Category Archives: Attention to the Unseen

Microbes that eat electricity

Emily Singer writes: [In 2015], biophysicist Moh El-Naggar and his graduate student Yamini Jangir plunged beneath South Dakota’s Black Hills into an old gold mine that is now more famous as a home to a dark matter detector. Unlike most scientists who make pilgrimages to the Black Hills these days, El-Naggar and Jangir weren’t there to hunt for subatomic particles. They came in search of life.

In the darkness found a mile underground, the pair traversed the mine’s network of passages in search of a rusty metal pipe. They siphoned some of the pipe’s ancient water, directed it into a vessel, and inserted a variety of electrodes. They hoped the current would lure their prey, a little-studied microbe that can live off pure electricity.

The electricity-eating microbes that the researchers were hunting for belong to a larger class of organisms that scientists are only beginning to understand. They inhabit largely uncharted worlds: the bubbling cauldrons of deep sea vents; mineral-rich veins deep beneath the planet’s surface; ocean sediments just a few inches below the deep seafloor. The microbes represent a segment of life that has been largely ignored, in part because their strange habitats make them incredibly difficult to grow in the lab.

Yet early surveys suggest a potential microbial bounty. A recent sampling of microbes collected from the seafloor near Catalina Island, off the coast of Southern California, uncovered a surprising variety of microbes that consume or shed electrons by eating or breathing minerals or metals. El-Naggar’s team is still analyzing their gold mine data, but he says that their initial results echo the Catalina findings. Thus far, whenever scientists search for these electron eaters in the right locations — places that have lots of minerals but not a lot of oxygen — they find them. [Continue reading…]

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The future of life necessitates that we rise way beyond the nationalist viewpoint

Yuval Noah Harari writes: Though human beings are social animals, for millions of years they lived in small, intimate communities numbering no more than a few dozen people. Even today, as the evolutionary biologist Robin Dunbar has shown, most human beings find it impossible properly to know more than 150 individuals, irrespective of how many Face­book “friends” they boast. Human beings easily develop loyalty to small, intimate groups such as a tribe, an infantry company or a family business, but it is hardly natural for them to be loyal to millions of strangers. Such mass loyalties have appeared only in the past few thousand years as a means of solving practical problems that no single tribe could solve by itself. Ancient Egypt was created to help human beings gain control of the River Nile, and ancient China coalesced to help the people restrain the turbulent Yellow River.

Nations solved some problems and created new ones. In particular, big nations led to big wars. Yet people were willing to pay the price in blood, because nations provided them with unprecedented levels of security and prosperity. In the 19th and early 20th centuries the nationalist deal still looked very attractive. Nationalism was leading to horrendous conflicts on an unprecedented scale, but modern nation states also built systems of health care, education and welfare. National health services made Passchendaele and Verdun seem worthwhile.

Yet the invention of nuclear weapons sharply tilted the balance of the deal. After Hiroshima, people no longer feared that nationalism would lead to mere war: they began to fear it would lead to nuclear war. Total annihilation has a way of ­sharpening people’s minds, and thanks in no small measure to the atomic bomb, the impossible happened and the nationalist genie was squeezed at least halfway back into its bottle. Just as the ancient villagers of the Yellow River Basin redirected some of their loyalty from local clans to a much bigger nation that restrained the dangerous river, so in the nuclear age a global community gradually developed over and above the various nations because only such a community could restrain the nuclear demon.

