One lab full of rats looks pretty much the same as another. But visiting a lab in Siberia, geneticist Alex Cagan can distinguish rats bred to be tame from those bred to be aggressive as soon as he opens the lab door.

“It’s a completely different response immediately,” he says. All of the tame rats “come to the front of the cage very inquisitively.” The aggressive rats scurry to the backs of their cages to hide. Exactly how 70 generations of breeding have ingrained friendly or hostile behaviors in the rats’ DNA is a mystery that domestication researchers are trying to solve. The rats, along with mink and silver foxes, are part of a long-running study at the Institute of Cytology and Genetics in Novosibirsk, Russia. The aim is to replay domestication to determine the genetic underpinnings that set domesticated animals apart from their wild ancestors.
For thousands of years, humans have lived with animals. Some of the creatures are companions — hopping onto laps, ready to play fetch. Some have jobs — carrying heavy loads, pulling wagons and plows, and herding other animals. Others provide meat, eggs or milk. Plants, too, have been tamed. On nearly every continent, fruits, vegetables, grains, nuts and tubers stand in soldier-straight rows and yield bounty on schedule.

There was a time when the species that now inhabit humans’ homes, fields and barnyards didn’t exist. Then some people, somewhere, brought wild things under human control. Or the wild creatures exploited new ecological niches created by humans, gradually habituating themselves to people and, in essence, domesticating themselves. Both paths — scientists are still debating which was more likely for different animals — led to the creation of domesticated species or subspecies genetically distinct from their wild ancestors.

Scientists studying evolution and human history want to know how ancient people domesticated animals and plants. What species did humans start with and where did it happen first? How long did it take? Does one group get credit for taming wild horses or subjugating aurochs into milk-giving cows? Or did multiple people in different places have the same idea?

Even for dogs, humans’ oldest, closest friends, “all those things are unknown,” says evolutionary geneticist Greger Larson of the University of Oxford. For many domesticated creatures, the questions outweigh the answers. As new studies flood in — some based on archaeology, others on modern or ancient DNA — the waters get muddy, with one study’s results contradicting another’s.

“Domestication research right now is really going through an exciting phase,” Larson says. Comparing the genetic instruction books, or genomes, of wild and domesticated species is giving evolutionary geneticists fresh clues about the changes that separate domesticated species from wild ones. New techniques (some developed in the last two to three years) for analyzing fragile DNA from ancient bones offer genetic snapshots of domestication as it played out long ago. Marrying that DNA data with archaeological findings, the context in which the bones were discovered, for example, may tell researchers more about when, where and how humans first engaged with plants and animals. Recent results are already rewriting the stories of rice, horse and chicken domestication.
A new hypothesis is also shining a light on core changes in the embryos of many domesticated species. The hypothesis aims to explain how the process of becoming close to people produces comparable changes in the appearance, reproduction and physiology of a whole range of domesticated animals. One central developmental change — in a temporary clump of cells called the neural crest — may be behind the suite of characteristics known as domestication syndrome.

The pace of research, much of it seemingly contradictory, will only increase in the near future, Larson predicts. “We’re going to get a lot more confused before we figure out what’s really going on.”
Defining domestication
Deciding when an animal can be called “domesticated” isn’t always easy.

Since 2002, Anna Kukekova has been making annual treks to Novosibirsk. A geneticist at the University of Illinois at Urbana-Champaign, she travels to Siberia each year to collect blood from hundreds of silver foxes to look for genetic changes that produce tame and aggressive behaviors.

These foxes are special. They are part of a long-running biological experiment to repeat domestication by turning a wild canid — from the family of animals including wolves, foxes, jackals and dogs — into a fox version of a domestic dog (SN: 5/13/17, p. 29). The project was the brainchild of geneticist Dmitry Belyaev. In the 1950s, Belyaev and colleagues started selecting and breeding the least aggressive and fearful silver foxes from those on a fur farm. Since 1960, researcher Lyudmila Trut and her team have selected the farm’s friendliest foxes to breed. Over more than 60 generations, the foxes have grown more and more tolerant of humans. Kukekova says she’s noticed a difference even in the 15 years she’s been visiting the farm.
In Kukekova’s early visits, about 70 percent of the tame foxes were considered “elite,” aquiver with excitement when people came around. The rest of the tame ones “didn’t mind if you petted them, but they weren’t super excited to interact with you,” she says. Now, almost every tame fox is in the super-friendly elite group. (Foxes bred to be aggressive, on the other hand, are definitely not happy to have people around, much like the fearful rats Cagan encountered at the institute.)

Even though the friendly Novosibirsk foxes are genetically tame — some are sold as pets — not everyone would call the animals domesticated. “In an apartment, they would probably be very difficult pets,” Kukekova says. The foxes have a strong odor, are more active at night and they aren’t easily house-trained. The combination of living with people plus inherited changes in the foxes’ genomes may eventually make them fully domesticated, but they aren’t there yet.

Researchers have set out several biological criteria that should determine when silver foxes, or other animals, cross the line that divides merely tame from fully domesticated. Number one: Domesticated animals are genetically distinct from their wild forebears, and they inherit their human-friendly demeanor. That’s different from wild animals that have been tamed but don’t pass on that tameness to the next generation.

