25. July 2012

Closely Watched Study Fails to Find Arsenic in Microbial DNA

by Elizabeth Pennisi on 2 February 2012, 1:50 PM

The debate over whether a bacterium can incorporate arsenic into its DNA just flared up again, with the posting yesterday of a paper refuting the idea on ArXiv, an electronic preprint archive primarily used by astronomers, mathematicians, and physicists. The controversy began in December 2010, when NASA astrobiology fellow Felisa Wolfe-Simon and colleagues described online in Science a microbe called GFAJ-1, which grew, albeit slowly, in the presence of arsenic, leading the authors to conclude the bacterium had taken up the toxic element and incorporated it into its cellular components. The report, amplified by a NASA press conference, quickly lit up the blogosphere and Twitter and led to the unprecedented publication of eight critical technical comments alongside the print version of the paper.

Wolfe-Simon and her colleagues agreed to make samples of GFAJ-1 available and now one vocal critic,Rosemary Redfield, a microbiologist at the University of British Columbia, Vancouver, in Canada, has grown the bacterium in the presence of arsenic and found no evidence of its uptake in the microbe's genetic material. "The data they have supports the conclusion there is no arsenic in the DNA," comments Michael Bartlett, a chemist at the University of Georgia, Athens, who is an expert in mass spectrometry of DNA, RNA, and related molecules.

Redfield, who chronicled every twist and turn of her experiments on her blog, and some other critics of the original paper are satisfied this resolves the matter and do not plan follow-up experiments. "We can do fancier analyses that push the limits of detection down, but I think the burden of proof is back on the authors," she says. "They are going to have to provide some better data than they did in their paper."

But Wolfe-Simon and her colleagues say the work on arsenic-based life is just beginning. They toldScienceInsider that they will not comment on the details of Redfield's work until it has been peer reviewed and published. They emphasize that the key point of their paper was that the microbe was able to use arsenic to grow, despite its toxicity, and that they only suggested arsenic was in the DNA. "What this is about is refuting an extreme interpretation of the paper," says John Tainer, a biochemist who was not an author on the original paper but is now working with Wolfe-Simon at the Lawrence Berkeley National Laboratory in California. "I would call it more of an attack than a paper. It aims to shut the door on additional research."

At the heart of the Wolfe-Simon paper was the finding that when starved of phosphorus, an element vital to life and a key component of DNA, and when provided with ample arsenic, GFAJ-1 was able to grow and use the arsenic instead of phosphorus. Analytical tests indicated that arsenic might have been used to make DNA. (The current assertion by Wolfe-Simon and her colleagues that the original paper did not specifically claim arsenic was in GFAJ-1's DNA has already drawn criticism and a detailed rebuttal from one scientist who had previously defended Wolfe-Simon.)

Yet Redfield and others argued that it was impossible for arsenic to be part of DNA and worried that the arsenic found associated with GFAJ-1 was contamination and not part of any of its biomolecules. They also suggested that the little bit of phosphorus already in the bacterial growth media would have been enough to fuel the growth attributed to arsenic.

When Redfield grew the microbe in her own lab, she got no growth at first. Then by adding an amount of phosphorus that she estimated to be equivalent to phosphorus found in the media used by Wolfe-Simon's team, Redfield saw growth rates equivalent to what Wolfe-Simon saw. Growth was similar in samples with and without added arsenic. Thus Redfield concludes that the minimal phosphorus, not the added arsenic, fueled the growth recorded by Wolfe-Simon.

Redfield has been blogging her day to day research for about 6 years, and she continued by posting regular updates on her attempts to grow GFAJ-1, eventually asking for collaborators on the project. Princeton University's Leonid Kruglyak answered Redfield's call for help as he has a mass spectrometry system able to analyze the constituents of DNA. Princeton graduate student Marshall Louis Reaves subjected isolated GFAJ-1 DNA to liquid chromatography-mass spectrometry and found no signs of arsenic in the DNA.

"This lab knows how to look at and detect these types of molecules," says Patrick A. Limbach, a chemist who studies mass spectrometry of nucleic acids at the University of Cincinnati. Based on the new data, "it's very clear there is no arsenate associated in the DNA backbones."

Redfield has suggested that the arsenic Wolfe-Simon's group claimed was in the microbe's DNA was contaminating arsenic that wasn't washed away when the DNA was purified. Redfield and her colleagues, says Bartlett, "have gone to significant lengths to make sure they remove any residual arsenic that might be associated with the [DNA]. The [Wolfe-Simon] paper did not."

However, Bartlett does take issue with how sensitive Redfield says her tests were to the presence of arsenic. He doesn't not think the limit of detection was 50-fold lower than what Wolfe-Simon found, as Redfield claims. There still could be some arsenic in the bacterium's biomolecules, he says, though not nearly as much as the Wolfe-Simon team originally reported finding.

