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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Chimpanzees learn to use tools on their own, no teaching required

Leah Froats writes: As it turns out, chimpanzees don’t need to see in order to do, no matter what the old mantra might lead you to believe.

A common belief among researchers is that chimps need to watch other members of their communities use tools before they can pick the behavior up. In a study published in PeerJ in September, researchers from the University of Birmingham, and the University of Tübingen challenged this belief and checked to see if it would hold for a specific kind of tool use.

They attempted to recreate a behavior commonly found in the wild: the use of sticks to scoop algae from the water to eat. Would chimpanzees that were unfamiliar with this behavior be able to figure it out on their own? [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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The stunning underwater picture this photographer wishes ‘didn’t exist’

Lindsey Bever writes: The powerful and poignant image shows a tiny sea horse holding tightly onto a pink, plastic cotton swab in blue-green waters around Indonesia.

California nature photographer Justin Hofman snapped the picture late last year off the coast of Sumbawa, an Indonesian island in the Lesser Sunda Islands chain. The 33-year-old, from Monterey, Calif., said a colleague pointed out the pocket-size sea creature, which he estimated to be about 1.5 inches tall — so small, in fact, that Hofman said he almost didn’t reach for his camera.

“The wind started to pick up and the sea horse started to drift. It first grabbed onto a piece of sea grass,” Hofman said Thursday in a phone interview.

Hofman started shooting.

“Eventually more and more trash and debris started to move through,” he said, adding that the critter lost its grip, then latched onto a white, wispy piece of a plastic bag. “The next thing it grabbed was a Q-Tip.”

Hofman said he wishes the picture “didn’t exist” — but it does; and now, he said, he feels responsible “to make sure it gets to as many eyes as possible.” [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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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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Beating the odds for lucky mutations

Jordana Cepelewicz writes: In 1944, a Columbia University doctoral student in genetics named Evelyn Witkin made a fortuitous mistake. During her first experiment in a laboratory at Cold Spring Harbor, in New York, she accidentally irradiated millions of E. coli with a lethal dose of ultraviolet light. When she returned the following day to check on the samples, they were all dead — except for one, in which four bacterial cells had survived and continued to grow. Somehow, those cells were resistant to UV radiation. To Witkin, it seemed like a remarkably lucky coincidence that any cells in the culture had emerged with precisely the mutation they needed to survive — so much so that she questioned whether it was a coincidence at all.

For the next two decades, Witkin sought to understand how and why these mutants had emerged. Her research led her to what is now known as the SOS response, a DNA repair mechanism that bacteria employ when their genomes are damaged, during which dozens of genes become active and the rate of mutation goes up. Those extra mutations are more often detrimental than beneficial, but they enable adaptations, such as the development of resistance to UV or antibiotics.

The question that has tormented some evolutionary biologists ever since is whether nature favored this arrangement. Is the upsurge in mutations merely a secondary consequence of a repair process inherently prone to error? Or, as some researchers claim, is the increase in the mutation rate itself an evolved adaptation, one that helps bacteria evolve advantageous traits more quickly in stressful environments?

The scientific challenge has not just been to demonstrate convincingly that harsh environments cause nonrandom mutations. It has also been to find a plausible mechanism consistent with the rest of molecular biology that could make lucky mutations more likely. Waves of studies in bacteria and more complex organisms have sought those answers for decades. [Continue reading…]

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How color vision came to the animals

Nick Stockton writes: Animals are living color. Wasps buzz with painted warnings. Birds shimmer their iridescent desires. Fish hide from predators with body colors that dapple like light across a rippling pond. And all this color on all these creatures happened because other creatures could see it.

The natural world is so showy, it’s no wonder scientists have been fascinated with animal color for centuries. Even today, the questions how animals see, create, and use color are among the most compelling in biology.

