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

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

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

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

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

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Cooperation is what makes us human

Kat McGowan writes: Tales about the origins of our species always start off like this: A small band of hunter-gatherers roams the savannah, loving, warring, and struggling for survival under the African sun. They do not start like this: A fat guy falls off a New York City subway platform onto the tracks.

But what happens next is a quintessential story of who we are as human beings.

On Feb. 17, 2013, around 2:30 a.m., Garrett O’Hanlon, a U.S. Air Force Academy cadet third class, was out celebrating his 22nd birthday in New York City. He and his sister were in the subway waiting for a train when a sudden silence came over the platform, followed by a shriek. People pointed down to the tracks.

O’Hanlon turned and saw a man sprawled facedown on the tracks. “The next thing that happened, I was on the tracks, running toward him,” he says. “I honestly didn’t have a thought process.”

O’Hanlon grabbed the unconscious man by the shoulders, lifting his upper body off the tracks, but struggled to move him. He was deadweight. According to the station clock, the train would arrive in less than two minutes. From the platform, O’Hanlon’s sister was screaming at him to save himself.

Suddenly other arms were there: Personal trainer Dennis Codrington Jr. and his friend Matt Foley had also jumped down to help. “We grabbed him, one by the legs, one by the shoulders, one by the chest,” O’Hanlon says. They got the man to the edge of the platform, where a dozen or more people muscled him up and over. More hands seized the rescuers’ arms and shoulders, helping them up to safety as well.

In the aftermath of the rescue, O’Hanlon says he has been surprised that so many people have asked him why he did it. “I get stunned by the question,” he says. In his view, anybody else would’ve done the same thing. “I feel like it’s a normal reaction,” he says. “To me that’s just what people do.”

More precisely, it is something only people do, according to developmental psychologist Michael Tomasello, codirector of the Max Planck Institute for Evolutionary Anthropology.

For decades Tomasello has explored what makes humans distinctive. His conclusion? We cooperate. Many species, from ants to orcas to our primate cousins, cooperate in the wild. But Tomasello has identified a special form of cooperation. In his view, humans alone are capable of shared intentionality—they intuitively grasp what another person is thinking and act toward a common goal, as the subway rescuers did. This supremely human cognitive ability, Tomasello says, launched our species on its extraordinary trajectory. It forged language, tools, and cultures—stepping-stones to our colonization of every corner of the planet. [Continue reading...]

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35,000 year-old Indonesian cave paintings suggest art came out of Africa

The Guardian reports: Paintings of wild animals and hand markings left by adults and children on cave walls in Indonesia are at least 35,000 years old, making them some of the oldest artworks known.

The rock art was originally discovered in caves on the island of Sulawesi in the 1950s, but dismissed as younger than 10,000 years old because scientists thought older paintings could not possibly survive in a tropical climate.

But fresh analysis of the pictures by an Australian-Indonesian team has stunned researchers by dating one hand marking to at least 39,900 years old, and two paintings of animals, a pig-deer or babirusa, and another animal, probably a wild pig, to at least 35,400 and 35,700 years ago respectively.

The work reveals that rather than Europe being at the heart of an explosion of creative brilliance when modern humans arrived from Africa, the early settlers of Asia were creating their own artworks at the same time or even earlier.

Archaeologists have not ruled out that the different groups of colonising humans developed their artistic skills independently of one another, but an enticing alternative is that the modern human ancestors of both were artists before they left the African continent.

“Our discovery on Sulawesi shows that cave art was made at opposite ends of the Pleistocene Eurasian world at about the same time, suggesting these practices have deeper origins, perhaps in Africa before our species left this continent and spread across the globe,” said Dr Maxime Aubert, an archaeologist at the University of Wollongong. [Continue reading...]

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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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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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Why do laughter, smiles and tears look so similar?