Tainer and Wolfe-Simon don't understand why Redfield didn't see arsenic-stimulated growth, but say the original paper stands up. "If there is no arsenic in DNA, [then] where is the arsenic going? That's the cool scientific question," says Tainer, one that he and Wolfe-Simon are pursuing by looking in the ribosome and elsewhere in the cell. And in her paper, Redfield also leaves open that possibility, suggesting that arsenic may be taken up by other molecules, just not DNA.

While the new work has not yet been formally reviewed by a journal—Redfield says it has been submitted toScience—other scientists have regularly commented and offered advice on her blog posts. As for the use of ArXiv, Kruglyak notes that posting papers on a preprint server has become commonplace in the physical sciences, but not in biology. Redfield says that Science's editors assured her that putting the paper on ArXiv would not jeopardize the paper's chance for publication there. Already several comments have come in with suggestions on improving the work. "I think it's a very positive thing," Kruglyak adds.

Not everyone agrees with Redfield's preprint and blogging approach, however. "To me it sort of looks like publicity hunting by Redfield," says Bartlett. "It's not the way I'd like to do science."

Tags: Roger, Biology, 12Jul

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Fri

Nov

2015

Are Languages Products of their Environment?

shutterstock_222422665_151112

DISCOVER MAGAZINE published this very interesting article:

Languages Are Products of Their Environments

The characteristics that make each language unique may actually be adaptations to the acoustics of different environments.

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Thu

Jun

2014

Fun with Newspaper Headlines

Newspaper Headlinigs

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Tue

Jun

2014

The Case for Reparations

The Case for Reparations

Two hundred fifty years of slavery. Ninety years of Jim Crow. Sixty years of separate but equal. Thirty-five years of racist housing policy. Until we reckon with our compounding moral debts, America will never be whole.

By Ta-Nehisi Coates

May 21, 2014

Chapters

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Mon

Jun

2014

A Look At 19th Century Children In The USA

PHILADELPHIA — DINNER with your children in 19th-century America often required some self-control. Berry stains in your daughter’s hair? Good for her. Raccoon bites running up your boy’s arms? Bet he had an interesting day.

As this year’s summer vacation begins, many parents contemplate how to rein in their kids. But there was a time when Americans pushed in the opposite direction, preserved in Mark Twain’s cat-swinging scamps. Parents back then encouraged kids to get some wildness out of their system, to express the republic’s revolutionary values.

The New York Times

Sunday Review

By JON GRINSPAN MAY 31, 2014

A late 19th century family taking a stroll down a set of railroad tracks

American children of the 19th century had a reputation. Returning British visitors reported on American kids who showed no respect, who swore and fought, who appeared — at age 10 — “calling for liquor at the bar, or puffing a cigar in the streets,” as one wrote. There were really no children in 19th-century America, travelers often claimed, only “small stuck-up caricatures of men and women.”

This was not a “carefree” nation, too rough-hewed to teach proper manners; adults deliberately chose to express new values by raising “go-ahead” boys and girls. The result mixed democracy and mob rule, assertiveness and cruelty, sudden freedom and strict boundaries. Visitors noted how American fathers would brag that their disobedient children were actually “young republicans,” liberated from old hierarchies. Children were still expected to be deferential to elders, but many were trained to embody their nation’s revolutionary virtues. “The theory of the equality” was present at the ballot box, according to one sympathetic Englishman, but “rampant in the nursery.”

Boys, in particular, spent their childhoods in a rowdy outdoor subculture. After age 5 or so they needed little attention from their mothers, but were not big enough to help their fathers work. So until age 10 or 12 they spent much of their time playing or fighting.

The writer William Dean Howells recalled his ordinary, violent Ohio childhood, immersed in his loose gang of pals, rarely catching a “glimpse of life much higher than the middle of a man.” Howells’s peers were “always stoning something,” whether friends, rivals or stray dogs. They left a trail of maimed animals behind them, often hurt in sloppy attempts to domesticate wild pets.

And though we envision innocents playing with a hoop and a stick, many preferred “mumbletypeg” — a game where two players competed to see who could throw a knife closer to his own foot. Stabbing yourself meant a win by default.

Left to their own devices, boys learned an assertive style that shaped their futures. The story of every 19th-century empire builder — Carnegie, Rockefeller, Vanderbilt — seems to begin with a striving 10-year-old. “Boy culture” offered training for the challenges of American manhood and a reprieve before a life of labor.

But these unsupervised boys also formed gangs that harassed the mentally ill, the handicapped and racial and ethnic minorities. Boys played an outsize role in the anti-Irish pogroms in 1840s Philadelphia, the brutal New York City draft riots targeting African-Americans during the Civil War and attacks on Chinese laborers in Gilded Age California. These children did not invent the bigotry rampant in white America, but their unrestrained upbringing let them enact what their parents mostly muttered.