In the 1964 US presidential campaign, Lyndon B Johnson aired the “Daisy” advertisement, one of the most successful pieces of propaganda in the annals of television. The advert opens with a little girl picking and counting the petals of a daisy, but when she reaches ten, a metallic male voice takes over, counting back from ten to zero as in a missile launch countdown. Upon it reaching zero, the bright flash of a nuclear explosion fills the screen, and Candidate Johnson addresses the American public: “These are the stakes – to make a world in which all of God’s children can live, or to go into the dark. We must either love each other. Or we must die.” We often associate the slogan “Make love, not war” with the late-1960s counterculture, but already in 1964 it was accepted wisdom, even among hard-nosed politicians such as Johnson. [Continue reading…]

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A physicist who models ISIS and the alt-right

Natalie Wolchover writes: Neil Johnson used to study electrons as a buttoned-up professor of physics at the University of Oxford. Then, a decade ago, he decamped to the University of Miami — a young institution that he sees as unconstrained by rigid traditions or barriers between disciplines — and branched out. In recent years, the 55-year-old physicist has published research on financial markets, crowds, superconductivity, earthquake forecasting, light-matter interactions, bacterial photosynthesis, quantum information and computation, neuron firing patterns, heart attacks, tumor growth, contagion and urban disasters, not to mention his extensive body of work on terrorism and other forms of insurgent conflict.

Johnson models the extreme events and behaviors that can arise in complex systems. The author of two books on complexity, he has found that the same principles often apply, regardless of whether a system consists of interacting electrons, humans or anything else. After the terrorist attacks of Sept. 11, 2001, he began modeling extremism in human society. He had also spent time in Colombia during the war against the FARC guerrilla army, and grew up near London during the era of IRA bombings. “I started wondering what the patterns of attacks in the respective places might be telling us about how humans do terrorism,” he said. “Terrorism suddenly became, for me, an urgent problem that I might be able to help society understand, and perhaps even one day predict.”

The rise of ISIS has served as both an impetus and test case for Johnson’s models. Even more recently, he has begun using his models to study the growth of white nationalist groups in the United States.

Quanta Magazine caught up with Johnson to discuss his findings by phone in June, before he left to spend the summer working with collaborators in Bogota, Colombia. A condensed and edited version of that conversation, and a subsequent email exchange after the events in Charlottesville, follows. [Continue reading…]

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Tool-wielding macaques are wiping out shellfish populations

Nathaniel Scharping reports: The advent of tools was a big deal for humanity. It made it far easier to manipulate our environment and mold the planet to serve our own interests—from the folsom point to the iPhone X.

Some animals use tools too, like the macaques of Thailand, who have figured out that their favorite shellfish snacks are much easier to eat if they bash them open with rocks first. They’ve become proficient shellfish smashers, so much so that the macaques are actually threatening the existence of oysters and snails an a small island there. It’s a tale of technology gone wrong — only this time, humans aren’t the villains.

Researchers from Thailand, Europe and Australia looked at two groups of long-tailed macaques on separate islands off the Thai coast. The two locations, both alike in shellfish populations, differed only in the number of macaques there. Koram is host to around 80 primates, while NomSao has but nine. Both groups have figured out how to use rocks to break open shellfish armor, behavior that has been observed among other groups of macaques in Thailand.

On Koram, though, the abundance of tool-wielding macaques has led to a crisis of sorts. In a paper published last week in the journal eLife, the researchers estimate that a single individual on the island slurps down 47 shellfish a day, mostly oysters. For the mere 26 macaques that the researchers studied, that works out to 441,000 a year. Looking at periwinkles, a small sea snail, the researchers estimated that the monkeys could eat the entire island’s population in just a year. On NomSao, the much smaller group eats only about an eighth of the available periwinkle population. [Continue reading…]

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Return of the city-state

Jamie Bartlett writes: If you’d been born 1,500 years ago in southern Europe, you’d have been convinced that the Roman empire would last forever. It had, after all, been around for 1,000 years. And yet, following a period of economic and military decline, it fell apart. By 476 CE it was gone. To the people living under the mighty empire, these events must have been unthinkable. Just as they must have been for those living through the collapse of the Pharaoh’s rule or Christendom or the Ancien Régime.

We are just as deluded that our model of living in ‘countries’ is inevitable and eternal. Yes, there are dictatorships and democracies, but the whole world is made up of nation-states. This means a blend of ‘nation’ (people with common attributes and characteristics) and ‘state’ (an organised political system with sovereignty over a defined space, with borders agreed by other nation-states). Try to imagine a world without countries – you can’t. Our sense of who we are, our loyalties, our rights and obligations, are bound up in them.

