How a guy from a Montana trailer park overturned 150 years of biology

Ed Yong writes: In 1995, if you had told Toby Spribille that he’d eventually overthrow a scientific idea that’s been the stuff of textbooks for 150 years, he would have laughed at you. Back then, his life seemed constrained to a very different path. He was raised in a Montana trailer park, and home-schooled by what he now describes as a “fundamentalist cult.” At a young age, he fell in love with science, but had no way of feeding that love. He longed to break away from his roots and get a proper education.

At 19, he got a job at a local forestry service. Within a few years, he had earned enough to leave home. His meager savings and non-existent grades meant that no American university would take him, so Spribille looked to Europe.

Thanks to his family background, he could speak German, and he had heard that many universities there charged no tuition fees. His missing qualifications were still a problem, but one that the University of Gottingen decided to overlook. “They said that under exceptional circumstances, they could enroll a few people every year without transcripts,” says Spribille. “That was the bottleneck of my life.”

Throughout his undergraduate and postgraduate work, Spribille became an expert on the organisms that had grabbed his attention during his time in the Montana forests — lichens.

You’ve seen lichens before, but unlike Spribille, you may have ignored them. They grow on logs, cling to bark, smother stones. At first glance, they look messy and undeserving of attention. On closer inspection, they are astonishingly beautiful. They can look like flecks of peeling paint, or coralline branches, or dustings of powder, or lettuce-like fronds, or wriggling worms, or cups that a pixie might drink from. They’re also extremely tough. They grow in the most inhospitable parts of the planet, where no plant or animal can survive.

Lichens have an important place in biology. In the 1860s, scientists thought that they were plants. But in 1868, a Swiss botanist named Simon Schwendener revealed that they’re composite organisms, consisting of fungi that live in partnership with microscopic algae. This “dual hypothesis” was met with indignation: it went against the impetus to put living things in clear and discrete buckets. The backlash only collapsed when Schwendener and others, with good microscopes and careful hands, managed to tease the two partners apart.

Schwendener wrongly thought that the fungus had “enslaved” the alga, but others showed that the two cooperate. The alga uses sunlight to make nutrients for the fungus, while the fungus provides minerals, water, and shelter. This kind of mutually beneficial relationship was unheard of, and required a new word. Two Germans, Albert Frank and Anton de Bary, provided the perfect one — symbiosis, from the Greek for ‘together’ and ‘living’. [Continue reading…]


Why most planets will either be lush or dead

David Grinspoon writes: Can a planet be alive? Lynn Margulis, a giant of late 20th-century biology, who had an incandescent intellect that veered toward the unorthodox, thought so. She and chemist James Lovelock together theorized that life must be a planet-altering phenomenon and the distinction between the “living” and “nonliving” parts of Earth is not as clear-cut as we think. Many members of the scientific community derided their theory, called the Gaia hypothesis, as pseudoscience, and questioned their scientific integrity. But now Margulis and Lovelock may have their revenge. Recent scientific discoveries are giving us reason to take this hypothesis more seriously. At its core is an insight about the relationship between planets and life that has changed our understanding of both, and is shaping how we look for life on other worlds.

Studying Earth’s global biosphere together, Margulis and Lovelock realized that it has some of the properties of a life form. It seems to display “homeostasis,” or self‐regulation. Many of Earth’s life‐sustaining qualities exhibit remarkable stability. The temperature range of the climate; the oxygen content of the atmosphere; the pH, chemistry, and salinity of the ocean—all these are biologically mediated. All have, for hundreds of millions of years, stayed within a range where life can thrive. Lovelock and Margulis surmised that the totality of life is interacting with its environments in ways that regulate these global qualities. They recognized that Earth is, in a sense, a living organism. Lovelock named this creature Gaia.

