Category Archives: Transhuman News

In a new book, University of North Carolina, Charlotte anthropologist Jonathan Marks says that racism in science is alive and well.

This stands in sharp contrast to creationist thinking, Marks says, which is, like racism, decidedly evident in our society but most certainly not welcome in science.

In Is Science Racist? Marks writes:

"If you espouse creationist ideas in science, you are branded as an ideologue, as a close-minded pseudo-scientist who is unable to adopt a modern perspective, and who consequently has no place in the community of scholars. But if you espouse racist ideas in science, that's not quite so bad. People might look at you a little askance, but as a racist you can coexist in science alongside them, which you couldn't do if you were a creationist. Science is racist when it permits scientists who advance racist ideas to exist and to thrive institutionally."

This is a strong set of claims, and Marks uses numerous examples to support them. For example, a 2014 book by science writer Nicholas Wade used genes and race to explain, as Michael Balter put it in Science magazine, "why some people live in tribal societies and some in advanced civilizations, why African-Americans are allegedly more violent than whites, and why the Chinese may be good at business."

The work of psychologist Philippe Rushton, who died in 2012, has been published and even celebrated in scientific circles, Marks explains. Rushton suggested that "the peoples of Africa had undergone eons of natural selection for high reproductive rate and low intelligence, which he measured via surrogate variables notably, sex drive, criminality rates, penis size, and brain size."

In other words, Wade, Rushton, and others working in the same vein take what is cultural, historical and political and conclude it is biologically natural. That's "rationalizing the economic and social disparities in the modern world," Marks notes.

"Race," Marks writes, "is not the discovery of difference; it is the imposition of difference." Inequality comes about because of unequal conditions imposed upon different groups of people through economic and cultural forces.

With this background, we can now tackle a part of Is Science Racist? that deconstructs an activity that has become more and more popular over the past 10 years: sending away our DNA for some type of ancestry testing.

The problem, Marks writes in the book, is the "fabricated meaning" that corporate science superimposes over the raw numbers that emerge from this process. Last week, Marks elaborated on this point in an email to me:

"To understand the ancestry tests, you have to begin by looking at the fine print. This [type of test] says 'for recreational purposes only' or something very similar. It obviously is written by lawyers, not scientists, and it's a way of saying that the results have no scientific or legal standing. This is privatized, corporate science, not ordinary science.

"How do they come up with numbers? They take DNA from people from disparate regions and compare yours to theirs. The numbers reflect a measure of your DNA similarity to those of the divergent gene pools. How do they calculate it? Don't know; the algorithms are protected intellectual property. Are they accurate? About as accurate as looking in the mirror."

OK, so it's a comparative process and we don't know the precise calculation methods. But what's the part about the fabricated meaning? Marks continues:

"Sociologists find that customers make sense of the results, and ignore the nonsense. For example, I've come out 95 percent Ashkenazi Jewish (not a geographical population, but a gene pool with its own minor genetic idiosyncrasies due to history) and 5 percent Korean. A good scientific question would be: +/- how much? 15 percent? 10 percent? Is my 5 percent Korean ancestry the same as 0 percent Korean ancestry?

"Scientific answer: Yes. Corporate answer: Wouldn't you like to know?

"So there is sense, but it blends into nonsense, and may be difficult to distinguish them."

Here's a second example of ancestry nonsense taken from Marks' book. The Denisovan people are named for a Siberian cave where an unusual finger bone, dated to 50,000 years ago, was reported in 2012. By now, we know more about the Denisovans, but still, not a lot.

Despite this, Marks notes, you can pay to find out what percentage Denisovan you are! What genuine meaning can this result possibly have when the meaning of "a Denisovan population" it itself in flux?

All this leads to a question Alva No asked here last year:

"Can it ever be more than fantasy to try to draw meaningful conclusions about an individual's origins on the basis of the sort of DNA information that is available to us now?"

Marks' answer is clearly negative. Again, from his email message:

"The tests often reify as 'natural' human populations that are actually natural/cultural, that is to say, human groups that are genetically different to some extent, but are actually bounded by history, language, politics, or religion, and are thus not 'natural' categories at all. These include particular African tribes, Ashkenazi Jews, or Vikings. The fact that one can detect ancestry in these identities does not mean that they are products of nature."

And as we've seen with work done by Wade and Rushton, the problem is that where we make a habit of seeing biologically natural units of some type instead of complex webs of variables at work, there's a risk of highly unscientific thinking and sometimes worse.