Which is all rather odd, since they’re not really that old. Until the mid-19th century, most of the world was a sprawl of empires, unclaimed land, city-states and principalities, which travellers crossed without checks or passports. As industrialisation made societies more complex, large centralised bureaucracies grew up to manage them. Those governments best able to unify their regions, store records, and coordinate action (especially war) grew more powerful vis-à-vis their neighbours. Revolutions – especially in the United States (1776) and France (1789) – helped to create the idea of a commonly defined ‘national interest’, while improved communications unified language, culture and identity. Imperialistic expansion spread the nation-state model worldwide, and by the middle of the 20th century it was the only game in town. There are now 193 nation-states ruling the world.

But the nation-state with its borders, centralised governments, common people and sovereign authority is increasingly out of step with the world. And as Karl Marx observed, if you change the dominant mode of production that underpins a society, the social and political structure will change too. [Continue reading…]

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Why the Cassini mission to Saturn must end in a fiery dive

Space.com reports: After examining Saturn from up close for 13 years, the Cassini spacecraft is ending its long career with a boom — and there’s an important reason why.

Friday morning (Sept. 15), Cassini will complete the orbital pirouettes of its seven-year Solstice Mission and complete a self-destructing descent into Saturn’s atmosphere. This fierce ending is dramatic for a purpose: It will prevent Earth microbes from contaminating Saturn’s nearby moons.

When NASA’s Cassini spacecraft completed its first tour of Saturn in 2008, the mission team had to decide what would come next. [Cassini’s Saturn Crash 2017: How to Watch Its ‘Grand Finale’]

Cassini could have parted ways with the ringed planet. In 2009, studies showed that Cassini had enough fuel to reach Uranus or Neptune. Cassini could have traveled in the other direction, toward Jupiter, or it could have been sent to visit an assembly of asteroids known as the Centaurs in the outer limits of the solar system.

Instead, scientists chose to continue making discoveries about Saturn and its moons — first through a two-year extended mission known as the Cassini Equinox Mission, and then with a second extension in 2010 that would bring the spacecraft to the very limit of the fuel it carried. That made it clear that Cassini’s third mission, the Solstice Mission, would be how the spacecraft would end its career. It was during these missions that scientists discovered that two of Saturn’s moons, Titan and Enceladus, showed signs that they were well suited to life. But why the fiery plummet?

“The spacecraft will burn up and disintegrate like a meteor in the upper atmosphere of Saturn,” Preston Dyches, of NASA’s Jet Propulsion Laboratory (JPL), told Space.com via email. “This was determined to be the best way to ensure the safe disposal of the spacecraft, so that there would be no chance of future contamination of Enceladus by any hardy microbes that might have stowed away on board all these years.” [Continue reading…]

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Our imaginative life today has access to the pre-linguistic, ancestral mind

Stephen T Asma writes: Richard Klein, Maurice Bloch and other prominent paleoanthropologists place the imagination quite late in the history of our species, thousands of years after the emergence of anatomically modern humans. In part, this theory reflects a bias that artistic faculties are a kind of evolutionary cheesecake – sweet desserts that emerge as byproducts of more serious cognitive adaptations such as language and logic. More importantly, it is premised on the relatively late appearance of cave art in the Upper Paleolithic period (c38,000 years ago). It is common for archaeologists to assume that imagination evolves late, after language, and the cave paintings are a sign of modern minds at work, thinking and creating just as we do today.

Contrary to this interpretation, I want to suggest that imagination, properly understood, is one of the earliest human abilities, not a recent arrival. Thinking and communicating are vastly improved by language, it is true. But ‘thinking with imagery’ and even ‘thinking with the body’ must have preceded language by hundreds of thousands of years. It is part of our mammalian inheritance to read, store and retrieve emotionally coded representations of the world, and we do this via conditioned associations, not propositional coding.