Two: Domestication makes animals dependent on humans for food and, for the most part, reproduction. Three: Breeding with wild counterparts becomes difficult, if not impossible. For example, domesticated plants don’t drop their seeds when ripe; they rely on humans to spread their progeny. Finally, domesticated animals and plants should bear the physical hallmarks of domestication syndrome, such as a smaller skull for animals, and a narrower footprint for plants.

By these criteria, some people argue that cats — popular pets worldwide — are not fully domesticated. Cats probably started taming themselves about 9,500 years ago by hunting vermin, infesting early farmers’ grain stores and feasting on food scraps. Farmers brought the mousers with them from the Middle East into Europe around 6,400 years ago, researchers reported June 19 in Nature Ecology & Evolution (SN Online: 06/19/17). But cats may not have been purring lap pets at that time, say molecular biologists Thierry Grange and Eva-Maria Geigl of the Institute Jacques Monod in Paris. That behavioral transformation may have happened later, perhaps in Egyptian cats that were quickly dispersed by boat around the ancient world.

In fact, cats haven’t changed much physically or genetically from their African wildcat ancestors (Felis silvestris lybica), Grange and Geigl say. Many felines still choose their own mates and hunt for food. Cats’ famed aloofness may be another clue that their domestication isn’t fully complete. Certainly, cats are more like their wild ancestors than dogs are, says Grange. But modern kitties are no longer wild cats, Geigl argues: “These couch potatoes are domesticated.”
Relationship status
Bonds between humans and their animal companions may be more important than rigid biological criteria, Larson and other researchers argue. Domestication, says zooarchaeologist Alan Outram of the University of Exeter in England, “is best looked at with a more cultural definition.”

Domestication is a gray area encompassing the point at which a hunter stops being interested in simply killing and eating an animal and starts being interested in controlling the animal, Outram says. The process probably starts slowly, first with animal herding and other forms of husbandry, such as controlling an animal’s food supply and movement, culling at specific ages and directing breeding. When people start using animals, such as horses, for labor, riding or milking (fermented horse milk is a staple in parts of Central Asia), the animals “start moving to being culturally domestic,” he says.
Outram has evidence that the Botai people, hunter-gatherers that lived in Central Asia, were milking and bridling horses about 5,500 years ago (SN: 3/28/09, p. 15). “I certainly wouldn’t want to make the argument that at the Botai time you’ve got anything like modern domesticated horses,” he says. It was “more like equine husbandry and herding.”

Scientists have to be careful not to judge how domestication happened in the past by the way animals are treated in modern Western cultures, says evolutionary biologist Ludovic Orlando of the University of Copenhagen. On a trip to collect DNA samples from ancient horse bones in Mongolia, Orlando got a whole new perspective on domestication.

“It completely changed my view of horse domestication, because I saw people interacting with this animal in ways I couldn’t imagine myself,” Orlando says. In Mongolia, horses roam free and their owners catch them, as needed, for riding or milking. “Once you’ve seen that, you can’t think that domestication is just about parking animals somewhere. It’s about the process of interacting with them and developing a relationship with them.”

Dog days
If it’s hard to pinpoint what domestication means in foxes tamed in controlled experiments, consider how difficult it is to decide whether the bones of a long-dead animal are from a wild or domesticated critter. That’s the task of paleontologist Mietje Germonpré of the Royal Belgian Institute of Natural Sciences in Brussels, who studies dog domestication. The beloved pets are the subjects of much domestication research.

Scientists used to think that dogs were domesticated toward the end of the Ice Age, about 14,000 years ago (SN Online: 7/22/10). Germonpré and colleagues have studied skulls and jawbones of even more ancient canids in caves and other places where Ice Age people lived more than 25,000 years ago. One skull, found in a Goyet cave in Belgium, may be one of the oldest dogs ever discovered — or at least the oldest wolf that looked like a dog. At 36,000 years old, the Goyet pooch pushed dog domestication back to well before glaciers reached their peak coverage of the Northern Hemisphere.
Those early dogs may have been used as pack animals to move mammoth carcasses from hunting grounds to living quarters, says Germonpré. Big dogs may have helped humans hunt dangerous carnivores, such as cave bears, hyenas and cave lions. It’s also possible the animals were used for fur or meat.
Germonpré’s assertion that the Goyet dog is in fact a dog comes from comparing its skull and jaws with those of wolves and modern dogs. Most domesticated mammals, including dogs, tend to have smaller bodies than their wild counterparts, with smaller skulls that have shorter, wider snouts and shorter, lower jaws. Those features make adult dogs look more puppylike than grown wolves do. That type of facial remodeling is part of the domestication syndrome, which also includes curly tails, floppy ears and other characteristics common among domesticated animals but not wild ones. By Germonpré’s measurements, the Goyet skull more closely resembles modern dogs than it does ancient or modern wolves.

She also has evidence of early dogs in Russia and the Czech Republic dating to 25,000 years ago or more. Other groups have reported data suggesting that a 33,000-year-old canid from the Altai Mountains of Russia was also an early dog.

Other researchers disagree, saying the animals were really wolves. Three-dimensional reconstructions of the skulls of the Goyet dog and another Ice Age dog show that the animals’ snouts didn’t angle from the skull the way modern dogs’ do, and the ancient versions didn’t have some other features of modern dogs (SN Online: 2/5/15).