Michael Graziano writes: About four thousand years ago, somewhere in the Middle East — we don’t know where or when, exactly — a scribe drew a picture of an ox head. The picture was rather simple: just a face with two horns on top. It was used as part of an abjad, a set of characters that represent the consonants in a language. Over thousands of years, that ox-head icon gradually changed as it found its way into many different abjads and alphabets. It became more angular, then rotated to its side. Finally it turned upside down entirely, so that it was resting on its horns. Today it no longer represents an ox head or even a consonant. We know it as the capital letter A.

The moral of this story is that symbols evolve.

Long before written symbols, even before spoken language, our ancestors communicated by gesture. Even now, a lot of what we communicate to each other is non-verbal, partly hidden beneath the surface of awareness. We smile, laugh, cry, cringe, stand tall, shrug. These behaviours are natural, but they are also symbolic. Some of them, indeed, are pretty bizarre when you think about them. Why do we expose our teeth to express friendliness? Why do we leak lubricant from our eyes to communicate a need for help? Why do we laugh?

One of the first scientists to think about these questions was Charles Darwin. In his 1872 book, The Expression of the Emotions in Man and Animals, Darwin observed that all people express their feelings in more or less the same ways. He argued that we probably evolved these gestures from precursor actions in ancestral animals. A modern champion of the same idea is Paul Ekman, the American psychologist. Ekman categorised a basic set of human facial expressions — happy, frightened, disgusted, and so on — and found that they were the same across widely different cultures. People from tribal Papua New Guinea make the same smiles and frowns as people from the industrialised USA.

Our emotional expressions seem to be inborn, in other words: they are part of our evolutionary heritage. And yet their etymology, if I can put it that way, remains a mystery. Can we trace these social signals back to their evolutionary root, to some original behaviour of our ancestors? To explain them fully, we would have to follow the trail back until we left the symbolic realm altogether, until we came face to face with something that had nothing to do with communication. We would have to find the ox head in the letter A.

I think we can do that. [Continue reading...]

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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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Can plants make choices?

a13-iconHelmholtz Centre for Environmental Research: Plants are also able to make complex decisions. At least this is what scientists from the Helmholtz Center for Environmental Research (UFZ) and the University of Göttingen have concluded from their investigations on Barberry (Berberis vulgaris), which is able to abort its own seeds to prevent parasite infestation. The results are the first ecological evidence of complex behaviour in plants. They indicate that this species has a structural memory, is able to differentiate between inner and outer conditions as well as anticipate future risks, scientists write in the renowned journal American Naturalist — the premier peer-reviewed American journal for theoretical ecology.

The European barberry or simply Barberry (Berberis vulgaris) is a species of shrub distributed throughout Europe. It is related to the Oregon grape (Mahonia aquifolium) that is native to North America and that has been spreading through Europe for years. Scientists compared both species to find a marked difference in parasite infestation: “a highly specialized species of tephritid fruit fly, whose larvae actually feed on the seeds of the native Barberry, was found to have a tenfold higher population density on its new host plant, the Oregon grape”, reports Dr. Harald Auge, a biologist at the UFZ.

This led scientists to examine the seeds of the Barberry more closely. Approximately 2000 berries were collected from different regions of Germany, examined for signs of piercing and then cut open to examine any infestation by the larvae of the tephritid fruit fly (Rhagoletis meigenii). This parasite punctures the berries in order to lay its eggs inside them. If the larva is able to develop, it will often feed on all of the seeds in the berry. A special characteristic of the Barberry is that each berry usually has two seeds and that the plant is able to stop the development of its seeds in order to save its resources. This mechanism is also employed to defend it from the tephritid fruit fly. If a seed is infested with the parasite, later on the developing larva will feed on both seeds. If however the plant aborts the infested seed, then the parasite in that seed will also die and the second seed in the berry is saved. [Read more...]

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The importance of consilience in science

OpinionPaul Willis writes: Science is not a democracy. A consensus of evidence may be interesting, but technically it may not be significant. The thoughts of a majority of scientists doesn’t mean a hill of beans. It’s all about the evidence. The science is never settled.

These are refrains that I and other science communicators have been using over and over again when we turn to analysing debates and discussions based on scientific principles. I think we get torn between remaining true to the philosophical principles by which science is conducted and trying to make those principles familiar to an audience that probably does not understand them.

