Evolution’s random paths lead to one place

Quanta Magazine: In his fourth-floor lab at Harvard University, Michael Desai has created hundreds of identical worlds in order to watch evolution at work. Each of his meticulously controlled environments is home to a separate strain of baker’s yeast. Every 12 hours, Desai’s robot assistants pluck out the fastest-growing yeast in each world — selecting the fittest to live on — and discard the rest. Desai then monitors the strains as they evolve over the course of 500 generations. His experiment, which other scientists say is unprecedented in scale, seeks to gain insight into a question that has long bedeviled biologists: If we could start the world over again, would life evolve the same way?

Many biologists argue that it would not, that chance mutations early in the evolutionary journey of a species will profoundly influence its fate. “If you replay the tape of life, you might have one initial mutation that takes you in a totally different direction,” Desai said, paraphrasing an idea first put forth by the biologist Stephen Jay Gould in the 1980s.

Desai’s yeast cells call this belief into question. According to results published in Science in June, all of Desai’s yeast varieties arrived at roughly the same evolutionary endpoint (as measured by their ability to grow under specific lab conditions) regardless of which precise genetic path each strain took. It’s as if 100 New York City taxis agreed to take separate highways in a race to the Pacific Ocean, and 50 hours later they all converged at the Santa Monica pier.

The findings also suggest a disconnect between evolution at the genetic level and at the level of the whole organism. [Continue reading...]

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The thermodynamic theory of ecology

Quanta Magazine: The Western Ghats in India rise like a wall between the Arabian Sea and the heart of the subcontinent to the east. The 1,000-mile-long chain of coastal mountains is dense with lush rainforest and grasslands, and each year, clouds bearing monsoon rains blow in from the southwest and break against the mountains’ flanks, unloading water that helps make them hospitable to numerous spectacular and endangered species. The Western Ghats are one of the most biodiverse places on the planet. They were also the first testing ground of an unusual new theory in ecology that applies insights from physics to the study of the environment.

John Harte, a professor of ecology at the University of California, Berkeley, has a wry, wizened face and green eyes that light up when he describes his latest work. He has developed what he calls the maximum entropy (MaxEnt) theory of ecology, which may offer a solution to a long-standing problem in ecology: how to calculate the total number of species in an ecosystem, as well as other important numbers, based on extremely limited information — which is all that ecologists, no matter how many years they spend in the field, ever have. Five years ago, the Ghats convinced him that what he thought was possible from back-of-the-envelope calculations could work in the real world. He and his colleagues will soon publish the results of a study that estimates the number of insect and tree species living in a tropical forest in Panama. The paper will also suggest how MaxEnt could give species estimates in the Amazon, a swath of more than 2 million square miles of land that is notoriously difficult to survey.
John Harte thinks it is possible to predict the behavior of ecosystems using just a few key attributes. His method ignores nature’s small-grained complexities, which makes many ecologists skeptical of the project.

If the MaxEnt theory of ecology can give good estimates in a wide variety of scenarios, it could help answer the many questions that revolve around how species are spread across the landscape, such as how many would be lost if a forest were cleared, how to design wildlife preserves that keep species intact, or how many rarely seen species might be hiding in a given area. Perhaps more importantly, the theory hints at a unified way of thinking about ecology — as a system that can be described with just a few variables, with all the complexity of life built on top. [Continue reading...]

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True Darwinism is all about chance

Noah Berlatsky writes: Chance is an uncomfortable thing. So Curtis Johnson argues in Darwin’s Dice: The Idea of Chance in the Thought of Charles Darwin, and he makes a compelling case. The central controversy, and the central innovation, in Darwin’s work is not the theory of natural selection itself, according to Johnson, but Darwin’s more basic, and more innovative, turn to randomness as a way to explain natural phenomena. This application of randomness was so controversial, Johnson argues, that Darwin tried to cover it up, replacing words like “accident” and “chance” with terms like “spontaneous variation” in later editions of his work. Nonetheless, the terminological shift was cosmetic: Randomness remained, and still remains, the disturbing center of Darwin’s theories.