Until the last few years, they were also at least partially unanswerable—because color researchers are only human, which means they can’t see the rich, vivid colors that other animals do. But now new technologies, like portable hyperspectral scanners and cameras small enough to fit on a bird’s head, are helping biologists see the unseen. And as described in a new Science paper, it’s a whole new world. [Continue reading…]

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Aliens in our midst

Douglas Fox writes: Leonid Moroz has spent two decades trying to wrap his head around a mind-boggling idea: even as scientists start to look for alien life in other planets, there might already be aliens, with surprisingly different biology and brains, right here on Earth. Those aliens have hidden in plain sight for millennia. They have plenty to teach us about the nature of evolution, and what to expect when we finally discover life on other worlds.

Moroz, a neuroscientist, saw the first hint of his discovery back in the summer of 1995, not long after arriving in the United States from his native Russia. He spent that summer at the Friday Harbor marine laboratory in Washington. The lab sat amid an archipelago of forested islands in Puget Sound – a crossroads of opposing tides and currents that carried hundreds of animal species past the rocky shore: swarms of jellyfish, amphipod crustaceans, undulating sea lilies, nudibranch slugs, flatworms, and the larvae of fish, sea stars and countless other animals. These creatures represented not just the far reaches of Puget Sound, but also the farthest branches of the animal tree of life. Moroz spent hours out on the pier behind the lab, collecting animals so he could study their nerves. He had devoted years to studying nervous systems across the animal kingdom, in hopes of understanding the evolutionary origin of brains and intelligence. But he came to Friday Harbor to find one animal in particular.

He trained his eyes to recognise its bulbous, transparent body in the sunlit water: an iridescent glint and fleeting shards of rainbow light, scattered by the rhythmic beating of thousands of hair-like cilia, propelling it through the water. This type of animal, called a ctenophore (pronounced ‘ten-o-for’ or ‘teen-o-for’), was long considered just another kind of jellyfish. But that summer at Friday Harbor, Moroz made a startling discovery: beneath this animal’s humdrum exterior was a monumental case of mistaken identity. From his very first experiments, he could see that these animals were unrelated to jellyfish. In fact, they were profoundly different from any other animal on Earth.

Moroz reached this conclusion by testing the nerve cells of ctenophores for the neurotransmitters serotonin, dopamine and nitric oxide, chemical messengers considered the universal neural language of all animals. But try as he might, he could not find these molecules. The implications were profound.

The ctenophore was already known for having a relatively advanced nervous system; but these first experiments by Moroz showed that its nerves were constructed from a different set of molecular building blocks – different from any other animal – using ‘a different chemical language’, says Moroz: these animals are ‘aliens of the sea’.

If Moroz is right, then the ctenophore represents an evolutionary experiment of stunning proportions, one that has been running for more than half a billion years. This separate pathway of evolution – a sort of Evolution 2.0 – has invented neurons, muscles and other specialised tissues, independently from the rest of the animal kingdom, using different starting materials. [Continue reading…]

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How to turn a fox into a dog

Lee Dugatkin and Lyudmila Trut: Deep inside my soul,” says Lyudmila Trut, “is a pathological love for animals.” She inherited this from her mother, who was a great dog lover. Lyudmila had grown up with dogs as pets, and even during World War II, when food was horribly scarce, her mother would feed starving stray dogs, telling her, “If we don’t feed them, Lyudmila, how will they survive? They need people.” Following her mother’s example, Lyudmila always carries some kind of treat in a pocket in case she encounters a stray dog. And she’s never forgotten that domesticated animals need people. She knows that this is how we’ve designed them.

In 1958, Lyudmila was just finishing up her studies at Moscow State University, home of Leonid Krushinsky, a pioneering Russian researcher in animal behavior. Dmitri Belyaev was friends with Krushinsky and admired his work. Belyaev had recently accepted a position as vice director of a new research institute in a giant Soviet city of science called Akademgorodok, near Novosibirsk, Siberia. He was searching for someone to lead an experiment he would begin in earnest at Akademgorodok. Dmitri intended to run an experiment domesticating silver foxes, and so the person he sought needed the kind of sophisticated skills in animal behavior that Krushinksy taught.

