While a certain bacterium that can thrive in arsenic has dominated the science press this week, the big story in the world at large is on the ongoing WikiLeaks saga. The release of an enormous trove of confidential documents from the U.S. State Department has provoked plenty of fall-out: there’s governmental embarrassment and anger, and WikiLeaks founder Julian Assange is now wanted in Sweden on alleged sex crimes. But we’re most interested in how the never-ending story touches several science and tech stories, some of which have unraveled here on 80beats.
Get That DNA
One embarrassing revelation of the leaked diplomatic cables was that American diplomats were supposed to be part spy; they were asked to try to gather genetic material from foreign governmental officials. Once the cables leaked, the State Department couldn’t exactly deny that this happened, but it now says that these suggestions came from intelligence agencies. And relax—the requests were voluntary.
A senior department official said the requests for DNA, iris scans and other biometric data on foreign government and U.N. diplomats came from American “intelligence community managers.” The official said American diplomats were free to ignore the requests and that virtually all do. [Washington Post]
China Source of Google Hack
Early in 2010 we reported on the large cyber-attack against Google. Though rumors swirled, the Chinese government denied its involvement; the country and the search engine giant went through months of tension before arriving at a truce in the summer. According to WikiLeaks, leaders of the Chinese Communist Party were directly connected to the hack.
China’s Politburo directed the intrusion into Google’s computer systems in that country, a Chinese contact told the American Embassy in Beijing in January, one cable reported. The Google hacking was part of a coordinated campaign of computer sabotage carried out by government operatives, private security experts and Internet outlaws recruited by the Chinese government. [The New York Times]
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The science world is abuzz with news of a strange new life form found in California’s Mono Lake: Researchers report that they’ve discovered a bacterium that can not only thrive in an arsenic-rich environment, it can actually use that arsenic to build its DNA. If the researchers, who published their findings in Science, are correct, then they’ve found a form of life unlike anything we’ve ever seen before.
As you might expect, DISCOVER’s blogs offered plenty of coverage of this exciting news.
At The Loom, Carl Zimmer writes: “Scientists have found a form of life that they claim bends the rules for life as we know it. But they didn’t need to go to another planet to find it. They just had to go to California.”
At Bad Astronomy, Phil Plait explains exactly how the bacteria can make use of arsenic to build their DNA. A few days ago, Phil also took NASA to task for its press release promising news of “an astrobiology finding that will impact the search for evidence of extraterrestrial life,” which fueled wild speculation on whether NASA had found little green men in the solar system.
At Not Exactly Rocket Science, Ed Yong debunks a few of the more breathless accounts. The bacteria do not “belong to a second branch of life on Earth…. They aren’t a parallel branch of life; they’re very much part of the same tree that the rest of us belong to. That doesn’t, however, make them any less extraordinary.”
At Gene Expression, Razib Khan has more thoughts on the wild speculation that preceded the announcement–which he compares to the hype surrounding the unveiling of the Segway.
Related Content:
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80beats: Do Asphalt-Loving Microbes Point the Way to Life on Titan?
80beats: Arsenic-Eating Bacteria May Resemble Early Life on Primordial Earth
DISCOVER: Renewed Hope for Life on the Red Planet
From Ed Yong:
The vast majority of people who are infected with HIV go on to develop AIDS. Their bodies become riddled with the virus, their immune systems falter, and they are besieged by life-threatening infections. But not everyone shares the same fate. Around 1 in every 300 people infected with HIV carry genetic trump cards that allow them to resist and control the virus. These “HIV controllers” can live with the virus for years. They never develop AIDS and they live long, healthy lives, even if they never take any medication. Their genetic secrets are slowly being revealed.
Researchers studying thousands of people with HIV, some with the controllers and some without, found something surprising:
Amazingly, every single one of these variants sits within a specific part of our sixth chromosome, among a set of genes called class I HLA genes. The proteins they produce form part of the internal security checks that defend us from infections. They grab small pieces of other proteins from inside our cells and display them on the outside, waving them under the noses of passing T-cells. If the T-cells recognise these pieces as parts of bacteria, viruses or other foreign invaders, they tell the infected cell to self-destruct and set the immune system on red alert.