Larson says he’s not bothered that the Goyet hound didn’t physically measure up in the 3-D study. The canid may have behaved very much like a dog and had close ties to humans. Those early dogs didn’t have thousands of years of intense breeding selection to sculpt them into the image of modern dogs. Even modern dogs have been transformed dramatically in just 200 to 300 years of breeding (SN Online: 4/26/17; SN: 1/31/09, p. 26). “What was a dog 15,000 to 30,000 years ago is not what a dog is now,” Larson says.
The timing of Fido’s taming isn’t the only dispute. Researchers also wrangle over where and how many times it happened. Dueling genetic studies based on the DNA of modern dogs and wolves suggest the fellowship between humans and dogs could have been forged in the Middle East, Central Asia, East Asia or, as Goyet’s archaeological evidence suggests, in Europe. Research reported by Larson and colleagues last year in Science suggests that dog domestication happened at least twice, once in Europe and once in East Asia (SN: 7/9/16, p. 15).

DNA evidence indicates that the Goyet dog and the 33,000-year-old Russian dog are not the ancestors of today’s dogs or wolves (SN: 12/14/13, p. 6). Scientists examined mitochondrial DNA, which is passed from mothers to offspring, to trace maternal lineages of ancient and modern dogs and wolves. The mitochondrial DNA of the Goyet and Russian dogs belongs to a maternal lineage that didn’t leave any modern descendants, researchers reported in Science in 2013. But it doesn’t mean the animals weren’t on the way toward being domesticated, Germonpré says.

Perhaps those dogs were part of an early, failed attempt at domestication, she says. “The domesticated animals became extinct, and domestication started up again somewhere else.”

Rice story shattered
Locating the cradle of most species’ domestication is difficult. Many were domesticated before writing was even invented. So scientists have to extract the story from artifacts and bones or from DNA.

The origin of Asian rice has been hotly debated for many years. Scientists used to think modern rice, Oryza sativa, was domesticated twice: sticky, short-grained japonica rice was domesticated in China, and in India, rice was domesticated into long-grained varieties indica and aus. Archaeological finds suggest that rice cultivation started about 9,000 years ago in China and 8,000 years ago in India. But true domestication probably happened only once — in China, says Dorian Fuller, an archaeobotanist at University College London.

People were certainly cultivating rice in India, but that’s just one step in the domestication process. The final threshold that separates a fully domesticated crop from a cultivated one is that domesticated plants require human intervention to spread their seeds, Fuller says. Wild grains, for instance, “shatter” their seed heads when ripe. But domesticated grains, including rice, wheat, barley, sorghum and millet, have mutations that prevent shattering. The only way the grain crops can propagate is if humans collect and plant the seeds.
It may have taken nearly 2,000 years for people in China’s Yangtze River basin to wrest complete control over rice, researchers reported last year in Scientific Reports. Scientists examined rice fossils to determine how easily the plant shattered its seed. Although people were growing an early rice 9,000 to 8,400 years ago, about 60 percent of plants were still dispersing seeds via shattering. It wasn’t until about 7,000 to 6,500 years ago that nonshattering rice began to edge out shattering varieties.

By examining DNA from modern rice strains, Fuller and evolutionary geneticist Michael Purugganan of New York University think they’ve pieced together the rest of the rice domestication story. DNA evidence clearly shows that China’s wild O. rufipogon was domesticated into O. sativa japonica. Traders carried domesticated japonica from China to India, where it was bred with the cultivated rice species O. nivara to produce domesticated aus about 4,000 years ago, Fuller, Purugganan and colleagues reported in January in Molecular Biology and Evolution. Indica’s story is less clear because its cultivated predecessor in India is still unknown. But the genetic evidence indicates that it got its domestication genes from China’s japonica.

Tails (and feathers) from the past
Working out the step-by-step history of domesticated animals is just as complicated. Until recently, researchers compared DNA from modern domestic animals with that of wild relatives, preferably the wild species that gave rise to the domesticated species. Sometimes that’s impossible to do. There are no wild cattle, for instance. Aurochs — massive cattle that eventually gave rise to domesticated cows — went extinct when the last one died in 1627 in Poland’s Jaktorów Forest.

Horses’ wild ancestors are also extinct, but remains from the warrior steeds of Genghis Khan and medieval knights, the Romans’ chariot horses and the mounts of the ancient Scythians, Greeks and Persians might fill in gaps in horse history and prehistory. Through the Pegasus project, begun in 2015, Orlando and colleagues have collected ancient DNA from horse fossils from a wide variety of time periods and cultures. “We’re looking at every possible ancient equine culture on the planet,” Orlando says.

Before the project, scientists mostly had to rely on DNA from modern horses to piece together the story of how the beasts of burden were domesticated. Findings of those studies may be misleading, Orlando and colleagues have concluded. For instance, studies of modern horses’ mitochondrial DNA plus Y chromosomes (passed from fathers to sons) told a nice, neat story: At the beginning of horse domestication, people must have captured just a few stallions and bred those stallions to many different mares.
But when Orlando and colleagues examined DNA of ancient horses, they found that the story started completely differently. Domesticated horses living 2,300 to 2,700 years ago — about the midpoint of horse domestication — had a wide variety of Y chromosomes, the researchers reported April 28 in Science (SN: 5/27/17, p. 10). That means many stallions contributed DNA to horses’ gene pool for at least the first few thousand years of domestication. It wasn’t until sometime after 2,300 years ago that people started winnowing down the number of stallions that were allowed to breed. Orlando doesn’t know yet when most Y chromosomes were lost.

