Category Archives: Biology

Resurrecting ancient proteins to illuminate the origins of life

Emily Singer writes: About 4 billion years ago, molecules began to make copies of themselves, an event that marked the beginning of life on Earth. A few hundred million years later, primitive organisms began to split into the different branches that make up the tree of life. In between those two seminal events, some of the greatest innovations in existence emerged: the cell, the genetic code and an energy system to fuel it all. All three of these are essential to life as we know it, yet scientists know disappointingly little about how any of these remarkable biological innovations came about.

“It’s very hard to infer even the relative ordering of evolutionary events before the last common ancestor,” said Greg Fournier, a geobiologist at the Massachusetts Institute of Technology. Cells may have appeared before energy metabolism, or perhaps it was the other way around. Without fossils or DNA preserved from organisms living during this period, scientists have had little data to work from.

Fournier is leading an attempt to reconstruct the history of life in those evolutionary dark ages — the hundreds of millions of years between the time when life first emerged and when it split into what would become the endless tangle of existence.

He is using genomic data from living organisms to infer the DNA sequence of ancient genes as part of a growing field known as paleogenomics. In research published online in March in the Journal of Molecular Evolution, Fournier showed that the last chemical letter added to the code was a molecule called tryptophan — an amino acid most famous for its presence in turkey dinners. The work supports the idea that the genetic code evolved gradually. [Continue reading…]

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The man who drank cholera and launched the yogurt craze

Lina Zeldovich writes: What do Jamie Lee Curtis, gut bacteria, and a long forgotten Russian scientist have in common? Why, yogurt, of course. But wait, the answer is not that easy. Behind it stretches a tale that shows you can never predict cultural influence. It wends its way through the Pasteur Institute, the Nobel Prize, one of the hottest fields of scientific research today, the microbiome, and one of the trendiest avenues in nutrition, probiotics. It all began in the 19th century with a hyperactive kid in Russia who had a preternatural ability to connect dots where nobody saw dots at all.

When Ilya Metchnikoff was 8 and running around on his parents’ Panassovka estate in Little Russia, now Ukraine, he was making notes on the local flora like a junior botanist. He gave science lectures to his older brothers and local kids whose attendance he assured by paying them from his pocket money. Metchnikoff earned the nickname “Quicksilver” because he was in constant motion, always wanting to see, taste, and try everything, from studying how his father played card games to learning to sew and embroider with the maids. His wife later wrote in The Life of Ellie Metchnikoff that Metchnikoff asked the “queerest” questions, often exasperating his caretakers. “He could only be kept quiet when his curiosity was awakened by observation of some natural objects such as an insect or a butterfly.”

At 16, Metchnikoff borrowed a microscope from a university professor to study the lower organisms. Darwin’s On the Origin of Species shaped his comparative approach to science during his university years — he viewed all organisms, and physiological processes that took place in them, as interconnected and related.

That ability led him to the discovery of a particular cell and enabled him to link digestive processes in primitive creatures to the human body’s immune defenses. In lower organisms, which lack the abdominal cavity and intestines, digestion is accomplished by a particular type of cells — mobile mesodermal cells — that move around engulfing and dissolving food particles. While staring at mesodermal cells inside transparent starfish larvae, Metchnikoff, 37 at the time, had a thought. “It struck me that similar cells might serve in the defense of the organisms against intruders,” he wrote. He fetched a few rose thorns from the garden and stuck them into the larvae. If his hypothesis was correct, the larva’s body would recognize thorns as intruders and mesodermal cells would aggregate around the thorns in an attempt to gobble them up. As Metchnikoff expected, the mesodermal cells surrounded the thorns, proving his theory. He named his cells phagocytes, which in Greek means “devouring cells,” and likened them to an “army hurling itself upon the enemy.” [Continue reading…]

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How artificial sweeteners could lead to obesity

Scientific American reports: Many of us, particularly those who prefer to eat our cake and look like we have not done so, have a love-hate relationship with artificial sweeteners. These seemingly magical molecules deliver a dulcet taste without its customary caloric punch. We guzzle enormous quantities of these chemicals, mostly in the form of aspartame, sucralose and saccharin, which are used to enliven the flavor of everything from Diet Coke to toothpaste. Yet there are worries. Many suspect that all this sweetness comes at some hidden cost to our health, although science has only pointed at vague links to problems.