Lions on the savanna, for example, learn and make predictions because experience forges strong associations between perception and feeling. Animals appear to use images (visual, auditory, olfactory memories) to navigate novel territories and problems. For early humans, a kind of cognitive gap opened up between stimulus and response – a gap that created the possibility of having multiple responses to a perception, rather than one immediate response. This gap was crucial for the imagination: it created an inner space in our minds. The next step was that early human brains began to generate information, rather than merely record and process it – we began to create representations of things that never were but might be. On this view, imagination extends back into the Pleistocene, at least, and likely emerged slowly in our Homo erectus cousins. [Continue reading…]

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‘Uncontacted’ Amazon tribe members are reported killed in Brazil

The New York Times reports: They were members of an uncontacted tribe gathering eggs along the river in a remote part of the Amazon. Then, it appears, they had the bad luck of running into gold miners.

Now, federal prosecutors in Brazil have opened an investigation into the reported massacre of about 10 members of the tribe, the latest evidence that threats to endangered indigenous groups are on the rise in the country.

The Brazilian agency on indigenous affairs, Funai, said it had lodged a complaint with the prosecutor’s office in the state of Amazonas after the gold miners went to a bar in a near the border with Colombia, and bragged about the killings. They brandished a hand-carved paddle that they said had come from the tribe, the agency said.

“It was crude bar talk,” said Leila Silvia Burger Sotto-Maior, Funai’s coordinator for uncontacted and recently contacted tribes. “They even bragged about cutting up the bodies and throwing them in the river.”

The miners, she said, claimed that “they had to kill them or be killed.”

Ms. Sotto-Maior said the killings were reported to have taken place last month. The indigenous affairs bureau conducted some initial interviews in the town and then took the case to the police.

“There is a lot of evidence, but it needs to be proven,” she said.

The prosecutor in charge of the case, Pablo Luz de Beltrand, confirmed that an investigation had begun, but said he could not discuss the details of the case while it was underway. He said the episode was alleged to have occurred in the Javari Valley — the second-largest indigenous reserve in Brazil — in the remote west.

“We are following up, but the territories are big and access is limited,” Mr. Beltrand said. “These tribes are uncontacted — even Funai has only sporadic information about them. So it’s difficult work that requires all government departments working together.”

Mr. Beltrand said it was the second such episode that he was investigating this year. The first reported killing of uncontacted Indians in the region occurred in February, and that case is still open. “It was the first time that we’d had this kind of case in this region,” he said in a telephone interview. “It’s not something that was happening before.”

Survival International, a global indigenous rights group, warned that given the small sizes of the uncontacted Amazon tribes, this latest episode could mean that a significant percentage of a remote ethnic group was wiped out.

“If the investigation confirms the reports, it will be yet another genocidal massacre resulting directly from the Brazilian government’s failure to protect isolated tribes — something that is guaranteed in the Constitution,” said Sarah Shenker, a senior campaigner with the rights group.

Under Brazil’s president, Michel Temer, funding for indigenous affairs has been slashed. In April, Funai closed five of the 19 bases that it uses to monitor and protect isolated tribes, and reduced staffing at others. The bases are used to prevent invasions by loggers and miners and to communicate with recently contacted tribes. [Continue reading…]

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Bacteria use brainlike bursts of electricity to communicate

Gabriel Popkin writes: Bacteria have an unfortunate — and inaccurate — public image as isolated cells twiddling about on microscope slides. The more that scientists learn about bacteria, however, the more they see that this hermitlike reputation is deeply misleading, like trying to understand human behavior without referring to cities, laws or speech. “People were treating bacteria as … solitary organisms that live by themselves,” said Gürol Süel, a biophysicist at the University of California, San Diego. “In fact, most bacteria in nature appear to reside in very dense communities.”

The preferred form of community for bacteria seems to be the biofilm. On teeth, on pipes, on rocks and in the ocean, microbes glom together by the billions and build sticky organic superstructures around themselves. In these films, bacteria can divide labor: Exterior cells may fend off threats, while interior cells produce food. And like humans, who have succeeded in large part by cooperating with each other, bacteria thrive in communities. Antibiotics that easily dispatch free-swimming cells often prove useless against the same types of cells when they’ve hunkered down in a film.

