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How Neanderthal DNA Helps Humanity

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Emily Singer reports in Quanta:

Eqrly human history was a promiscuous affair. As modern humans began to spread out of Africa roughly 50,000 years ago, they encountered other species that looked remarkably like them — the Neanderthals and Denisovans, two groups of archaic humans that shared an ancestor with us roughly 600,000 years earlier. This motley mix of humans coexisted in Europe for at least 2,500 years, and we now know that they interbred, leaving a lasting legacy in our DNA. The DNA of non-Africans is made up of roughly 1 to 2 percent Neanderthal DNA, and some Asian and Oceanic island populations have as much as 6 percent Denisovan DNA.

Over the last few years, scientists have dug deeper into the Neanderthal and Denisovan sections of our genomes and come to a surprising conclusion. Certain Neanderthal and Denisovan genes seem to have swept through the modern human population — one variant, for example, is present in 70 percent of Europeans — suggesting that these genes brought great advantage to their bearers and spread rapidly.

“In some spots of our genome, we are more Neanderthal than human,” saidJoshua Akey, a geneticist at the University of Washington. “It seems pretty clear that at least some of the sequences we inherited from archaic hominins were adaptive, that they helped us survive and reproduce.”

But what, exactly, do these fragments of Neanderthal and Denisovan DNA do? What survival advantage did they confer on our ancestors? Scientists are starting to pick up hints. Some of these genes are tied to our immune system, to our skin and hair, and perhaps to our metabolism and tolerance for cold weather, all of which might have helped emigrating humans survive in new lands.

“What allowed us to survive came from other species,” said Rasmus Nielsen, an evolutionary biologist at the University of California, Berkeley. “It’s not just noise, it’s a very important substantial part of who we are.”

The Neanderthal Within

The Tibetan plateau is a vast stretch of high-altitude real estate isolated by massive mountain ranges. The scant oxygen at 14,000 feet — roughly 40 percent lower than the concentrations at sea level — makes it a harsh environment. People who move there suffer higher rates of miscarriage, blood clots and stroke on account of the extra red blood cells their bodies produce to feed oxygen-starved tissue. Native Tibetans, however, manage just fine. Despite the meager air, they don’t make as many red blood cells as the rest of us would at those altitudes, which helps to protect their health.

In 2010, scientists discovered that Tibetans owe their tolerance of low oxygen levels in part to an unusual variant in a gene known as EPAS1. About 90 percent of the Tibetan population and a smattering of Han Chinese (who share a recent ancestor with Tibetans) carry the high-altitude variant. But it’s completely absent from a database of 1,000 human genomes from other populations.

In 2014, Nielsen and colleagues found that Tibetans or their ancestors likely acquired the unusual DNA sequence from Denisovans, a group of early humans first described in 2010 that are more closely related to Neanderthals than to us. The unique gene then flourished in those who lived at high altitudes and faded away in descendants who colonized less harsh environments. “That’s one of the most clear-cut examples of how [interbreeding] can lead to adaptation,” said Sriram Sankararaman, a geneticist and computer scientist at the University of California, Los Angeles.

The idea that closely related species can benefit from interbreeding, known in evolutionary terms as adaptive introgression, is not a new one. As a species expands into a new territory, it grapples with a whole new set of challenges — different climate, food, predators and pathogens. Species can adapt through traditional natural selection, in which spontaneous mutations that happen to be helpful gradually spread through the population. But such mutations strike rarely, making it a very slow process. A more expedient option is to mate with species that have already adapted to the region and co-opt some of their helpful DNA. (Species are traditionally defined by their inability to mate with one another, but closely related species often interbreed.)

This phenomenon has been well documented in a number of species, including mice that adopted other species’ tolerance to pesticides and butterflies that appropriated other species’ wing patterning. But it was difficult to study adaptive introgression in humans until the first Neanderthal genome was sequenced in 2010, providing scientists with hominin DNA to compare to our own.

Neanderthals and Denisovans would have been a good source of helpful DNA for our ancestors. They had lived in Europe and Asia for hundreds of thousands of years — enough time to adjust to the cold climate, weak sun and local microbes. “What better way to quickly adapt than to pick up a gene variant from a population that had probably already been there for 300,000 years?” Akey said. Indeed, the Neanderthal and Denisovan genes with the greatest signs of selection in the modern human genome . . .

Continue reading.

Written by LeisureGuy

26 May 2016 at 10:29 am

Another way a functional Congress would come in handy: Scientists say nuclear fuel pools around the country pose safety and health risks

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Read to see how we seem to be waiting to see what happens when the fuse burns up.

