Everything we thought we knew about the genome is turning out to be wrong

Claire Ainsworth writes: Ask me what a genome is, and I, like many science writers, might mutter about it being the genetic blueprint of a living creature. But then I’ll confess that “blueprint” is a lousy metaphor since it implies that the genome is two-dimensional, prescriptive and unresponsive.

Now two new books about the genome show the limitation of that metaphor for something so intricate, complex, multilayered and dynamic. Both underscore the risks of taking metaphors too literally, not just in undermining popular understanding of science, but also in trammelling scientific enquiry. They are for anyone interested in how new discoveries and controversies will transform our understanding of biology and of ourselves.

John Parrington is an associate professor in molecular and cellular pharmacology at the University of Oxford. In The Deeper Genome, he provides an elegant, accessible account of the profound and unexpected complexities of the human genome, and shows how many ideas developed in the 20th century are being overturned.

Take DNA. It’s no simple linear code, but an intricately wound, 3D structure that coils and uncoils as its genes are read and spliced in myriad ways. Forget genes as discrete, protein-coding “beads on a string”: only a tiny fraction of the genome codes for proteins, and anyway, no one knows exactly what a gene is any more.[Continue reading…]

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U.S. government starts to unmuzzle the CIA’s torture victims

Huffington Post reports: For years, Guantanamo Bay prisoners’ memories of their time in CIA custody have been considered classified state secrets. Abu Zubaydah’s lawyers can’t talk publicly about how he lost his left eye. Lawyers for Mustafa al Hawsawi, who can now only sit on a pillow, can’t tell the press or the public about anal feedings that left him with a rectal prolapse. And until recently, Majid Khan’s lawyers couldn’t bring up the time he was hung from a pole for two days, naked and hooded, while interrogators threw ice water on him.

The government argued that by talking about what had happened to them, the CIA’s former prisoners, who are now detained at the Guantanamo Bay prison facility, would risk revealing classified information about the agency’s torture program.

But as James Connell, a lawyer who represents detainee Ammar al Baluchi, wrote more than three years ago in a motion to declassify the prisoners’ accounts, “A person’s own experiences — whether the smell of a rose or the click of a gun near one’s head — are what make them a person, and the government can never own or control them.”

The notion that a torture survivor’s memories can be classified, Connell wrote, “contravenes the most basic principles of human rights.” He added that detainees “were exposed to classified interrogation techniques only in the sense that Hiroshima was exposed to the classified Manhattan Project.”

Now, the government is starting to change course. A Senate Intelligence Committee report, which began to pull back the curtain on the CIA’s use of torture in secret prisons known as “black sites,” compelled the government to change its rules about keeping former CIA prisoners’ memories secret. Khan became the first to successfully test the new rules by going public with his account of his imprisonment, which included details not previously disclosed in the Senate report. Citing the success of Khan’s team, defense attorneys for other Guantanamo detainees are now cautiously optimistic that they can bring their clients’ memories of their time in CIA black sites to light. [Continue reading…]

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Republicans’ leading climate denier tells the pope to butt out of climate debate

The Guardian reports: Washington’s notorious snowball-thrower was at it again – even on a June day with forecast highs of 92 degrees – as the Senate’s most powerful environmental leader delivered a pep talk to activists who deny the science behind climate change.

Oklahoma senator James Inhofe, who now chairs the Senate environment and public works committee despite famously calling global warming “the greatest hoax ever perpetrated on the American people”, took a star turn on Thursday at the Heartland Institute, whose conferences function as a hub for climate deniers.

His message – that “God is still up there” and that Pope Francis should mind his own business – sent a clear signal to his fellow conservatives: climate sceptics have a loyal – and newly powerful – friend in Congress. [Continue reading…]

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Stop using China as an excuse for inaction on climate change

George Monbiot writes: to suggest that China is an inherent and insuperable threat, as many of my correspondents do (mostly those who alternate between insisting that man-made climate change isn’t happening and insisting that we can’t do anything about it anyway), is grievously to misrepresent the people of that nation.

First, of course, much of its energy use is commissioned by other nations. As manufacturing has declined in countries like the US and Britain, and the workforce is mostly engaged in other activities, the fossil fuel burning caused by our consumption of stuff has shifted overseas, along with the blame. Even so, when China’s total greenhouse gas production is divided by its population, you discover that it is still producing much less per head than we are.

Partly as a result of a massive investment in renewables, the Chinese demand for coal dropped for the first time last year, and is likely to drop again this year. Perhaps because of the bureaucratic chaos of China’s centralised, unwieldy government, there is a gulf between the energy transition rapidly taking place within China and its negotiating positions in international meetings, which are “in the hands of completely different sets of bureaucrats.”