"Scientific racism," Marks told me, "often begins by highlighting (and misrepresenting) patterns of difference in the human species; but regardless of how different they may be from one another, people are entitled to equality."

Yes, they are. Humans vary, and our genes vary. But not very much: The chimpanzee gene pool shows a lot more genetic variation than the human gene pool does.

What can our genome tell us?

Less than we may like to think.

Barbara J. King is an anthropology professor emerita at the College of William and Mary. She often writes about the cognition, emotion and welfare of animals, and about biological anthropology, human evolution and gender issues. Barbara's new book is Personalities on the Plate: The Lives and Minds of Animals We Eat. You can keep up with what she is thinking on Twitter: @bjkingape

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Why You Should Think Twice About Those DNA-By-Mail Results ... - NPR

A female baboon presents to a male, a form of sexual solicitation. Alice Baniel

Why does it matter? If such behavior is found in humanity's closest relatives the chimpanzees and other social primates, it suggests roots deep in evolutionary history, as opposed to behavior that has arisen recently.

"Because sexual intimidation where aggression and matings are not clustered in time is discreet, it may easily go unnoticed," Baniel said.

Related:

"It may therefore be more common than previously appreciated in mammalian societies, and constrain female sexuality even in some species where they seem to enjoy relative freedom."

There's another factor size. The behavior may be more common in species whose males are markedly bigger than females, such as chimpanzees, baboons and humans.

Humanity's other close relative, the bonobo, doesn't have this sexual size difference, and bonobos are notoriously egalitarian when it comes to sex.

"This study adds to growing evidence that males use coercive tactics to constrain female mating decisions in promiscuous primates," Baniel said.

"Such behavior, previously reported only in chimpanzees, may therefore occur in a wider range of primates, strengthening the case for an evolutionary origin of human sexual intimidation," Baniel's team concluded.

Baniel plans to study the two troupes further. She's hoping at least some of the females stand up for better relationships.

"I would like to understand if several mating strategies could coexist among males, i.e., being chosen by females versus intimidating them," she said.

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Baboon Study Shows Sexual Bullying May Lie Deep in Our DNA - NBCNews.com

The Khoe-San in Southern Africa split off early from other Africans, but carry DNA from East African herders.

Roger de la Harpe/Newscom

By Elizabeth PennisiJul. 6, 2017 , 12:45 PM

AUSTINThe study of ancient human DNA has not been an equal opportunity endeavor. Early Europeans and Asians have had portions of their genomes sequenced by the hundreds over the past decade, rewriting Eurasian history in the process. But because genetic material decays rapidly in warm, moist climates, scientists had sequenced the DNA of just one ancient African. Until now.

This week, at the annual meeting of the Society for Molecular Biology & Evolution here, scientists announced that they had partially sequenced 15 ancient African genomes, with representatives from all over sub-Saharan Africa. And another groupwhose work is still unpublishedhas sequenced seven more ancient humans from South Africa. [Finding] ancient genomes from Africa is pretty amazing, says Anna-Sapfo Malaspinas, a population geneticist at the University of Bern, who was not involved in either project.

Africa has long been called the cradle of humanity, from which our earliest human ancestors spread across the rest of the world some 50,000 years ago. Africa is also where peopleancient and modernare most genetically diverse. But how such groups, from the Hadza of East Africa to the Khoe-San of Southern Africa, came to be is a mystery. Thats in part because some 2000 years ago, early adopters of agriculture known as the Bantu spread across the continent, erasing the genetic footprint of other Africans. The one ancient African genome that has been sequencedan Ethiopian who lived some 4500 years agohas shed little light on this mystery.

Pontus Skoglund knew there had to be more to the story. So the Harvard University evolutionary geneticist and his colleagues obtained DNA from 15 ancient Africans from between 500 and 6000 years ago, some before the Bantu expansion. In addition, Skoglunds team got DNA data from 19 modern populations across Africa for comparison, including from large groups like the Bantu and smaller ones like the Khoe-San and the Hadza.

For the most part, the ancient DNA was most similar to that of people living in the same places where the bones were found, Skoglund reported. But some interesting exceptions showed intermingling among various groups. Its really exciting to see in Africa that there was already this ancient admixture, says Simon Aeschbacher, a population geneticist from the University of Bern who was not involved with the work. There must have been population movements in early Africa.

