Ed Yong writes: Evolution works on a strict energy budget. Each adaptation burns through a certain number of calories, and each individual can only acquire so many calories in the course of a day. You can’t have flapping wings and a huge body and venom and fast legs and a big brain. If you want to expand some departments, you need to make cuts in others. That’s why, for example, animals that reproduce faster tend to die earlier. They divert energy towards making new bodies, and away from maintaining their own.
But humans, on the face of it, are exceptional. Compared to other apes, we reproduce more often (or, at least, those of us in traditional societies do) and our babies are bigger when they’re born and we live longer. And, as if to show off, our brains are much larger, and these huge organs sap some 20 percent of our total energy.
“We tend to have our cake and eat it too,” says Herman Pontzer from Hunter College. “These traits that make us human are all energetically costly. And until now, we didn’t really understand how we were fueling them.” [Continue reading…]
Veronique Greenwood writes: The millimeter-long roundworm Caenorhabditis elegans has about 20,000 genes — and so do you. Of course, only the human in this comparison is capable of creating either a circulatory system or a sonnet, a state of affairs that made this genetic equivalence one of the most confusing insights to come out of the Human Genome Project. But there are ways of accounting for some of our complexity beyond the level of genes, and as one new study shows, they may matter far more than people have assumed.
For a long time, one thing seemed fairly solid in biologists’ minds: Each gene in the genome made one protein. The gene’s code was the recipe for one molecule that would go forth into the cell and do the work that needed doing, whether that was generating energy, disposing of waste, or any other necessary task. The idea, which dates to a 1941 paper by two geneticists who later won the Nobel Prize in medicine for their work, even has a pithy name: “one gene, one protein.”
Over the years, biologists realized that the rules weren’t quite that simple. Some genes, it turned out, were being used to make multiple products. In the process of going from gene to protein, the recipe was not always interpreted the same way. Some of the resulting proteins looked a little different from others. And sometimes those changes mattered a great deal. There is one gene, famous in certain biologists’ circles, whose two proteins do completely opposite things. One will force a cell to commit suicide, while the other will stop the process. And in one of the most extreme examples known to science, a single fruit fly gene provides the recipe for more than 38,000 different proteins.
But these are dramatic cases. It was never clear just how common it is for genes to make multiple proteins and how much those differences matter to the daily functioning of the cell. Many researchers have assumed that the proteins made by a given gene probably do not differ greatly in their duties. It’s a reasonable assumption — many small-scale tests of sibling proteins haven’t suggested that they should be wildly different.
It is still an assumption, however, and testing it is quite an endeavor. Researchers would have to take a technically tricky inventory of the proteins in a cell and run numerous tests to see what each one does. In a recent paper in Cell, however, researchers at the Dana-Farber Cancer Institute in Boston and their collaborators reveal the results of just such an effort. They found that in many cases, proteins made by a single gene are no more alike in their behavior than proteins made by completely different genes. Sibling proteins often act like strangers. It’s an insight that opens up an interesting new set of possibilities for thinking about how the cell — and the human body — functions. [Continue reading…]
Ed Yong writes: There are tens of trillions of bacteria in my gut and they are different from those in yours. Why?
This is a really basic question about the human microbiome and, rather vexingly, we still don’t have a good answer. Sure, we know some of the things that influence the roll call of species — diet and antibiotics, to name a few — but their relative importance is unclear and the list is far from complete. That bodes poorly for any attempt to work out whether these microbes are involved in diseases, and whether they can be tweaked to improve our health.
Two new studies have tried to address the problem. They’re the largest microbiome studies thus far published, looking at 1,135 Dutch adults and 1,106 Belgians respectively. Both looked at how hundreds of factors affect the microbiome, including age, height, weight, sleep, medical history, smoking, allergies, blood levels of various molecules, and a long list of foods. Both found dozens of factors that affect either the overall diversity of microbial species, or the abundance of particular ones. And encouragingly, their respective lists overlap considerably.
But here’s the important thing: Collectively, the factors they identified explain a tiny proportion of the variation between people’s microbiomes — 19 percent in the Dutch study, and just 8 percent in the Belgian. Which means we’re still largely in the dark about what makes my microbiome different from yours, let alone whether one is healthier than the other. [Continue reading…]
When we’re born, our lungs are thought to be sterile. But from the moment we take our first breath, our pristine lungs are exposed to all the bugs that are in the air. It has become clear in the last 10 years that the lungs rapidly acquire a population of many different microorganisms (mostly bacteria and viruses) that colonise the lungs and remain with us for the rest of our lives. This population of bugs is called the lung microbiome.