Belyaev went to visit Krushinsky at his office at Moscow State’s Sparrow Hill campus for advice about who might work with him on this experiment. Ensconced in the grand setting of Krushinsky’s building, with its palatial ceilings, marble floors, ornate columns, and fine art statues, he described his plans for the experiment and explained that he was looking for talented graduates to assist with the work. Krushinsky put the word out, and when Lyudmila heard about the opportunity, she was immediately captivated. Her own undergraduate work had been on the behavior of crabs, and as fascinating as their complex behavior could be, the prospect of working with foxes, so closely related to her beloved dogs, and with such a well-respected scientist as Belyaev, was tantalizing.

In early 1958, Lyudmila went to meet with Belyaev at his office. She was immediately struck by how unusual he was for a male Soviet scientist, especially one of his rank. Many were quite high-handed, and condescending to women. Lyudmila, who has a genial, smiling manner and stands just five feet tall, with her wavy brown hair cropped quite short, looked young for her age, and she hadn’t even finished her undergraduate studies, but Dmitri spoke to her as an equal. She was riveted, she recalls, by his piercing blue eyes, which so strongly communicated his intelligence and drive, but also emanated an extraordinary empathy.

She felt privileged to be invited into the confidence of this extraordinary man, who shared with her so openly about the bold work he was proposing. She had never experienced such a distinctive combination of confidence and warmth in a person. Dmitri told Lyudmila what he had in mind. “He told me that he wanted to make a dog out of a fox,” she recalls. Probing how creative she would be about conducting the experiment, Belyaev asked her, “You are now located on a fox farm that has several hundred foxes, and you need to select the 20 calmest ones for the experiment. How will you do it?” She had no experience whatsoever with foxes, and had only a vague notion of what the fox farms might be like and what sort of welcome she might receive at them. But she was a confident young woman, and she did the best she could to suggest some reasonable possibilities. She would try different methods, she said, talk to people who had worked with foxes, read up on what was known in the literature. Dmitri sat back and listened, gauging how committed she would be to the work and to developing techniques for such a novel study. She must be not only rigorously scientific, but also quite inventive. Was she really ready to go to Novosibirsk, to move to Akademgorodok, he asked her? After all, moving to the heart of Siberia was a life change not to be taken lightly. [Continue reading…]

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New study finds as many as ‘50% of the number of animal individuals that once shared Earth with us are already gone’

Ed Yong writes: Imagine if every animal and plant on the planet collapsed into a single population each, says ecologist Gerardo Ceballos. If lions disappeared except from one small corner of Kenya, the prey they keep in check would run amok everywhere else. If sparrows were no more except in one Dutch forest, the seeds that sparrows disperse would stay in place everywhere else. If honeybees became isolated to one American meadow, the flowers that they pollinate would fail to reproduce everywhere else. None of those species would be extinct per se, “but we’d still be in very bad shape,” says Ceballos.

He uses this thought experiment to show that fixating on the concept of extinction can lead scientists to overestimate the state of the planet’s health. Extinction obviously matters. If a species is completely wiped out, that’s an important and irreversible loss. But that flip from present to absent, extant to extinct, is just the endpoint of a long period of loss. Before a species disappears entirely, it first disappears locally. And each of those local extinctions—or extirpations—also matters.

“If jaguars become extinct in Mexico, it doesn’t matter if there are still jaguars in Brazil for the role that jaguars play in Mexican ecosystems,” says Ceballos. “Or we might able to keep California condors alive forever, but if there are just 10 or 12 individuals, they won’t be able to survive without human intervention. We’re missing the point when we focus just on species extinction.”