Last year, though, a team of Israeli scientists put together a stronger case. The researchers concluded from studies of mice that ingesting artificial sweeteners might lead to—of all things—obesity and related ailments such as diabetes. This study was not the first to note this link in animals, but it was the first to find evidence of a plausible cause: the sweeteners appear to change the population of intestinal bacteria that direct metabolism, the conversion of food to energy or stored fuel. And this result suggests the connection might also exist in humans.

In humans, as well as mice, the ability to digest and extract energy from our food is determined not only by our genes but also by the activity of the trillions of microbes that dwell within our digestive tract; collectively, these bacteria are known as the gut microbiome. The Israeli study suggests that artificial sweeteners enhance the populations of gut bacteria that are more efficient at pulling energy from our food and turning that energy into fat. In other words, artificial sweeteners may favor the growth of bacteria that make more calories available to us, calories that can then find their way to our hips, thighs and midriffs, says Peter Turnbaugh of the University of California, San Francisco, an expert on the interplay of bacteria and metabolism. [Continue reading…]

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Stardust

Ray Jayawardhana writes: Joni Mitchell beat Carl Sagan to the punch. She sang “we are stardust, billion-year-old carbon” in her 1970 song “Woodstock.” That was three years before Mr. Sagan wrote about humans’ being made of “star-stuff” in his book “The Cosmic Connection” — a point he would later convey to a far larger audience in his 1980 television series, “Cosmos.”

By now, “stardust” and “star-stuff” have nearly turned cliché. But that does not make the reality behind those words any less profound or magical: The iron in our blood, the calcium in our bones and the oxygen we breathe are the physical remains — ashes, if you will — of stars that lived and died long ago.

That discovery is relatively recent. Four astrophysicists developed the idea in a landmark paper published in 1957. They argued that almost all the elements in the periodic table were cooked up over time through nuclear reactions inside stars — rather than in the first instants of the Big Bang, as previously thought. The stuff of life, in other words, arose in places and times somewhat more accessible to our telescopic investigations.

Since most of us spend our lives confined to a narrow strip near Earth’s surface, we tend to think of the cosmos as a lofty, empyrean realm far beyond our reach and relevance. We forget that only a thin sliver of atmosphere separates us from the rest of the universe. [Continue reading…]

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How useful is the idea of the Anthropocene?

Jedediah Purdy writes: As much as a scientific concept, the Anthropocene is a political and ethical gambit. Saying that we live in the Anthropocene is a way of saying that we cannot avoid responsibility for the world we are making. So far so good. The trouble starts when this charismatic, all-encompassing idea of the Anthropocene becomes an all-purpose projection screen and amplifier for one’s preferred version of ‘taking responsibility for the planet’.

Peter Kareiva, the controversial chief scientist of the Nature Conservancy, uses the theme ‘Conservation in the Anthropocene’ to trash environmentalism as philosophically naïve and politically backward. Kareiva urges conservationists to give up on wilderness and embrace what the writer Emma Marris calls the ‘rambunctious garden’. Specifically, Kareiva wants to rank ecosystems by the quality of ‘ecosystem services’ they provide for human beings instead of ‘pursuing the protection of biodiversity for biodiversity’s sake’. He wants a pro‑development stance that assumes that ‘nature is resilient rather than fragile’. He insists that: ‘Instead of scolding capitalism, conservationists should partner with corporations in a science-based effort to integrate the value of nature’s benefits into their operations and cultures.’ In other words, the end of nature is the signal to carry on with green-branded business as usual, and the business of business is business, as the Nature Conservancy’s partnerships with Dow, Monsanto, Coca-Cola, Pepsi, J P Morgan, Goldman Sachs and the mining giant Rio Tinto remind us.

Kareiva is a favourite of Andrew Revkin, the roving environmental maven of The New York Times Magazine, who touts him as a paragon of responsibility-taking, a leader among ‘scholars and doers who see that new models for thinking and acting are required in this time of the Anthropocene’. This pair and their friends at the Breakthrough Institute in California can be read as making a persistent effort to ‘rebrand’ environmentalism as humanitarian and development-friendly (and capture speaking and consultancy fees, which often seem to be the major ecosystem services of the Anthropocene). This is itself a branding strategy, an opportunity to slosh around old plonk in an ostentatiously shiny bottle. [Continue reading…]

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Inside the new social science of genetics

David Dobbs writes: A few years ago, Gene Robinson, of Urbana, Illinois, asked some associates in southern Mexico to help him kidnap some 1,000 newborns. For their victims they chose bees. Half were European honeybees, Apis mellifera ligustica, the sweet-tempered kind most beekeepers raise. The other half were ligustica’s genetically close cousins, Apis mellifera scutellata, the African strain better known as killer bees. Though the two subspecies are nearly indistinguishable, the latter defend territory far more aggressively. Kick a European honeybee hive and perhaps a hundred bees will attack you. Kick a killer bee hive and you may suffer a thousand stings or more. Two thousand will kill you.