We now know more about the lung microbiome thanks to genetics. In the past, identifying the types of bugs present in the lungs depended on being able to grow them in a laboratory, and for many types of bug this was difficult. The big change that happened recently is our ability to recognise both the different bug species, and their relative abundance, by using DNA sequencing. This can be done either from a sample taken from the lungs or from sputum (the mucus we cough up when we have an infection).
Is the lung microbiome a good or a bad thing?
We all know that bacteria in the lungs can be harmful. When harmful bacteria multiply, they cause pneumonia which, despite the existence of antibiotics, can still be deadly. However, it seems that the lung microbiome usually exists in a balanced state, such that harmful types of bugs do not increase in number sufficiently to cause pneumonia. In fact, it’s possible that the very presence of such a diverse range of bugs in the lungs is one of the reasons it’s quite difficult for harmful bugs to multiply and cause disease.
Stephen T Asma writes: After you spend time with wild animals in the primal ecosystem where our big brains first grew, you have to chuckle a bit at the reigning view of the mind as a computer. Most cognitive scientists, from the logician Alan Turing to the psychologist James Lloyd McClelland, have been narrowly focused on linguistic thought, ignoring the whole embodied organism. They see the mind as a Boolean algebra binary system of 1 or 0, ‘on’ or ‘off’. This has been methodologically useful, and certainly productive for the artifical intelligence we use in our digital technology, but it merely mimics the biological mind. Computer ‘intelligence’ might be impressive, but it is an impersonation of biological intelligence. The ‘wet’ biological mind is embodied in the squishy, organic machinery of our emotional systems — where action-patterns are triggered when chemical cascades cross volumetric tipping points.
Neuroscience has begun to correct the computational model by showing how our rational, linguistic mind depends on the ancient limbic brain, where emotions hold sway and social skills dominate. In fact, the cognitive mind works only when emotions preferentially tilt our deliberations. The neuroscientist Antonio Damasio worked with patients who had damage in the communication system between the cognitive and emotional brain. The subjects could compute all the informational aspects of a decision in detail, but they couldn’t actually commit to anything. Without clear limbic values (that is, feelings), Damasio’s patients couldn’t decide their own social calendars, prioritise jobs at work, or even make decisions in their own best interest. Our rational mind is truly embodied, and without this emotional embodiment we have no preferences. In order for our minds to go beyond syntax to semantics, we need feelings. And our ancestral minds were rich in feelings before they were adept in computations.
Our neo-cortex mushroomed to its current size less than one million years ago. That’s a very recent development when we remember that the human clade or group broke off from the great apes in Africa 7 million years ago. That future-looking, tool-wielding, symbol-juggling cortex grew on top of the limbic system. Older still is the reptile brain — the storehouse of innate motivational instincts such as pain-avoidance, exploration, hunger, lust, aggression and so on. Walking around (very carefully) on the Serengeti is like visiting the nursery of our own mind. [Continue reading…]
Kensy Cooperrider writes: ome metaphors end up forgotten by all but the most dedicated historians, while others lead long, productive lives. It’s only a select few, though, that become so entwined with how we understand the world that we barely even recognize them as metaphors, seeing them instead as something real. Of course, why some fizzle and others flourish can be tricky to account for, but their career in science provides some clues.
Metaphors, as we all by now know, aren’t just ornamental linguistic flourishes — they’re basic building blocks of everyday reasoning. And they’re at their most potent when they recast a difficult-to-understand phenomenon as something familiar: The brain becomes a computer; the atom, a tiny solar system; space-time, a fabric. Metaphors that tap into something familiar are the ones that generally gain traction.
Charles Darwin gave us both kinds, big winners and total flops. Natural selection, his best-known metaphor, is still a fixture of evolutionary biology. Though it’s not always recognized as a metaphor today, that’s exactly what it was to Darwin and his contemporaries. After all, evolution was a foreign and unwieldy concept. So Darwin set out to make it accessible by comparing it to a method employed in farmyards around the world.