The ancient genomes indicate that Southern Africans split off from Western Africans several thousand years ago, and subsequently evolved key adaptations that honed their taste buds and protected them from the sun. Around 3000 years ago, herderspossibly from todays Tanzaniaspread far and wide, reaching Southern Africa centuries before the first farmers. But modern Malawians, who live just south of Tanzania, are likely descended from West African farmers rather than local hunter-gatherers, Skoglund says. Indeed, the analysis suggests that West Africans were early contributors to the DNA of sub-Saharan Africans. But even these DNA donors were a hodgepodge of what are now two modern groupsthe Mende and the Yoruba. And one ancient African herder showed influence from even farther abroad, with 38% of their DNA coming from outside Africa.

Another study focused on Southern Africa, where some researchers think modern Homo sapiens evolved. Evolutionary geneticist Carina Schlebusch and her colleagues at Uppsala University in Sweden partially sequenced seven ancient genomes: three from 2000-year-old hunter-gatherers and four from 300- to 500-year-old farmers. They also included modern DNA in their analyses.

The more modern farmers did have Bantu DNA in their genomes, but the ancient hunter-gatherers predated the spread of the Bantu, she and her colleagues reported last month on the preprint server bioRxiv. Their other findings parallel Skoglunds discoveries: Nine percent to 22% of the DNA of these farmers modern descendantsincluding the southern Khoe-Sancomes from East Africans and Eurasian herders.

Schlebuschs analysis reaches even deeper into human history than does Skoglunds, as her team used the ancient and modern genomes to estimate that the hunter-gatherers she studied split off from other groups some 260,000 years ago, about the age of the oldest H. sapiens fossil. Having that date lets us start to think about questions like where, and how, anatomically and behaviorally modern humans evolved, says Iain Mathieson, an evolutionary geneticist at Harvard. Whether this date survives peer review after publication is yet to be seen.

Aeaschbacher has a simple solution to resolve such uncertainties: sequencing more ancient African genomes. Theres a deep-seated need to understand this, he says. How ancient Africans divided into groups and when and how they moved around could have a strong impact on what shapes present-day humans.

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First big efforts to sequence ancient African DNA reveal how early ... - Science Magazine

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.

Its 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.

Over thousands of years, humans have found ways to put other species to work, from spinning silk to storing water. These short stories reveal how humans got to know some of their closest companions.

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 didnt 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 studys results contradicting anothers.

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. Were going to get a lot more confused before we figure out whats really going on.

Deciding when an animal can be called domesticated isnt 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 farms friendliest foxes to breed. Over more than 60 generations, the foxes have grown more and more tolerant of humans. Kukekova says shes noticed a difference even in the 15 years shes been visiting the farm.

In China, people began domesticating the larvae of silk moths for the fine, strong threads of their cocoons as early as 7,500 years ago, genetic evidence suggests. People bred the larvae to produce more silk and to tolerate human handling and extreme crowding (SN Online: 8/27/09). For more than 2,000 years, the Chinese kept their silk-making methods top secret, and smuggling silkworms out of the country was punishable by death. Silk makers traded their monopolized fabric throughout Eurasia along the Silk Road (SN:5/27/17, p. 4). To this day, the only other insect that is domesticated is the honeybee. Erika Engelhaupt

In Kukekovas 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 didnt mind if you petted them, but they werent 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 arent easily house-trained. The combination of living with people plus inherited changes in the foxes genomes may eventually make them fully domesticated, but they arent 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. Thats different from wild animals that have been tamed but dont 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 dont 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 havent 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 isnt 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.

Dogs appear to have been the first species domesticated by humans, followed by many others in Asia and the Middle East. As people spread to the New World, they continued to domesticate animals. Some were domesticated more than once in different locations.

Sources: D.E. MacHugh et al/Annu. Rev. Anim. Biosci. 2017; M. Germonpr et al/J. Archaeol. Sci. 2009

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 animals 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.

Many domestication stories have vague beginnings, but we know exactly when the Syrian golden hamster, now a popular pet, first came under human control. On April 12, 1930, zoologist Israel Aharoni had workers dig up a mother hamster and her 11 babies spied by a farmer in his wheat field near Aleppo, Syria. Aharoni wanted a convenient animal to rear in the laboratory, but the creatures were so easily tamed that breeders began selling them as pets. Now, more than a million hamsters, descended from that first litter, run in wheels and transparent balls in homes across the United States. Erika Engelhaupt

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 wouldnt want to make the argument that at the Botai time youve 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 couldnt imagine myself, Orlando says. In Mongolia, horses roam free and their owners catch them, as needed, for riding or milking. Once youve seen that, you cant think that domestication is just about parking animals somewhere. Its about the process of interacting with them and developing a relationship with them.