Working carefully, Robinson’s conspirators — researchers at Mexico’s National Center for Research in Animal Physiology, in the high resort town of Ixtapan de la Sal — jiggled loose the lids from two African hives and two European hives, pulled free a few honeycomb racks, plucked off about 250 of the youngest bees from each hive, and painted marks on the bees’ tiny backs. Then they switched each set of newborns into the hive of the other subspecies.

Robinson, back in his office at the University of Illinois at Urbana-Champaign’s Department of Entomology, did not fret about the bees’ safety. He knew that if you move bees to a new colony in their first day, the colony accepts them as its own. Nevertheless, Robinson did expect the bees would be changed by their adoptive homes: He expected the killer bees to take on the European bees’ moderate ways and the European bees to assume the killer bees’ more violent temperament. Robinson had discovered this in prior experiments. But he hadn’t yet figured out how it happened.

He suspected the answer lay in the bees’ genes. He didn’t expect the bees’ actual DNA to change: Random mutations aside, genes generally don’t change during an organism’s lifetime. Rather, he suspected the bees’ genes would behave differently in their new homes — wildly differently.

This notion was both reasonable and radical. Scientists have known for decades that genes can vary their level of activity, as if controlled by dimmer switches. Most cells in your body contain every one of your 22,000 or so genes. But in any given cell at any given time, only a tiny percentage of those genes is active, sending out chemical messages that affect the activity of the cell. This variable gene activity, called gene expression, is how your body does most of its work. [Continue reading…]

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Your gut tells your mind, more than you may imagine

Charles Schmidt writes: The notion that the state of our gut governs our state of mind dates back more than 100 years. Many 19th- and early 20th-century scientists believed that accumulating wastes in the colon triggered a state of “auto-intoxication,” whereby poisons emanating from the gut produced infections that were in turn linked with depression, anxiety and psychosis. Patients were treated with colonic purges and even bowel surgeries until these practices were dismissed as quackery.

The ongoing exploration of the human microbiome promises to bring the link between the gut and the brain into clearer focus. Scientists are increasingly convinced that the vast assemblage of microfauna in our intestines may have a major impact on our state of mind. The gut-brain axis seems to be bidirectional — the brain acts on gastrointestinal and immune functions that help to shape the gut’s microbial makeup, and gut microbes make neuroactive compounds, including neurotransmitters and metabolites that also act on the brain. These interactions could occur in various ways: microbial compounds communicate via the vagus nerve, which connects the brain and the digestive tract, and microbially derived metabolites interact with the immune system, which maintains its own communication with the brain. Sven Pettersson, a microbiologist at the Karolinska Institute in Stockholm, has recently shown that gut microbes help to control leakage through both the intestinal lining and the blood-brain barrier, which ordinarily protects the brain from potentially harmful agents.

Microbes may have their own evolutionary reasons for communicating with the brain. They need us to be social, says John Cryan, a neuroscientist at University College Cork in Ireland, so that they can spread through the human population. Cryan’s research shows that when bred in sterile conditions, germ-free mice lacking in intestinal microbes also lack an ability to recognize other mice with whom they interact. In other studies, disruptions of the microbiome induced mice behavior that mimics human anxiety, depression and even autism. In some cases, scientists restored more normal behavior by treating their test subjects with certain strains of benign bacteria. Nearly all the data so far are limited to mice, but Cryan believes the findings provide fertile ground for developing analogous compounds, which he calls psychobiotics, for humans. “That dietary treatments could be used as either adjunct or sole therapy for mood disorders is not beyond the realm of possibility,” he says. [Continue reading…]

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The genetic code is less like a blueprint than a first draft

Nessa Carey writes: When President Obama delivered a speech at MIT in 2009, he used a common science metaphor: “We have always been about innovation,” he said. “We have always been about discovery. That’s in our DNA.” Deoxyribonucleic acid, the chemical into which our genes are encoded, has become the metaphor of choice for a whole constellation of ideas about essence and identity. A certain mystique surrounds it. As Evelyn Fox Keller argues in her book The Century of the Gene, the genome is, in the popular imagination at least, the secret of life, the holy grail. It is a master builder, the ultimate computer program, and a modern-day echo of the soul, all wrapped up in one. This fantasy does not sit easily, however, with geneticists who have grown more aware over the last several decades that the relationship between genes and biological traits is much less than certain.