So let me introduce a concept that is all-too-often overlooked in science discussions, that can actually shed some light deep into the mechanisms of science and explain the anatomy of a scientific debate. It’s the phonically beautiful term ‘consilience’.

Consilience means to use several different lines of inquiry that converge on the same or similar conclusions. The more independent investigations you have that reach the same result, the more confidence you can have that the conclusion is correct. Moreover, if one independent investigation produces a result that is at odds with the consilience of several other investigations, that is an indication that the error is probably in the methods of the adherent investigation, not in the conclusions of the consilience.

Let’s take an example to unpack this concept, an example where I first came across the term and it is a beautiful case of consilience at work. Charles Darwin’s On Origin Of Species is a masterpiece of consilience. Each chapter is a separate line of investigation and, within each chapter there are numerous examples, investigations and experiments that all join together to reach the same conclusion: that life changes through time and that life has evolved on Earth. Take apart On Origin Of Species case by case and no single piece of evidence that Darwin mustered conclusively demonstrates that evolution is true. But add those cases back together and the consilience is clear: evidence from artificial breeding, palaeontology, comparative morphology and a host of other independent lines of investigation combine to confirm the same inescapable conclusion.

That was 1859. Since then yet more investigations have been added to the consilience for evolution. What’s more, these investigations within the biological and geological sciences have been joined with others from physics and chemistry as well as completely new areas of science such as genetics, radiometric dating and molecular biology. Each independent line of investigation builds the consilience that the world and the universe are extremely old and that life has evolved through unfathomable durations of time here on our home planet.

So, when a new line of investigation comes along claiming evidence and conclusions contrary to evolution, how can that be accommodated within the consilience? How does it relate to so many independent strains conjoined by a similar conclusion at odds with the newcomer? Can one piece of evidence overthrow such a huge body of work?

Such is the thinking of those pesky creationists who regularly come up with “Ah-Ha!” and “Gotcha!” factoids that apparently overturn, not just evolution, but the whole consilience of science. [Continue reading...]

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A new theory about the origin of life

origin-life

Evolution explains how life changes, but it doesn’t explain how it came into existence. A young physicist at MIT has now come up with a mathematical formula which suggests that given the right set of conditions, the emergence of living forms is not merely possible; it almost seems inevitable.

Let there be light, shining on atoms, and there will eventually be life.

Quanta magazine: Why does life exist?

Popular hypotheses credit a primordial soup, a bolt of lightning and a colossal stroke of luck. But if a provocative new theory is correct, luck may have little to do with it. Instead, according to the physicist proposing the idea, the origin and subsequent evolution of life follow from the fundamental laws of nature and “should be as unsurprising as rocks rolling downhill.”

From the standpoint of physics, there is one essential difference between living things and inanimate clumps of carbon atoms: The former tend to be much better at capturing energy from their environment and dissipating that energy as heat. Jeremy England, a 31-year-old assistant professor at the Massachusetts Institute of Technology, has derived a mathematical formula that he believes explains this capacity. The formula, based on established physics, indicates that when a group of atoms is driven by an external source of energy (like the sun or chemical fuel) and surrounded by a heat bath (like the ocean or atmosphere), it will often gradually restructure itself in order to dissipate increasingly more energy. This could mean that under certain conditions, matter inexorably acquires the key physical attribute associated with life.

“You start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant,” England said.

England’s theory is meant to underlie, rather than replace, Darwin’s theory of evolution by natural selection, which provides a powerful description of life at the level of genes and populations. “I am certainly not saying that Darwinian ideas are wrong,” he explained. “On the contrary, I am just saying that from the perspective of the physics, you might call Darwinian evolution a special case of a more general phenomenon.”

His idea, detailed in a recent paper and further elaborated in a talk he is delivering at universities around the world, has sparked controversy among his colleagues, who see it as either tenuous or a potential breakthrough, or both.