Check out the rest of this post at DISCOVER blog Not Exactly Rocket Science.
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Image: Wikimedia / HIV Budding
Rosalind Franklin would probably not have appreciated her posthumous reputation. First there was the colossal insult of being denied due credit for her role in the discovery of DNA’s double helix shape, a breakthrough that revealed not only the form of our genetic material, but also how it functioned. James Watson and Francis Crick received the lion’s share of the glory for that finding, and for decades Franklin was a historical footnote.
But it seems likely that this no-nonsense scientist wouldn’t have appreciated being reduced to a feminist cartoon either–more recently, she’s been held up as an example of a woman crushed by the good old boys network.
That’s why a new play at New York’s Ensemble Studio Theatre is so necessary, and so right on the money. The play, called Photograph 51, honors Franklin’s achievements and rues her relative obscurity, but it also returns to her the ambiguities and complexities that a real human being deserves.
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Almost 50 years after they won the Nobel Prize for defining the structure of DNA, Maurice Wilkins, James Watson, and Francis Crick are in the news again.
Nine boxes of “lost” correspondence (from the days before email!) between two competing groups of researchers have been unearthed. The letters, between Wilkins and Rosalind Franklin of King’s College and Watson and Crick at Cambridge University, provide insight into the researchers’ mindsets while they were making these historic, game-changing discoveries.
“The [letters] give us much more flavor and examples illuminating the characters and the relations between them,” said study researcher Alexander Gann, editorial director at Cold Spring Harbor Laboratory Press in New York. “They’re consistent with what we already believed, but they add important details.” [MSNBC.com]
Gann and Jan Witkowski published a commentary on the new material in the September 30 issue of Nature. The letters highlight the different mentalities between the two groups as they approached the project: an attitude of spirited excitement on the side of the Cambridge clan, and an air of anxiety from Wilkins.
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Is it medicine, or is it not?
In May, the University of California, Berkeley unveiled its “Bring Your Genes To Cal” program. The idea was, Berkeley’s 5,500 or so incoming freshman would have the option to have their DNA tested for three particular characteristics: Their metabolism of folate, tolerance of lactose, and metabolism of alcohol. Though the program was limited, it raised privacy hackles. And now the State of California has ruled: This is a medical test, and Cal can’t do it unless it’s in a clinical setting.
Mark Schlissel, UC Berkeley’s dean of biological sciences and an architect of the DNA program, said he disagreed with the state Department of Public Health’s ruling that the genetic testing required advance approval from physicians and should be done only by specially-licensed clinical labs, not by university technicians. The campus could not find labs willing to do the work and probably could not afford it anyway, Schlissel said. He also contended that the project deserved an exemption from those rules because it was an educational exercise [Los Angeles Times].
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Andrew Crawford and his colleagues discovered 11 new species of amphibians in Panama. But they wish it hadn’t happened this way.
The team just completed a long-term study of amphibians in Panama’s Omar Torrijos National Park, published in the Proceedings of the National Academy of Sciences, showing the startling disappearance of species there. Co-author Karen Lips began the study back before the disease chytridiomycosis, which is caused by a fungus called Batrachochytrium dendrobatidis and has devastated amphibian populations, reached that place and began to afflict its inhabitants.
The pre-decline surveys identified 63 species of amphibians within just a 1.5-square-mile (4-square-kilometer) area. After 2004, 25 of those species had disappeared from the site. As of 2008, none had reappeared. An additional nine species saw an 85 percent to 99 percent decline in their abundance [MSNBC].
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Identical twins don’t share everything. The mix of viruses in a person’s gut, a new study says, is unique to each of us, even if we share nearly all our DNA with another person. That is, at least according to our poop.
This year scientists have been working to decode the genetics of the beneficial microbes that live inside us, like the bacteria that help us digest food. But those trillions of bacteria have partners of their own—beneficial viruses. Jeffrey Gordon and colleagues wanted to see what those viruses were like, and how they differed from person to person. To do it, they studied fecal samples that came from four sets of identical twins, as well as their mothers.