Johnson, a political theorist at Lewis & Clark College, explains that there are two basic kinds of chance in Darwin’s thought. The first—most familiar and least disconcerting—is chance as probability. According to the theory of natural selection, individuals with advantageous adaptations are most likely to survive. A giraffe with a longer neck has a better shot of reaching those lofty leaves and living to munch another day; a polar bear blessed with a warmer coat has a higher probability of surviving a frigid winter than one with less hair. The long-necked giraffe may not always win—it may, for example, be pulverized by a meteor before it can pass on its long-necked genes. But over time, the odds will go its way. There is randomness here, but it is controlled and predictable: It works in accordance with a rule. Natural selection makes sense.

The second kind of chance in Darwin’s work, though, is more mysterious. For natural selection to work, you need to have a range of traits to select among. That range is provided by individual variation, the fact that two different animals (whether giraffe or bear) are different from each other. Some giraffes have longer necks than others. Some bears have thicker fur than others. Why should this be? Darwin’s answer was chance. [Continue reading...]

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How to save Earth from a cataclysmic extinction event

Tony Hiss talks to E.O. Wilson, the great evolutionary biologist, about how to save life on Earth: Throughout the 544 million or so years since hard-shelled animals first appeared, there has been a slow increase in the number of plants and animals on the planet, despite five mass extinction events. The high point of biodiversity likely coincided with the moment modern humans left Africa and spread out across the globe 60,000 years ago. As people arrived, other species faltered and vanished, slowly at first and now with such acceleration that Wilson talks of a coming “biological holocaust,” the sixth mass extinction event, the only one caused not by some cataclysm but by a single species—us.

Wilson recently calculated that the only way humanity could stave off a mass extinction crisis, as devastating as the one that killed the dinosaurs 65 million years ago, would be to set aside half the planet as permanently protected areas for the ten million other species. “Half Earth,” in other words, as I began calling it—half for us, half for them. A version of this idea has been in circulation among conservationists for some time.

“It’s been in my mind for years,” Wilson told me, “that people haven’t been thinking big enough—even conservationists. Half Earth is the goal, but it’s how we get there, and whether we can come up with a system of wild landscapes we can hang onto. I see a chain of uninterrupted corridors forming, with twists and turns, some of them opening up to become wide enough to accommodate national biodiversity parks, a new kind of park that won’t let species vanish.”

I had also begun to think about such wildland chains as “Long Landscapes,” and Wilson said he liked the idea that they could meet climate change head on: Those that run north-south, like the initiative in the West known as Yellowstone-to-Yukon, can let life move north as things warm up, and those that run east-west may have the benefit of letting life move east, away from the west, which in the future may not see as much rain. “Why, when this thing gets really going,” Wilson said, “you’ll be so surrounded, so enveloped by connected corridors that you’ll almost never not be in a national park, or at any rate in a landscape that leads to a national park.”

Is this Half Earth vision even possible, I wondered, and what might it look like? [Continue reading...]

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Is the world making you sick?

Jill Neimark writes: In 1962, physicist and historian Thomas Kuhn proposed that science makes progress not just through the gradual accumulation and analysis of knowledge, but also through periodic revolutions in perspective. Anomalies and incongruities that may have been initially ignored drive a field into crisis, he argued, and eventually force a new scientific framework. Copernicus, Darwin, Newton, Galileo, Pasteur—all have spearheaded what Kuhn has called a “paradigm shift.”

Thomas Kuhn is Claudia Miller’s hero. An immunologist and environmental health expert at the University of Texas School of Medicine in San Antonio, and a visiting senior scientist at Harvard University, Miller lives by Kuhn’s maxim that “the scientist who embraces a new paradigm is like the man wearing inverting lenses…[he] has undergone a revolutionary transformation of vision.”

Miller has spent 30 years hammering out a theory to explain the contemporary surge in perplexing, multi-symptom illnesses — from autism to Gulf War Syndrome — which represent a Kuhnian shift in medicine. She calls her theory “TILT,” short for Toxicant Induced Loss of Tolerance.

TILT posits that a surprising range of today’s most common chronic conditions are linked to daily exposure to very low doses of synthetic chemicals that have been in mass production since World War II. These include organophosphate pesticides, flame-retardants, formaldehyde, benzene, and tens of thousands of other chemicals.

TILT, says Miller, is a two-step process. Genetically susceptible individuals get sick after a toxic exposure or series of exposures. Instead of recovering, their neurological and immune systems become “tilted.” Then, they lose tolerance to a wide range of chemicals commonly found at low doses in everyday life and develop ongoing illnesses. [Continue reading...]