Their sisters followed a different path. Girls were usually assigned more of their mothers’ tasks. An 8-year-old girl would be expected to help with the wash or other physically demanding tasks, while her brother might simply be too small, too slow or too annoying to drive the plow with his father. But despite their drudgery, 19th-century American girls still found time for tree climbing, bonfire building and waterfall-jumping antics. There were few pretty pink princesses in 19th-century America: Girls were too rowdy and too republican for that.

So how did we get from “democratic sucklings” to helicopter parents? Though many point to a rise of parental worrying after the 1970s, this was an incremental change in a movement that began a hundred years earlier.

In the last quarter of the 19th century, middle-class parents launched a self-conscious project to protect children. Urban professionals began to focus on children’s vulnerabilities. Well-to-do worriers no longer needed to raise tough dairymaids or cunning newsboys; the changing economy demanded careful managers of businesses or households, and restrained company men, capable of navigating big institutions.

Demographics played a role as well: By 1900 American women had half as many children as they did in 1800, and those children were twice as likely to live through infancy as they were in 1850. Ironically, as their children faced fewer dangers, parents worried more about their protection.

Instead of seeing boys and girls as capable, clever, knockabout scamps, many reconceived children as vulnerable, weak and naïve. Reformers introduced child labor laws, divided kids by age in school and monitored their play. Jane Addams particularly worked to fit children into the new industrial order, condemning “this stupid experiment of organizing work and failing to organize play.”

There was good reason to tame the boys and girls of the 19th century, if only for stray cats’ sake. But somewhere between Jane Addams and Nancy Grace, Americans lost track of their larger goal. Earlier parents raised their kids to express values their society trumpeted.

“Precocious” 19th-century troublemakers asserted their parents’ democratic beliefs and fit into an economy that had little use for 8-year-olds but idealized striving, self-made men. Reformers designed their Boy Scouts to meet the demands of the 20th century, teaching organization and rebalancing the relationship between play and work. Both movements agreed, in their didactic ways, that playtime shaped future citizens.

Does the overprotected child articulate values we are proud of in 2014? Nothing is easier than judging other peoples’ parenting, but there is a side of contemporary American culture — fearful, litigious, controlling — that we do not brag about but that we reveal in our child rearing, and that runs contrary to our self-image as an open, optimistic nation. Maybe this is why sheltering parents come in for so much easy criticism: A visit to the playground exposes traits we would rather not recognize.

There is, however, a saving grace that parents will notice this summer. Kids are harder to guide and shape, as William Dean Howells put it, “than grown people are apt to think.” It is as true today as it was two centuries ago: “Everywhere and always the world of boys is outside of the laws that govern grown-up communities.” Somehow, they’ll manage to go their own way.

________________________________

A National Endowment for the Humanities fellow at the Massachusetts Historical Society who is writing a book on the role of young people in 19th-century American democracy.

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Mon

Apr

2014

Investigating Family's Wealth, China's Leader Signals a Change

From The New York Times

By CHRISTOPHER DREW and JAD MOUAWAD

APRIL 19, 2014

HONG KONG — His son landed contracts to sell equipment to state oil fields and thousands of filling stations across China. His son’s mother-in-law held stakes in pipelines and natural gas pumps from Sichuan Province in the west to the southern isle of Hainan. And his sister-in-law, working from one of Beijing’s most prestigious office buildings, invested in mines, property and energy projects.

In thousands of pages of corporate documents describing these ventures, the name that never appears is his own: Zhou Yongkang, the formidable Chinese Communist Party leader who served as China’s top security official and the de facto boss of its oil industry.

A visitor at the Zhou family's ancestral graves in Xiqliantou, eastern China. Intrigue surrounds the family after a spate of arrests. Sim Chi Yim for the New York Times

But President Xi Jinping has targeted Mr. Zhou in an extraordinary corruption inquiry, a first for a Chinese party leader of Mr. Zhou’s rank, and put his family’s extensive business interests in the cross hairs.

Even by the cutthroat standards of Chinese politics, it is a bold maneuver. The finances of the families of senior leaders are among the deepest and most politically delicate secrets in China. The party has for years followed a tacit rule that relatives of the elite could prosper from the country’s economic opening, which rewarded loyalty and helped avert rifts in the leadership.

Zhou Family Ties

Zhou Yongkang, a member of China’s ruling Politburo Standing Committee from 2007 to 2012, is the subject of one of the highest-level corruption investigations in the history of the People’s Republic of China. Several members of his family, over the years Mr. Zhou was in power, made investments in companies with ties to the China National Petroleum Corp., the state oil company formerly run by Mr. Zhou, although there is no evidence to show that Mr. Zhou was personally involved in the dealings.

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Fri

Nov

2015