He and his colleagues, Paul Ehrlich and Rodolfo Dirzo, have now tried to quantify those local losses. First, they analyzed data for some 27,600 species of land-based vertebrates, and found that a third of these are in decline. That doesn’t mean they are endangered: A third of these declining species are listed as “low concern” by the International Union for Conservation of Nature, meaning that they aren’t in immediate peril. But that, according to Ceballos’s team, provides a false sense of security. Barn swallows, for example, still number in the millions, but those numbers are going down, and the birds are disappearing from many parts of their range. “Even these common species are declining,” says Ceballos. “Eventually, they’ll become endangered, and eventually they’ll be extinct.”

The team also analyzed detailed historical data for 177 species of mammals. In the last century, every one of these species has lost at least 30 percent of its historical range, and almost half have lost more than 80 percent. Consider the lion. If you divide the world’s land into a grid of 22,000 sectors, each containing 10,000 square kilometers, around 2,000 of those would have been home to lions at the start of the 20th century. Now, just 600 of them are. These royal beasts, which once roamed all over Africa and all the way from southern Europe to northern India, are now confined to pockets of sub-Saharan Africa, and a single Indian forest. Their numbers have fallen by 43 percent in the last two decades.

Several other species that were once thought to be safe are also now endangered. Since the 1980s, the giraffe population has fallen by up to 40 percent, from at least 152,000 animals to just 98,000 in 2015. In the last decade, savanna elephant numbers have fallen by 30 percent, and 80 percent of forest elephants were slaughtered in a national park that was one of their last strongholds. Cheetahs are down to their last 7,000 individuals, and orangutans to their last 5,000.

All told, “as much as 50 percent of the number of animal individuals that once shared Earth with us are already gone, as are billions of populations,” Ceballos and his colleagues write. “While the biosphere is undergoing mass species extinction, it is also being ravaged by a much more serious and rapid wave of population declines and extinctions.” [Continue reading…]

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Can microbes encourage altruism?

Elizabeth Svoboda writes: Parasites are among nature’s most skillful manipulators — and one of their specialties is making hosts perform reckless acts of irrational self-harm. There’s Toxoplasma gondii, which drives mice to seek out cats eager to eat them, and the liver fluke Dicrocoelium dendriticum, which motivates ants to climb blades of grass, exposing them to cows and sheep hungry for a snack. There’s Spinochordodes tellinii, the hairworm that compels crickets to drown themselves so the worm can access the water it needs to breed. The hosts’ self-sacrifice gains them nothing but serves the parasites’ hidden agenda, enabling them to complete their own life cycle.

Now researchers are beginning to explore whether parasitic manipulations may spur host behaviors that are selfless rather than suicidal. They are wondering whether microbes might be fundamentally responsible for many of the altruistic behaviors that animals show toward their own kind. Altruism may seem easy to justify ethically or strategically, but explaining how it could have persisted in a survival-of-the-fittest world is surprisingly difficult and has puzzled evolutionary theorists going all the way back to Darwin. If microbes in the gut or other tissues can nudge their hosts toward generosity for selfish reasons of their own, altruism may become less enigmatic.

A recently developed mathematical model and related computer simulations by a trio of researchers at Tel Aviv University appear to validate this theory. The researchers showed that transmissible microbes that promoted altruism in their hosts won the survival battle over microbes that did not — and when this happened, altruism became a stable trait in the host population. The research was published in Nature Communications earlier this year.

“The story is fascinating, because we don’t think of altruism in terms of the host-microbiome relationship,” said John Bienenstock, a biologist at McMaster University in Hamilton, Ontario, and director of the Brain-Body Institute at St. Joseph’s Healthcare Hamilton, who was not involved with the simulation work. “You can’t ignore the possible effect of what your bug population is doing.” [Continue reading…]

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What hyenas can tell us about the origins of intelligence

David Z. Hambrick writes: Physical similarities aside, we share a lot in common with our primate relatives. For example, as Jane Goodall famously documented, chimpanzees form lifelong bonds and show affection in much the same way as humans. Chimps can also solve novel problems, use objects as tools, and may possess “theory of mind”—an understanding that others may have different perspectives than oneself. They can even outperform humans in certain types of cognitive tasks.