The popular understanding of DNA as a blueprint for organisms, with a one-to-one correspondence between genes and traits (called phenotypes), is the legacy of the early history of genetics. The term “gene” was coined in 1909 to refer to abstract units of inheritance, predating the discovery of DNA by forty years. Biologists came to think of genes like beads on a string that lined up neatly into chromosomes, with each gene determining a single phenotype. But, while some genes do correspond to traits in a straightforward way, as in eye color or blood group, most phenotypes are far more complex, set in motion by many different genes as well as by the environment in which the organism lives.

It turns out that the genetic code is less like a blueprint and more like a movie script, subject to revision and reinterpretation by a director. This process is called epigenetic modification (“epi” meaning “above” or “in addition to”). Just as a script can be altered with crossed-out words, sentences or scenes, epigenetic editing allows entire sections of DNA to be activated or de-activated. Genes can be as finely tuned as actors responding to stage directions to shout, whisper, or cackle. [Continue reading…]

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Darwin learned more about evolution from plants than Galapagos Finches

Henry Nicholls writes: When the HMS Beagle dropped anchor on San Cristobal, the easternmost island in the Galapagos archipelago, in September 1835, the ship’s naturalist Charles Darwin eagerly went ashore to gather samples of the insects, birds, reptiles, and plants living there. At first, he didn’t think much of the arid landscape, which appeared to be “covered by stunted, sun-burnt brushwood…as leafless as our trees during winter” But this did not put him off. By the time the Beagle left these islands some five weeks later, he had amassed a spectacular collection of Galapagos plants.

It is fortunate that he took such trouble. Most popular narratives of Darwin and the Galapagos concentrate on the far more celebrated finches or the giant tortoises. Yet when he finally published On the Origin of Species almost 25 years later, Darwin made no mention of these creatures. In his discussion of the Galapagos, he dwelt almost exclusively on the islands’ plants.

By the early 19th century, there was increasing interest in what we now refer to as biogeography, the study of the distribution of species around the globe. Many people still imagined that God had been involved in the creation of species, putting fully formed versions down on Earth that continued to reproduce themselves, dispersing from a divine “center of creation” to occupy their current habitats. To explain how the plants and animals reached far-flung places such as the isolated Galapagos, several naturalists imagined that there had to have been land bridges, long-since subsided, that had once connected them to a continent. But in the wake of the Beagle voyage, the collection of Galapagos plants suggested an alternate scenario.

Even if there had once been a land bridge to the islands, it could not account for the fact that half of the plant species Darwin collected were unique to the Galapagos, and that most of them were particular to just one island. “I never dreamed that islands, about fifty or sixty miles apart, and most of them in sight of each other, formed of precisely the same rocks, placed under a quite similar climate, rising to a nearly equal height, would have been differently tenanted,” wrote Darwin in his Journal of Researches. His observations could be best explained if species were not fixed in nature but somehow changed as the seeds traveled to different locations. [Continue reading…]

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DNA contains no information

Regan Penaluna writes: When we talk about genes, we often use expressions inherited from a few influential geneticists and evolutionary biologists, including Francis Crick, James Watson, and Richard Dawkins. These expressions depict DNA as a kind of code telling bodies how to form. We speak about genes similarly to how we speak about language, as symbolic and imbued with meaning. There is “gene-editing,” and there are “translation tables” for decoding sequences of nucleic acid. When DNA replicates, it is said to “transcribe” itself. We speak about a message — such as, build a tiger! or construct a female! — being communicated between microscopic materials. But this view of DNA has come with a price, argue some thinkers. It is philosophically misguided, they say, and has even led to scientific blunders. Scratch the surface of this idea, and below you’ll find a key contradiction.