England has taken “a very brave and very important step,” said Alexander Grosberg, a professor of physics at New York University who has followed England’s work since its early stages. The “big hope” is that he has identified the underlying physical principle driving the origin and evolution of life, Grosberg said.

“Jeremy is just about the brightest young scientist I ever came across,” said Attila Szabo, a biophysicist in the Laboratory of Chemical Physics at the National Institutes of Health who corresponded with England about his theory after meeting him at a conference. “I was struck by the originality of the ideas.”

Others, such as Eugene Shakhnovich, a professor of chemistry, chemical biology and biophysics at Harvard University, are not convinced. “Jeremy’s ideas are interesting and potentially promising, but at this point are extremely speculative, especially as applied to life phenomena,” Shakhnovich said.

England’s theoretical results are generally considered valid. It is his interpretation — that his formula represents the driving force behind a class of phenomena in nature that includes life — that remains unproven. But already, there are ideas about how to test that interpretation in the lab. [Continue reading...]

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Less than one third of Americans believe in evolution

(Note: Because of the misleading way in which Pew presents its own findings, multiple reports run with a headline similar to this one in USA Today: “One-third of Americans reject human evolution.” That would appear to imply that two-thirds of Americans accept the theory of evolution that provides the foundation for evolutionary biology. However, the rejectionists that the survey identifies are those who believe in the literal truth of Genesis, Adam and Eve etc.. Those who subscribe to Intelligent Design or other non-scientific Creationist evolutionary narratives are viewed by Pew as believing in human evolution.)

I am not a militant atheist. I have little patience for the anti-religion campaigning engaged in by Richard Dawkins, Sam Harris, and their ilk. The idea of trying to rid the world of religion makes no more sense than trying to abolish sport.

Human beings are not governed by reason and people who become enslaved by rationality, inevitably become emotionally malformed. The human capacity to express and experience love is a capacity without which we would cease to be human. As Pascal said: “The heart has its reasons which reason knows not.”

We live in a world constructed by thought and shared ideas and our ability to make sense of life springs in large part from the fact that we continuously filter our experience through stories — stories through which we tell ourselves who we are, where we live, and why we live.

Because of this, I don’t think that science should or can be thrust down anyone’s throat…

And yet to learn that less than a third of Americans believe in evolution is deeply depressing — even if not surprising.

Those who want to put a strong political spin on the results of a new Pew Research Center poll on views about evolution are emphasizing the fact that the greatest concentration of skepticism on evolution is among Republicans while pointing to the figure of 67% of Democrats believing in evolution.

The pollsters, however, fudged the basic question by implying that it’s possible to believe in evolution without accepting its scientific basis.

Pew’s primary interest was in differentiating between those Americans who take Genesis literally and those who don’t. Those Americans who believe “a supreme being guided the evolution of living things for the purpose of creating humans and other life in the form it exists today” are counted as believing in evolution, even though they don’t believe in natural selection.

The fact that Pew chose to slice the question in this way is itself illustrative of the weak influence science has in American culture. “Evolution” is being treated as an object of belief coming in many varieties, rather than as hard, incontrovertibly proven scientific fact.

No one would conduct a poll asking Americans whether they believe the Earth revolves around the Sun and yet when it comes to the subject of evolution, the deference to religious belief is so engrained that evolution is treated as a completely subjective term — evolution, whatever that means to you.

Why does this matter?

The world cannot tackle climate change if America turns its back on science. And yet as a culture, America currently stands somewhere between the sixteenth and the twentieth century. Copernicus was successful but the jury’s still out on Darwin.

If two-thirds of the population is skeptical about evolution, what chance is there of persuading them that climate change is caused by human activity?

It hardly seems coincidental that almost exactly the same number of Americans who believe in human-caused climate change also believe in evolution through natural selection. (I would hazard a guess that it’s not just the same number, but also the same Americans.)

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The society of microbes that make us what we are

Earth Island Journal: In your new book, Cooked, you explore the art of cooking through the elements of Fire, Water, Air, and Earth. I’m sure you love all your children equally, but of those four, which taught you the most?