But perhaps the biggest surprise for those who unwittingly invoke the old Yellow Peril tropes is that the Chinese people care more about climate change than we do. A survey released on Monday reveals that 26% of respondents in the UK and 32% in the US believe that climate change is “not a serious problem”, while in China the figure is only 4%. In the UK, 7% don’t want their government to endorse any international agreement addressing climate change. In the US the proportion rises to 17%. But in China, Hong Kong, Indonesia, Singapore, Malaysia and Thailand, only 1% want no action taken. [Continue reading…]

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Why technocracy won’t save the world

Benjamin Cohen writes: In a 2014 New Yorker profile of twenty-five year old entrepreneur Rob Rhinehart, Lizzie Widdicombe explained the millenial’s motives for inventing a new caloric infusion named for the 1973 film. Rhinehart thought that “food was an inefficient way of getting what he needed to survive.” He “began to resent the fact that he had to eat at all.” It was becoming too problematic for him to invest the effort in food shopping, preparation, or even, apparently, consumption. For the lifehacker, these were the wrong kind of disruptive. Widdicombe resisted editorializing on the shocking arrogance of the view that food was a hindrance to life. But I won’t. When a Bay Area twenty-something understands food as an obstacle to daily life, that person conceives of the environment as a constraint on rather than the basis of living. The dream of efficiency and the view that food is but a calorie delivery vehicle is all too familiar as resting on assumptions of a technocratic worldview.

I question whether anything is best pursued by technocratic means, let alone environmentalism; the political character of technocracy is ethically tenuous for the governance of people, not to mention nature. Technocratic thinking is based on logic of dehumanized values. It’s pinned to strictly technical criteria measured by disembodied quantitative metrics — efficiency, speed, yield, productivity, for example. Anything non-technical is not of significance: if it can’t be stated as a technical problem then it isn’t a problem at all. Values beyond that of a thin and narrow register — consider empowerment, dignity, justice, fulfillment, nourishment, honor, harmony — have no place in such a discussion because they’re too difficult to shoehorn into technical metrics. As for environmental virtues, good luck. Biodiversity, environmental knowledge, or the organic tenets of sustainable ecosystems find little space in technocratic pursuits. [Continue reading…]

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How technology is damaging our brains

The New York Times reports: When one of the most important e-mail messages of his life landed in his in-box a few years ago, Kord Campbell overlooked it.

Not just for a day or two, but 12 days. He finally saw it while sifting through old messages: a big company wanted to buy his Internet start-up.

“I stood up from my desk and said, ‘Oh my God, oh my God, oh my God,’ ” Mr. Campbell said. “It’s kind of hard to miss an e-mail like that, but I did.”

The message had slipped by him amid an electronic flood: two computer screens alive with e-mail, instant messages, online chats, a Web browser and the computer code he was writing.

While he managed to salvage the $1.3 million deal after apologizing to his suitor, Mr. Campbell continues to struggle with the effects of the deluge of data. Even after he unplugs, he craves the stimulation he gets from his electronic gadgets. He forgets things like dinner plans, and he has trouble focusing on his family.

His wife, Brenda, complains, “It seems like he can no longer be fully in the moment.”

This is your brain on computers.

Scientists say juggling e-mail, phone calls and other incoming information can change how people think and behave. They say our ability to focus is being undermined by bursts of information.

These play to a primitive impulse to respond to immediate opportunities and threats. The stimulation provokes excitement — a dopamine squirt — that researchers say can be addictive. In its absence, people feel bored.

The resulting distractions can have deadly consequences, as when cellphone-wielding drivers and train engineers cause wrecks. And for millions of people like Mr. Campbell, these urges can inflict nicks and cuts on creativity and deep thought, interrupting work and family life.

While many people say multitasking makes them more productive, research shows otherwise. Heavy multitaskers actually have more trouble focusing and shutting out irrelevant information, scientists say, and they experience more stress.

And scientists are discovering that even after the multitasking ends, fractured thinking and lack of focus persist. In other words, this is also your brain off computers. [Continue reading…]

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Humanity’s destructive thirst

Nautilus reports: A sliver here, a spot there. That’s all the water that’s left of the great Aral Sea, once the fourth largest lake in the world by surface area. Recent images of the dry Aral Sea show camels sheltering from the sun beside the rusting husks of fishing boats, perched permanently on the dried-up lakebed. The extreme transformation took all of 50 years.

The Aral Sea wasn’t historically fragile. Humans have been using the saltwater lake for at least 3,000 years, the water level only fluctuating by about four meters during the 300 years prior to 1960. And the water provided for neighboring communities, offering a sustainable and profitable way of life for early 20th-century fishermen who caught carp, pike, and perch in numbers great enough to export them widely. Fish were so abundant that Aralsk fishermen, when called upon by Soviet leader Lenin, were able to load up 14 train cars bound for starved regions of the Soviet Union with fresh Aral Sea fish in October of 1921.