The story of chicken domestication is being retold as well, also thanks to DNA evidence. Modern chickens carry a version of the thyroid-stimulating hormone receptor gene, TSHR, that has been linked to several domesticated chicken characteristics: year-round egg laying, faster egg production at sexual maturity, reduced aggression toward other chickens and less fear of people. Because that version of the gene is ubiquitous in present-day chickens and is responsible for those attractive traits, researchers thought that people probably selected the most prolific egg layers right from the very beginning, about 4,000 years ago. Picking better laying hens would also mean unwittingly choosing the domesticated version of TSHR.

But, the egg-laying version of the gene didn’t become popular among chickens in Europe until about A.D. 920, around the time that Christians started giving up meat on fasting days in favor of fish and fowl, Larson and colleagues reported May 2 in Molecular Biology and Evolution. (Rabbit domestication followed a religious proclamation, as well. In 600, Pope Gregory I declared that fetal rabbits, called laurices, are aquatic, which made them fish, suitable to eat during Lent. Rabbit breeding took off in monasteries in southern France, and bunnies quickly became domesticated.)
If Larson’s calculations are correct, egg laying wasn’t the main criterion for selecting which chickens to keep until the Middle Ages. By that time, the birds had been domesticated for thousands of years. So what were ancient people looking for when striking up friendships with the feathered animals — or any other creatures? Many people think it was about the relationship; tameness and docility were the most attractive qualities in potential animal pals. It’s hard to be buddies with a creature that constantly runs from you, or worse, attacks.

Docility makeover
A breeding experiment with wild red jungle fowl, the precursor to the domesticated chicken, may help explain whether selecting for tameness is the triggering event of domestication and all its characteristics. Behavioral geneticist Per Jensen of Linköping University in Sweden is in the middle of a domestication redo. He and colleagues have bred eight generations of the rust-feathered birds. Like the rats, mink and foxes in Novosibirsk, Jensen’s jungle fowl are bred to be more (or less) fearful of humans than their ancestors were.

From the beginning, the researchers took great pains to select birds only for their behavior: Jungle fowl were tested for tameness at 12 weeks old, before they reached sexual maturity. One researcher would approach the fowl and attempt to touch it, while an outside observer scored the bird’s reaction. Neither researcher knew whether they were testing a jungle fowl from the tame or fearful line.

“Mind you, this went well for two or three generations but then the difference started to be so big it was difficult to keep a secret,” Jensen says. After that, the tame birds were so calm they didn’t react when a human entered the room. “You basically had to kick them out of your way,” he jokes. By the sixth generation, tame birds were bigger and had a higher metabolism than their fearful counterparts, Jensen and colleagues reported in Biology Letters in 2015. Changes in body size, reproduction and metabolism happened quickly, even though the researchers were only choosing birds for tameness.

The tame birds, Jensen says, “show a lot of traits that you really associate with domesticated animals, but I’m not sure anyone would accept that,” he says. Becoming what other people think of as domesticated chickens may take more time: jungle fowl hens that lay eggs year-round and are big enough to eat. “I don’t think we’re talking about hundreds of generations, maybe dozens. It’s a much faster process than we used to think.”

Again and again, animals of various species domesticated at different times in different parts of the world develop the same domestication syndrome characteristics: more extensive breeding periods; smaller brains, hearts and teeth; small or floppy ears; spotted coats; curly hair and tails; variable numbers of vertebrae in the spine; and juvenile faces with shorter snouts. Researchers have found evidence that pigmentation genes differ between domestic and wild animals. Others have pinpointed changes in brain chemistry or genes involved in face development that may separate tame and wild animals. But scientists didn’t have a unifying explanation for why the physical traits of domestication syndrome were linked to tameness until three years ago.
That’s when geneticist Adam Wilkins of Humboldt University of Berlin, primatologist Richard Wrangham of Harvard University and evolutionary biologist and cognitive scientist W. Tecumseh Fitch of the University of Vienna introduced a new hypothesis. Selecting animals for tameness, they said, could alter genes that control a group of developmentally important cells called neural crest cells. Those embryonic cells migrate in the embryo and contribute to tissues involved in the fight-or-flight response, facial development and coloring.

Choosing animals for tameness might be selecting for ones that have changes in how their neural crest cells function, the researchers proposed in Genetics in 2014 (SN: 8/23/14, p. 7). Calmer domesticated animals might have neural crest cells that move or work differently than the cells in more fearful wild animals. Because neural crest cells contribute to so many tissues in the body, altering their function could change an animal’s behavior, appearance and biology, the researchers reasoned. For the first time, domestication researchers had a hypothesis about the link between tameness and physical traits that could really be put to the scientific test.
Since the neural crest hypothesis surfaced, geneticists have found tantalizing clues that Wilkins, Wrangham and Fitch are onto something. Analysis of cat DNA found that house cats and wild cats have different versions of genes implicated in neural crest cell migration (SN: 12/13/14, p. 7). When Orlando and colleagues examined horse DNA for genes that may have rapidly changed during domestication, they too found genes involved in neural crest cell function.

While at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, Cagan compared DNA from the tame rats and mink at Novosibirsk, and from other domesticated species, with DNA from aggressive counterparts and wild ancestors. In unpublished research, Cagan (now at the Wellcome Trust Sanger Institute in Hinxton, England) found that genes involved in helping neural crest cells migrate differed between the tame and wild animals (SN: 6/13/15, p. 11). That might explain the white patches of fur, shorter snouts and curly tails of the tame animals.