Written by LeisureGuy

24 May 2016 at 12:24 pm

Absolutely brilliant: Coaching parents as a way to help impoverished children

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A direct attack on dysfunctional memes by inoculation with a benign meme, and one that is self-sustaining at that. Paul Tough writes in the NY Times:

IN 1986, in a few of the poorest neighborhoods in Kingston, Jamaica, a team of researchers from the University of the West Indies embarked on an experiment that has done a great deal, over time, to change our thinking about how to help children succeed, especially those living in poverty. Its message: Help children by supporting and coaching their parents.

The researchers divided the families of 129 infants and toddlers into groups. The first group received hourlong home visits once a week from a trained researcher who encouraged the parents to spend more time playing actively with their children: reading picture books, singing songs, playing peekaboo. A second group of children received a kilogram of a milk-based nutritional supplement each week. A control group received nothing. The interventions themselves ended after two years, but the researchers have followed the children ever since.

The intervention that made the big difference in the children’s lives, as it turned out, wasn’t the added nutrition; it was the encouragement to the parents to play. The children whose parents were counseled to play more with them did better, throughout childhood, on tests of I.Q., aggressive behavior and self-control. Today, as adults, they earn an average of 25 percent more per year than the subjects whose parents didn’t receive home visits.

The Jamaica experiment helps make the case that if we want to improve children’s opportunities for success, one of the most powerful potential levers for change is not the children themselves, but rather the attitudes, beliefs and behaviors of the adults who surround them [i.e., their defining memes – LG].

More recent research has helped to uncover exactly how that change can take place. Psychologists including Mary Dozier at the University of Delaware and Philip Fisher at the University of Oregon have studied home-visiting interventions in which parents of infants and young children are provided with supportive, personalized coaching that identifies and reinforces the small moments — such as the face-to-face exchanges sometimes called “serve and return” interactions — that encourage attachment, warmth and trust between parent and child.

The impact of this coaching can be powerful. In one series of experiments, infants and toddlers whose foster parents received just 10 home visits showed fewer behavior problems than a control group and significantly higher rates of “secure attachment” (a close, stable connection with the adults in their lives). The children’s ability to process stress improved, too. In fact, the daily patterns in their levels of cortisol, a key stress hormone, came to resemble those of typical, well-functioning, non-foster-care children.

These positive influences in children’s early lives can have a profound effect on the development of what are sometimes called noncognitive skills.

These capacities may be harder to measure on tests of kindergarten readiness than skills like number and letter recognition, but they are inordinately valuable in school, beginning on the first day of kindergarten. Unlike reading and math skills, though, they aren’t primarily developed through deliberate practice and explicit training. Instead, researchers have found, they are mostly shaped by children’s daily experience of their environment. And they have their roots in the first few years of life. When children spend their early years in communities and homes where life is unstable and chaotic — which is true of a disproportionate number of children growing up in poverty — the intense and chronic stress they often experience as a result can seriously disrupt, on a neurobiological level, their development of these important capacities.

This is why interventions such as home visits with parents can be so effective. . .

Continue reading.

One’s self really does seem to be a collection of memes, and it turns out to make a big difference which memes you acquire.

Written by LeisureGuy

22 May 2016 at 1:48 pm

New Support for Alternative Quantum View

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Perhaps quantum mechanics is not so mysterious as the Copenhagen interpretation would have it. Dan Falk reports in Quanta:

Of the many counterintuitive features of quantum mechanics, perhaps the most challenging to our notions of common sense is that particles do not have locations until they are observed. This is exactly what the standard view of quantum mechanics, often called the Copenhagen interpretation, asks us to believe. Instead of the clear-cut positions and movements of Newtonian physics, we have a cloud of probabilities described by a mathematical structure known as a wave function. The wave function, meanwhile, evolves over time, its evolution governed by precise rules codified in something called the Schrödinger equation. The mathematics are clear enough; the actual whereabouts of particles, less so. Until a particle is observed, an act that causes the wave function to “collapse,” we can say nothing about its location. Albert Einstein, among others, objected to this idea. As his biographer Abraham Pais wrote: “We often discussed his notions on objective reality. I recall that during one walk Einstein suddenly stopped, turned to me and asked whether I really believed that the moon exists only when I look at it.”

But there’s another view — one that’s been around for almost a century — in which particles really do have precise positions at all times. This alternative view, known as pilot-wave theory or Bohmian mechanics, never became as popular as the Copenhagen view, in part because Bohmian mechanics implies that the world must be strange in other ways. In particular, a 1992 study claimed to crystalize certain bizarre consequences of Bohmian mechanics and in doing so deal it a fatal conceptual blow. The authors of that paper concluded that a particle following the laws of Bohmian mechanics would end up taking a trajectory that was so unphysical — even by the warped standards of quantum theory — that they described it as “surreal.”