As in all communities, cohabiting bacteria need ways to exchange messages. Biologists have known for decades that bacteria can use chemical cues to coordinate their behavior. The best-known example, elucidated by Bonnie Bassler of Princeton University and others, is quorum sensing, a process by which bacteria extrude signaling molecules until a high enough concentration triggers cells to form a biofilm or initiate some other collective behavior. [Continue reading…]

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Massive black hole discovered near heart of the Milky Way

The Guardian reports: An enormous black hole one hundred thousand times more massive than the sun has been found hiding in a toxic gas cloud wafting around near the heart of the Milky Way.

If the discovery is confirmed, the invisible behemoth will rank as the second largest black hole ever seen in the Milky Way after the supermassive black hole known as Sagittarius A* that is anchored at the very centre of the galaxy.

Astronomers in Japan found evidence for the new object when they turned a powerful telescope in the Atacama desert in Chile towards the gas cloud in the hope of understanding the strange movement of its gases. Unlike those that make up other interstellar clouds, the gases in this cloud – including hydrogen cyanide and carbon monoxide – move at wildly different speeds.

Observations from the Alma telescope in Chile showed that molecules in the elliptical cloud, which is 200 light years from the centre of the Milky Way and 150 trillion kilometres wide, were being pulled around by immense gravitational forces. The most likely cause, according to computer models, was a black hole no more than 1.4 trillion km across. [Continue reading…]

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The modern state, not ideas, brought about religious freedom

Mark Koyama writes: Religious freedom has become an emblematic value in the West. Embedded in constitutions and championed by politicians and thinkers across the political spectrum, it is to many an absolute value, something beyond question. Yet how it emerged, and why, remains widely misunderstood.

According to the conventional narrative, freedom of religion arose in the West in the wake of devastating wars fought over religion. It was catalysed by powerful arguments from thinkers such as John Locke, Baruch Spinoza, Pierre Bayle and Voltaire. These philosophers and political theorists responded to the brutality of the religious wars with support for radical notions of toleration and religious freedom. Their liberal ideals then became embedded in the political institutions of the West, following the American and French Revolutions.

In broad outline, such is the account accepted by most political philosophers and social scientists. But the evidence does not support this emphasis on the power of ideas in shaping the rise of religious freedom, and underestimates the decisive role played by institutions.

The ideas of the philosophers were indeed important. In his Dictionnaire Historique et Critique (1697), Bayle pointed out that if one religion claimed to be the only true faith, it by implication possessed the right to persecute all the others, and all other faiths possessed an equal right to make such a claim. Showing the inherent volatility, for society, of such religious-truth claims, Bayle also argued that if people turned out to be mistaken about their religion, they could hardly be guilty of sin for nonetheless trying, in their sincerity, to observe its dictates.

Locke argued that true faith could not be compelled. It followed, he claimed, that restricting the rights of religious minorities should only be done for reasons of state, that is, not for reasons of faith or salvation. Voltaire took a no less effective course, relentlessly documenting and mocking cases of religious persecution. Time and again, he made zealots and enforcers of religious dogma look ridiculous. These are compelling and consequential ideas, and worthy of continued study and reading.

But focusing on these ideas does not fully explain how religious freedom came to the West. The intellectual importance of Bayle, Locke and Voltaire does not mean that their ideas were central to religious freedom as it developed and came to be in actual political and social life. [Continue reading…]

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How the Folsom point became an archaeological icon

Stephen E. Nash writes: The Folsom spear point, which was excavated in 1927 near the small town of Folsom, New Mexico, is one of the most famous artifacts in North American archaeology, and for good reason: It was found in direct association with the bones of an extinct form of Ice Age bison. The Folsom point therefore demonstrated conclusively, and for the first time, that human beings were in North America during the last Ice Age—thousands of years earlier than previously thought.