Margulis and Lovelock showed that the Darwinian picture of biological evolution is incomplete. Darwin identified the mechanism by which life adapts due to changes in the environment, and thus allowed us to see that all life on Earth is a continuum, a proliferation, a genetic diaspora from a common root. In the Darwinian view, Earth was essentially a stage with a series of changing backdrops to which life had to adjust. Yet, what or who was changing the sets? Margulis and Lovelock proposed that the drama of life does not unfold on the stage of a dead Earth, but that, rather, the stage itself is animated, part of a larger living entity, Gaia, composed of the biosphere together with the “nonliving” components that shape, respond to, and cycle through the biota of Earth. Yes, life adapts to environmental change, shaping itself through natural selection. Yet life also pushes back and changes the environment, alters the planet. This is now as obvious as the air you are breathing, which has been oxygenated by life. So evolution is not a series of adaptations to inanimate events, but a system of feedbacks, an exchange. Life has not simply molded itself to the shifting contours of a dynamic Earth. Rather, life and Earth have shaped each other as they’ve co-evolved. When you start looking at the planet in this way, then you see coral reefs, limestone cliffs, deltas, bogs, and islands of bat guano as parts of this larger animated entity. You realize that the entire skin of Earth, and its depths as well, are indeed alive. [Continue reading…]


Dino-killing asteroid may have punctured Earth’s crust

Live Science reports: After analyzing the crater from the cosmic impact that ended the age of dinosaurs, scientists now say the object that smacked into the planet may have punched nearly all the way through Earth’s crust, according to a new study.

The finding could shed light on how impacts can reshape the faces of planets and how such collisions can generate new habitats for life, the researchers said.

Asteroids and comets occasionally pelt Earth’s surface. Still, for the most part, changes to the planet’s surface result largely from erosion due to rain and wind, “as well as plate tectonics, which generates mountains and ocean trenches,” said study co-author Sean Gulick, a marine geophysicist at the University of Texas at Austin.

In contrast, on the solar system’s other rocky planets, erosion and plate tectonics typically have little, if any, influence on the planetary surfaces. “The key driver of surface changes on those planets is constantly getting hit by stuff from space,” Gulick told Live Science. [Continue reading…]


How industrialization brought about the decline of vertebrate species

Nathan Collins writes: With climate change and deforestation threatening biodiversity around the world, it’s fair to wonder just how rapidly threatened species have been declining, and when exactly those declines began. The answer is bleak: Among threatened vertebrates, rapid losses began in the late 19th century, and numbers have since declined by about 25 percent per decade, according to a new study.

“Although preservation of biodiversity is vital to a sustainable human society, rapid population decline (RPD) continues to be widespread” across plant and animal populations, Haipeng Li and a team of Chinese and American biologists write in Proceedings of the National Academy of Sciences.

Understanding the severity and origins of these population losses could help conservationists protect endangered species and possibly help promote public awareness of the threat, the researchers argue. But there’s a problem: Good data on plant and animal population sizes only goes back about four decades, and populations surely declined prior to that.

Fortunately, modern biologists have a way to circumvent that: DNA. [Continue reading…]


Huddled mice could change the way we think about evolution

Stuart P Wilson, University of Sheffield and James V Stone, University of Sheffield

Adapt or die. That’s the reality for an animal species when it is faced with a harsh environment. Until now, many scientists have assumed that the more challenging an animal’s environment, the greater the pressure to adapt and the faster its genes evolve. But we have just published new research in Royal Society Open Science that shows that genes might actually evolve faster when the pressure to adapt is reduced.

We built a simple computer model of how evolution may be affected by the way animals interact with each other when they’re in groups. Specifically, we looked at what happens to animals that huddle together to keep warm.

We found that when animals huddle in larger groups, their genes for regulating temperature evolve faster, even though there is less pressure to adapt to the cold environment because of the warmth of the huddle. This shows that an organism’s evolution doesn’t just depend on its environment but also on how it behaves.

When animals such as rats and mice huddle together in groups, they can maintain a high body temperature without using as much energy as they would on their own. We wanted to understand how this kind of group behaviour would affect a species’ evolution.