For years, Darwin — a fancy pigeon breeder — obsessed over what he called artificial selection, what cattle-breeders, gardeners, and crop-growers did to create new varieties of plant and animal: allowing just the ones with desirable traits to reproduce. Darwin’s first-hand experience with breeding set the stage for his now-famous metaphoric leap. [Continue reading…]
Susie Neilson writes: To Hawaiian speakers, vowels reign supreme. Only eight consonants exist in the language’s 13-letter alphabet, so most of its meaning is derived from oohs and aahs, ohs and eehs. One might say Hawaiian sounds a lot like the sea that surrounds it; the bulk of its words are simple and spare, flowing smoothly from vowel to vowel. Mahalo.
On the opposite end of the spectrum, we have German. With its 30-letter alphabet, clipped consonants, and “uvulars”—sounds made by constricting the tongue against the back wall of the throat—German is famously harsh and guttural. Auf Wiedehrsen! One might say — if one weren’t German, that is — that the language is cold and craggy, just like the country.
What accounts for how discrepant these languages sound? Ian Maddieson, a linguist at the University of New Mexico, had a hunch that the differences were not purely coincidental. He and a colleague, Christophe Coupe, analyzed more than 600 regional dialects around the world by topography, weather, and climate. Their findings, presented last November at the 170th Meeting of the Acoustical Society of America (ASA), claimed that the variations among the dialects exhibited a phenomenon previously only seen in birdcalls and other animal noises—acoustic adaptation. Put simply, acoustic adaptation maintains that the land where a language is born is also instrumental to how it evolves. [Continue reading…]
Emily Singer writes: For the past 40 years, David Deamer has been obsessed with membranes. Specifically, he is fascinated by cell membranes, the fatty envelopes that encase our cells. They may seem unremarkable, but Deamer, a biochemist at the University of California, Santa Cruz, is convinced that membranes like these sparked the emergence of life. As he envisions it, they corralled the chemicals of the early Earth, serving as an incubator for the reactions that created the first biological molecules.
One of the great initial challenges in the emergence of life was for simple, common molecules to develop greater complexity. This process resulted, most notably, in the appearance of RNA, long theorized to have been the first biological molecule. RNA is a polymer — a chemical chain made up of repeating subunits — that has proved extremely difficult to make under conditions similar to those on the early Earth.
Deamer’s team has shown not only that a membrane would serve as a cocoon for this chemical metamorphosis, but that it might also actively push the process along. Membranes are made up of lipids, fatty molecules that don’t dissolve in water and can spontaneously form tiny packages. In the 1980s, Deamer showed that the ingredients for making these packages would have been readily available on the early Earth; he isolated membrane-forming compounds from the Murchison meteorite, which exploded over Australia in 1969. Later, he found that lipids can help form RNA polymers and then enclose them in a protective coating, creating a primitive cell. [Continue reading…]
Phys.org reports: Previous analyses of the hominins from Sima de los Huesos in 2013 showed that their maternally inherited mitochondrial DNA was distantly related to Denisovans, extinct relatives of Neandertals in Asia. This was unexpected since their skeletal remains carry Neandertal-derived features. Researchers of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have since worked on sequencing nuclear DNA from fossils from the cave, a challenging task as the extremely old DNA is degraded to very short fragments. The results now show that the Sima de los Huesos hominins were indeed early Neandertals. Neandertals may have acquired different mitochondrial genomes later, perhaps as the result of gene flow from Africa.
Until now it has been unclear how the 28 400,000-year-old individuals found at the Sima de los Huesos (“pit of bones”) site in Northern Spain were related to Neandertals and Denisovans who lived until about 40,000 years ago. A previous report based on analyses of mitochondrial DNA from one of the specimens suggested a distant relationship to Denisovans, which is in contrast to other archaeological evidence, including morphological features that the Sima de los Huesos hominins shared with Neandertals.