The Folsom discovery marked the end of a long series of sometimes serendipitous, sometimes deliberate actions by an intriguing cast of characters. As such, it helps us understand that archaeology—like most fields of study—has very few “Eureka!” moments in which a brilliant sage comes upon an insight that suddenly changes the world. Instead, archaeology is cumulative, often slow, and painstaking. And while an individual artifact can indeed be important, it’s context (where it was found) and association (what it was found with) are often more important than the object itself.

The story begins in 1908. In the late afternoon heat of August 27, an unusually strong summer thunderstorm dropped 13 inches of rain—75 percent of the yearly average—on Johnson Mesa, northwest of Folsom. The resulting flash flood swept through the town and the usually dry drainages in the vicinity. In so doing, it exposed buried features and artifacts that hadn’t seen the light of day in thousands of years. [Continue reading…]

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Yearning for the end of the world

As a child in Iran, Dina Nayeri belonged to a secret Christian church where the Rapture was welcomed as a rescue. She writes: In my mid-20s, after years of grappling with my identity as a refugee and my place in the world, I stopped believing in the Rapture. By then I had embraced all the secular, corporeal things I had secretly desired: a rigorous education, travel, great food, the admission that I do believe in science and that the Bible is at most a metaphor to me. I watched that old movie, A Thief in the Night, on my laptop and was fumed at the heavy-handed messages that had colonised my adolescent brain. The Christian characters benefit from the goodwill and love of their secular friends, then dismiss human love as insufficient. Ever blase, their lives never progress; they only wait. This was the detail in the movie that struck me most as an adult: the two primary Christian characters don’t have jobs or romances. They live in the next life.

This fetishisation of waiting was the final straw. Because here is something that only refugees (and people newly in love) can tell you: there is no painful business quite like waiting. Roland Barthes calls it subjection. For me, waiting for the Rapture and for political asylum felt much the same: the constant anticipation of a new start, of vanishing, of having already smelled the tiny yellow roses that draped our garden walls or tasted my grandmother’s celery stew for the final time. Being a refugee is dismantling home, setting out into the desert and becoming stateless in pursuit of a better life. Refugees are seekers of a sort of Rapture, and, in leaving their known world for something unimaginably good beyond, they enact a small apocalypse.

When I said this to my mother recently, she balked. Though she believes in the Rapture – it is her “living hope” – and has suffered long bouts as a refugee, she doesn’t like the comparison. “I didn’t choose to leave my home,” she said. “Being a refugee is being homeless, not having hope. In those years I lived in constant numbness, because while you’re waiting, there is nothing. No way back and no way forward. With the Rapture, going back isn’t an option, but what’s ahead is beautiful.”

The Rapture story offers a known future that you don’t have to build yourself. It happens in an instant: before you’re done with one life, you’re whisked into another. And that is everything – skipping that in-between space, the country of purgatory where the refugee lingers. “If you’ve ever been a refugee,” my mother says, “you know how much that matters.”

She’s right: I do know that. I understand now that eschatological promises provide closure, the end of mankind’s story on Earth, at once terrible and necessary. They are designed to assuage a universal fear: the fate of the refugee. To set off as an asylum seeker is to endure a carousel of embassy visits and interviews and application papers without any idea of what comes next. It’s life without a heaven or hell, just recurring cycles that lead nowhere. Refugees live out the ancient themes of purgatory and banishment literally, and that – not the guillotine’s blade or the antichrist or oblivion – is the ultimate nightmare: life without closure, forever in limbo.

But I also know that being rescued from the nightmare of waiting is not only the refugee’s greatest desire, but also her greatest dread, because then home is no longer home and she’s no longer who she once was; she is transformed. Maybe that’s why I was so much more afraid in Oklahoma than in Isfahan – by then, I had tasted that transformation. I knew what it was like to be taken away, never to smell the yellow roses or taste the celery stew again. [Continue reading…]

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Introducing ‘dark DNA’ – the phenomenon that could change how we think about evolution

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By Adam Hargreaves, University of Oxford

DNA sequencing technology is helping scientists unravel questions that humans have been asking about animals for centuries. By mapping out animal genomes, we now have a better idea of how the giraffe got its huge neck and why snakes are so long. Genome sequencing allows us to compare and contrast the DNA of different animals and work out how they evolved in their own unique ways.

