A molecule deep in space could help explain the origins of life

Discover Magazine reports: A peculiar new molecule hovering within a star-forming dust cloud in deep in space could help explain why life on Earth is the way it is.

The cloud, called Sagittarius B2, resides near the center of the Milky Way, and it’s there that researchers from the California Institute of Technology discovered an organic element that displays a key property shared by all life. Propylene oxide is the first element discovered outside of our solar system to exhibit chirality, or the presence of two distinct, mirror-image forms. Many complex molecules have this property, including myriad organic molecules necessary for life. The chemical formula of these two versions is exactly the same, but the structure is flipped.

All life on Earth is composed of chiral molecules, and the versions organisms use, either right- or left-handed, determines fundamental properties of their biology. For example, all living things only use the right-handed form of the sugar ribose to form the backbone of DNA, giving it that the signature twist. You can think of molecular handedness by picturing gloves — hence the “handed terminology”. The gloves, or molecules, may look similar, but you could never put a left-handed glove on your right hand. [Continue reading…]

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RIP Bob Paine, a keystone among ecologists

Ed Yong writes: I’m deeply saddened to learn that Bob Paine, a giant of ecology, passed away yesterday. You may not know his name, but you almost certainly know the ideas that he pioneered.

Back in 1963, Paine began prying ochre starfish off a rocky beach in Washington and hurling them into the sea. After a year, the mussels that the starfish would normally have eaten had overrun the beach, turning a wonderland of limpets, anemones, and barnacles into a monoculture of black gaping shells.

The experiment was ground-breaking. It showed that not all species are equal, and that some — like the starfish—are secret lynchpins of the natural world. Their absence can ripple outwards, triggering the rise and fall of connected species and can even reshape the landscape. For example, when sea otters vanish, the sea urchins they eat transform lush forests of kelp into desolate barrens, dooming the fish, crabs, and other animals that once lived there. Paine called these ripples “trophic cascades”, and he billed the animals behind them — the starfish, otters, and others — as “keystone species”, after the central stone that stops an arch from collapsing. These concepts are so familiar today that we take them for granted, but we didn’t always know about them. We only do because of Paine. [Continue reading…]

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Yes, there have been aliens

Adam Frank writes: Last month astronomers from the Kepler spacecraft team announced the discovery of 1,284 new planets, all orbiting stars outside our solar system. The total number of such “exoplanets” confirmed via Kepler and other methods now stands at more than 3,000.

This represents a revolution in planetary knowledge. A decade or so ago the discovery of even a single new exoplanet was big news. Not anymore. Improvements in astronomical observation technology have moved us from retail to wholesale planet discovery. We now know, for example, that every star in the sky likely hosts at least one planet.

But planets are only the beginning of the story. What everyone wants to know is whether any of these worlds has aliens living on it. Does our newfound knowledge of planets bring us any closer to answering that question?

A little bit, actually, yes. In a paper published in the May issue of the journal Astrobiology, the astronomer Woodruff Sullivan and I show that while we do not know if any advanced extraterrestrial civilizations currently exist in our galaxy, we now have enough information to conclude that they almost certainly existed at some point in cosmic history. [Continue reading…]

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Theophrastus: The unsung hero of Western Science

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Andrea Wulf writes: In 345 B.C.E., two men took a trip that changed the way we make sense of the natural world. Their names were Theophrastus and Aristotle, and they were staying on Lesbos, the Greek island where tens of thousands of Syrian refugees have recently landed.

Theophrastus and Aristotle were two of the greatest thinkers in ancient Greece. They set out to bring order to nature by doing something very unusual for the time: they examined living things and got their hands dirty. They turned away from Plato’s idealism and looked at the real world. Both Aristotle and Theophrastus believed that the study of nature was as important as metaphysics, politics, or mathematics. Nothing was too small or insignificant. “There is something awesome in all natural things.” Aristotle said, “inherent in each of them there is something natural and beautiful.”