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The super-abundant virus controlling your gut bacteria

The New Scientist reports: The common cold, hepatitis C… crAssphage? A new virus has been discovered that could lurk in the guts of almost three-quarters of people around the world, making it one of the most ubiquitous viruses you never knew you had.

The virus, which replicates by infecting a species of common gut bacteria, is six times more abundant than all other known gut viruses combined. Its discovery supports the idea that viruses may be the puppet masters of our intestines, regulating the teeming bacterial communities that call our gut home.

“The idea is that viruses can control the levels of bacteria in the gut, to make sure that no one type gets the upper hand,” says Bas Dutilh of Radboud University Medical Centre in Nijmegen, the Netherlands. “Viruses could maintain the biodiversity within us.”

The fact that the virus is found in so many different people, regardless of where they live or what they eat, overturns the previously held belief that each person’s viral signature is unique, says Dutilh. [Continue reading...]

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Human microbes. Who is the host?

Imagine New York City with the lights all on, but nobody home — indeed, nobody anywhere. A city fully intact and yet uninhabited. Would it still be a city, or would we refer to it as the place formerly known as New York City?

The image I’m conjuring up is not meant to represent the aftermath of some catastrophe, but rather, if we were to think of NYC as representing a human body, what that body would be like if it was stripped of its microbial life.

When the human body is described as being a host to a multitude of microbial organisms, by implication those organisms are viewed as guests. We might have some sense that we need these guests — even that we cannot survive without them — but they belong to us rather than us to them.

Why?

The “I” that stands at the center, possessed — or so it imagines — with some kind of regal authority over this domain called a person, is really a fiction.

Life in the city which is the body, continues just the same whether the monarch is awake or unconscious.

Jane Brody writes: We may think of ourselves as just human, but we’re really a mass of microorganisms housed in a human shell. Every person alive is host to about 100 trillion bacterial cells. They outnumber human cells 10 to one and account for 99.9 percent of the unique genes in the body.

Katrina Ray, a senior editor of Nature Reviews, recently suggested that the vast number of microbes in the gut could be considered a “human microbial ‘organ’” and asked, “Are we more microbe than man?

Our collection of microbiota, known as the microbiome, is the human equivalent of an environmental ecosystem. Although the bacteria together weigh a mere three pounds, their composition determines much about how the body functions and, alas, sometimes malfunctions.

Like ecosystems the world over, the human microbiome is losing its diversity, to the potential detriment of the health of those it inhabits.

Dr. Martin J. Blaser, a specialist in infectious diseases at the New York University School of Medicine and the director of the Human Microbiome Program, has studied the role of bacteria in disease for more than three decades. His research extends well beyond infectious diseases to autoimmune conditions and other ailments that have been increasing sharply worldwide.

In his new book, “Missing Microbes,” Dr. Blaser links the declining variety within the microbiome to our increased susceptibility to serious, often chronic conditions, from allergies and celiac disease to Type 1 diabetes and obesity. He and others primarily blame antibiotics for the connection. [Continue reading...]

Want to diversify your own ecosystem?

It’s easier than you might imagine. Just start making your own kefir — a fermented milk drink. There’s very little skill required.

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When we were fish

Nautilus: Neil Shubin has been going backward his whole life. “I teach anatomy but I want to understand why things look the way they do,” says the paleontologist and professor of organismal biology and anatomy at the University of Chicago. “And to understand the fundamental questions you have to go ever deeper into history. So I have gone backward from humans to fish to planets.”

Shubin, 53, is referring to his two books, Your Inner Fish and The Universe Within, which detail the atoms and molecules, genes and cells, sculpted by evolution into the common bonds of life. In 2004, on Ellesmere Island in the Arctic, Shubin discovered one of the key links in animal evolution, the fish known as Tiktaalik, that, he writes, “was specialized for a rather extraordinary function: it was capable of doing push-ups.”

Shubin and his team learned from Tiktaalik fossils that the big fish with the flat head had a shoulder, elbow, and wrist composed of the same bones in a human’s upper arm, forearm, and wrist. Tiktaalik used those bones to navigate shallow streams and ponds “and even to flop around on the mudflats along the banks.” Here was the creature from the lagoon that revealed how animals evolved from fish to us. [Continue reading...]

