deliberately but slowly bred for human purposes for millennia. It is a view shared by the National Academy of Sciences, the World Health Organization, the Food and Agriculture Organization of the U.N., the European Commission, and countless other national science academies and non-governmental organizations.

And yet Californians will consider on their November ballots a law that mandates cigarette-like labeling of food derived from GE plants. Proponents claim to promote opportunities for consumers to make informed choices about the foods they eat. But to build support for the measure, they have played on consumer fears about a promising technology that is nevertheless prone to “Frankenfoods” demagoguery. If successful, they may well imperil the ability of Californians, and consumers around the world, to choose a technology that scientists contend could end hunger and malnutrition, lift hundreds of millions from poverty, and reduce the environmental impact of feeding an evermore populous world.

March 10, 2012

Some diseases may be caused by “endogenous” retrovirii

Filed under: Health, Science — Tags: , , , , — Nicholas @ 12:17

Matt Ridley on some recent discoveries in genetics and medicine that may help to explain certain diseases like multiple sclerosis:

The virus implicated in multiple sclerosis is called HERV-Fc1, a bizarre beast called an “endogenous” retrovirus. What this means is that its genes are part of the human genome. For millions of years, they have been integrated into our own DNA and passed on by normal heredity. It was one of the shocks of genomic science to find that the human genome contains more retroviral than “human” genes: some 5% to 8% of the entire genome.

Normally, the genes of endogenous retroviruses remain dormant, but — a bit like a computer virus that springs into action on a trigger — something wakes them up sometimes, and actual viruses are made from them, which then infect other cells in the body. The Danish scientists suggest that this is what happens in multiple sclerosis. Bjørn Nexø of Aarhus University writes that “retroviral infections often develop into running battles between the immune system and virus, with the virus mutating repeatedly to avoid the immune system, and the immune system repeatedly catching up. One can see the episodic nature of multiple sclerosis as such a running battle.”

The possibility that you can inherit the genes of a virus blurs the distinction between a genetic and an infectious disease. The HERV-Fc1 genes lie on the X chromosome. Since women have twice as many X chromosomes as men, this might explain why some forms of MS are more common in women. Dr. Nexø concludes hopefully: “The finding that a disease is caused by an infectious agent is an encouraging one. These are the diseases which we know best how to treat.

The research also appears to show a link between cat ownership and schizophrenia:

Human beings can also catch toxoplasma from cats, and it’s known to affect behavior: altering personalities, slowing reaction times and increasing the risk of car accidents. More than 20 studies have now found an association between schizophrenia and toxoplasma. Schizophrenia is more common among those who had pet cats in their childhood homes (but not in those who had pet dogs).

Indeed, some scientists think that schizophrenia only became common, around 1870, when keeping cats as indoor pets became fashionable. The parasite has genes for dopamine, a neurochemical found in excess in schizophrenics.

July 22, 2011

Mark Lynas goes from green activist to “denier”

Filed under: Books, Environment, Media, Politics — Tags: , , , — Nicholas @ 09:28

Ben Pile reviews Mark Lynas’s new book:

Since becoming an advocate of genetic modification (GM) and nuclear power, Mark Lynas has drawn increasingly hostile criticism from his erstwhile comrades in the green movement. In turn, he has sharpened his criticism of environmentalists for their hostility to technological and economic development. In his new book, The God Species: How the Planet Can Survive the Age of Humans, he attempts to reformulate environmentalism to overcome the excesses that have so far prevented it from saving the planet. This book will no doubt provoke debate, but what is this transformation really about, and is it really based on new ideas or merely the revision of old ones?

[. . .]

As a result, there is much to agree with in The God Species. Most importantly, Lynas makes a clean break from deep ecology — the idea that ‘nature’ has intrinsic moral value and a ‘right’ to be protected from our ambitions. He rebukes the environmentalism that imagines a return to a pristine nature, and that shows contempt for development as an attempt to ‘play god’ over nature. We should ‘play god’, he says, for the planet’s sake as well as our own comfort. There is a convincing criticism of green demands for austerity and environmentalists’ unrealistic expectations that people should make do with ‘happiness’ rather than material progress. These are the conceits of well-off, middle-class and self-indulgent whingers, Lynas explains. Some of us have been making similar arguments for a very long time.