Aristotle is the more famous of the two men, but Theophrastus deserves equal bidding in any history of naturalism. Born around 372 B.C.E. in Eresos, a town on the southwestern coast of Lesbos, Theophrastus was 13 years younger than Aristotle. According to Diogenes Laërtius — a biographer who wrote his Eminent Philosophers more than 400 years afterwards but who is the main source for what we know about Theophrastus’ life — Theophrastus was one of Aristotle’s pupils at Plato’s Academy. For many years they worked closely together until Aristotle’s death in 322 B.C.E. when Theophrastus became his successor at the Lyceum school in Athens and inherited his magnificent library. [Continue reading…]

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‘Gene drives’ that tinker with evolution are an unknown risk, researchers say

MIT Technology Review reports: With great power — in this case, a technology that can alter the rules of evolution — comes great responsibility. And since there are “considerable gaps in knowledge” about the possible consequences of releasing this technology, called a gene drive, into natural environments, it is not yet responsible to do so. That’s the major conclusion of a report published today by the National Academies of Science, Engineering, and Medicine.

Gene drives hold immense promise for controlling or eradicating vector-borne diseases like Zika virus and malaria, or in managing agricultural pests or invasive species. But the 200-page report, written by a committee of 16 experts, highlights how ill-equipped we are to assess the environmental and ecological risks of using gene drives. And it provides a glimpse at the challenges they will create for policymakers.

The technology is inspired by natural phenomena through which particular “selfish” genes are passed to offspring at higher rate than is normally allowed by nature in sexually reproducing organisms. There are multiple ways to make gene drives in the lab, but scientists are now using the gene-editing tool known as CRISPR to very rapidly and effectively do the trick. Evidence in mosquitoes, fruit flies, and yeast suggests that this could be used to spread a gene through nearly 100 percent of a population.

The possible ecological effects, intended or not, are far from clear, though. How long will gene drives persist in the environment? What is the chance that an engineered organism could pass the gene drive to an unintended recipient? How might these things affect the whole ecosystem? How much does all this vary depending on the particular organism and ecosystem?

Research on the molecular biology of gene drives has outpaced ecological research on how genes move through populations and between species, the report says, making it impossible to adequately answer these and other thorny questions. Substantially more laboratory research and confined field testing is needed to better grasp the risks. [Continue reading…]

Jim Thomas writes: If there is a prize for the fastest emerging tech controversy of the century the ‘gene drive’ may have just won it. In under eighteen months the sci-fi concept of a ‘mutagenic chain reaction’ that can drive a genetic trait through an entire species (and maybe eradicate that species too) has gone from theory to published proof of principle to massively-shared TED talk (apparently an important step these days) to the subject of a US National Academy of Sciences high profile study – complete with committees, hearings, public inputs and a glossy 216 page report release. Previous technology controversies have taken anywhere from a decade to over a century to reach that level of policy attention. So why were Gene Drives put on the turbo track to science academy report status? One word: leverage.

What a gene drive does is simple: it ensures that a chosen genetic trait will reliably be passed on to the next generation and every generation thereafter. This overcomes normal Mendelian genetics where a trait may be diluted or lost through the generations. The effect is that the engineered trait is driven through an entire population, re-engineering not just single organisms but enforcing the change in every descendant – re-shaping entire species and ecosystems at will.

It’s a perfect case of a very high-leverage technology. Archimedes famously said “Give me a lever long enough and a fulcrum on which to place it, and I shall move the world. ” Gene drive developers are in effect saying “Give me a gene drive and an organism to put it in and I can wipe out species, alter ecosystems and cause large-scale modifications.” Gene drive pioneer Kevin Esvelt calls gene drives “an experiment where if you screw up, it affects the whole world”. [Continue reading…]

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Genes are overrated

Nathaniel Comfort writes: In the Darwinian struggle of scientific ideas, the gene is surely among the select. It has become the foundation of medicine and the basis of vigorous biotechnology and pharmaceutical industries. Media coverage of recent studies touts genes for crime, obesity, intelligence — even the love of bacon. We treat our genes as our identity. Order a home genetic-testing kit from the company 23andMe, and the box arrives proclaiming, “Welcome to you.” Cheerleaders for crispr, the new, revolutionarily simple method of editing genes, foretell designer babies, the end of disease, and perhaps even the transformation of humanity into a new and better species. When we control the gene, its champions promise, we will be the masters of our own destiny.