Since the earliest days of molecular biology, scientists describe genetic material to be unlike all other biological material, because it supposedly carries something that more workaday molecules don’t: information. In a 1958 paper, Crick presented his ideas on the importance of proteins for inheritance, and said that they were composed of energy, matter, and information. Watson called DNA the “repository” of information.

Less than a decade later, George Williams, an influential evolutionary biologist, elaborated on this idea. He described genes to have a special status distinct from DNA, and to be the message that the DNA delivers. In a later work, he likened genes to ideas contained in books. A book can be destroyed, but the story inside is not identical to the physical book. “The same information can be recorded by a variety of patterns in many different kinds of material. A message is always coded in some medium, but the medium is really not the message.” In his book The Blind Watchmaker, Dawkins gives perhaps the most forthright description of this view: “airborne willow seeds… are, literally, spreading instructions for making themselves… It is raining instructions out there; it’s raining programs; it’s raining tree-growing, fluff-spreading, algorithms. That is not a metaphor, it is the plain truth. It couldn’t be any plainer if it were raining floppy discs.”

But do genes truly contain information in the same sense as words, books, or floppy discs? It depends on what we mean by information. If it’s the meaning represented by the words, books, or floppy disks, then no. Many philosophers agree that this kind of semantic information requires communication: an agent to create the message and another to interpret it. “Genes don’t carry semantic information, though. They weren’t made as part of an act of communication. So genes don’t literally represent anything, as people sometimes say,” explains Peter Godfrey-Smith, a professor of philosophy at CUNY. [Continue reading…]

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Crows understand analogies

crow

Scientific American reports: People are fascinated by the intelligence of animals. In fact, cave paintings dating back some 40,000 years suggest that we have long harbored keen interest in animal behavior and cognition. Part of that interest may have been practical: animals can be dangerous, they can be sources of food and clothing, and they can serve as sentries or mousers.

But, another part of that fascination is purely theoretical. Because animals resemble us in form, perhaps they also resemble us in thought. For many philosophers — including René Descartes and John Locke — granting intelligence to animals was a bridge too far. They especially deemed abstract reasoning to be uniquely human and to perfectly distinguish people from “brutes.” Why? Because animals do not speak, they must have no thoughts.

Nevertheless, undeterred by such pessimistic pronouncements, informed by Darwin’s theory of evolution, and guided by the maxim that “actions speak more loudly than words,” researchers today are fashioning powerful behavioral tests that provide nonverbal ways for animals to disclose their intelligence to us. Although animals may not use words, their behavior may serve as a suitable substitute; its study may allow us to jettison the stale convention that thought without language is impossible. [Continue reading…]

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Humans and animals — the power and limitations of language

Stassa Edwards writes: In his Apology for Raymond Sebond (1576), Michel de Montaigne ascribed animals’ silence to man’s own wilful arrogance. The French essayist argued that animals could speak, that they were in possession of rich consciousness, but that man wouldn’t condescend to listen. ‘It is through the vanity of the same imagination that [man] equates himself with God,’ Montaigne wrote, ‘that he attributes divine attributes for himself, picks himself out and separates himself from the crowd of other creatures.’ Montaigne asked: ‘When I play with my cat, who knows if she is making more of a pastime of me than I of her?’

Montaigne’s question is as playful as his cat. Apology is not meant to answer the age-old question, but rather to provoke; to tap into an unending inquiry about the reasoning of animals. Perhaps, Montaigne implies, we simply misunderstand the foreign language of animals, and the ignorance is not theirs, but ours.

Montaigne’s position was a radical one – the idea the animals could actually speak to humans was decidedly anti-anthropocentric – and when he looked around for like-minded thinkers, he found himself one solitary essayist. But if Montaigne was a 16th century loner, then he could appeal to the Classics. Apology is littered with references to Pliny and a particular appeal to Plato’s account of the Golden Age under Saturn. But even there, Montaigne had little to work with. Aristotle had argued that animals lacked logos (meaning, literally, ‘word’ but also ‘reason’) and, therefore, had no sense of the philosophical world inhabited and animated by humans. And a few decades after Montaigne, the French philosopher René Descartes delivered the final blow, arguing that the uniqueness of man stems from his ownership of reason, which animals are incapable of possessing, and which grants him dominion over them.

Everyone know what it’s like to forget someone’s name. It could be the name of a celebrity and the need to remember might be non-existent, and yet, as though finding this name might be an antidote to looming senility, it’s hard to let go of such a compulsion until it is satisfied.