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Systemic pesticides pose global threat to biodiversity, harming bees, butterflies, fish and birds

AFP reports: Neurotoxic pesticides blamed for the world’s bee collapse are also harming butterflies, worms, fish and birds, said a scientific review that called Tuesday for tighter regulation to curb their use.

Analysing two decades of reports on the topic, an international panel of 29 scientists found there was “clear evidence of harm” from use of two pesticide types, neonicotinoids and fipronil.

And the evidence was “sufficient to trigger regulatory action”.

“We are witnessing a threat to the productivity of our natural and farmed environment,” said Jean-Marc Bonmatin of France’s National Centre for Scientific Research, co-author of the report entitled the Worldwide Integrated Assessment.

Far from protecting food production, these nerve-targeting insecticides known as neonics were “imperilling the pollinators, habitat engineers and natural pest controllers at the heart of a functioning ecosystem.”

The four-year assessment was carried out by The Task Force on Systemic Pesticides, which advises the International Union for Conservation of Nature, the world’s watchdog on species loss.

Neonics are widely used insecticides whose effects can be instant and lethal, or chronic. Exposure can impair smell and memory in some species, curb procreation, reduce foraging, cause flight difficulties and increase disease susceptibility.

Used for insect pest management in farming, but also in pet flea control, they have been fingered in the recent decline in bees — crucial pollinators of human food crops — in Europe, the Americas and Asia.

The latest study says these pesticides, absorbed by plants, are also harming other insect pollinators, fish and birds as they leach into soil and water.

The most affected species were terrestrial invertebrates such as earthworms, which are crucial soil-enrichers, said a press statement.

Bees and butterflies were next, followed by aquatic invertebrates like freshwater snails and water fleas, then birds, and finally fish, amphibians and certain microbes. [Continue reading...]

Imidacloprid, primarily manufactured by Bayer CropScience, is not only the most widely used neonicotinoid pesticide but also the most widely used insecticide of any type in the world.

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How malnutrition affects the microbiome

The Scientist reports: The gut microbiomes of young children don’t fully recover from the trauma of early-life malnourishment, even after they are treated with more-complete diets, according to a study published in Nature. A team led by Jeffrey Gordon of the Washington University in St. Louis sampled the gut microbiomes of healthy and malnourished children in Bangladesh and found that the microbiomes of children who were underfed and whose diets lacked essential nutrients looked less like those of adults and more like those of younger, healthy children.

“This is actually a real step forward in terms of having a technique to look at development of the microbiome in children,” said Josef Neu, a pediatrician at the University of Florida who studies gastrointestinal health of neonates and was not involved in the work.

The findings present a possible explanation for the commonly observed complications that malnourished children suffer even after they are treated with a standardized food regimen, including stunted growth, cognitive delays, and immune system problems. The researchers suggested that the immature gut microbiomes of malnourished children may be partially responsible for some of these long-term impairments. [Continue reading...]

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The language of life

vegetables

Within the mechanistic worldview that shapes the way most of us view life, each human being and other living organism is seen as a discrete entity — a form that possesses and is animated by its own life.

Lives come into existence, go out of existence, and between times interact with each other, while all along retaining autonomy in varying degrees.

Human beings, as creatures whose powers have been extended and amplified through technology, supposedly possess the highest degree of autonomy, living lives steered by the exercise of our freewill.

Having become so full of ourselves we have mostly lost the sense of life forming a seamless whole. We fail to see that human being is a conceptual construct fabricated through a leap of imagination.

But this thing called life is unfathomably complex and the more we learn about it, the more we discover its interactive nature.

Just as people talk to each other and those conversations produce societies, it turns out that inside our bodies another kind of conversation — this one through molecular exchanges facilitated by exosomes — allows plant cells to “talk” to our cells and thereby regulate the homeostatic foundations of health.

GreenMedInfo reports: A groundbreaking new study published in Molecular Nutrition & Food Research titled, “Interspecies communication between plant and mouse gut host cells through edible plant derived exosome-like nanoparticles,” reveals a new way that food components ‘talk’ to animal cells by regulating gene expression and conferring significant therapeutic effects. With the recent discovery that non-coding microRNA’s in food are capable of directly altering gene expression within human physiology, this new study further concretizes the notion that the age old aphorism ‘you are what you eat’ is now consistent with cutting edge molecular biology.

This is the first study of its kind to look at the role of exosomes, small vesicles secreted by plant and animal cells that participate in intercellular communication, in interspecies (plant-animal) communication.