The gene has now found a fittingly high-profile chronicler in Siddhartha Mukherjee, the oncologist-author of the Pulitzer Prize–winning The Emperor of All Maladies, a history of cancer. The Gene’s dominant traits are historical breadth, clinical compassion, and Mukherjee’s characteristic graceful style. He calls it “an intimate history” because he shares with us his own dawning awareness of heredity and his quest to make meaning of it. The curtain rises on Kolkata, where he has gone to visit Moni, his paternal cousin, who has been diagnosed with schizophrenia. In addition to Moni, two of the author’s uncles were afflicted with “various unravelings of the mind.” Asked for a Bengali term for such inherited illness, Mukherjee’s father replies, “Abheder dosh” — a flaw in identity. Schizophrenia becomes a troubling touchstone throughout the book. But the Indian interludes are tacked onto an otherwise conventional triumphalist account of European-American genetics, written from the winners’ point of view: a history of the emperor of all molecules. [Continue reading…]

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Eagles take down drones

The New York Times reports: Its wings beating against a gathering breeze, the eagle moves gracefully through a cloudy sky, then swoops, talons outstretched, on its prey below.

The target, however, is not another bird but a small drone, and when the eagle connects, there is a metallic clunk. With the device in its grasp, the bird of prey returns to the ground.

At a disused military airfield in the Netherlands, hunting birds like the eagle are being trained to harness their instincts to help combat the security threats stemming from the proliferation of drones.

The birds of prey learn to intercept small, off-the-shelf drones — unmanned aerial vehicles — of the type that can pose risks to aircraft, drop contraband into jails, conduct surveillance or fly dangerously over public events.

The thought of terrorists using drones haunts security officials in Europe and elsewhere, and among those who watched the demonstration at Valkenburg Naval Air Base this month was Mark Wiebes, a detective chief superintendent in the Dutch police.

Mr. Wiebes described the tests as “very promising,” and said that, subject to a final assessment, birds of prey were likely to be deployed soon in the Netherlands, along with other measures to counter drones. The Metropolitan Police Service in London is also considering using trained birds to fight drones. [Continue reading…]

This has been described as a “a low-tech solution for a high-tech problem” but, on the contrary, what it highlights is the fact that in terms of maneuverability, the flying skills of an eagle (and most other flying creatures) are vastly superior to any form of technology.

In this, as in so many other instances, technology crudely imitates nature.

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What the songs of wolves reveal about language

Holly Root-Gutteridge writes: Dialects, or regional differences in the form and use of vocalisations, have been observed in birds, bats, chimpanzees and now an increasingly long list of other species. This has been most beautifully heard in whales, where the songs of humpbacks are transmitted across hundreds of miles, telling a listener which part of the ocean the whale lives in, and tracing its family group by the influences on song formations. The bioacousticians Katharine Payne and Roger Payne first listened to the whales on underwater microphone recordings in the 1960s, and used musical notation to explore the changes that occurred in each male’s song, year on year. Whalesong, heard by humans as long ago as Aristotle, became the subject of intense study and public interest. Their research showed that there were geographic differences in humpback whale songs and that we could tell apart populations just by using those songs, which change throughout their lives. So the whales were controlling their singing and subject to cultural influences. The Paynes had found dialects in whale song. Would we find the same for canids?

Despite their cultural popularity, wolf howls haven’t been the subject of focussed research until recently. Now, following the lead of marine biologists and ornithologists, and with improved sound recording equipment and analysis programs, researchers can study them in depth. The first step in understanding what animals are saying to one another is to figure out what aspects of the voice are functional and what parts are formed by the structure of the throat and mouth, or what is the piano and what is the tune. Studies since the 1960s have shown that the howls that have haunted our dreams for centuries can tell us a lot about the particular wolf vocalising. Like humans, each wolf has its own voice. Each pack also shares howl similarities, making different families sound distinct from each other (wolves respond more favourably to familiar howls). This much we knew. What we didn’t know was whether the differences seen between packs were true of subspecies or of species, and if an Indian wolf howl would be distinct from a Canadian one.