Around 1960 the land began to change. The erstwhile Soviet Union expanded irrigation projects aimed at increasing the yield of profitable cotton. The crop’s thirst for the freshwater in the rivers replenishing the Aral Sea meant less water ended up in the lake. Over time, one of the rivers — the Amu Darya — stopped making it to the lake. And as the water depleted, the salt in the lake’s water became more concentrated. Salinity went up, killing off several fish species that couldn’t cope in the changing environment. Now the fishermen can’t make a living, and those not impoverished by decreasing opportunities in the barren land can only find continuous work in feeding, growing, and picking cotton or other water-guzzling crops. The dry basin itself, doused with farming chemicals and prone to rise up in dust storms, threatens the health of any who live nearby. And since Uzbekistan is today the second-biggest cotton exporter in the world, the Aral Sea has little hope of recovering its former size. [Continue reading…]

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Documenting evil: Inside Assad’s hospitals of horror

Adam Ciralsky reports: On a stifling day in August 2013, a police photographer with chiseled features and a military bearing moved hurriedly about his office in Damascus. For two years, as Syria’s civil war became ever more deadly, he lived a double life: regime bureaucrat by day, opposition spy by night. Now he had to flee. Having downloaded thousands of high-resolution photographs onto flash drives, he snuck into the empty office of his boss and took cell-phone pictures of the papers on the man’s desk. Among them were execution orders and directives to falsify death certificates and dispose of bodies. Armed with as much evidence as he could safely carry, the photographer—code-named Caesar—fled the country.

Since then, the images that Caesar secreted out of Syria have received wide circulation, having been touted by Western officials and others as clear evidence of war crimes. The pictures, most of them taken in Syrian military hospitals, show corpses photographed at close range — one at a time as well as in small groupings. Virtually all of the bodies — thousands of them—betray signs of torture: gouged eyes; mangled genitals; bruises and dried blood from beatings; acid and electric burns; emaciation; and marks from strangulation. Caesar took a number of these pictures, working with roughly a dozen other photographers assigned to the same military-police unit.

But Caesar himself, like the intelligence operation of which he became a part, has remained in the shadows. He appeared only once in public, last summer, before the House Foreign Affairs Committee, where he wore a hood and spoke through a translator. He spoke briefly, and in a restricted setting, though I have been able to obtain a copy of his complete testimony. He sought and was granted asylum in a Western European country whose name Vanity Fair has agreed not to disclose, for his personal safety. [Continue reading…]

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ISIS: Blend of religious fervor and technical know-how makes a formidable foe

By Paul Rogers, University of Bradford

At the end of G7, Barack Obama repeated his admission that the United States did not yet have a complete strategy for responding to IS. Republican opponents were quick to criticise him but few were prepared to say what should be done.

Some in US military circles believe an intensive air war can succeed, but not many, given that the months of air attacks have had so little effect. Indeed there is now an increasingly widespread view that one of the main effects of the air attacks has been to increase support for IS, ever ready to present itself as the guardian of Islam under attack from the “crusaders” of the far enemy and their cohorts from the apostate regimes in Jordan, Saudi Arabia and other parts of the Middle East.

Even so, the Pentagon this week announced the deployment of another 450 US troops to assist the Iraqi army, taking the total to 3,550, less than four years after the US withdrew all its forces.

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Jailed for ‘Twitter terrorism’ supporting ISIS and Al Qaeda

The Daily Beast reports: American and British counter-terror officers have turned their fire on the keyboard warriors waging jihad from their bedrooms in Western capitals.

A teenage boy from the D.C. area and a woman living in South London admitted Thursday in courtrooms 3,000 miles apart that they were “Twitter terrorists”—part of a growing online army that encourages Western citizens to travel to the so-called Islamic State; take up arms; or martyr themselves in the name of jihad.

Such is the perceived threat from these social media recruiting sergeants that judges on both sides of the Atlantic have dispensed with free speech arguments and now characterize Twitter or Instagram propaganda sites for al Qaeda and Islamic State (also known as ISIS and ISIL) as providing “material support” for terrorists. [Continue reading…]

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Back from Syria and Iraq, Bosnian fighters pose threat at home

Reuters reports: Bosnian fighters returning from Syria and Iraq are forming regional militant networks that pose a direct threat to security in the Balkans and beyond, a study warned on Thursday.

The returnees have formed links extending to Serbia, Montenegro, Macedonia, Albania and Kosovo, said the non-profit Sarajevo-based Atlantic Initiative, and may be radicalizing youngsters on the margins of society.