The study explained the biological properties of exosomes as follows:

“Exosomes are produced by a variety of mammalian cells including immune, epithelial, and tumor cells [11–15]. Exosomes play a role in intercellular communication and can transport mRNA, miRNA, bioactive lipids, and proteins between cells [16–19]. Upon contact, exosomes transfer molecules that can render new properties and/or reprogram their recipient cells.”

While most of the research on exosomes has focused on their role in pathological states such as tumor promotion, they were recently found to play a key role in stimulating regeneration within damaged cardiac tissue, and are known to be found in human breast milk, further underscoring how irreplaceable it is vis-à-vis synthesized infant formula. [Continue reading...]

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Mice run for fun

James Gorman writes: If an exercise wheel sits in a forest, will mice run on it?

Every once in a while, science asks a simple question and gets a straightforward answer.

In this case, yes, they will. And not only mice, but also rats, shrews, frogs and slugs.

True, the frogs did not exactly run, and the slugs probably ended up on the wheel by accident, but the mice clearly enjoyed it. That, scientists said, means that wheel-running is not a neurotic behavior found only in caged mice.

They like the wheel.

Two researchers in the Netherlands did an experiment that it seems nobody had tried before. They placed exercise wheels outdoors in a yard and in an area of dunes, and monitored the wheels with motion detectors and automatic cameras.

They were inspired by questions from animal welfare committees at universities about whether mice were really enjoying wheel-running, an activity used in all sorts of studies, or were instead like bears pacing in a cage, stressed and neurotic. Would they run on a wheel if they were free?

Now there is no doubt. Mice came to the wheels like human beings to a health club holding a spring membership sale. They made the wheels spin. They hopped on, hopped off and hopped back on. [Continue reading...]

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Why does life resist disorder?

Addy Pross writes: Biology is wondrously strange – so familiar, yet so strikingly different to physics and chemistry. We know where we are with inanimate matter. Ever since Isaac Newton, it has answered to a basically mechanical view of nature, blindly following its laws without regard for purposes. But could there be, as Immanuel Kant put it, a Newton of the blade of grass? Living things might be made of the same fundamental stuff as the rest of the material world – ‘dead’ atoms and molecules – but they do not behave in the same way at all. In fact, they seem so purposeful as to defy the materialist philosophy on which the rest of modern science was built.

Even after Charles Darwin, we continue to struggle with that difference. As any biologist will acknowledge, function and purpose remain central themes in the life sciences, though they have long been banished from the physical sciences. How, then, can living things be reconciled with our mechanical-mechanistic universe? This is a conceptual question, of course, but it has a historical dimension: how did life on Earth actually come about? How could it have? Both at the abstract level and in the particular story of our world, there seems to be a chasm between the animate and inanimate realms.

I believe that it is now possible to bridge that gap. [Continue reading...]

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Hunter-gatherers have healthier guts than urban dwellers

Nature Communications reports: The gut microbiota is responsible for many aspects of human health and nutrition, but most studies have focused on “western” populations. An international collaboration of researchers, including researchers of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, has for the first time analysed the gut microbiota of a modern hunter-gatherer community, the Hadza of Tanzania. The results of this work show that Hadza harbour a unique microbial profile with features yet unseen in any other human group, supporting the notion that Hadza gut bacteria play an essential role in adaptation to a foraging subsistence pattern. The study further shows how the intestinal flora may have helped our ancestors adapt and survive during the Paleolithic.

Bacterial populations have co-evolved with humans over millions of years, and have the potential to help us adapt to new environments and foods. Studies of the Hadza offer an especially rare opportunity for scientists to learn how humans survive by hunting and gathering, in the same environment and using similar foods as our ancestors did.

The research team, composed of anthropologists, microbial ecologists, molecular biologists, and analytical chemists, and led in part by Stephanie Schnorr and Amanda Henry of the Max Planck Institute for Evolutionary Anthropology, compared the Hadza gut microbiota to that of urban living Italians, representative of a “westernized” population. Their results, published recently in Nature Communications, show that the Hadza have a more diverse gut microbe ecosystem, i.e. more bacterial species compared to the Italians. “This is extremely relevant for human health”, says Stephanie Schnorr. “Several diseases emerging in industrialized countries, like IBS, colorectal cancer, obesity, type II diabetes, Crohn’s disease and others, are significantly associated with a reduction in gut microbial diversity.” [Continue reading...]