But in some cases we’re faced with a mystery. Some animal genomes seem to be missing certain genes, ones that appear in other similar species and must be present to keep the animals alive. These apparently missing genes have been dubbed “dark DNA”. And its existence could change the way we think about evolution.

My colleagues and I first encountered this phenomenon when sequencing the genome of the sand rat (Psammomys obesus), a species of gerbil that lives in deserts. In particular we wanted to study the gerbil’s genes related to the production of insulin, to understand why this animal is particularly susceptible to type 2 diabetes.

But when we looked for a gene called Pdx1 that controls the secretion of insulin, we found it was missing, as were 87 other genes surrounding it. Some of these missing genes, including Pdx1, are essential and without them an animal cannot survive. So where are they?

The first clue was that, in several of the sand rat’s body tissues, we found the chemical products that the instructions from the “missing” genes would create. This would only be possible if the genes were present somewhere in the genome, indicating that they weren’t really missing but just hidden.

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Why have we taken so long to catch up with animal consciousness?

Brandon Keim writes: I met my first semipalmated sandpiper in a crook of Jamaica Bay, an overlooked shore strewn with broken bottles and religious offerings at the edge of New York City. I didn’t know what it was called, this small, dun-and-white bird running the flats like a wind-up toy, stopping to peck mud and racing to join another bird like itself, and then more. Soon a flock formed, several hundred fast-trotting feeders that at some secret signal took flight, wheeling with the flashing synchronisation that researchers observing starlings have mathematically likened to avalanche formation and liquids turning to gas.

Entranced, I spent the afternoon watching them. The birds were too wary to approach, but if I stayed in one spot they would eventually come to me. They followed the tideline, retreating when waves arrived, and rushing forward as they receded, a strangely affecting parade. When they came very close, their soft, peeping vocalisations enveloped me. That night I looked at photographs I’d taken, marvelling as the birds’ beauty emerged from stillness and enlargement, each tiny feather on their backs a masterpiece of browns. I looked up their scientific classification, Calidris pusilla, conversationally known as the semipalmated sandpiper — a name derived from a combination of their piping signal calls and the partially webbed feet that keep them from sinking in the tidal sand flats of their habitat, where they eat molluscs, insect larvae and diatom algae growing in shallow, sun-heated seawater.

I learned that semipalmated sandpipers are the most common shorebird in North America, with an estimated population around 1.9 million. My copy of Lives of North American Birds (1996) described them as ‘small and plain in appearance’, which seemed unappreciative, especially in light of their migratory habits. Small enough to fit in my hand, they breed in the Arctic and winter on South America’s northern coasts, flying several thousand miles each spring and fall, stopping just once or twice. The flock I’d watched was a thread in a string of globe-encircling energy and life, fragile yet ancient, linking my afternoon to Suriname and the tundra. At that fact, I felt the sense of wonder and connection that all migratory birds inspire. Yet not once did I wonder what they thought and felt along the way. How did they experience their own lives, not just as members of a species, but as individuals? [Continue reading…]

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The Anna Karenina hypothesis says that every unbalanced microbiome is unbalanced in its own way

Ed Yong writes: In 2012, Rebecca Vega Thurber looked at the results of the large underwater experiment she had been running for three years—and was disappointed.

Since 2009, her team had been traveling to the coral reefs of the Florida Keys. In some spots, they exposed the corals to nitrogen and phosphorus, to simulate the agricultural runoffs that often pollute these reefs. In other areas, they used wire mesh to keep fish away, mimicking the effects of overfishing. They wanted to know if these sources of stress disrupt the relationship between the corals and the trillions of microbes that live with them—and whether these disruptions lead to the corals’ demise.