From infancy we are taught that success in life requires an unceasing commitment to colonize the world with language. To be lost for words, is to be left out.

Without the ability to speak or understand, we would lose our most vital connection with the rest of humanity.

Montaigne understood that it was a human conceit to imagine that among all creatures, we were the only ones endowed with the capacity to communicate:

Can there be a more formall and better ordained policie, divided into so severall charges and offices, more constantly entertained, and better maintained, than that of Bees? Shall we imagine their so orderly disposing of their actions, and managing of their vocations, have so proportioned and formall a conduct without discourse, reason, and forecast?

What Montaigne logically inferred in the 1500s, science would confirm centuries later.

While Stassa Edwards enumerates the many expressions of a human desire for animals to speak, my sense is that behind this desire there is an intuition about the limitations of language: that our mute companions often see more because they can say less.

We view language as a prism that allows us perceive order in the world and yet this facility in representation is so successful and elegantly structured that most of the time we see the representations much more clearly than we see the world.

Our ability to describe and analyze the world has never been more advanced than it is today and yet for millennia, humans have observed that animals seem to be able to do something that we cannot: anticipate earthquakes.

Perhaps our word-constructed world only holds together on condition that our senses remain dull.

The world we imagine we can describe, quantify, and control, is in truth a world we barely understand.

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Birds can hear sounds hundreds of miles away

The Atlantic: In April, a massive thunderstorm unleashed a series of tornadoes that tore through the central and southern United States. The 84 twisters decimated homes and buildings, causing more than $1 billion in damage across 17 states. In the wake of the natural disaster, 35 people lost their lives.

Now, scientists say a peculiar event took place just two days before the storm: Flocks of songbirds fled the area en masse. Many golden-winged warblers had just finished a 1,500-mile migration to Tennessee when they suddenly flew south on a 900-mile exodus to Florida and Cuba. At that time, the storm was somewhere between 250 and 560 miles away. The researchers said that the birds somehow knew about the impending storm.

“At the same time that meteorologists on The Weather Channel were telling us this storm was headed in our direction, the birds were apparently already packing their bags and evacuating the area,” Henry Streby, a population ecologist from the University of California, Berkeley, said in a statement. He and his research team had been examining the birds’ migratory patterns when they made their discovery.

Initially, the team was studying if warblers, which weigh the same as four dimes, could carry half-gram geo-locators over long distances. After retrieving data from five of the 20 tagged birds, the team noticed the birds were nowhere near the path they’d expected. Why, the researchers wondered, would these tiny birds travel so far from their already-grueling migratory route? Upon further inspection, the scientists found that the dates the birds broke with the pattern coincided with the beginnings of the storm. In a paper reported today in the journal Current Biology, the team suggests that the birds made their “evacuation migration” because their keen sense of hearing alerted them to the incoming natural disaster. [Continue reading…]

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What is it like to be a bee?

honey-bee

In the minds of many humans, empathy is the signature of humanity and yet if this empathy extends further and includes non-humans we may be suspected of indulging in anthropomorphism — a sentimental projection of our own feelings into places where similar feelings supposedly cannot exist.

But the concept of anthropomorphism is itself a strange idea since it seems to invalidate what should be one of the most basic assumptions we can reasonably make about living creatures: that without the capacity to suffer, nothing would survive.

Just as the deadening of sensation makes people more susceptible to injury, an inability to feel pain would impede any creature’s need to avoid harm.

The seemingly suicidal draw of the moth to a flame is the exception rather than the rule. Moreover the insect is driven by a mistake, not a death wish. It is drawn towards the light, not the heat, oblivious that the two are one.

If humans indulge in projections about the feelings of others — human and non-human — perhaps we more commonly engage in negative projections: choosing to assume that feelings are absent where it would cause us discomfort to be attuned to their presence.

Our inclination is to avoid feeling too much and thus we construct neat enclosures for our concerns.

These enclosures shut out the feelings of strangers and then by extension seal away boundless life from which we have become even more estranged.

Heather Swan writes: It was a warm day in early spring when I had my first long conversation with the entomologist and science studies scholar Sainath Suryanarayanan. We met over a couple of hives I had recently inherited. One was thriving. Piles of dead bees filled the other. Parts of the comb were covered with mould and oozing something that looked like molasses.