Jeff Leach recently accompanied some Hadza hunters and observed the way they handled a recently killed adult Impala: Before the two Hadza men I was with jumped in to help skin and gut the Impala, I quickly took swabs of each of their hands (and 1 hour after, 3 hours after, and so on) to assess how the skin (palm) microbiota change throughout the day/week of a typical Hadza (We’ve sampled the hands [and stools] of 150+ Hadza men, women, and children so far). As they slowly and methodically dismembered the animal, they carefully placed the stomach and its still steaming contents on the fleshy side of the recently removed hide. In a separate area, they piled the fatty internal organs (which men are only allowed to eat by the way). Once the animal had been processed more or less, I was amazed to see all three men take a handful of the partially digested plant material from the recently removed stomach to scrub off the copious amounts of blood that now covered their hands and foreman’s. This was followed by a final “cleaning” with dry grass for good measure.

While I was fascinated by the microbe-laden stomach contents being used as hand scrubber – presumably transferring an extraordinary diversity of microbes from the Impala gut to the hands of the Hadza – I was not prepared for what they did next. Once they had cleaned out – by hand – the contents of the stomach (“cleaned” is a generous word), they carved pieces of the stomach into bite-sized chunks and consumed it sushi-style. By which I mean they didn’t cook it or attempt to kill or eliminate the microbes from the gut of the Impala in anyway. And if this unprecedented transfer of microbes from the skin, blood, and stomach of another mammal wasn’t enough, they then turned their attention to the colon of the Impala.

After removing the poo pellets (which we collect samples of as well), they tossed the tubular colon onto a hastily built fire. However, it only sat on the fire for a minute at best and clearly not long enough to terminate the menagerie of invisible microbes clinging to the inside wall of the colon. They proceeded to cut the colon into chunks and to eat more or less raw. For myself, I kindly turned down offers to taste either the raw stomach or the partially cooked colon – but did eat some tasty Impala ribs I thoroughly turned on a stick over the fire to a microbial-free state of well done.

The Hadza explained that this is what they always do, and have always done (though I suspect sushi-style eating of innards is not an every-kill ritual. But….). Whether it’s an Impala, Dik Dik, Zebra, bush pig, Kudu or any other of the myriad of mammals they hunt and eat, becoming one with the deceased’s microbes in any number of ways is common place – same goes for 700 plus species of birds they hunt (minus abundant amounts of stomach contents for hand sanitizer!). While less obvious than at the “kill site,” the transfer of microbes continued back in camp when women, children and other men handled the newly arrived raw meat, internal organs, and skin. The transfer continued as the hunters engaged (touching) other members of the camp.

The breathtaking exchange (horizontal transfer) of microbes between the Hadza and their environment is more or less how it’s been for eons until humans started walling ourselves off from the microbial world through the many facets of globalization. Rather than think of ourselves as isolated islands of microbes, the Hadza teach us that we are better thought of as an archipelago of islands, once seamlessly connected to one another and to a larger metacommunity of microbes via a microbial super highway that runs through the gut and skin/feathers of every animal and water source on the landscape (for those of you keeping up with your homework, this is Macroecology 101). The same can be said for plants and their extraordinary diversity of microbes above (phyllosphere) and below ground (rhizosphere) that the Hadza, and once all humans, interacted with on a nearly continuous basis.

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Methane-producing microbes may have triggered the largest mass extinction in Earth’s history

MIT News Office: Evidence left at the crime scene is abundant and global: Fossil remains show that sometime around 252 million years ago, about 90 percent of all species on Earth were suddenly wiped out — by far the largest of this planet’s five known mass extinctions. But pinpointing the culprit has been difficult, and controversial.

Now, a team of MIT researchers may have found enough evidence to convict the guilty parties — but you’ll need a microscope to see the killers.

The perpetrators, this new work suggests, were not asteroids, volcanoes, or raging coal fires, all of which have been implicated previously. Rather, they were a form of microbes — specifically, methane-producing archaea called Methanosarcina — that suddenly bloomed explosively in the oceans, spewing prodigious amounts of methane into the atmosphere and dramatically changing the climate and the chemistry of the oceans.