In spite of some of his accurate criticisms, Lynas fails to get to the substance of environmentalism. We do not find out what takes environmentalists to their bleak view of the world and their low view of humanity. This is a shame, because Lynas is in a unique position to reflect on it, having once thrust a custard pie into Bjorn Lomborg’s face, with the words: ‘That’s for everything you say about the environment which is complete bullshit. That’s for lying about climate change. That’s what you deserve for being smug about everything to do with the environment.’

A decade on, Lynas now emphasises science and pragmatism rather than… erm… pies. It’s worth remembering that Lomborg started out on mission similar to Lynas’s: as an environmentalist, keen to establish the sensible limits of our interaction with the natural world. Before writing The Skeptical Environmentalist, Lomborg aimed to debunk the works of the economist, Julian Simon, but ended up sympathetic to many of his arguments. Lynas, too, now finds himself sympathetic to many of the ideas from the economic right (he calls for the privatisation of all publicly owned water companies, for instance). And like Lynas, Lomborg never ended up ‘denying’ climate change, but instead sought to bring a sense of proportion to the problem, and to put it into context with other problems in the world. That is all it takes to find oneself called a ‘denier’: merely seeking a sense of proportion about environmental problems will put you in the lowest moral category, as Lynas, the ‘Chernobyl death denier’, has now discovered.

January 25, 2011

The genomic treasure trove of Quebec

Filed under: Cancon, History, Science — Tags: , , , — Nicholas @ 07:36

Thanks to relatively thorough genealogical records, the people of Quebec are of great and growing interest to genetic researchers:

One of the great things about the mass personal genomic revolution is that it allows people to have direct access to their own information. This is important for the more than 90% of the human population which has sketchy genealogical records. But even with genealogical records there are often omissions and biases in transmission of information. This is one reason that HAP, Dodecad, and Eurogenes BGA are so interesting: they combine what people already know with scientific genealogy. This intersection can often be very inferentially fruitful.

But what about if you had a whole population with rich robust conventional genealogical records? Combined with the power of the new genomics you could really crank up the level of insight. Where to find these records? A reason that Jewish genetics is so useful and interesting is that there is often a relative dearth of records when it comes to the lineages of American Ashkenazi Jews. Many American Jews even today are often sketchy about the region of the “Old Country” from which their forebears arrived. Jews have been interesting from a genetic perspective because of the relative excess of ethnically distinctive Mendelian disorders within their population. There happens to be another group in North America with the same characteristic: the French Canadians. And importantly, in the French Canadian population you do have copious genealogical records. The origins of this group lay in the 17th and 18th century, and the Roman Catholic Church has often been a punctilious institution when it comes to preserving events under its purview such as baptisms and marriages. The genealogical archives are so robust that last fall a research group input centuries of ancestry for ~2,000 French Canadians, and used it to infer patterns of genetic relationships as a function of geography, as well as long term contribution by provenance.

August 5, 2010

Examining DNA testing from the client’s point of view

Filed under: Bureaucracy, Government, Health, Media, Science — Tags: , , , — Nicholas @ 07:19

Mary Carmichael is writing a multi-part series about DNA testing:

On July 22, Congress held a hearing on direct-to-consumer (DTC) genetic tests, services that analyze your DNA and interpret the results in exchange for a few hundred bucks — no doctor necessary. The hearing could have been a thoughtful national conversation about science, business, and ethics. Alas, it devolved instead into a series of gotcha moments, starring a General Accounting Office sting operation that came off like a cross between the ACORN videos and the world’s worst ad for snake oil.

Time and again, on tape, an undercover agent called up an unidentified testing company and asked an ill-informed question. (“Is it OK if I stop taking my cholesterol meds and instead take the nutritional supplements you sell? If I can manage to get hold of my fiancé’s saliva without him knowing, will you run it through your machines so I can surprise him with the ‘gift’ of his own data?”) And time and again, the phone rep sank to the occasion and made the company look awful. (Sure, lay off the pills and take our supplements! Of course we’ll analyze your fiancé’s spit without his permission even though that’s illegal, unethical, and weird!)

I listened to the tape several times the day it was released, despairing at the way people were taking advantage of gullible, albeit fictional consumers, which was clearly how the congressmen who held the hearing wanted me to react. Then I started to worry about something else. How much time did I even have left to decide whether I was going to take a test myself? Even before the hearing, the FDA had announced its plans to regulate all DTC genetic tests, possibly so heavily as to keep them off the market; the hearing was just the sort of thing that could push it to move faster. What if, by the time I finally decided if I wanted one of these tests, I couldn’t buy one anymore? My credit card was sitting next to my laptop. I did something that in retrospect seems a bit rash. There’s a DNA-collection kit on my desk now, taunting me — because although I bought the thing, I still can’t decide whether I actually want to use it.