Having recently attended a class for hobby beekeepers with Marla Spivak, an entomologist at the University of Minnesota, I was aware of the many different diseases to which bees are susceptible. American foulbrood, which was a mean one, concerned me most. Beekeepers recommended burning all of your equipment if you discovered it in your hives. Some of these bees were alive, but obviously in low spirits, and I didn’t want to destroy them unnecessarily. I called Sainath because I thought he could help me with the diagnosis.

Beekeeping, these days, is riddled with risks. New viruses, habitat loss, pesticides and mites all contribute to creating a deadly labyrinth through which nearly every bee must travel. Additionally, in 2004, mysterious bee disappearances began to plague thousands of beekeepers. Seemingly healthy bees started abandoning their homes. This strange disappearing act became known as colony collapse disorder (CCD).

Since then, the world has seen the decline of many other pollinating species, too. Because honeybees and other pollinators are responsible for pollinating at least one-third of all the food we eat, this is a serious problem globally. Diagnosing bee problems is not simple, but some answers are emerging. A ubiquitous class of pesticides called neonicotinoids have been implicated in pollinator decline, which has fuelled conversations among beekeepers, scientists, policy-makers and growers. A beekeeper facing a failing hive now has to consider not only the health of the hive itself, but also the health of the landscape around the hive. Dead bees lead beekeepers down a path of many questions. And some beekeepers have lost so many hives, they feel like giving up.

When we met at my troubled hives, Sainath brought his own hive tool and veil. He had already been down a path of many questions about bee deaths, one that started in his youth with a fascination for observing insects. When he was 14, he began his ‘Amateur Entomologist’s Record’, where he kept taxonomic notes on such things as wing textures, body shapes, colour patterns and behaviours. But the young scientist’s approach occasionally slipped to include his exuberance, describing one moment as ‘a stupefying experience!’ All this led him to study biology and chemistry in college, then to work on the behavioural ecology of paper wasps during his doctoral studies, and eventually to Minnesota to help Spivak investigate the role of pesticides in CCD.

Sainath had spent several years doing lab and field experiments with wasps and bees, but ultimately wanted to shift from traditional practices in entomology to research that included human/insect relationships. It was Sainath who made me wonder about the role of emotion in science – both in the scientists themselves and in the subjects of their experiments. I had always thought of emotion as something excised from science, but this was impossible for some scientists. What was the role of empathy in experimentation? How do we, with our human limitations, understand something as radically different from us as the honeybee? Did bees have feelings, too? If so, what did that mean for the scientist? For the science? [Continue reading…]

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How broken sleep can unleash creativity

Karen Emslie writes: It is 4.18am. In the fireplace, where logs burned, there are now orange lumps that will soon be ash. Orion the Hunter is above the hill. Taurus, a sparkling V, is directly overhead, pointing to the Seven Sisters. Sirius, one of Orion’s heel dogs, is pumping red-blue-violet, like a galactic disco ball. As the night moves on, the old dog will set into the hill.

It is 4.18am and I am awake. Such early waking is often viewed as a disorder, a glitch in the body’s natural rhythm – a sign of depression or anxiety. It is true that when I wake at 4am I have a whirring mind. And, even though I am a happy person, if I lie in the dark my thoughts veer towards worry. I have found it better to get up than to lie in bed teetering on the edge of nocturnal lunacy.

If I write in these small hours, black thoughts become clear and colourful. They form themselves into words and sentences, hook one to the next – like elephants walking trunk to tail. My brain works differently at this time of night; I can only write, I cannot edit. I can only add, I cannot take away. I need my day-brain for finesse. I will work for several hours and then go back to bed.

All humans, animals, insects and birds have clocks inside, biological devices controlled by genes, proteins and molecular cascades. These inner clocks are connected to the ceaseless yet varying cycle of light and dark caused by the rotation and tilt of our planet. They drive primal physiological, neural and behavioural systems according to a roughly 24-hour cycle, otherwise known as our circadian rhythm, affecting our moods, desires, appetites, sleep patterns, and sense of the passage of time.

The Romans, Greeks and Incas woke up without iPhone alarms or digital radio clocks. Nature was their timekeeper: the rise of the sun, the dawn chorus, the needs of the field or livestock. Sundials and hourglasses recorded the passage of time until the 14th century when the first mechanical clocks were erected on churches and monasteries. By the 1800s, mechanical timepieces were widely worn on neck chains, wrists or lapels; appointments could be made and meal- or bed-times set.