Scientists have conducted hundreds of similar studies in humans. They compare healthy and sick people and look for differences in their microbiomes—the vast community of bacteria and other microbes that share our bodies. They aren’t looking for a specific disease-causing bug, like the ones behind classic infections like plague, leprosy, or tuberculosis. Instead, they’re looking for imbalances, where certain species rise to the fore, others slink into obscurity, and the entire community changes for the worse.

That’s what Vega Thurber expected to find in the corals. But that’s not what her postdoc Jesse Zaneveld found when he analyzed the results. The extra nutrients and the missing fish both changed the coral microbiomes—but not in any consistent ways. “It was a pretty dark day after three years of work,” says Vega Thurber. “A lot of students would have thrown up their hands and cried a bit. But Jesse said: You know what, I think I see something strange. It’s a pattern but one we didn’t predict.”

The microbiomes of the stressed corals had become more varied. They didn’t shift in any particular direction—they changed in every direction. And shortly after Zaneveld realized this, he spotted the same pattern—but this time in chimpanzees. Researchers at Yale University had studied the gut microbiomes of chimps that were infected with an HIV-like virus, and found that their microbiomes had also become more variable. [Continue reading…]

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We can’t thrive in a world without darkness

Rebecca Boyle writes: Sound dominated my senses as we left the village of San Pedro de Atacama and walked into the desert night. The crunch of shoes on gravel underlay our voices, which were hushed to avoid waking any households or street dogs. Our small group of astronomy writers was escaping from light and, without any flashlights or streetlamps, we struggled to see, so our other senses were heightened. Land that looked red by day was now monochromatic, the rods in our retinas serving as our only visual input.

After about 15 minutes of hiking, we stopped to take some pictures of the sky. I fumbled with my gear and tried to get my bearings, but everything was alien. I was horribly jet-lagged after 10 hours hunched against the window of a 757, another two-hour flight north from Santiago and a two-hour bus ride, and it wan’t just my oxygen-hungry brain that put me out of sorts. The Atacama Desert looked like Mars as drawn by Dr Seuss; I was surrounded by wrong-coloured cliffs and swirling rock formations. But I was determined to photograph something even more bizarre: the Large Magellanic Cloud, a dwarf galaxy you can see only from the southern hemisphere. I perched my camera on a rock and aimed at the sky, but the cosmic smudge would not resolve in my viewfinder. I stood, brushed dirt from my jeans, and looked up.

The unfamiliar sky momentarily took away what little breath I had left at 8,000 feet in elevation. Above the horizon was the conspicuous Southern Cross. Orion was there, too, but looked as disoriented as I felt, upside down to the world. And there were so many constellations I’d never seen, with hopeful, Latinate names such as Dorado and Reticulum. Countless stars blazed into view as I stared into the smear of the Milky Way.

To most people who have travelled outside the developed world – whether to camp or to meditate or to hunt – such bright and plentiful stars are a glorious sight. But this beauty instilled in me a creeping sense of guilt. At home, 1,500 miles north, I wouldn’t recognise such spangled heavens. From where I live in the American Midwest, the stars might as well not exist. After journeying millions of years, their light is swallowed by city glare and my porch lantern. Those that make it through will still fail: not even bright Betelgeuse can outshine my iPhone. Yet I am an astronomy writer, a person who thinks about stars and planets all the time. What does my neglect of the night sky say about the rest of humanity?

‘We are all descended from astronomers,’ the astrophysicist Neil deGrasse Tyson intones in the rebooted version of the TV show Cosmos. This is as poetic as it is true. Everyone owns the night sky; it was the one natural realm all our ancestors could see and know intimately. No river, no grand mountain or canyon, not even the oceans can claim that. But since Edison’s light bulbs colonised our cities, the vast majority of humans has ceased to see those skies. More than 60 per cent of the world, and fully 99 per cent of the US and Europe, lives under a yellowy sky polluted with light. [Continue reading…]

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