Jensen calls the neural crest cell hypothesis “a very speculative idea that may not be applicable across species.” He is looking more closely at the neural crest in the jungle fowl. He and colleagues are collecting eggs to track the cells’ movements in tame and fearful birds. Even if the researchers find differences, he says, “we still need to find the genetic mechanisms that are causing the neural crest cells to act as they do.”

Larson expects many revelations in the next year or two about when, where and how domestication happened. “Even the big themes are going to be radically revised,” he says. Domestication is likely to be a far more complicated process than researchers expected, but Larson hopes people will find it all the more interesting for its lack of simplicity. “We want to get people to embrace the ambiguity and to love the complexity.”

Water bears may be Earth’s last animal standing.

These tough little buggers, also known as tardigrades, could keep calm and carry on until the sun boils Earth’s oceans away billions of years from now, according to a new study that examined water bears’ resistance to various astronomical disasters. This finding, published July 14 in Scientific Reports, suggests that complex life can be extremely difficult to destroy, which bodes well for anyone hoping Earthlings have cosmic company.
Most previous studies of apocalyptic astronomical events — like asteroid impacts, neighboring stars going supernova or insanely energetic explosions called gamma-ray bursts — focused on their threat to humankind. But researchers wanted to know what it would take to annihilate one of the world’s most resilient creatures, so they turned to tardigrades.

The tardigrade is basically the poster child for extremophiles. These hardy, microscopic critters are up for anything. Decades without food or water? No problem. Temperatures plummeting to –272° Celsius or skyrocketing to 150°? Bring it on. Even the crushing pressure of deep seas, the vacuum of outer space and exposure to extreme radiation don’t bother water bears.

Water bears are so sturdy that they probably won’t succumb to nuclear war, global warming or any astronomical events that wreak havoc on Earth’s atmosphere — all of which could doom humans, says Harvard University astrophysicist Avi Loeb. To exterminate tardigrades, something would have to boil the oceans away (no more water means no more water bears). So Loeb and colleagues calculated just how big an asteroid, how strong a supernova, or how powerful a gamma-ray burst would have to be to inject that much energy into Earth’s oceans.

“They actually ran the numbers on everyone’s favorite natural doomsday weapons,” marvels Seth Shostak, an astronomer at the SETI Institute in Mountain View, Calif.

Loeb’s team found that there are only 19 asteroids in the solar system sufficiently massive enough to eradicate water bears, and none are on a collision course with Earth. A supernova — the explosion of a massive star after it burns through its fuel — would have to happen within 0.13 light-years of Earth, and the closest star big enough to go supernova is nearly 147 light-years away. And gamma-ray bursts — thought to result from especially powerful supernovas or stellar collisions — are so rare that the researchers calculated that, over a billion years, there’s only about a 1 in 3 billion chance of one killing off tardigrades.
“Makes me wish I were an extremophile like a tardigrade,” says Edward Guinan, an astrophysicist at Villanova University in Pennsylvania who was not involved in the work.

But even tardigrades can’t cheat death forever. In the next seven billion years, the sun will swell into a red giant star, potentially engulfing Earth and surely sizzling away its water. But the fact that tardigrades are so resistant to other potential apocalypses in the interim implies that “life is tough, once it gets going,” Shostak says.

Scientists pour a lot of brainpower into understanding how their experimental equipment works.

You don’t want to be fooled into thinking you’ve made a great discovery because of some quirk in the apparatus you didn’t know about. Just the other day, a new paper published online suggested that the instruments used to detect gravitational waves exhibited such a quirk, tricking scientists into claiming the detection of waves that maybe weren’t really there.

It appears that gravity wave fans can relax, though. A response to the challenge pretty much establishes that the new criticism doesn’t undermine the wave discoveries. Of course, you never know — supposedly well-established results sometimes do fade away. Often that’s because scientists have neglected to understand the most important part of the entire experimental apparatus — their own brains.

It’s the brain, after all, that devises experiments and interprets their results. How the brain perceives, how it makes decisions and judgments, and how those judgments can go awry are at least as important to science as knowing the intricacies of nonbiotic experimental machinery. And as any brain scientist will tell you, there’s still a long way to go before understanding the brain will get crossed off science’s to-do list. But there has been progress. A recent special issue of the journal Neuron offers a convenient set of “perspective” papers exploring the current state of understanding of the brain’s inner workings. Those papers show that a lot is known. But at the same time they emphasize that there’s a lot we don’t know.

Glancing at the table of contents reveals the first lesson about understanding the brain: It’s a complex problem that needs to be approached from multiple perspectives.

On one level, there’s the dynamics of electrical currents that constitute the main signaling method of the brain’s nerve cells. Then on a higher level there’s the need to figure out the rules by which nerve cells make connections (synapses) and create the neural circuitry for processing sensory input, learning and behaving. Another challenge is understanding how nerve cell networks represent memories and how you recall what you’ve learned. And it’s essential to understand how neurobiological processing conducted by molecules and cells and electrical signaling gets translated into behaviors, from simple bodily movements to complex social interactions.