Michael Pollan: Fermentation – without a doubt. I began this education about microbiology. I’ve always been interested in nature and other species, and this symbiotic relationship we have with them, and I have mostly paid attention to it in the plant world. I just had no idea of how rich our engagement with microbes was, and how invisible it is to us. I began it when I was doing the Air section and learning about sourdough cultures. But then I got into that last chapter and started learning about fermentation: how much of our food is fermented, the fact that you could cook without the use of any heat, and the fact that we are dependent on these microbes. They’re using us; we’re using them. For me that was most fascinating.

You point out that our feelings about microbes are an expression of our attitude toward the natural world.

Yeah, and our drive for control, at all costs. Microbes are frightening for a couple reasons. One is, they’re invisible. They’re an unseen enemy. And they are pathogens, I mean some of them. You know, conquering infectious disease was a tremendous achievement for our civilization. But as so often happens, we cast things in black and white. So microbes are all bad because some microbes cause disease, and we fail to realize how dependent we are on them for our health. I think we’re going to get to a point where we will discover the unit in evolution and natural selection is not the species as an individual, but what is called the “holobiont,” the group of species that travel together. And that’s what selection is acting on very often, is the super-organism of humans or cats or plants.

Plants, you know, they, too, have their own microbiome; I didn’t talk about this in the piece, but their microbiome is outside their bodies. It surrounds their roots. It’s in what’s called the rhizosphere. There’s a little ecosystem around the root of every plant, and I think we’re going to come to learn that it’s as important to plant health as our flora is to us. I think we’re going to start looking at all species as collectivities, and microbes will be the part of that. And that changes a lot. It changes how you approach agriculture. It certainly changes how you approach health. So I think we’re really on the verge of a paradigm shift around that. [Continue reading...]

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The misleading metaphor of the selfish gene

David Dobbs writes: A couple of years ago, at a massive conference of neuroscientists — 35,000 attendees, scores of sessions going at any given time — I wandered into a talk that I thought would be about consciousness but proved (wrong room) to be about grasshoppers and locusts. At the front of the room, a bug-obsessed neuroscientist named Steve Rogers was describing these two creatures — one elegant, modest, and well-mannered, the other a soccer hooligan.

The grasshopper, he noted, sports long legs and wings, walks low and slow, and dines discreetly in solitude. The locust scurries hurriedly and hoggishly on short, crooked legs and joins hungrily with others to form swarms that darken the sky and descend to chew the farmer’s fields bare.

Related, yes, just as grasshoppers and crickets are. But even someone as insect-ignorant as I could see that the hopper and the locust were wildly different animals — different species, doubtless, possibly different genera. So I was quite amazed when Rogers told us that grasshopper and locust are in fact the same species, even the same animal, and that, as Jekyll is Hyde, one can morph into the other at alarmingly short notice.

Not all grasshopper species, he explained (there are some 11,000), possess this morphing power; some always remain grasshoppers. But every locust was, and technically still is, a grasshopper — not a different species or subspecies, but a sort of hopper gone mad. If faced with clues that food might be scarce, such as hunger or crowding, certain grasshopper species can transform within days or even hours from their solitudinous hopper states to become part of a maniacally social locust scourge. They can also return quickly to their original form.

In the most infamous species, Schistocerca gregaria, the desert locust of Africa, the Middle East and Asia, these phase changes (as this morphing process is called) occur when crowding spurs a temporary spike in serotonin levels, which causes changes in gene expression so widespread and powerful they alter not just the hopper’s behaviour but its appearance and form. Legs and wings shrink. Subtle camo colouring turns conspicuously garish. The brain grows to manage the animal’s newly complicated social world, which includes the fact that, if a locust moves too slowly amid its million cousins, the cousins directly behind might eat it.

How does this happen? Does something happen to their genes? Yes, but — and here was the point of Rogers’s talk — their genes don’t actually change. That is, they don’t mutate or in any way alter the genetic sequence or DNA. Nothing gets rewritten. Instead, this bug’s DNA — the genetic book with millions of letters that form the instructions for building and operating a grasshopper — gets reread so that the very same book becomes the instructions for operating a locust. Even as one animal becomes the other, as Jekyll becomes Hyde, its genome stays unchanged. Same genome, same individual, but, I think we can all agree, quite a different beast.