More questions follow. If howls from different subspecies are different, do the howls convey the same message? Is there a shared culture of howl-meanings, where an aggressive howl from a European wolf means the same thing as an aggressive howl of a Himalayan? And can a coyote differentiate between a red wolf howling with aggressive intent and one advertising the desire to mate? Even without grammar or syntax, howls can convey intent, and if the shape of the howl changes enough while the intent remains constant, the foundations of distinctive culture can begin to appear. [Continue reading…]

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The ex-anarchist construction worker who became a world-renowned scientist

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Daniel Gumbiner writes: “See these lichens here? I don’t know how you see them but, to me, I see them as a surrealist.”

I am sitting in the UC Riverside herbarium, speaking to Kerry Knudsen, Southern California’s only professional lichenologist. We are looking at his collection of lichens, which consists of over 16,000 individual specimens, all of them neatly organized in large green file cabinets. Knudsen has published over 200 peer-reviewed scientific papers on lichens, and discovered more than 60 species that are new to science. It is an extraordinary output, for any scientist, but Knudsen has achieved it in only fifteen years. Science is his second career. For more than two decades he worked in construction. Before that, he was a teenage runaway living in an anarchist commune in Chicago.

“He’s amazing,” said Shirley Tucker, a retired professor of botany at LSU. “He came out of nowhere and became an expert in the most difficult genera.”

A lichen is a fungus in a symbiotic relationship with an algae or a cyanobacteria. The fungus essentially farms the algae or cyanobacteria, who are able to harvest energy from the sun through photosynthesis. In return, the fungus provides the algae or cyanobacteria with protection, but the relationship is a little one-sided.

“The algae is trapped,” Knudsen explained. “It has a lot of tubes going into it. It’s controlled by chemical signals … The first time I saw it under the microscope, I wanted to join the Algae Liberation Front. I mean, it looked bad.”

Scientists believe that lichen evolved over 500 million years ago, about the same time as fish. Although lichen make up 8 percent of the world’s biomass, they are rarely considered by the amateur naturalist, and therefore have very few common names. [Continue reading…]

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Animals are us

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Tania Lombrozo writes: Researchers have studied how people think about humans in relation to the natural world, and how the way we reason about humans and other animals changes over the course of development and as a function of education and culture.

The findings from this body of work suggest that by age 5, Western children growing up in urban environments are anomalous in the extent to which they regard humans as central to the biological world. Much of the rest of the world — including 3-year-olds, 5-year-olds in rural environments and adults from indigenous populations in South America — are more inclined to think about humans as one animal species among others, at least when it comes to reasoning about the properties that human and non-human animals are likely to possess.

To illustrate, consider a study by Patricia Herrmann, Sandra Waxman and Douglas Medin published in the Proceedings of the National Academy of Sciences in 2010. In one experiment, 64 urban children, aged 3 or 5, were asked a series of questions that assessed their willingness to generalize an unknown property from one object to another. For instance, they might be told that people “have andro inside,” and would then have to guess whether it’s right or wrong to say that dogs “have andro inside.”

The findings with 5-year-olds replicated classic work in developmental psychology and suggested a strong “anthropocentric” bias: The children were more likely to generalize from humans to non-humans than the other way around, consistent with a privileged place for humans in the biological world. The 3-year-olds, by contrast, showed no signs of this bias: They generalized from humans to non-humans and from non-humans to humans in just the same way. These findings suggest that an anthropocentric perspective isn’t a necessary starting point for human reasoning about the biological world, but rather a perspective we acquire through experience.

So what happens between the ages of 3 and 5 to induce an anthropocentric bias?

Perhaps surprisingly, one influence seems to be anthropomorphism in storybooks. [Continue reading…]

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The birth and death of a landscape

Justin Nobel writes: To reach the youngest land in the United States you need a boat. Robert Twilley still vividly remembers the first time he made the trip. The Louisiana State University coastal ecologist piled into a 24-foot Boston Whaler with a bunch of geomorphologists from Minnesota and motored out to an arc of spongy islands along the central coast of Louisiana called the Wax Lake Delta. It was the best place to learn about how a delta develops. The way the land eventually stabilizes and becomes home to a unique ecosystem that changes as the delta gets older is a process that ecologists call succession. “Succession is one of the most fascinating concepts in ecology,” said Twilley, “though one of the hardest to study. But in the Wax Lake Delta you can see it all. Biologic communities link up A to Z; it is the holy grail of ecosystem succession.”