To do this, we built a computer model simulating how the species’ genes changed and were passed on over multiple generations. When the effects of huddling were built into the computer model, the reduced pressure to adapt was actually found to accelerate evolution of the genes controlling heat production and heat loss.

[Read more…]


China is at the forefront of manipulating DNA to create a new class of superhumans

G. Owen Schaefer writes: Would you want to alter your future children’s genes to make them smarter, stronger, or better looking? As the state of science brings prospects like these closer to reality, an international debate has been raging over the ethics of enhancing human capacities with biotechnologies such as so-called smart pills, brain implants, and gene editing. This discussion has only intensified in the past year with the advent of the CRISPR-cas9 gene editing tool, which raises the specter of tinkering with our DNA to improve traits like intelligence, athleticism, and even moral reasoning.

So are we on the brink of a brave new world of genetically enhanced humanity? Perhaps. And there’s an interesting wrinkle: It’s reasonable to believe that any seismic shift toward genetic enhancement will not be centered in Western countries like the US or the UK, where many modern technologies are pioneered. Instead, genetic enhancement is more likely to emerge out of China.

Numerous surveys among Western populations have found significant opposition to many forms of human enhancement. For example, a recent Pew study of 4,726 Americans found that most would not want to use a brain chip to improve their memory, and a plurality view such interventions as morally unacceptable. [Continue reading…]


A unified theory of evolution requires input from Darwin and Lamarck


Michael Skinner writes: The unifying theme for much of modern biology is based on Charles Darwin’s theory of evolution, the process of natural selection by which nature selects the fittest, best-adapted organisms to reproduce, multiply and survive. The process is also called adaptation, and traits most likely to help an individual survive are considered adaptive. As organisms change and new variants thrive, species emerge and evolve. In the 1850s, when Darwin described this engine of natural selection, the underlying molecular mechanisms were unknown. But over the past century, advances in genetics and molecular biology have outlined a modern, neo-Darwinian theory of how evolution works: DNA sequences randomly mutate, and organisms with the specific sequences best adapted to the environment multiply and prevail. Those are the species that dominate a niche, until the environment changes and the engine of evolution fires up again.

But this explanation for evolution turns out to be incomplete, suggesting that other molecular mechanisms also play a role in how species evolve. One problem with Darwin’s theory is that, while species do evolve more adaptive traits (called phenotypes by biologists), the rate of random DNA sequence mutation turns out to be too slow to explain many of the changes observed. Scientists, well-aware of the issue, have proposed a variety of genetic mechanisms to compensate: genetic drift, in which small groups of individuals undergo dramatic genetic change; or epistasis, in which one set of genes suppress another, to name just two.

Yet even with such mechanisms in play, genetic mutation rates for complex organisms such as humans are dramatically lower than the frequency of change for a host of traits, from adjustments in metabolism to resistance to disease. The rapid emergence of trait variety is difficult to explain just through classic genetics and neo-Darwinian theory. To quote the prominent evolutionary biologist Jonathan B L Bard, who was paraphrasing T S Eliot: ‘Between the phenotype and genotype falls the shadow.’

And the problems with Darwin’s theory extend out of evolutionary science into other areas of biology and biomedicine. For instance, if genetic inheritance determines our traits, then why do identical twins with the same genes generally have different types of diseases? And why do just a low percentage (often less than 1 per cent) of those with many specific diseases share a common genetic mutation? If the rate of mutation is random and steady, then why have many diseases increased more than 10-fold in frequency in only a couple decades? How is it that hundreds of environmental contaminants can alter disease onset, but not DNA sequences? In evolution and biomedicine, the rates of phenotypic trait divergence is far more rapid than the rate of genetic variation and mutation – but why?