“Once a destination country for foreign fighters in the 1990s, Bosnia is now the country of origin for volunteers in other people’s wars,” said Vlado Azinovic, a co-author of the report. [Continue reading…]

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Israel rules out legal action against its soldiers who killed children in Gaza

The Washington Post reports: The Israeli military has decided not to pursue criminal charges against soldiers involved in missile strikes in the Gaza Strip last summer that killed four children playing on a beach.

The Military Advocate General Corps investigated the notorious incident, which took place on July 16 in view of the hotels where international journalists were staying, and concluded that there was no criminal wrongdoing.

The four young cousins who were killed were sons of the extended Bakr fishing family, ages 9 to 11. Four other youths were injured by shrapnel. Images of the dead and wounded children being rushed from the beach toward ambulances were broadcast around the world. A reporter for The Washington Post witnessed the attack.

The children were playing on the breakwater jetty in the Gaza City harbor when the aerial assault began. After the first salvo was fired, they ran toward a beach hotel where journalists were working, and a second Israeli strike was fired directly at the group.

In a summary of the criminal investigation released Thursday night, the Israel Defense Forces said its troops believed they were targeting militants from the Hamas navy. [Continue reading…]

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Russia has inherited only one thing from the Soviet Union — the love its leader holds for the pomp of military ceremony

Ivan Sukhov writes: Modern Russia is not positioning itself as a welfare state: The government now sees it as a burden to feed millions of people directly dependent on the state. Modern Russia is ostensibly trying to invest in development, but its space program is crumbling with every failed rocket launch, and lawmakers are scaring away potential investors with ill-conceived laws.

Modern Russia is definitely not the free and prosperous country that dissidents dreamed it would become when the Soviet regime collapsed in 1991 — but, beyond a doubt, it is also not the Soviet Union. The contours of the social and political system now unfolding before our eyes are far harsher, the political taboos preventing society from degenerating into primitive obscurantism far fewer and the barriers separating the country from the rest of the world far higher.

Meanwhile, the honor guard embodying Great Russia continues marching at the Kremlin walls and the country’s nuclear missiles — capable of destroying half the planet — stand ready. [Continue reading…]

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Myanmar to bar Rohingya from fleeing, but won’t address their plight

The New York Times reports: The government of Myanmar says it is determined to stop the departures of migrants fleeing religious persecution in places like this bitterly divided port city, but it will not budge in its refusal to address the conditions driving the exodus across the sea.

Tens of thousands of Rohingya, a Muslim ethnic group, fled the country in recent months, setting off a regional crisis when boatloads of migrants were abandoned at sea or abused and held for ransom by traffickers.

But the government insists that most of the migrants do not belong in Myanmar, referring to them as Bengalis, and says it has no plans to alter policies that strip them of basic rights and confine more than 140,000 to a crowded, squalid government camp here.

“There is no change in the government’s policy toward the Bengalis,” U Zaw Htay, a deputy director general of the Myanmar president’s office, said in an interview this week.

Under international pressure, as crowded vessels baked and bobbed in the ocean for days with no country willing to take them in, regional leaders met in Bangkok last month, and the immediate crisis was relieved when the migrants were granted temporary refuge.

But any hope that Myanmar might have been persuaded to soften its position was quickly dispelled.

When a government delegation returned from the talks, the state news media hailed the officials as managing “to refute accusations that the boat people were from Myanmar.”

And those people, despite the reports of horror stories at sea, are no less desperate to leave. [Continue reading…]

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Pakistan expels aid agency Save the Children

The Washington Post reports: Pakistani authorities expelled the U.S.-based aid agency Save the Children from the country on Thursday, sealing its office in the capital and giving staff members 15 days to leave because of “anti-Pakistan activities,” according to the Interior Ministry.

The move, which could have a chilling effect on dozens of charities that work in Pakistan, was carried out after extensive monitoring of the group’s members and activities, a ministry official said in an interview.

The official, who spoke on the condition of anonymity because he was not authorized to discuss the matter, declined to discuss the specific reason for the action. But the move appeared to be related to long-standing allegations of Save the Children’s ties to the Pakistani physician recruited to help the CIA gain information about Osama bin Laden’s whereabouts prior to the 2011 U.S. military mission that killed him in northwestern Pakistan. [Continue reading…]

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British police carrying guns almost never use them

The Washington Post reports: To join the few and the proud who police Britain’s streets with a gun, first you have to walk the beat unarmed for years.

Then there is the rigorous selection process — an unforgiving complement of fitness tests, psychological appraisals and marksmanship exams. Finally, there is the training, which involves endless drilling on even the most routine scenarios.

“They rehearse those situations like a SEAL team trying to get into Osama bin Laden’s compound,” Cambridge University criminologist Lawrence Sherman said.

Yet, in a country where the vast majority of police officers patrol with batons and pepper spray, the elite cadre of British cops who are entrusted with guns almost never use them. Police in Britain have fatally shot two people in the past three years. [Continue reading…]

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