What is remarkable for scientists like Twilley is that with good muck boots, a small boat, and a non-aversion to intense sun, freak thunderstorms, biting insects, and devastating humidity, the aging process of this new land can be studied in a human lifespan. In just over 40 years, the Wax Lake Delta has grown from nothing to an area twice the size of Manhattan. Meanwhile, since the European settlement of North America, the Mississippi River Delta has lost approximately one-third of its original wetland area. A delta that was once about twice the size of Delaware and on maps resembled a head of cauliflower now looks more like a string bean. The slow death of the Mississippi River Delta has severe consequences, including reduced hurricane protection for cities like New Orleans. Not only an important food source for humans and wildlife, this rich habitat also helps filter pollutants and absorb excess nutrients that would deplete the oxygen in the Gulf of Mexico’s water.

As one delta dies, another one grows. The budding Wax Lake Delta has allowed Twilley and his team of researchers to study how a delta ages. First, the nascent delta takes shape as lobes of sediment accumulate below the water. The delta is born when it breaches the surface of the water. Colonized by plants that gradually enhance the soil’s organic content and raise its elevation, it rolls through childhood. And eventually, it grows into a landscape able to support large shrubs and black willow trees. “The delta is almost like an organism,” says Twilley, “There is a birthing, there is an aging process, and there is a death.” [Continue reading…]

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Missing mitochondria show life doesn’t relentlessly pursue complexity

Sarah Kaplan writes: Life on Earth used to be simple.

Once upon a time, every organism on the planet was a single, simple cell. Scientists call them prokaryotes. They are about as basic as a living thing can be — just little balloons of DNA and protein, with no grander goals in life than to swim around, eat and occasionally duplicate themselves to produce more swimmers and eaters.

Then, about 1.5 billion years ago, something strange and spectacular happened. One prokaryote engulfed another, and instead of digesting it, he put the little guy to work. They established an endosymbiotic relationship: The smaller internal cell performed lots of helpful tasks — such as making energy and building proteins — and in exchange, the bigger cell kept it safe and well-fed. This lucky bit of teamwork gave rise to the complex (a.k.a. eukaryotic) cell that exists today, from curious single-celled protists to the cells that make up all plants, fungi and animals — including us.

The eukaryotes are a weird and diverse lot, but at the cellular level we’ve all got the same basic components: a nucleus to store our DNA, and mitochondria — the descendants of that ancient swallowed organism — to make energy and perform other essential functions. Other internal structures, called organelles, may vary, but those two are so universal that biologists assumed we couldn’t exist without them.

“They’re part of the definition of eukaryotic cell,” said Anna Karnkowska, an evolutionary biologist at the University of British Columbia. “If you open a biology textbook to a picture of a eukaryotic cell, that’s what you’ll see.”

Which is why she was so shocked to find a eukaryote that didn’t have any mitochondria at all: a single-celled relative of the giardia parasite called Monocercomonoides.

The discovery, which Karnkowska made with other biologists when she was a post-doctoral fellow at Charles University in Prague, seems to rip up that textbook illustration. One of her co-authors compared it to finding a city with no utilities or public works department.

“This is the first example of a eukaryote lacking any form of a mitochondrion,” the researchers write in their study, which was published Thursday in the journal Current Biology, “demonstrating that this organelle is not absolutely essential for the viability of a eukaryotic cell.” [Continue reading…]

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Ancient space dust hints at a mysterious period in Earth’s early history

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Rebecca Boyle writes: Geologists tell a pretty broad-brush narrative of Earth’s 4.5 billion-year history. For its first half-billion years, the newly formed planet was a seething ball of lava constantly pelted by giant space rocks, including a Mars-sized object that sheared off a chunk that became the moon. Things calmed down when the Late Heavy Bombardment tapered off some 3.8 billion years ago, but volcanoes ensured Earth’s atmosphere remained a toxic stew of gases with almost no oxygen to speak of. It stayed that way for another billion years, when single-celled bacteria filled the oceans. Around 2.5 billion years ago, at the end of the Archean era, algae figured out how to make energy from sunlight, and the Great Oxygenation Event gave Earth its lungs. Complex life took its time, finally exploding in the Cambrian era some 500 million years ago. Evolution moved a lot faster after that, resulting in dinosaurs, then mammals, then us.