These commonalities may not seem all that surprising given what we now know from the field of comparative genomics: We share nearly all of our DNA with chimpanzees and other primates. However, social and cognitive complexity is not unique to our closest evolutionary cousins. In fact, it is abundant in species with which we would seem to have very little in common—like the spotted hyena.

For more than three decades, the Michigan State University zoologist Kay Holekamp has studied the habits of the spotted hyena in Kenya’s Masai Mara National Reserve, once spending five years straight living in a tent among her oft-maligned subjects. One of the world’s longest-running studies of a wild mammal, this landmark project has revealed that spotted hyenas not only have social groups as complex as those of many primates, but are also capable of some of the same types of problem solving.

This research sheds light on one of science’s greatest mysteries—how intelligence has evolved across the animal kingdom. [Continue reading…]

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Jumping genes play a big role in what makes us human

Science News reports: Face-to-face, a human and a chimpanzee are easy to tell apart. The two species share a common primate ancestor, but over millions of years, their characteristics have morphed into easily distinguishable features. Chimps developed prominent brow ridges, flat noses, low-crowned heads and protruding muzzles. Human noses jut from relatively flat faces under high-domed crowns.

Those facial features diverged with the help of genetic parasites, mobile bits of genetic material that insert themselves into their hosts’ DNA. These parasites go by many names, including “jumping genes,” “transposable elements” and “transposons.” Some are relics of former viruses assimilated into a host’s genome, or genetic instruction book. Others are self-perpetuating pieces of genetic material whose origins are shrouded in the mists of time.

“Transposable elements have been with us since the beginning of evolution. Bacteria have transposable elements,” says evolutionary biologist Josefa González. She doesn’t think of transposons as foreign DNA. They are parts of our genomes — like genes.

“You cannot understand the genome without understanding what transposable elements are doing,” says González, of the Institute of Evolutionary Biology in Barcelona. She studies how jumping genes have influenced fruit fly evolution.

Genomes of most organisms are littered with the carcasses of transposons, says Cédric Feschotte, an evolutionary geneticist at the University of Utah in Salt Lake City. Fossils of the DNA parasites build up like the remains of ancient algae that formed the white cliffs of Dover. One strain of maize, the organism in which Nobel laureate Barbara McClintock first discovered transposable elements in the 1940s, is nearly 85 percent transposable elements (SN: 12/19/09, p. 9). Corn is an extreme example, but humans have plenty, too: Transposable elements make up nearly half of the human genome.

Most of the transposons in the genomes of humans and other creatures are now “dead,” meaning they are no longer able to jump. The majority are in bits and pieces scattered throughout the genome like so much confetti. Many researchers used to think these broken transposons were just genetic garbage.

Far from junk, however, jumping gene remnants have been an evolutionary treasure trove. Some of the control switches transposons once used for their own hopping have been recycled over time into useful tools that help species, including Homo sapiens, adapt to their environments or take on new characteristics. [Continue reading…]

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The thoughts of a spiderweb

Joshua Sokol writes: Millions of years ago, a few spiders abandoned the kind of round webs that the word “spiderweb” calls to mind and started to focus on a new strategy. Before, they would wait for prey to become ensnared in their webs and then walk out to retrieve it. Then they began building horizontal nets to use as a fishing platform. Now their modern descendants, the cobweb spiders, dangle sticky threads below, wait until insects walk by and get snagged, and reel their unlucky victims in.

In 2008, the researcher Hilton Japyassú prompted 12 species of orb spiders collected from all over Brazil to go through this transition again. He waited until the spiders wove an ordinary web. Then he snipped its threads so that the silk drooped to where crickets wandered below. When a cricket got hooked, not all the orb spiders could fully pull it up, as a cobweb spider does. But some could, and all at least began to reel it in with their two front legs.