Volcanoes are not entirely off the hook, according to this new scenario; they have simply been demoted to accessories to the crime. The reason for the sudden, explosive growth of the microbes, new evidence shows, may have been their novel ability to use a rich source of organic carbon, aided by a sudden influx of a nutrient required for their growth: the element nickel, emitted by massive volcanism at just that time.

The new solution to this mystery is published this week in the Proceedings of the National Academy of Science by MIT professor of geophysics Daniel Rothman, postdoc Gregory Fournier, and five other researchers at MIT and in China.

The researchers’ case builds upon three independent sets of evidence. First, geochemical evidence shows an exponential (or even faster) increase of carbon dioxide in the oceans at the time of the so-called end-Permian extinction. Second, genetic evidence shows a change in Methanosarcina at that time, allowing it to become a major producer of methane from an accumulation of organic carbon in the water. Finally, sediments show a sudden increase in the amount of nickel deposited at exactly this time. [Continue reading...]

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Devasting consequences of losing ‘knowledgeable elders’ in non-human cultures

bluefin-tuna

Culture — something we generally associate with its expressions through art, music, literature and so forth — is commonly viewed as one of the defining attributes of humanity. We supposedly rose above animal instinct when we started creating bodies of knowledge, held collectively and passed down from generation to generation.

But it increasingly appears that this perspective has less to do with an appreciation of what makes us human than it has with our ignorance about non-human cultures.

Although non-human cultures don’t produce the kind of artifacts we create, the role of knowledge-sharing seems to be just as vital to the success of these societies as it is to ours. In other words, what makes these creatures what they are cannot be reduced to the structure of their DNA — it also involves a dynamic and learned element: the transmission of collective knowledge.

The survival of some species doesn’t simply depend on their capacity to replicate their DNA; it depends on their ability to pass on what they know.

Scuola Internazionale Superiore di Studi Avanzati: Small changes in a population may lead to dramatic consequences, like the disappearance of the migratory route of a species. A study carried out in collaboration with the SISSA has created a model of the behaviour of a group of individuals on the move (like a school of fish, a herd of sheep or a flock of birds, etc.) which, by changing a few simple parameters, reproduces the collective behaviour patterns observed in the wild. The model shows that small quantitative changes in the number of knowledgeable individuals and availability of food can lead to radical qualitative changes in the group’s behaviour.

Until the ’50s, bluefin tuna fishing was a thriving industry in Norway, second only to sardine fishing. Every year, bluefin tuna used to migrate from the eastern Mediterranean up to the Norwegian coasts. Suddenly, however, over no more than 4-5 years, the tuna never went back to Norway. In an attempt to solve this problem, Giancarlo De Luca from SISSA (the International School for Advanced Studies of Trieste) together with an international team of researchers (from the Centre for Theoretical Physics — ICTP — of Trieste and the Technical University of Denmark) started to devise a model based on an “adaptive stochastic network.” The physicists wanted to simulate, simplifying it, the collective behaviour of animal groups. Their findings, published in the journal Interface, show that the number of “informed individuals” in a group, sociality and the strength of the decision of the informed individuals are “critical” variables, such that even minimal fluctuations in these variables can result in catastrophic changes to the system.

“We started out by taking inspiration from the phenomenon that affected the bluefin tuna, but in actual fact we then developed a general model that can be applied to many situations of groups “on the move,” explains De Luca.

The collective behaviour of a group can be treated as an “emerging property,” that is, the result of the self-organization of each individual’s behaviour. “The majority of individuals in a group may not possess adequate knowledge, for example, about where to find rich feeding grounds” explains De Luca. “However, for the group to function, it is enough that only a minority of individuals possess that information. The others, the ones who don’t, will obey simple social rules, for example by following their neighbours.”

The tendency to comply with the norm, the number of knowledgeable individuals and the determination with which they follow their preferred route (which the researchers interpreted as being directly related to the appeal, or abundance, of the resource) are critical variables. “When the number of informed individuals falls below a certain level, or the strength of their determination to go in a certain direction falls below a certain threshold, the migratory pathway disappears abruptly.”

“In our networks the individuals are “points,” with interconnections that form and disappear in the course of the process, following some established rules. It’s a simple and general way to model the system which has the advantage of being able to be solved analytically,” comments De Luca.