Each identical twin had virus populations that didn’t resemble those of their sibling—or anybody else, for that matter.
Remarkably, more than 80 percent of the viruses in the stool samples had not been previously discovered. “The novelty of the viruses was immediately apparent,” Gordon said. The intestinal viromes of identical twins were about as different as the viromes of unrelated individuals [MSNBC].
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Los Angeles police say that Lonnie Franklin Jr. may be the “grim sleeper” serial killer they have sought for more than 20 years. And if indeed they do have their man, they have his son to thank—for getting arrested himself.
Franklin is one of the first major suspects nabbed by police using familial DNA. With this controversial method, investigators look for partial matches between DNA left at a crime scene and DNA profiles that are stored in police databases; a partial match may indicate that the person is related to the target individual sought by the cops.
The trail began to heat up when the DNA of Franklin’s son was entered in a state database after he was convicted in a weapons case, authorities said. The son’s DNA was similar to genetic material found on the victims, and authorities soon began following around Franklin to get his DNA and see if he was the suspected killer [AP].
The cops posed as waiters at a restaurant where the elder Franklin ate, which is how they obtained a complete DNA sample from him–they grabbed a plate and napkin he tossed after eating a slice of pizza. The investigators say that when they found the match to the samples in their evidence, it eased 25 years of frustration at not being able to track him down.
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Clearly, the people of Tibet must have evolved quickly to tolerate a life spent living at the top of the world. How quickly? A study out in this week’s Science, which compared Tibetans to Han Chinese to see the differences in their DNA, says that the two groups may have diverged no more than 3,000 years ago. If natural selection has changed Tibetans in such a short time, it would be the fastest known example of human evolution. But not everybody is buying this time line.
As DISCOVER noted when a similar study by another team came out in May, natives of the Tibetan plateau seem to survive the altitude because their bodies make less hemoglobin. It’s somewhat counter-intuitive:
In theory higher levels of haemoglobin would be beneficial, because this would improve oxygen transport. But high levels could make the blood thicker and less efficient at carrying oxygen, says Jay Storz of the University of Nebraska-Lincoln [New Scientist]. (Storz writes the accompanying commentary in Science.)
Looking at the differences in genes that regulate that, the team found vast differences between the Han and the Tibetans, with one version appearing in 87 percent of Tibetans studied but only 9 percent of Chinese. However, the assertion by the scientists at the Beijing Genome Institute—that their findings mean the two group broke apart just three millennia ago—has ruffled archaeologists who believe that the Tibetan plateau has been continuously occupied for much, much longer: more like 7,000 to 21,000 years.
For more about all of this, check out Razib Khan’s post at Gene Expression.
Related Content:
Gene Expression: Very Recent Altitude Adaptation in Tibet
Gene Expression: Tibet & Tibetans, Not Coterminus
80beats: Found: The Genes That Help Tibetans Live at the Top of the World
DISCOVER: High-Altitude Determines Who Survives in Tibet
Image: Wikimedia Commons
It doesn’t take much to be a vile, bloodsucking pest. You, human, have three billion base pairs in your genome, but the body louse—which has been a typhus-spreading scourge of humanity for millennia—carries just 108 million. That’s what scientists say today in a study in the Proceedings of the National Sciences that describes how they sequenced the body louse genome.
Because the body louse (a separate creature from the head or pubic louse) lives entirely on humans, hatching in our clothes and eating our blood, its genome can get away with being so streamlined, study author Barry Pittendrigh says:
“Most of the genes that are responsible for sensing or responding to the environment are very much reduced,” Pittendrigh said. The body louse was found to have “significantly fewer genes” for smell and taste, as well as minimal genes responsible for a “simple visual system,” the study authors wrote. They found just 10 genes to code for odor receptors [Scientific American].