Societies built around industrialisation and clock-time brought with them urgency and the concept of being ‘on time’ or having ‘wasted time’. Clock-time became increasingly out of synch with natural time, yet light and dark still dictated our working day and social structures.

Then, in the late 19th century, everything changed. [Continue reading…]

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The life cycles of flowers and bees are getting thrown out of balance by climate change

bee-pollination

The Guardian reports: Sexual deceit, pressed flowers and Victorian bee collectors are combined in new scientific research which demonstrates for the first time that climate change threatens flower pollination, which underpins much of the world’s food production.

The work used museum records stretching back to 1848 to show that the early spider orchid and the miner bee on which it depends for reproduction have become increasingly out of sync as spring temperatures rise due to global warming.

The orchid resembles a female miner bee and exudes the same sex pheromone to seduce the male bee into “pseudocopulation” with the flower, an act which also achieves pollination. The orchids have evolved to flower at the same time as the bee emerges.

But while rising temperatures cause both the orchid and the bee to flower or fly earlier in the spring, the bees are affected much more, which leads to a mismatch.

“We have shown that plants and their pollinators show different responses to climate change and that warming will widen the timeline between bees and flowers emerging,” said Dr Karen Robbirt, at the Royal Botanic Gardens, Kew and the University of East Anglia (UEA). “If replicated in less specific systems, this could have severe implications for crop productivity.”

She said the research, published in Current Biology on Thursday, is “the first clear example, supported by long-term data, of the potential for climate change to disrupt critical [pollination] relationships between species.” [Continue reading…]

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The complex, varied, ever changing and context-dependent microbiome

Ed Yong writes: In the late 17th century, the Dutch naturalist Anton van Leeuwenhoek looked at his own dental plaque through a microscope and saw a world of tiny cells “very prettily a-moving.” He could not have predicted that a few centuries later, the trillions of microbes that share our lives — collectively known as the microbiome — would rank among the hottest areas of biology.

These microscopic partners help us by digesting our food, training our immune systems and crowding out other harmful microbes that could cause disease. In return, everything from the food we eat to the medicines we take can shape our microbial communities — with important implications for our health. Studies have found that changes in our microbiome accompany medical problems from obesity to diabetes to colon cancer.

As these correlations have unfurled, so has the hope that we might fix these ailments by shunting our bugs toward healthier states. The gigantic probiotics industry certainly wants you to think that, although there is little evidence that swallowing a few billion yogurt-borne bacteria has more than a small impact on the trillions in our guts. The booming genre of microbiome diet books — self-help manuals for the bacterial self — peddles a similar line, even though our knowledge of microbe-manipulating menus is still in its infancy.

This quest for a healthy microbiome has led some people to take measures that are far more extreme than simply spooning up yogurt. [Continue reading…]

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The biology of deceit

Daniel N Jones writes: It’s the friend who betrays you, the lover living a secret life, the job applicant with the fabricated résumé, or the sham sales pitch too good to resist. From the time humans learnt to co‑operate, we also learnt to deceive each other. For deception to be effective, individuals must hide their true intentions. But deception is hardly limited to humans. There is a never-ending arms race between the deceiver and the deceived among most living things. By studying different patterns of deception across the species, we can learn to better defend ourselves from dishonesty in the human world.

My early grasp of human deception came from the work of my adviser, the psychologist Delroy Paulhus at the University of British Columbia in Canada, who studied what he called the dark triad of personality: psychopathy, recognised by callous affect and reckless deceit; narcissism, a sense of grandiose entitlement and self-centered overconfidence; and Machiavellianism, the cynical and strategic manipulation of others.

If you look at the animal world, it’s clear that dark traits run through species from high to low. Some predators are fast, mobile and wide-ranging, executing their deceptions on as many others as they can; they resemble human psychopaths. Others are slow, stalking their prey in a specific, strategic (almost Machiavellian) way. Given the parallels between humans and other animals, I began to conceive my Mimicry Deception Theory, which argues that long- and short-term deceptive strategies cut across species, often by mimicking other lifestyles or forms.

Much of the foundational work for this idea comes from the evolutionary biologist Robert Trivers, who noted that many organisms gain an evolutionary advantage through deception. [Continue reading…]

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