If its 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. Thats the task of paleontologist Mietje Germonpr 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). Germonpr 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 Germonpr. Big dogs may have helped humans hunt dangerous carnivores, such as cave bears, hyenas and cave lions. Its also possible the animals were used for fur or meat.

The ancestor of todays enormous, fleshy sweet watermelons was a surprisingly small, hard and bitter melon with pale green flesh. Just where this fruit was first grown is debatedall thats agreed on is that it was somewhere in Africa. An image of a watermelon appears in an Egyptian tomb dating to at least 4,000 years ago, and five watermelon seeds were found in King Tuts tomb. Its thought that the Egyptians bred the fruit as a tasty, and portable, water supply. Erika Engelhaupt

Germonprs 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 Germonprs 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 didnt angle from the skull the way modern dogs do, and the ancient versions didnt have some other features of modern dogs (SN Online: 2/5/15).

Larson says hes not bothered that the Goyet hound didnt 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 didnt 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 Fidos taming isnt 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 Goyets 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 todays 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 didnt leave any modern descendants, researchers reported in Science in 2013. But it doesnt mean the animals werent on the way toward being domesticated, Germonpr 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.

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 thats 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.

Though the Inca built great cities and had a sophisticated understanding of astronomy, they didnt use wheels to transport goods. Instead, llamas carried the heavy loads along the empires vast road system. And llama dung fertilized Inca fields, possibly helping to grow maize at high altitudes. South Americas llamas and alpacas are domesticated versions of two wild camel species: guanaco (ancestor of llamas) and the smaller vicua (alpacas ancestor). The earliest evidence of the animals domestication is from bones found at archaeological sites in the Peruvian Andes, dating to at least 6,000 years ago. Erika Engelhaupt

It may have taken nearly 2,000 years for people in Chinas 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 wasnt 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 theyve pieced together the rest of the rice domestication story. DNA evidence clearly shows that Chinas 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. Indicas 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 Chinas japonica.

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 thats 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 Polands Jaktorw 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. Were 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 wasnt until sometime after 2,300 years ago that people started winnowing down the number of stallions that were allowed to breed. Orlando doesnt 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 didnt 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.)

Turkeys are one of the most recently domesticated animals. In 2016, researchers found 1,500-year-old turkey eggs plus bones of both chicks and adult birds in the Oaxaca region of Mexico. The presence of turkeys at all life stages suggests they were being raised as food. They may have been important symbolically too; remains have been found buried alongside humans. The birds have changed a great deal since those early days: Some commercially bred turkeys have breast muscles so large that the birds cant get close enough to mate. Humans must artificially inseminate them, a sign of true domestication. Erika Engelhaupt

If Larsons calculations are correct, egg laying wasnt 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. Its hard to be buddies with a creature that constantly runs from you, or worse, attacks.

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 Linkping 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, Jensens 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 birds 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 didnt 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 Im 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 dont think were talking about hundreds of generations, maybe dozens. Its 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 didnt have a unifying explanation for why the physical traits of domestication syndrome were linked to tameness until three years ago.

Humans may have selected animals for tameness (left column), with those choices leading to unintended features seen in many domesticated species (right column). One hypothesis is that tameness, which involves a calmer nervous system and a dampened stress hormone response, results from alterations in neural crest cells. Those cells migrate throughout the embryo to form many tissues. Changes in the cells migration might account for many physical traits linked to tameness in domesticated animals.

Source: A.S. Wilkins, R.W. Wrangham and W.T. Fitch/Genetics 2014

Thats 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 animals 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.

It would be hard to recognize todays toothsome corncobs from the plants wild progenitor, a grass called teosinte. When Native Americans began domesticating teosinte, its ears were two or three inches long, holding a sparse five to 12 kernels each. In fact, teosinte looks so different from maize that scientists questioned the link, first proposed in the 1930s, until genetics could prove it more than half a century later. In 2009, archaeologists found the earliest known evidence of domesticated maize at an 8,700-year-old site in southwestern Mexico, alongside stone tools used to grind the plants. Erika Engelhaupt

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.

This article appears in the July 8, 2017, issue of Science News with the headline: "The road to tameness: Fresh ideas emerge about the origins of humans' relationships with their favorite species."

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DNA evidence is rewriting domestication origin stories - Science News Magazine

A simple tweak to a tool for making macrocyclic compounds could help increase the diversity of DNA-encoded libraries used by drug developers to rapidly screen and identify promising drug candidates (Bioconjugate Chem. 2017, DOI: 10.1021/acs.bioconjchem.7b00292).