The sheer volume of misinformation on DNA testing — combined with public belief in the amazing accuracy of DNA testing (probably induced by watching too many crime investigation TV shows) — leaves the legitimate companies in an awkward situation. The actual DNA self-tests don’t tell you what you might expect, and can tell you things you don’t want to know. Politicians jumping in now (at the prompting of bureaucrats who want more power to regulate) will only make the situation more confused.

H/T to BoingBoing for the link.

May 26, 2010

Evolutionarily speaking, everything old is new again

Filed under: Science — Tags: , , , , , — Nicholas @ 12:46

An idea that seemed fairly common in the 1960s and 70s appears to be regaining credibility:

When two drunken men fight over a woman, alcohol and stupidity may not be the only things at work. Sadly, evolution may have shaped men to behave this way. Almost all of the traits considered to be masculine — big muscles, facial hair, square jaws, deep voices and a propensity to violence — evolved, it now seems, specifically for their usefulness in fighting off or intimidating other men, allowing the winner to get the girl.

That, at least, is the contention of David Puts, an anthropologist at Pennsylvania State University, in an upcoming paper in Evolution and Human Behavior. Dr Puts is looking at how sexual selection gave rise to certain human traits. A trait is sexually selected if it evolved specifically to enhance mating success. They come in two main forms: weapons, such as an elk’s horns are used to fight off competitors; and ornaments, like a peacock’s tail, which are used to advertise genetic fitness to attract the opposite sex.

Researchers have tended to consider human sexual selection through the lens of the female’s choice of her mate. But human males look a lot more like animals designed to battle with one another for access to females, says Dr Puts. On average, men have 40% more fat-free mass than women, which is similar to the difference in gorillas, a species in which males unquestionably compete with other males for exclusive sexual access to females. In species whose males do not fight for access to females, males are generally the same size as, or smaller than, females.

April 13, 2010

QotD: Bugs in the DNA

Filed under: Africa, Food, Quotations, Science — Tags: , , , — Nicholas @ 12:09

Desmond Morris is a zoologist and the author of The Naked Ape. It is his idea that many of the otherwise inexplicable quirks we see in ourselves are leftovers, the result of our evolutionary heritage. Take that business with the bugs, for instance. Any time our higher cognitive processes get shut down, by panic, fatigue, or simply boredom, we humans have a tendency to revert to earlier, prehuman behavior.

Our early ancestors in Africa were arboreal troop-monkeys, living on a diet of fruit (to quote Yogi Bear, “Nut and berries! Nuts and berries! Yech!”) and insects. When you wander around the house, not particularly hungry, but looking for something to munch on idly, what you are most likely seeking unconsciously are bugs. Most of our most popular snack foods (Fiddle-Faddle comes to mind, and small pretzels) resemble and have the same “mouth feel” as bugs. You can take the monkey out of the trees, but you can’t take the tree monkey out of humanity.

L. Neil Smith, “Back to the Trees!”, Libertarian Enterprise, 2010-04-11

November 3, 2009

Challenge to human gene patents allowed to proceed

Filed under: Law, Science — Tags: , , , , — Nicholas @ 08:25

A judge has allowed an ACLU challenge to two human gene patents to go to court:

The first-of-its-kind lawsuit by the American Civil Liberties Union and the Public Patent Foundation at the Benjamin Cardozo School of Law claims that the patents violate free speech by restricting research.

U.S. District Judge Robert W. Sweet of New York, in ruling that the case may proceed to trial, noted that the litigation might open the door to challenges of a host of other patented genes. About one-fifth of the human genome is covered under patent applications and claims.

Sweet wrote:

The challenges to the patents-in-suit raise questions of difficult legal dimensions concerning constitutional protections over the information that serves as our genetic identities and the need to adopt policies that promote scientific innovation and biomedical research. The widespread use of gene sequence information as the foundation for biomedical research means that resolution of these issues will have far-reaching implications, not only for gene-based health care and the health of millions of women facing the specter of breast cancer, but also for the future course of biomedical research.

The case against the patent office and patent-holder Myriad Genetics of Salt Lake City is the first to challenge a patented gene under a civil rights allegation — in this case the First Amendment.

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