Nerve cells in the brain, or neurons, are known to communicate among themselves by transmitting electrical signals, aided by chemical signaling at the synapses connecting the neurons. But there are gaps in understanding how that process takes the brain from perceptions to thoughts to actions. Each of Neuron’s perspective papers both describes what’s already known about how the brain works and offers speculations where scientists lack full knowledge about how the brain does it jobs.

Much of the effort to explain the brain involves mapping the electrical signaling throughout the entire network of nerve cell connections. Per Roland of the University of Copenhagen, for instance, discusses how those signals vary in space and time. He emphasizes the important balance between signaling that incites neurons to send signals and the messaging that inhibits signaling, keeping some neurons quiet.
Sophie Denève and colleagues of the Ecole Normale Supérieure in Paris also emphasize the balance between excitation and inhibition in neural circuitry. That balance is important, they say, for understanding how the whole brain can learn to do things based on changes in the connections between individual neurons. Somehow the rules governing synaptic connections between cells enable such “local” activity to modify the “global” neural circuitry that carries out the brain’s many functions. Excitation-inhibition balance, plus feedback from the global network influencing synapse strength, “can ensure that global functions can be learned with local learning rules,” Denève and colleagues write.

Almost all these approaches to figuring out the brain involve how it manipulates information. In a sense, the ultimate key question is how the brain conducts the mysterious process by which it absorbs information in the form of lights and colors, sounds, smells and tactile inputs and transforms them into physical actions — ideally behaviors that are appropriate responses to the inputs. Just (OK, not “just,” but sort of) as in a computer, the brain transforms input into output; information about the external world is manipulated to produce information about how to react to it.

But because sensory input has its limits, and some of it is ambiguous, the informational variables of the external world cannot be gauged with certainty, Xaq Pitkow and Dora Angelaki of Baylor College of Medicine and Rice University in Houston point out in their perspective. So the brain’s behavioral choices must be based on some method of computing probabilities to infer the likely state of the world — and then choosing the wisest (probably) actions in response.

“It is widely accepted that the brain somehow approximates probabilistic inference,” Pitkow and Angelaki write. But nobody really knows how the brain does it. Pitkow and Angelaki propose that multiple populations of the brain’s neurons perform various computations to make appropriate behavioral decisions.

Patterns of electrical signaling by these neurons must represent the original sensory stimuli — that is, the patterns in the stimuli are encoded in the patterns of electrical signaling among the neurons. Those neural signaling patterns, in Pitkow and Angelaki’s description, are then recoded into another set of patterns; that process sorts out the important variables in the environment from those that don’t matter. Those patterns are then decoded in the process of generating behavioral actions.

In sum, the brain appears to implement algorithms for collecting and assessing information about the environment and encoding that information in messages that tell the body what to do. Somehow those algorithms allow the brain to conduct statistical computations that combine beliefs about the environment with the expected outcome of different behaviors.

Pitkow and Angelaki present sophisticated speculation about the possible ways the brain could accomplish this task. It’s clearly an unimaginably complicated process, and figuring out how the brain does it will require more sophisticated experiments than neuroscientists have so far imagined. Much research on brain function in animals, for instance, offers the animal a choice of two options, given various external conditions. But tasks of that nature are vastly simpler than the jobs that evolution optimized brains for.

“The real benefit of complex inferences like weighing uncertainty may not be apparent unless the uncertainty has complex structure,” Pitkow and Angelaki argue. “Overly simple tasks” are “ill-suited to expose the inferential computations that make the brain special.”

And so truly understanding the brain, it seems, will require better experiments — using apparatus that is more fully understood than the brain now is — of sufficient complexity to be worthy of probing the brain’s abilities.

Some deep-sea tube worms get long in the tooth … er, tube. Living several decades longer than its shallow-water relatives, Escarpia laminata has the longest known life span for a tube worm, aging beyond 300 years, researchers report in the August Science of Nature.

E. laminata lives 1,000 to 3,300 meters deep in the Gulf of Mexico, near seafloor vents that seep energy-rich compounds that feed bacteria that feed the tube worms. In 2006, biologists marked 356 E. laminata in their natural habitat and measured how much the creatures had grown a year later. To estimate the ages of tube worms of different sizes, the researchers plugged E. laminata’s average yearly growth rate — along with estimates of birthrates and death rates, based on observations of another 1,046 tube worms — into a simulation. The species’s typical life span is 100 to 200 years, the researchers calculate, but some larger tube worms may be more than 300 years old.

With few large predators, deep-sea tube worms have got it good, says study coauthor Alanna Durkin, a biologist at Temple University in Philadelphia. “Once they find a seat at the buffet, they’re pretty set for hundreds of years.” The researchers’ methodology appears robust, says ocean scientist David Reynolds of Cardiff University in Wales, who was not involved in the work. Although variable environmental conditions could affect growth rate over time, he says.

Everybody poops, but the poop of bloblike filter feeders called giant larvaceans could be laced with microplastics.

Every day, these gelatinous creatures (Bathochordaeus stygius) build giant disposable mucus mansions to round up zooplankton into their stomachs — sometimes sifting through around 80 liters of seawater per hour. Kakani Katija and her colleagues at the Monterey Bay Aquarium Research Institute now suggest that tiny plastic particles also make their way in — and out — of giant larvaceans’ guts.

Microplastics pervade the ocean. Their combined mass could reach 250 million metric tons by 2025. Scientists don’t know a lot about where microplastics stick around in open water ecosystems.