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Behold La conversione di San Paolo (The Conversion of St. Paul), one of the masterworks of Caravaggio. The Italian artist of the Baroque era was famous for the chiaroscuro shading—dramatic contrasts of light and dark—evident in this conversion scene. But he was also renowned for living hard and dying young. Four centuries after his death, Italian researchers say they’ve found his bones, and they might know what actually killed him: the lead in his paints.
First, the researchers had to find his remains. Caravaggio died in 1610 in the Tuscan town of Porto Ercole, but his remains were whereabouts unknown until a researcher claimed to turn up a death certificate in 2001 pointing to the crypts there. The bones the scientists found there matched a man aged 38 to 40 (Caravaggio’s age range at his death) and dated to his era. And the DNA matched combinations found in people from the painter’s hometown and sharing his original surname, Merisi or Merisio.
“There can’t be the scientific certainty because when one works on ancient DNA, it is degraded,” Giorgio Gruppioni, an anthropologist on the team, told The Associated Press. “But only in one set of bones did we find all the elements necessary for it to be Caravaggio’s — age, period in which he died, gender, height.” The group says there is an 85 percent probability they are right, though team leader Silvano Vinceti says that is conservative. “We are being cautious,” he said. “As a historian I can say we have found the remains… All evidence concurs” [AP].
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The Food and Drug Administration has a message for the personal genomics revolution: slow down.
Personal DNA tests have been available for years now from companies like 23andMe and Pathway Genomics, and the direct-to-consumer tests have sold briskly even while the companies tried to sort out whether or how their systems would be regulated by the FDA. Then last month, Pathway took the next big step, offering to sell their tests over the counter in the nation’s largest drugstore chain, Walgreens.
For the FDA, that was one step too far, and it began to make noise about regulation. Now the agency’s leader in this field, Alberto Gutierrez, has sent official letters to all the major personal DNA-testing companies saying it intends to regulate the tests as medical devices, and that the companies must provide evidence of their scientific validity.
The letters, posted on the F.D.A. Web site on Friday, say the companies must apply for approval or discuss with the agency why certain test claims do not require such approval. But the letters stop short of saying the tests must be taken off the market until they are approved. Dr. Gutierrez said in an interview that it would be unfair to remove the tests from the market because the agency had not clearly told the companies that the devices needed approval [The New York Times].
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Just how connected are the Jews, genetically speaking? Despite the fact that pockets of Jewish people are spread around the globe, the new genetic analysis by Harry Ostrer and his team says that they share genetic markers that go back thousands of years.
In the study in the American Journal of Human Genetics, Ostrer investigated Jewish people from all over the world:
Historians divide the world’s 13 million living Jews into three groups: Middle Eastern, or Oriental, Jews; Sephardic Jews from Spain and Portugal; and Ashkenazi Jews from Europe [ScienceNOW].
Taking nuclear DNA samples from 237 Jews—some from each group—the team compared them to samples from more than 400 non-Jewish people who lived in the same regions.
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Show them the money: The winners of the Kavli Prizes have been announced, and the eight scientists will split a total of $3 million in prize money.
No, these aren’t the Nobels. The Kavlis are a relatively new award created to award scientists whose fields don’t get much recognition in Stockholm:
These are only the second ever recipients of Kavli Prizes, the biennial awards launched in 2008 by Fred Kavli. Recipients in the fields of astrophysics, neuroscience and nanoscience each receive a scroll, a gold medal and (perhaps most importantly) a share of the $1 million pot for each discipline [Nature].
1. Astrophysics
The prize recognized three men—Jerry Nelson, Roger Angel, and Raymond Wilson—not for finding new phenomena deep in the cosmos, but for engineering the telescopes to make those searches possible. Nelson and Angel are renowned for their prowess in casting the mirrors for the largest telescopes on Earth; Nelson’s work will go into the Thirty Meter Telescope, for which Mauna Kea in Hawaii was just chosen as the preferred location.
Dr. Wilson pioneered the use of a technology known as active optics, in which computer-controlled supports correct the shapes of telescope mirrors to cancel the distortions caused by gravity, wind and temperature, allowing astronomers to build mirrors that are thinner and lighter [The New York Times].
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