Why?

Transforming the hopper is gene expression — a change in how the hopper’s genes are ‘expressed’, or read out. Gene expression is what makes a gene meaningful, and it’s vital for distinguishing one species from another. We humans, for instance, share more than half our genomes with flatworms; about 60 per cent with fruit flies and chickens; 80 per cent with cows; and 99 per cent with chimps. Those genetic distinctions aren’t enough to create all our differences from those animals — what biologists call our particular phenotype, which is essentially the recognisable thing a genotype builds. This means that we are human, rather than wormlike, flylike, chickenlike, feline, bovine, or excessively simian, less because we carry different genes from those other species than because our cells read differently our remarkably similar genomes as we develop from zygote to adult. The writing varies — but hardly as much as the reading.

This raises a question: if merely reading a genome differently can change organisms so wildly, why bother rewriting the genome to evolve? How vital, really, are actual changes in the genetic code? Do we even need DNA changes to adapt to new environments? Is the importance of the gene as the driver of evolution being overplayed?

You’ve probably noticed that these questions are not gracing the cover of Time or haunting Oprah, Letterman, or even TED talks. Yet for more than two decades they have been stirring a heated argument among geneticists and evolutionary theorists. As evidence of the power of rapid gene expression mounts, these questions might (or might not, for pesky reasons we’ll get to) begin to change not only mainstream evolutionary theory but our more everyday understanding of evolution. [Continue reading...]

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Are we alone in the Universe?

Paul Davies writes: The recent announcement by a team of astronomers that there could be as many as 40 billion habitable planets in our galaxy has further fueled the speculation, popular even among many distinguished scientists, that the universe is teeming with life.

The astronomer Geoffrey W. Marcy of the University of California, Berkeley, an experienced planet hunter and co-author of the study that generated the finding, said that it “represents one great leap toward the possibility of life, including intelligent life, in the universe.”

But “possibility” is not the same as likelihood. If a planet is to be inhabited rather than merely habitable, two basic requirements must be met: the planet must first be suitable and then life must emerge on it at some stage.

What can be said about the chances of life starting up on a habitable planet? Darwin gave us a powerful explanation of how life on Earth evolved over billions of years, but he would not be drawn out on the question of how life got going in the first place. “One might as well speculate about the origin of matter,” he quipped. In spite of intensive research, scientists are still very much in the dark about the mechanism that transformed a nonliving chemical soup into a living cell. But without knowing the process that produced life, the odds of its happening can’t be estimated.

When I was a student in the 1960s, the prevailing view among scientists was that life on Earth was a freak phenomenon, the result of a sequence of chemical accidents so rare that they would be unlikely to have happened twice in the observable universe. “Man at last knows he is alone in the unfeeling immensity of the universe, out of which he has emerged only by chance,” wrote the biologist Jacques Monod. Today the pendulum has swung dramatically, and many distinguished scientists claim that life will almost inevitably arise in Earthlike conditions. Yet this decisive shift in view is based on little more than a hunch, rather than an improved understanding of life’s origin. [Continue reading...]

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Social complexity and facial diversity among primates

UCLA Newsroom: Why do the faces of some primates contain so many different colors — black, blue, red, orange and white — that are mixed in all kinds of combinations and often striking patterns while other primate faces are quite plain?

UCLA biologists reported last year on the evolution of 129 primate faces in species from Central and South America. This research team now reports on the faces of 139 Old World African and Asian primate species that have been diversifying over some 25 million years.

With these Old World monkeys and apes, the species that are more social have more complex facial patterns, the biologists found. Species that have smaller group sizes tend to have simpler faces with fewer colors, perhaps because the presence of more color patches in the face results in greater potential for facial variation across individuals within species. This variation could aid in identification, which may be a more difficult task in larger groups.