Part of the explanation can be found in some concepts that Jean-Baptiste Lamarck proposed 50 years before Darwin published his work. Lamarck’s theory, long relegated to the dustbin of science, held, among other things, ‘that the environment can directly alter traits, which are then inherited by generations to come’. [Continue reading…]


Digging our own graves in deep time

By David Farrier, Aeon, October 31, 2016

Late one summer night in 1949, the British archaeologist Jacquetta Hawkes went out into her small back garden in north London, and lay down. She sensed the bedrock covered by its thin layer of soil, and felt the hard ground pressing her flesh against her bones. Shimmering through the leaves and out beyond the black lines of her neighbours’ chimney pots were the stars, beacons ‘whose light left them long before there were eyes on this planet to receive it’, as she put it in A Land (1951), her classic book of imaginative nature writing.

We are accustomed to the idea of geology and astronomy speaking the secrets of ‘deep time, the immense arc of non-human history that shaped the world as we perceive it. Hawkes’s lyrical meditation mingles the intimate and the eternal, the biological and the inanimate, the domestic with a sense of deep time that is very much of its time. The state of the topsoil was a matter of genuine concern in a country wearied by wartime rationing, while land itself rises into focus just as Britain is rethinking its place in the world. But in lying down in her garden, Hawkes also lies on the far side of a fundamental boundary. A Land was written at the cusp of the Holocene; we, on the other hand, read it in the Anthropocene.

The Anthropocene, or era of the human, denotes how industrial civilisation has changed the Earth in ways that are comparable with deep-time processes. The planet’s carbon and nitrogen cycles, ocean chemistry and biodiversity – each one the product of millions of years of slow evolution – have been radically and permanently disrupted by human activity. The development of agriculture 10,000 years ago, and the Industrial Revolution in the middle of the 19th century, have both been proposed as start dates for the Anthropocene. But a consensus has gathered around the Great Acceleration – the sudden and dramatic jump in consumption that began around 1950, followed by a huge rise in global population, an explosion in the use of plastics, and the collapse of agricultural diversity.

[Read more…]


The Sixth Extinction: Two-thirds of global wildlife population expected to be lost by the end of this decade


Marco Lambertini, Director General,WWF International, writes [PDF]: The evidence has never been stronger and our understanding never been clearer. Not only are we able to track the exponential increase in human pressure over the last 60 years — the so-called “Great Acceleration” and the consequent degradation of natural systems, but we also now better understand the interdependencies of Earth’s life support systems and the limits that our planet can cope with.

Take biodiversity. The richness and diversity of life on Earth is fundamental to the complex life systems that underpin it. Life supports life itself. We are part of the same equation. Lose biodiversity and the natural world and the life support systems, as we know them today, will collapse. We completely depend on nature, for the quality of the air we breathe, water we drink, climate stability, the food and materials we use and the economy we rely on, and not least, for our health, inspiration and happiness.

For decades scientists have been warning that human actions are pushing life on our shared planet toward a sixth mass extinction. Evidence in this year’s Living Planet Report supports this. Wildlife populations have already shown a concerning decline, on average by 58 per cent since 1970 and are likely to reach 67 per cent by the end of the decade. [Continue reading…[PDF]]


Mice feel each other’s pain

Science magazine reports: To most people, the phrase “I feel your pain” is just an expression of sympathy. But it’s also a real biological phenomenon, a new study in rodents suggests. Healthy mice living in the same room with mice experiencing pain are up to 68% more sensitive to pain themselves, regardless of their stress levels, according to the new study, which found that mice could scent when their fellows were suffering. The discovery suggests that current methods for studying rodent pain may need to be overhauled, and it may even point to a novel mechanism for pain transmission between humans, the authors say.

Andrey Ryabinin, a behavioral neuroscientist at Oregon Health & Science University in Portland, and colleagues stumbled on the phenomenon largely by accident. They were studying the effects of alcohol withdrawal in mice, looking for new ways to help people overcome addiction. One of the most common, but challenging, symptoms of alcohol withdrawal is an intense, generalized pain throughout the body—a difficult-to-define condition that often leads people back to drinking, he says. Recreating those painful withdrawal symptoms in mice is difficult, leading some researchers to question whether the rodents are a good model for alcohol addiction.