To see if plastics could end up on the larvacean menu, Katija and colleagues tried feeding the animals brightly colored microplastics. An underwater robot equipped with camera gear helped the researchers monitor plastic intake from above. Some animals did end up scarfing down the particles, and some of those particles ended up in the organism’s waste, which showers down on the seafloor, Katija and colleagues report August 16 in Science Advances.

“Plastics are sometimes seen as a sea surface issue, and more and more we’re seeing that’s not necessarily true,” Katija says.

Just how much plastic ends up passing through giant larvaceans in the wild remains unclear. But the researchers suspect that the creatures’ poop, as well as their mucus houses, could transfer microplastics from the water’s surface to the depths of the sea (along with nutrients such as carbon that cycle through the environment). And that pollution transfer may impact the ecosystems at either end.

The story of how Charles Darwin’s trip around the world on the HMS Beagle inspired his ideas about evolution is well-known. Less familiar, however, may be the decades of detailed research that he conducted after that 1830s voyage. As biologist James Costa chronicles in Darwin’s Backyard, many of those studies took place at Down House, Darwin’s country home southeast of London.

The estate’s relative isolation enabled Darwin to conduct in-depth anatomical analyses of everything from barnacles to birds. Darwin supplemented that work with hands-on experiments. He bred and raised 16 varieties of pigeons, trying to show that the fancy types preferred by breeders had developed from only a few ancestral wild types.
In his gardens, Darwin laid out intricate plots where he studied the diversity and growth of grasses and weeds, as well as how earthworms churn the soil. On nearby hillsides, he investigated orchid pollination and reproduction. (Not all of his experiments were successful: One year, cows ate and trampled his orchids.) Some experiments were considered quirky by 19th century standards, but the work provided data supporting Darwin’s notions about trait variability in a population and how natural selection drives changes in populations over time.

Stories of Darwin’s rich — and in some cases, tragic — family life are woven throughout Costa’s account. Without appreciating this aspect of his life, Costa claims, neither Darwin nor his accomplishments can be fully understood. For example, he enlisted his wife, cousins and nieces — and even his butler and governess — in assisting with his homespun field studies.

One outstanding aspect of the book: Each chapter ends with a description of some of Darwin’s experiments that nonscientists can perform on their own. Readers will enjoy the tales Costa tells and the experience of re-creating some of the famous naturalist’s most enlightening work.

People hunted giant sloths in the center of South America around 23,120 years ago, researchers say — a find that adds to evidence that humans reached South America well before Clovis hunters roamed North America 13,000 years ago.

Evidence of people’s presence at Santa Elina rock-shelter, in central-west Brazil, so long ago raises questions about how people first entered South America. Early settlers may have floated down the Pacific Coast in canoes before heading 2,000 kilometers east to the remote rock-shelter, or they might have taken an inland route from North America, Denis Vialou of the National Museum of Natural History in Paris and colleagues report in the August Antiquity. Other proposed Stone Age South American sites lie much closer to the coast than Santa Elina does.

Excavations revealed remains of hearths, stone artifacts and bones of giant sloths. Sloth remains included small, bony plates from the skin that humans apparently made into ornaments of some kind by adding notches and holes.

Three different dating methods indicate that people reached Santa Elina over 20,000 years ago.

Journalist Maryn McKenna opens Big Chicken by teasing our taste buds with a description of the succulent roasted chickens she bought at an open-air market in Paris. The birds tasted nothing like the bland, uniform chicken offered at U.S. grocery stores. This meat had an earthy, lush, animal flavor. From this tantalizing oh-so-European tableau, McKenna hits us with a sickening contrast — scientists chasing outbreaks of drug-resistant Salmonella infections in humans, and ailing chickens living in crowded conditions and never seeing the light of day.

Antibiotics are at the root of both nightmares, McKenna argues. She draws clear connections between several dramatic foodborne outbreaks and the industrialization of chicken production, made possible, in large part, by the heavy use of the drugs. That reliance on antibiotics has also spurred the rise of drug-resistant bacteria. In fact, the overuse of antibiotics in livestock is a bigger driver of resistance than the overuse of antibiotics in people.

Farmers began using the drugs after studies in the 1940s showed that antibiotics boosted muscle mass. For chickens, that meant the birds got bigger and grew faster with less feed. Today, a meat chicken weighs twice what it did 70 years ago at slaughter and reaches that weight in half the time. Once farmers saw opportunity for growth and packed more birds into barns, the drugs took on a new role: to protect crowded animals from illness.

McKenna weaves in real people’s stories with clearly explained scientific details and regulatory history. If this story has a villain, it’s Thomas Jukes, whose noble goal was to feed the world with cheap protein. In the ’50s, Jukes was a researcher at Lederle Laboratories, one of the first manufacturers of antibiotics. He did some of the early studies testing the drugs as growth promoters. He saw signs that bacteria were developing resistance, but he saw no risk to the chickens, McKenna writes. Jukes railed against efforts in the ’70s to regulate antibiotic use in livestock and, up until he died in 1999, refused to acknowledge any downsides.

In addition to profiling farmers who embraced industrialization, McKenna introduces those who have turned their backs on antibiotics. These farmers, including many in the United States, have learned to raise drug-free chickens, mainly by going back to the old ways — letting chickens roam free, day and night, pecking at grubs in the ground. Some farms in the Netherlands even manage to raise industrial numbers of chickens without propping them up with antibiotics.