Species that live in the same habitat with other closely related species tend to have more complex facial patterns, suggesting that complex faces may also aid in species recognition, the life scientists found.

“Humans are crazy for Facebook, but our research suggests that primates have been relying on the face to tell friends from competitors for the last 50 million years and that social pressures have guided the evolution of the enormous diversity of faces we see across the group today,” said Michael Alfaro, an associate professor of ecology and evolutionary biology in the UCLA College of Letters and Science and senior author of the study.

“Faces are really important to how monkeys and apes can tell one another apart,” he said. “We think the color patterns have to do both with the importance of telling individuals of your own species apart from closely related species and for social communication among members of the same species.” [Continue reading...]

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Moore’s law and the origin of life

I recently offered some commentary on a scientific paper, “Life before Earth,” written by a couple of geneticists, Alexei Sharov of the National Institute on Aging in Baltimore, and Richard Gordon of the Gulf Specimen Marine Laboratory in Florida, who suggest that the rate at which evolution advances necessitates that life must be much older than the Earth and may trace back to within the first 2 billion years of the universe’s existence.

Sharov and Gordon base their analysis on the claim that genetic complexity advances exponentially and they draw a comparison with Moore’s law which, though not actually a law, describes the fact that roughly every two years semiconductor manufacturers are able to double the number of transistors that can be crammed onto a microprocessor. Sharov and Gordon say that genetic complexity doubles every 376 million years.

The idea that life began long before the existence of our planet is certainly a view well outside orthodox views of evolution. And science is inherently conservative in its approach to radical new ideas. So, the fact that Sharov and Gordon’s paper has either been ignored or dismissed does not in and of itself indicate it is worthless.

However, I’m not a geneticist, so I’m not in a position to provide any critical analysis on what they wrote. Massimo Pigliucci, on the other hand, is a rare combination: he’s both a geneticist and a philosopher. So, unlike some other scientists, he doesn’t contemptuously dismiss the paper, but he does have the wherewithal to pick it apart.

Pigliucci writes:

[T]he first highly questionable statement … is that “the core of the macroevolutionary process … is the increase of functional complexity of organisms.” No, it isn’t. Stephen Gould long ago persuasively argued that there is no necessary direction of increased complexity throughout evolution. The only reason why complexity historically follows simplicity is because life had to start simple, so it only had “more complex” as a direction of (stochastic, not directed) movement. It’s a so-called “left wall” effect: if you start walking (randomly, even) from near a wall, the place you end up is away from the wall. And of course, as Gould again pointed out, life on earth was (relatively) simple and bacterial for a long, long time — and none the worse for it either. Moreover, the most complex organism on earth — us — though very successful in certain respects, is actually a member of a very small and often struggling group of large brained social animals. Measured by criteria such as biomass, bacteria still beat the crap out of us “superior” beings.

But the real problems begin for the Sharov and Gordon paper when they finally get to the business at hand: correlating genomic complexity with time of origin of the respective organisms, and then extrapolating back in time. [As a commenter on my Twitter stream pointed out, they could just as “reasonably” have extrapolated into the far future, arriving at the conclusion that the entire universe will eventually be made of DNA...]

The authors realize that simple genome length won’t cut it, because what matters is functional complexity, and there are some portions of the genomes of various organisms that are redundant and possibly without function. Nonetheless, they end up plotting the log-10 of genome size against time, which is how they arrive at the figure of 9.7 billion years ago for the origin of life. As PZ Myers quickly pointed out, however, even if we accept the procedure at face value, they simply cherry picked the data: plenty of organisms that don’t show up on the graph (plants and fungi, for instance) would completely scramble the results. Make no mistake about it: this is a fatal blow to the entire enterprise, and one that the authors ought to have thought about well before posting the paper. [Continue reading...]

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Problem-solving and pattern recognition

The Telegraph reports: The apes, which are our closest relatives in the animal kingdom, seem to get the same level of satisfaction out of solving brain teasers as their human evolutionary cousins.

A study published by the Zoological Society of London shows that six chimpanzees who were given a game which involved moving red dice or Brazil through a maze of pipes enjoyed solving the puzzle whether they got a reward or not.