Building such libraries involves attaching short, unique DNA sequences to small molecules and then reacting those DNA-tagged building blocks together to create myriad products, which are tagged with additional unique DNA sequences. The chain of DNA markers serves as a sort of bar code to identify the compounds in a library that successfully bind to a particular drug target and to trace their synthesis history. However, these libraries generally have not been able to include ring compounds in the drug screening because transition-metal catalysts essential for ring-closing reactions are incompatible with DNA. These catalysts are central to many important organic transformations such as olefin metathesis, but they can bind to charged DNA backbones and cause the strands to fall apart.

A team led by Xiaojie Lu and Lijun Fan at GlaxoSmithKline has found that by protecting the DNA tags with magnesium ions, they can produce a variety of DNA-encoded heterocycles and macrocycles using ruthenium-catalyzed ring-closing metathesis. The team hypothesizes that because the magnesium ions occupy all the DNAs binding sites, the ruthenium catalyst is forced to react with the substrates instead of the DNA. Preliminary tests to perform cross-metathesis reactions between two DNA-tagged primary alkenes to produce a secondary alkene were also successful.

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Making macrocyclic compounds for DNA-encoded libraries - The Biological SCENE

July 6, 2017 Sequence-specific, twist-induced, kinked elastic configurations, generated by molecular dynamics simulations on supercomputers at the Texas Advanced Computing Center, help explain how long strands of DNA can fit in small spaces. Credit: Christopher G. Myers, B. Montgomery Pettitt, University of Texas Medical Branch

A biological mystery lies at the center of each of our cells, namely: how one meter of DNA can be wadded up into the space of a micron (or one millionth of a meter) within each nucleus of our body.

The nuclei of human cells are not even the most crowded biological place that we know of. Some bactiophagesviruses that infect and replicate within a bacteriumhave even more concentrated DNA.

"How does it get in there?" B. Montgomery (Monte) Pettitt, a biochemist and professor at the University of Texas Medical Branch, asks. "It's a charged polymer. How does it overcome the repulsion at its liquid crystalline density? How much order and disorder is allowed, and how does this play a role in nucleic acids?"

Using the Stampede and Lonestar5 supercomputers at The University of Texas at Austin's Texas Advanced Computing Center (TACC), Pettitt investigates how phages' DNA folds into hyper-confined spaces.

Writing in the June 2017 issue of the Journal of Computational Chemistry, he explained how DNA may overcome both electrostatic repulsion and its natural stiffness.

The key to doing so? Kinks.

The introduction of sharp twists or curves into configurations of DNA packaged within a spherical envelope significantly reduces the overall energies and pressures of the molecule, according to Pettitt.

He and his collaborators used a model that deforms and kinks the DNA every 24 base pairs, which is close to the average length that is predicted from the phage's DNA sequence. The introduction of such persistent defects not only reduces the total bending energy of confined DNA, but also reduces the electrostatic component of the energy and pressure.

"We show that a broad ensemble of polymer configurations is consistent with the structural data," he and collaborator Christopher Myers, also of University of Texas Medical Branch, wrote.

Insights like these cannot be gained strictly in the lab. They require supercomputers that serve as molecular microscopes, charting the movement of atoms and atomic bonds at length- and time-scales that are not feasible to study with physical experiments alone.

"In the field of molecular biology, there's a wonderful interplay between theory, experiment and simulation," Pettitt said. "We take parameters of experiments and see if they agree with the simulations and theories. This becomes the scientific method for how we now advance our hypotheses."

Problems like the ones Pettitt is interested in cannot be solved on a desktop computer or a typical campus cluster, but require hundreds of computer processors working in parallel to mimic the minute movements and physical forces of molecules in a cell.

Pettitt is able to access TACC's supercomputers in part because of a unique program known as the Journal of Computational Chemistry initiative, which makes TACC's computing resources, expertise and training available to researchers within the University of Texas Systems' 14 institutions.

"Computational research, like that of Dr. Pettitt, which seeks to bridge our understanding of physical, chemical, and ultimately biological phenomena, involves so many calculations that it's only really approachable on large supercomputers like TACC's Stampede or Lonestar5 systems," said Brian Beck, a life sciences researcher at TACC.

"Having TACC supercomputing resources available is critical to this style of research," Pettitt said.

FINDING THE ORDER IN DISORDERED PROTEINS

Another phenomenon that has long interested Pettitt is the behavior of Intrinsically Disordered Proteins (IDPs) and intrinsically disordered domains, where parts of a protein have a disordered shape.