Their ability to recapitulate the ancient spiders’ innovation got Japyassú, a biologist at the Federal University of Bahia in Brazil, thinking. When the spider was confronted with a problem to solve that it might not have seen before, how did it figure out what to do? “Where is this information?” he said. “Where is it? Is it in her head, or does this information emerge during the interaction with the altered web?”

In February, Japyassú and Kevin Laland, an evolutionary biologist at the University of Saint Andrews, proposed a bold answer to the question. They argued in a review paper, published in the journal Animal Cognition, that a spider’s web is at least an adjustable part of its sensory apparatus, and at most an extension of the spider’s cognitive system.

This would make the web a model example of extended cognition, an idea first proposed by the philosophers Andy Clark and David Chalmers in 1998 to apply to human thought. In accounts of extended cognition, processes like checking a grocery list or rearranging Scrabble tiles in a tray are close enough to memory-retrieval or problem-solving tasks that happen entirely inside the brain that proponents argue they are actually part of a single, larger, “extended” mind.

Among philosophers of mind, that idea has racked up citations, including supporters and critics. And by its very design, Japyassú’s paper, which aims to export extended cognition as a testable idea to the field of animal behavior, is already stirring up antibodies among scientists. “I got the impression that it was being very careful to check all the boxes for hot topics and controversial topics in animal cognition,” said Alex Jordan, a collective behaviorial scientist at the Max Planck Institute in Konstanz, Germany (who nonetheless supports the idea).

While many disagree with the paper’s interpretations, the study shouldn’t be confused for a piece of philosophy. Japyassú and Laland propose ways to test their ideas in concrete experiments that involve manipulating the spider’s web — tests that other researchers are excited about. “We can break that machine; we can snap strands; we can reduce the way that animal is able to perceive the system around it,” Jordan said. “And that generates some very direct and testable hypotheses.” [Continue reading…]

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The language of prairie dogs

Ferris Jabr writes: [Con] Slobodchikoff, an emeritus professor of biology at Northern Arizona University, has been analyzing the sounds of prairie dogs for more than 30 years. Not long after he started, he learned that prairie dogs had distinct alarm calls for different predators. Around the same time, separate researchers found that a few other species had similar vocabularies of danger. What Slobodchikoff claimed to discover in the following decades, however, was extraordinary: Beyond identifying the type of predator, prairie-dog calls also specified its size, shape, color and speed; the animals could even combine the structural elements of their calls in novel ways to describe something they had never seen before. No scientist had ever put forward such a thorough guide to the native tongue of a wild species or discovered one so intricate. Prairie-dog communication is so complex, Slobodchikoff says — so expressive and rich in information — that it constitutes nothing less than language.

That would be an audacious claim to make about even the most overtly intelligent species — say, a chimpanzee or a dolphin — let alone some kind of dirt hamster with a brain that barely weighs more than a grape. The majority of linguists and animal-communication experts maintain that language is restricted to a single species: ourselves. Perhaps because it is so ostensibly entwined with thought, with consciousness and our sense of self, language is the last bastion encircling human exceptionalism. To concede that we share language with other species is to finally and fully admit that we are different from other animals only in degrees not in kind. In many people’s minds, language is the “cardinal distinction between man and animal, a sheerly dividing line as abrupt and immovable as a cliff,” as Tom Wolfe argues in his book “The Kingdom of Speech,” published last year.

Slobodchikoff thinks that dividing line is an illusion. To him, the idea that a human might have a two-way conversation with another species, even a humble prairie dog, is not a pretense; it’s an inevitability. And the notion that animals of all kinds routinely engage in sophisticated discourse with one another — that the world’s ecosystems reverberate with elaborate animal idioms just waiting to be translated — is not Doctor Dolittle-inspired nonsense; it is fact. [Continue reading…]

 

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