McKenna’s story almost has a happy ending. In 2014, the fast-food restaurant Chick-fil-A announced it would, within five years, stop serving chicken raised with antibiotics. Chicken producers, as well as McDonald’s, Subway, Costco and Walmart, followed suit.
But we’re not out of the woods yet, McKenna warns. She likens antibiotic resistance to climate change, calling it “an overwhelming threat, created over decades by millions of individual decisions and reinforced by the actions of industries.” The book might not make you give up chicken, but you may be more likely to look for sustainably raised birds to put on the dinner table.

When things heat up, spinning electrons go their separate ways.

Warming one end of a strip of platinum shuttles electrons around according to their spin, a quantum property that makes them behave as if they are twirling around. Known as the spin Nernst effect, the newly detected phenomenon was the only one in a cadre of related spin effects that hadn’t previously been spotted, researchers report online September 11 in Nature Materials.

“The last missing piece in the puzzle was spin Nernst and that’s why we set out to search for this,” says study coauthor Sebastian Goennenwein, a physicist at the Technical University of Dresden in Germany.
The effect and its brethren — with names like the spin Hall effect, the spin Seebeck effect and the spin Peltier effect — allow scientists to create flows of electron spins, or spin currents. Such research could lead to smaller and more efficient electronic gadgets that use electrons’ spins to store and transmit information instead of electric charge, a technique known as “spintronics.”

In the spin Nernst effect, named after Nobel laureate chemist Walther Nernst, heating one end of a metal causes electrons to flow toward the other end, bouncing around inside the material as they go. Within certain materials, that bouncing has a preferred direction: Electrons with spins pointing up (as if twirling counterclockwise) go to the right and electrons with spins pointing down (as if twirling clockwise) go to the left, creating an overall spin current. Although the effect had been predicted, no one had yet observed it.

Finding evidence of the effect required disentangling it from other heat- and charge-related effects that occur in materials. To do so, the researchers coupled the platinum to a layer of a magnetic insulator, a material known as yttrium iron garnet. Then, they altered the direction of the insulator’s magnetization, which changed whether the spin current could flow through the insulator. That change slightly altered a voltage measured along the strip of platinum. The scientists measured how this voltage changed with the direction of the magnetization to isolate the fingerprints of the spin Nernst effect.

“The measurement was a tour de force; the measurement was ridiculously hard,” says physicist Joseph Heremans of Ohio State University in Columbus, who was not involved with the research. The effect could help scientists to better understand materials that may be useful for building spintronic devices, he says. “It’s really a new set of eyes on the physics of what’s going on inside these devices.”

A relative of the spin Nernst effect called the spin Hall effect is much studied for its potential use in spintronic devices. In the spin Hall effect, an electric field pushes electrons through a material, and the particles veer off to the left and right depending on their spin. The spin Nernst effect relies on the same basic physics, but uses heat instead of an electric field to get the particles moving.
“It’s a beautiful experiment. It shows very nicely the spin Nernst effect,” says physicist Greg Fuchs of Cornell University. “It beautifully unifies our understanding of the interrelation between charge, heat and spin transport.”

Contrary to popular opinion, humans didn’t shed a harsh existence as hunter-gatherers and herders for the good life of stay-in-place farming. Year-round farming villages and early agricultural states, such as those that cropped up in Mesopotamia, exchanged mobile groups’ healthy lifestyles for the back-breaking drudgery of cultivating crops, exposure to infectious diseases, inadequate diets, taxes and conscription into armies.

In Against the Grain, political anthropologist James C. Scott offers a disturbing but enlightening defense of that position. He draws on past and recent archaeological studies indicating that the emergence of state-run societies around 6,000 years ago represented a cultural step backward in some important ways. Scott has previously written about modern states’ failed social engineering projects and the evasion of state control by present-day mountain peoples in Southeast Asia. Exploring the roots of state-building was a logical next step.
Neither agriculture nor large settlements, on their own, stimulated state formation, Scott argues. Middle Eastern foragers cultivated grains thousands of years before year-round villages appeared. Large, permanent settlements depending substantially on wild plants and marine food materialized in Mesopotamia well before agricultural states formed there.

Scott proposes that early states represented a shotgun marriage of farming and huge communities presided over by a new class of hyperambitious rulers. State-building began in wetland areas, such as the Fertile Crescent, with huge expanses of fertile soil. There, grain farming squeezed enough people and storable food into a small enough space to enable state control and tax collection.

Fledgling states were fragile, often breaking into smaller entities or falling apart entirely. Researchers have tended to overlook the possibility that apparent state “collapses” in the archaeological record involved intentional flights of subjects fed up with war, taxes, epidemics and crop failures, Scott says.

He ends with a look at how herding groups both raided and abetted early agricultural states in Asia. Nomads deftly robbed stores of food and goods from their neighbors, then negotiated steep bribes in exchange for not attacking. Mobile pastoralists eventually became trading partners, bringing sedentary societies copper, horses and slaves, to name a few. Herders were also mercenaries, catching runaway slaves and repressing revolts. Ironically, Scott writes, “barbarians” helped states become the dominant political players they are today.

Scott writes in a straightforward style largely free of scientific jargon. He doesn’t portray foraging and mobile lifestyles as utopian systems, but a closer look at their cons as well as their pros would have painted a fuller picture of these people. Still, Scott’s depiction of early centralized states’ problems rings true in a modern world of nation-states.