It’s a great story, and scientists have been telling it for decades, but tiny fossilized space pebbles from Australia may upend it entirely, giving us a new narrative about Earth’s adolescence. These pebbles rained down on our planet’s surface 2.7 billion years ago. As they passed through the upper atmosphere, they melted and rusted, making new crystal shapes and minerals that only form where there is plenty of oxygen. A new paper describing the space pebbles will be published today in the journal Nature. It suggests the atmosphere’s upper reaches were surprisingly rich in oxygen during the Archean, when Earth’s surface had practically none.

“If they’re right, a lot of people have had misconceptions, or have been wrong,” says Kevin Zahnle, a planetary scientist at NASA’s Ames Research Center. Moreover, if the research holds up, geologists will have a new mystery on their hands: How did all that oxygen get there, and why didn’t it reach the ground? [Continue reading…]

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Are oxygen-depleted oceans from California to Namibia a harbinger of the next mass extinction?

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Moises Velasquez-Manoff writes: It was crabbers who first reported something amiss. In 2002, they began pulling in traps full of corpses. (Crabs should be alive when you catch them.) And they mentioned something else: Little octopuses had followed their crab lines to the surface, as if fleeing inhospitable conditions below.

Then heaps of dead crustaceans began washing ashore along a stretch of Oregon’s coast. When scientists sent a robotic submersible offshore, they discovered mile upon mile of dead crustaceans, the water brown and murky with detritus.

The killer was low oxygen, or hypoxia. Nearly all animals require oxygen to live, and, that year, dissolved oxygen had fallen so low off Oregon’s coast that whatever mobile creatures could had fled, while more-sessile life had simply suffocated.

Every year since, those hypoxic waters have appeared in late summer and early autumn. In 2006, they became anoxic, meaning they lost all their oxygen. “You didn’t see a single fish in a day,” says Jack Barth, a professor at Oregon State University, “just the piles of crab carcasses and worms that had come out of the bottom, sort of wafting in the current.” When scientists examined the roughly 50-year record of oxygen measurements from the region, they couldn’t find a single comparable event in the past. The hypoxia, it seemed, was unprecedented.

And then it spread.

In 2013, low-oxygen water showed up off the California coast just north of San Francisco. The following year, crabbers pulled in dead crabs in Half Moon Bay, just below San Francisco. Further south, the Monterey Bay Aquarium registered a decline in the oxygen content of the water it pumps in from the ocean.

“It seems like something has changed,” says John Largier, head of the Coastal Oceanography Group at the University of California-Davis. He tries to remain skeptical, but he suspects “large-scale global change.”

These suffocated patches of ocean aren’t just bad for fishermen and their catch; they represent a change in the ocean that has, at times in Earth’s past, heralded mass extinction. [Continue reading…]

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One in five of world’s plant species at risk of extinction

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Phys.org reports: The first annual State of the World’s Plants report, which involved more than 80 scientists and took a year to produce, is a baseline assessment of current knowledge on the diversity of plants on earth, the global threats these plants currently face, as well as the policies in place and their effectiveness in dealing with threats.

“This is the first ever global assessment on the state of the world’s plants. We already have a ‘State of the World’s …birds, sea-turtles, forests, cities, mothers, fathers, children even antibiotics’ but not plants. I find this remarkable given the importance of plants to all of our lives- from food, medicines, clothing, building materials and biofuels, to climate regulation. This report therefore provides the first step in filling this critical knowledge gap.” said Professor Kathy Willis, Director of Science at the Royal Botanic Gardens, Kew at the report launch on Monday.

“But to have effect, the findings must serve to galvanise the international scientific, conservation, business and governmental communities to work together to fill the knowledge gaps we’ve highlighted and expand international collaboration, partnerships and frameworks for plant conservation and use,” she added.

The status of plants outlined in the report is based on the most up to date knowledge from around the world as of 2016 and is divided into three sections; describing the world’s plants, global threats to plants and policies and international trade. [Continue reading…]

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