So what ever happened to the Norwegian tuna? “Based on our results we formulated some hypotheses which will, however, have to be tested experimentally,” says De Luca. In the’50s Norway experienced a reduction in biomass and in the quantity of herrings, the main prey of tuna, which might have played a role in their disappearance. “This is consistent with our model, but there’s more to the story. In a short time the herring population returned to normal levels, whereas the tuna never came back. Why?”

One hypothesis is that, although the overall number of Mediterranean tuna has not changed, what has changed is the composition of the population: “The most desirable tuna specimens for the fishing industry are the larger, older individuals, which are presumably also those with the greater amount of knowledge, in other words the knowledgeable elders.” concludes De Luca.

Another curious fact: what happens if there are too many knowledgeable elders? “Too many know-alls are useless,” jokes De Luca. “In fact, above a certain number of informed individuals, the group performance does not improve so much as to justify the “cost” of their training. The best cost-benefit ratio is obtained by keeping the number of informed individuals above a certain level, provided they remain a minority of the whole population.”

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We need to understand the language of nature

o13-iconMycologist, Paul Stamets, discusses the important role mushrooms play in the survival and health of the earth and human species.

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A Siberian giant virus and the butterfly effect

Omulyakhskaya and Khromskaya Bays lie along the northern Siberian coast, where permafrost blankets the land around the bays. Photo: NASA Earth Observatory

Omulyakhskaya and Khromskaya Bays lie along the northern Siberian coast, where permafrost blankets the land around the bays. Photo: NASA Earth Observatory

Embedded in the mud, glistening green and gold and black, was a butterfly, very beautiful and very dead.

“Not a little thing like that! Not a butterfly!” cried Eckels.

It fell to the floor, an exquisite thing, a small thing that could upset balances and knock down a line of small dominoes and then big dominoes and then gigantic dominoes, all down the years across Time. Eckels’ mind whirled. It couldn’t change things. Killing one butterfly couldn’t be that important! Could it? — Ray Bradbury, A Sound of Thunder, 1952

As one of the massive and probably irreversible consequences of climate change, the melting of the Northern Hemisphere’s permafrost is not an example of the butterfly effect. Yet the discovery of a giant virus which has come back to life after 30,000 years of frozen dormancy, suggests many possibilities including some akin to those envisaged by Ray Bradbury is his famous science fiction story.

Whereas his narrative required that the reader suspend disbelief by entertaining the idea of time travel, the thawing tundra may produce a very real kind of time travel if any viruses or other microbes were to emerge as new invasive species.

Rather than being transported geographically as a result of human activity, these will spring suddenly from a distant past into an environment that may lack necessary evolutionary adaptations to accommodate their presence.

We are assured that Pithovirus sibericum poses no threat to humans — it just attacks amoebas. But our concern shouldn’t be limited to fears about the reemergence of something like an ancient strain of smallpox.

The rebirth of a pathogen that could strike phytoplankton — producers of half the world’s oxygen — would have a devastating impact on the planet.

BBC News reports: The ancient pathogen was discovered buried 30m (100ft) down in the frozen ground.

Called Pithovirus sibericum, it belongs to a class of giant viruses that were discovered 10 years ago.

These are all so large that, unlike other viruses, they can be seen under a microscope. And this one, measuring 1.5 micrometres in length, is the biggest that has ever been found.

The last time it infected anything was more than 30,000 years ago, but in the laboratory it has sprung to life once again.

Tests show that it attacks amoebas, which are single-celled organisms, but does not infect humans or other animals.

Co-author Dr Chantal Abergel, also from the CNRS, said: “It comes into the cell, multiplies and finally kills the cell. It is able to kill the amoeba – but it won’t infect a human cell.”

However, the researchers believe that other more deadly pathogens could be locked in Siberia’s permafrost.

“We are addressing this issue by sequencing the DNA that is present in those layers,” said Dr Abergel.

“This would be the best way to work out what is dangerous in there.”

The researchers say this region is under threat. Since the 1970s, the permafrost has retreated and reduced in thickness, and climate change projections suggest it will decrease further.

It has also become more accessible, and is being eyed for its natural resources.

Prof Claverie warns that exposing the deep layers could expose new viral threats.

He said: “It is a recipe for disaster. If you start having industrial explorations, people will start to move around the deep permafrost layers. Through mining and drilling, those old layers will be penetrated and this is where the danger is coming from.”

He told BBC News that ancient strains of the smallpox virus, which was declared eradicated 30 years ago, could pose a risk. [Continue reading...]

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