“Sima de los Huesos is currently the only non-permafrost site that allow us to study DNA sequences from the Middle Pleistocene, the time period preceding 125,000 years ago”, says Matthias Meyer of the Max Planck Institute for Evolutionary Anthropology, lead author of an article that was published in Nature today. “The recovery of a small part of the nuclear genome from the Sima de los Huesos hominins is not just the result of our continuous efforts in pushing for more sensitive sample isolation and genome sequencing technologies”, Meyer adds. “This work would have been much more difficult without the special care that was taken during excavation.” [Continue reading…]
Regan Penaluna writes: In a recent Sunday, at my local Italian market, I considered the octopus. To eat the tentacle would be, in a way, like eating a brain — the eight arms of an octopus contain two-thirds of its half billion neurons. Delicious for some, yes — but for others, a jumping off point for the philosophical question of other minds.
“I do think it feels like something to be an octopus,” says Peter Godfrey-Smith, a professor of philosophy at CUNY Graduate Center, who has spent almost a decade considering the idea. Stories of octopuses’ remarkable ability to solve puzzles, open bottles, and interact with aquarium caretakers, suggest an affinity between their intelligence and our own. He wonders: What, if anything, is going on in its head — or as may be the case, its arms? The rest of its neurons are contained in lobes wrapping around its esophagus and sitting behind its eyes. This alien-like physiology is the result of almost 600 million years of evolution that separate us.
Since a 2008 dive off the coast of Sydney, Australia, where Godfrey-Smith encountered curious, 3-foot long cuttlefish, he’s been fascinated by the minds of cephalopods, which have the largest nervous systems of all the invertebrates. He’s teamed up with scientists to uncover their secret lives and behaviors, publishing in scientific journals and also a blog, where you can follow his adventures with posts that blend “natural history and philosophy.” He has a book coming out at the end of the year called Other Minds, which digs into how the octopus helps us understand the evolution of subjective experience. “I think cephalopods have a special kind of otherness, because they are organized so differently from us and diverged evolutionarily from our line so long ago,” he says. “If they do have minds, theirs are the most other minds of all.” [Continue reading…]
Brian Gallagher writes: The staunch atheist and essayist Christopher Hitchens once said that “the most overrated of the virtues is faith.” It’s a reasonable conclusion if you believe, as the astrophysicist Carl Sagan did, that “extraordinary claims require extraordinary evidence.” To believe something without evidence — or have faith — is, in their view, something to avoid (and, when called for, to mock).
Yet it was arguably faith — rather than reason — that had been instrumental to our ancestors’ survival. That’s just one of the many intriguing and paradoxical claims that Joseph Henrich, an evolutionary anthropologist at Harvard University, defends in his new book, The Secret of Our Success: How Culture Is Driving Human Evolution, Domesticating Our Species, and Making Us Smarter. His central thesis, reiterated confidently, is that natural selection — the mechanism of biological evolution — is not the “only process capable of creating complex adaptations.” Cultural evolution, he says, is quite capable of generating “complex adaptive products” essential to our survival, which no one designed or understood “before they emerged.”
Consider, for example, the art of hunting, a complex adaptive product that Henrich unpacks in a section titled “Divination and Game Theory.” To decide where to go looking for caribou, the hunters of the Naskapi tribe, in Labrador, Canada, would not do something most would consider common sense: Go to the spot where you last killed some. That tactic would be ineffective because the caribou know to avoid places where their comrades were last slayed. Of course, the Naskapi don’t realize this; the reason they don’t go to the spot of their last kill is because they rely on the result of a ritual to point the way instead. [Continue reading…]
Nature reports: The discovery of yet another period of interbreeding between early humans and Neanderthals is adding to the growing sense that sexual encounters among different ancient human species were commonplace throughout their history.
“As more early modern humans and archaic humans are found and sequenced, we’re going to see many more instances of interbreeding,” says Sergi Castellano, a population geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. His team discovered the latest example, which they believe occurred around 100,000 years ago, by analysing traces of Homo sapiens DNA in a Neanderthal genome extracted from a toe bone found in a cave in Siberia.
“There is this joke in the population genetics community — there’s always one more interbreeding event,” Castellano says. So before researchers discover the next one, here’s a rundown of the interbreeding episodes that they have already deduced from studies of ancient DNA. [Continue reading…]
Over the past 25 years, scientists have supported the view that modern humans left Africa around 50,000 years ago, spreading to different parts of the world by replacing resident human species like the Neanderthals. However, rapid advances in genetic sequencing have opened up a whole new window into the past, suggesting that human history is much more complicated.