Ryabinin and his team were using a standard setup: The mice are allowed to lap freely at an ethanol and water solution, but then go into withdrawal after the bottle is removed. A control group, housed in the same room, drinks only water. Using multiple measures of pain sensitivity—including brushing their forepaws with a thin hair and dipping their tails into hot water, the researchers attempted to gauge how withdrawal might be affecting the addicted rodents.

The initial results were disappointing, showing no significant difference between the two groups. Before giving up, however, the scientists decided to cage the control mice in a different room. This time, the sober controls showed far less pain sensitivity than the controls in the previous experiment, suggesting that the latter group had somehow acquired a heightened pain sensitivity from their roommates, Ryabinin says. [Continue reading…]


Hints of tool use, culture seen in bumble bees

Science magazine reports: For years, cognitive scientist Lars Chittka felt a bit eclipsed by his colleagues at Queen Mary University of London. Their studies of apes, crows, and parrots were constantly revealing how smart these animals were. He worked on bees, and at the time, almost everyone assumed that the insects acted on instinct, not intelligence. “So there was a challenge for me: Could we get our small-brained bees to solve tasks that would impress a bird cognition researcher?” he recalls. Now, it seems he has succeeded at last.

Chittka’s team has shown that bumble bees can not only learn to pull a string to retrieve a reward, but they can also learn this trick from other bees, even though they have no experience with such a task in nature. The study “successfully challenges the notion that ‘big brains’ are necessary” for new skills to spread, says Christian Rutz, an evolutionary ecologist who studies bird cognition at the University of St. Andrews in the United Kingdom.

Many researchers have used string pulling to assess the smarts of animals, particularly birds and apes. So Chittka and his colleagues set up a low clear plastic table barely tall enough to lay three flat artificial blue flowers underneath. Each flower contained a well of sugar water in the center and had a string attached that extended beyond the table’s boundaries. The only way the bumble bee could get the sugar water was to pull the flower out from under the table by tugging on the string. [Continue reading…]


Something is shifting out there in the ocean

Rebecca Kessler writes: ‘It’s hard to believe that a 40-ton animal can get hidden. They’re sneaky.’ Charles ‘Stormy’ Mayo was scanning the sea from the deck of the R/V Shearwater searching for omens: a cloud of vapour, a patch of white water, a fluke. A few minutes earlier someone had spotted the first North Atlantic right whales of the day. But now they were down below and out of sight in 80 feet of murky seawater. Feeding, most likely.

Finally, a whale’s head emerged briefly on the sea surface. Then a slab of black back followed by the silhouette of flukes, signaling another deep dive. The appearance lasted maybe a second and a half. Groans from the crew, who did not quite manage to snap a photo that could help identify the whale, one of an early March influx that foretold another strong season in Cape Cod Bay. ‘There’s probably a bunch of whales here but it’s going to drive us crazy,’ Mayo chimed in. ‘I’m going to say there are probably three. It’s hard as hell to tell.’

The world’s rarest whales – Eubalaena glacialis – have been visiting the bay in late winter and early spring for as long as anyone can remember. But Mayo and his team at the Center for Coastal Studies (CCS) in Provincetown documented a puzzling uptick in recent years. Not just a few dozen animals, as was typical, but hundreds were showing up and, in one year, darn-near two-thirds of the world’s entire living population of around 500 North Atlantic right whales. ‘Right Whale Kingdom’ Mayo has called the bay. Simultaneously, the whales went AWOL from their usual summer feeding grounds 300 miles to the northeast in Canada’s Bay of Fundy and elsewhere, further mystifying researchers.

The Shearwater idled, waiting. The whales remained deep down, scooping up patches of zooplankton and straining out the seawater through the long strips of baleen in their mouths. Scooping and straining, scooping and straining. A change in the location of their preferred food is the most likely explanation for the whales’ wandering itinerary, Mayo said. Something is shifting out there in the ocean. As with so much else about their lives, only the whales know what it is. [Continue reading…]