Unlike crystals or the highly-packed DNA in viruses, which have distinct, rigid shapes, IDPs "fold up into a gooey mess," according to Pettitt. And yet they're critical for all forms of life.

It is believed that in eukaryotes (organisms whose cells have complex substructures like nuclei), roughly 30 percent of proteins have an intrinsically disordered domain. More than 60 percent of proteins involved in cell signaling (molecular processes that take signals from outside the cell or across cells that tell the cell what behaviors to turn on and off in response) have disordered domains. Similarly, 80 percent of cancer-related signaling proteins have IDP regions - making them important molecules to understand.

Among the IDPs Pettitt and his group are studying are nuclear transcription factors. These molecules control the expression of genes and have a signaling domain that is rich in the flexible amino acid, glycine.

The folding of the nuclear transcription factor signaling domain is not brought about by hydrogen bonding and hydrophobic effects, like most protein molecules, according to Pettitt. Rather, when the longer molecules find too many glycines in a space, they go beyond their solubility and start associating with each other in unusual ways.

"It's like adding too much sugar in your tea," Pettitt explains. "It won't get any sweeter. The sugar must fall out of solution and find a partner - precipitating into a lump."

Writing in Protein Science in 2015, he described molecular simulations performed on Stampede that helped to explain how and why IDPs collapse into globule-like structures.

The simulations calculated the forces from carbonyl (CO) dipole-dipole interactionsattractions between the positive end of one polar molecule and the negative end of another polar molecule. He determined that these interactions are more important in the collapse and aggregation of long strands of glycine than the formation of H-bonds.

"Given that the backbone is a feature of all proteins, CO interactions may also play a role in proteins of nontrivial sequence where structure is eventually determined by interior packing and the stabilizing effects of H-bonds and CO-CO interactions," he concluded.

The research was enabled by an allocation of compute time on Stampede through the Extreme Science and Engineering Discovery Environment (XSEDE) which is supported by the National Science Foundation.

Pettitt, a long-time champion of supercomputing, doesn't only use TACC resources himself. He encourages other scholars, including his colleagues at the Sealy Center for Structural Biology and Molecular Biophysics, to use supercomputers as well.

"Advanced computing is important for data analysis and data refinement from experiments, X-ray and electron microscopy, and informatics," he says. "All of these problems have big data processing issues that can be addressed using advanced computing."

When it comes to uncovering the mysteries of biology on the tiniest scales, nothing quite beats a giant supercomputer.

Explore further: Rosetta online server that includes everyone

More information: Christopher G. Myers et al, Phage-like packing structures with mean field sequence dependence, Journal of Computational Chemistry (2017). DOI: 10.1002/jcc.24727

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Researchers explore DNA folding, cellular packing with supercomputer simulations - Phys.Org

LEBANON, Ohio -- A DNA sample solved a rape cold case about 16 years after the crime, Warren County Prosecutor David Fornshell announced Thursday.

Sixteen years ago, nurses at Brookside Extended Care discovered one of their residents -- a 29-year-old woman with developmental disabilities so severe she could neither walk nor speak -- had been violently sexually assaulted by an unknown man overnight. Not one of them,Fornshell said, has ever been able to forget it.

"It's sickening to think that anybody would be capable of doing that to someone so vulnerable," he said.

The victim died in 2011. The only DNA evidence of the culprit's identity -- blood and semen found in the victim's diaper after the assault -- languished without matches for over a decade, and $6,000 in reward money didn't coax leads out of the surrounding community. Brookside made improvements to its security, including the installation of many alarms and surveillance cameras, but no suspects emerged.

Until Thursday.

Fornshell believes a DNA cross-check has successfully identified the culprit as Brian Sundin, a 42-year-old whose DNA was on file with the Florida Department of Corrections.

Sundin was with charged the rape in February after the match was made, but his indictment remained sealed while he was at large. According to a news release from Fornshell, he was recently arrested and convicted of a theft offense in Williamson County, Tennessee.

With Sundin already behind bars, Warren County authorities unsealed the indictment and began the process of extraditing him to Ohio.

Authorities believeSundin, who lived nearby at the time, entered Brookside through an unlocked door and assaulted the victim, according to the news release.

Although the victim is no longer living, Fornshell said everyone from doctors to detectives agreed the county should seek justice for her sake and that of her family.

"It's going to be a situation where no jury is going to believe she in any way consented to any of this happening," he said.

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DNA solved 'cold case' rape of developmentally disabled woman 16 ... - WCPO