In fact, genetic studies in the last few years have revealed that since our African exodus, humans have moved and mixed a lot more than previously thought – particularly over the last 10,000 years.
Our ability to sequence DNA has increased dramatically since the human genome was first sequenced 15 years ago. In its most basic form, genetic analysis involves comparing DNA from different sets of people, whether between people with or without a particular type of cancer, or individuals from different regions of the world.
The human genome is 3 billion letters long, but as people differ at just one letter in every thousand, on average, we don’t have to look at them all. Instead, we can compare people where we know there are these differences, known as genetic markers. Millions of these markers have been discovered and, together with a genetic sequencing technology that allows us to cheaply look at these markers in lots of people, there has been an explosion in the data available to geneticists.
Tim Requarth writes: Mike Russell found his moment of inspiration on a warm spring evening in Glasgow in 1983, when his 11-year-old son broke a new toy. The toy in question was a chemical garden, a small plastic tank in which stalactite-like tendrils grew out of seed crystals placed in a mineral solution. Although the tendrils appeared solid from the outside, when shattered they revealed their true nature: each one was actually a network of hollow tubes, like bundles of tiny cocktail straws.
At the time, Russell, a geologist, was struggling to understand an unusual rock he had recently found. It, too, was solid on the outside but inside was full of hollow tubes, their thin walls riddled with microscopic compartments. It dawned on him then that this rock – like the formations in his son’s toy – must have formed in some unusual kind of liquid solution. Russell posited a whole new geological phenomenon to explain it: undersea hydrothermal hotspots where mineral-rich water spewed from Earth’s interior and then precipitated in the cool surrounding water, creating chemical gardens of towering, hollow rocks growing up from the ocean floor.
That was a huge intuitive leap, but it soon led Russell to an even more outlandish thought. ‘I had the epiphany that life emerged from those rocks,’ he said. ‘Many years later, people would tell me the idea was amazing, but it wasn’t to me. I was just thinking in a different realm, in the light of what I knew as a geologist. I didn’t set out to study the origin of life, but it just seemed so obvious.’
What seemed obvious to Russell was that his hypothetical chemical gardens could solve one of the deepest riddles of life’s origin: the energy problem. Then as now, many leading theories of life’s origins had their roots in Charles Darwin’s speculation of a ‘warm little pond’, in which inanimate matter, energised by heat, sunlight or lightning, formed complex molecules that eventually began reproducing themselves. For decades, most origin-of-life research has focused on how such self-replicating chemistry could have arisen. They largely brushed aside the other key question, how the first living things obtained the energy to grow, reproduce and evolve to greater complexity.
But in Russell’s mind, the origin of life and the source of the energy it needed were a single issue, the two parts inextricably intertwined. As a geologist (now working at NASA’s Jet Propulsion Laboratory in California), he came at the problem with a very different perspective from his biology-trained colleagues. Undersea chemical gardens, Russell realised, would have provided an abundant flux of matter and energy in the same place – a setting conducive for self-replicating reactions, and also a free lunch for fledgling creatures. It has long troubled researchers that the emergence of life seems to rely on highly improbable chemical events that lead toward greater complexity. By considering energy first, Russell believed he could address that. In his view, the emergence of biological complexity was not improbable but inevitable. [Continue reading…]
New Scientist reports: We may have lived alongside an archaic human species just 10,500 years ago in China. Controversial bone discoveries suggest we even interbred with and cannibalised these mystery hominins.
Some think the findings could overturn our understanding of what it means to be human. “If true, this would be rather spectacular and it would make the finds of truly global importance,” says Michael Petraglia at the University of Oxford, who wasn’t involved in the discoveries.
One of the most exciting finds is a hominin femur found in Muladong cave in south-west China, alongside other human and animal bones. It shows evidence of having been burned in a fire that was used for cooking other meat, and has marks consistent with it being butchered. It has also been broken in a way that is used to access bone marrow. Unusually, it has been painted with a red clay called ochre, associated with burial rituals (PLoS One, doi.org/97c).
Things got more interesting when the team tried to identify the bone. “Our work shows clearly that the femur resembles archaic humans,” says Darren Curnoe of the University of New South Wales in Sydney, Australia, who led the team behind the discoveries. Yet the sediment the bone was found in dates to just 14,000 years ago. This would make it the most recent human species to go extinct. [Continue reading…]