The researchers claim this suggests they got the same kind of psychological reward as humans get when solving problems.

Most problem solving witnessed in the animal kingdom, where animals use tools or navigate mazes, are with the aim of reaching food. Hyenas, octopuses and birds such as crows all show the ability to solve problems.

Chimpanzees have also been witnessed in the wild using tools such as a stick to forage for insects or honey in hard to reach places like tree stumps.

But ZSL researcher Fay Clark said their research said they could be motivated by more than just food.

She said: “We noticed that the chimps were keen to complete the puzzle regardless of whether or not they received a food reward.

“This strongly suggests they get similar feelings of satisfaction to humans who often complete brain games for a feel-good reward.”

It seems like research repeatedly demonstrates that we share more similarities with other primates than we previously recognized, and as I’ve suggested before, this says as much about our preconceptions about human uniqueness as it says about the human-like qualities of our close relatives. Moreover, in this case, just as the research indicates chimps experience a human-like satisfaction in problem-solving, I suspect that in both instances this trait relates to something shared by all animate creatures: an interest in discerning order.

Chaos is immobilizing and the ability to turn one direction rather than another rests in part in the ability to see patterns and repetition. In pure pristine perception, every moment would be unique, but in reality, the ground of perception is not blank — present is mapped onto past.

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How a quarter of the cow genome came from snakes

Ed Yong writes: Genomes are often described as recipe books for living things. If that’s the case, many of them badly need an editor. For example, around half of the human genome is made up of bits of DNA that have copied themselves and jumped around, creating vast tracts of repetitive sequences. The same is true for the cow genome, where one particular piece of DNA, known as BovB, has run amok. It’s there in its thousands. Around a quarter of a cow’s DNA is made of BovB sequences or their descendants.

BovB isn’t restricted to cows. If you look for it in other animals, as Ali Morton Walsh from the University of Adelaide did, you’ll find it in elephants, horses, and platypuses. It lurks among the DNA of skinks and geckos, pythons and seasnakes. It’s there in purple sea urchin, the silkworm and the zebrafish.

The obvious interpretation is that BovB was present in the ancestor of all of these animals, and stayed in their genomes as they diversified. If that’s the case, then closely related species should have more similar versions of BovB. The cow version should be very similar to that in sheep, slightly less similar to those in elephants and platypuses, and much less similar to those in snakes and lizards.

But not so. If you draw BovB’s family tree, it looks like you’ve entered a bizarre parallel universe where cows are more closely related to snakes than to elephants, and where one gecko is more closely related to horses than to other lizards.

This is because BovB isn’t neatly passed down from parent to offspring, as most pieces of animal DNA are. This jumping gene not only hops around genomes, but between them.

This type of “horizontal gene transfer” (HGT) is an everyday event for bacteria, which can quickly pick up important abilities from each other by swapping DNA. Such trades are supposedly much rarer among more complex living things, but every passing year brings new examples of HGT among animals. For example, in 2008, Cedric Feschotte (now at the University of Utah) discovered a group of sequences that have jumped between several mammals, an anole lizard, and a frog. He called them Space Invaders.

The Space Invaders belong to a group of jumping genes called DNA transposons. They jump around by cutting themselves out of their surrounding DNA, and pasting themselves in somewhere new. They’re also relatively rare—they make up just 2 to 3 percent of our genome. BovB belongs to a different class of jumping genes called retrotransposons. They move through a copy-and-paste system rather than a cut-and-paste one, so that every jump produces in a new copy of the gene. For that reason, they spread like wildfire.

BovB was first discovered in the genomes of cows and other cud-chewing mammals in the 1980s, and seemed to be a signature of that group. Then, in the 1990s, Dusan Kordis and Franc Gubensek detected an extremely similar version of BovB amid the genes of the horned viper. It looked like this piece of DNA had jumped between species. Now, with complete genomes of the cow and other animals at hand, Walsh has more fully mapped BovB’s voyage through the animal kingdom. [Continue reading...]

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