Nearly a quarter-century later, a group of scientists has carried out an experiment in a Toronto laboratory that aims to test this idea. And if their results, first reported earlier this year, hold up to scrutiny, the Bohmian view of quantum mechanics — less fuzzy but in some ways more strange than the traditional view — may be poised for a comeback.

Saving Particle Positions

Bohmian mechanics was worked out by Louis de Broglie in 1927 and again, independently, by David Bohm in 1952, who developed it further until his death in 1992. (It’s also sometimes called the de Broglie–Bohm theory.) As with the Copenhagen view, there’s a wave function governed by the Schrödinger equation. In addition, every particle has an actual, definite location, even when it’s not being observed. Changes in the positions of the particles are given by another equation, known as the “pilot wave” equation (or “guiding equation”). The theory is fully deterministic; if you know the initial state of a system, and you’ve got the wave function, you can calculate where each particle will end up.

That may sound like a throwback to classical mechanics, but there’s a crucial difference. Classical mechanics is purely “local” — stuff can affect other stuff only if it is adjacent to it (or via the influence of some kind of field, like an electric field, which can send impulses no faster than the speed of light). Quantum mechanics, in contrast, is inherently nonlocal. The best-known example of a nonlocal effect — one that Einstein himself considered, back in the 1930s — is when a pair of particles are connected in such a way that a measurement of one particle appears to affect the state of another, distant particle. The idea was ridiculed by Einstein as “spooky action at a distance.” But hundreds of experiments, beginning in the 1980s, have confirmed that this spooky action is a very real characteristic of our universe.

In the Bohmian view, nonlocality is even more conspicuous. The trajectory of any one particle depends on what all the other particles described by the same wave function are doing. And, critically, the wave function has no geographic limits; it might, in principle, span the entire universe. Which means that the universe is weirdly interdependent, even across vast stretches of space. The wave function “combines — or binds — distant particles into a single irreducible reality,” as Sheldon Goldstein, a mathematician and physicist at Rutgers University, has written.

The differences between Bohm and Copenhagen become clear when we look at the classic “double slit” experiment, in which particles (let’s say electrons) pass through a pair of narrow slits, eventually reaching a screen where each particle can be recorded. When the experiment is carried out, the electrons behave like waves, creating on the screen a particular pattern called an “interference pattern.” Remarkably, this pattern gradually emerges even if the electrons are sent one at a time, suggesting that each electron passes through both slits simultaneously.

Those who embrace the Copenhagen view have come to live with this state of affairs — after all, it’s meaningless to speak of a particle’s position until we measure it. Some physicists are drawn instead to the Many Worlds interpretation of quantum mechanics, in which observers in some universes see the electron go through the left slit, while those in other universes see it go through the right slit — which is fine, if you’re comfortable with an infinite array of unseen universes.

By comparison, the Bohmian view sounds rather tame: The electrons act like actual particles, their velocities at any moment fully determined by the pilot wave, which in turn depends on the wave function. In this view, each electron is like a surfer: It occupies a particular place at every specific moment in time, yet its motion is dictated by the motion of a spread-out wave. Although each electron takes a fully determined path through just one slit, the pilot wave passes through both slits. The end result exactly matches the pattern one sees in standard quantum mechanics.

For some theorists, the Bohmian interpretation holds an irresistible appeal. “All you have to do to make sense of quantum mechanics is to say to yourself: When we talk about particles, we really mean particles. Then all the problems go away,” said Goldstein. “Things have positions. They are somewhere. If you take that idea seriously, you’re led almost immediately to Bohm. It’s a far simpler version of quantum mechanics than what you find in the textbooks.”Howard Wiseman, a physicist at Griffith University in Brisbane, Australia, said that the Bohmian view “gives you a pretty straightforward account of how the world is…. You don’t have to tie yourself into any sort of philosophical knots to say how things really are.”

But not everyone feels that way, and over the years the Bohm view has struggled to gain acceptance, trailing behind Copenhagen and, these days, behind Many Worlds as well. A significant blow came with the paper known as “ESSW,” an acronym built from the names of its four authors. The ESSW paper claimed that particles can’t follow simple Bohmian trajectories as they traverse the double-slit experiment. Suppose that someone placed a detector next to each slit, argued ESSW, recording which particle passed through which slit. ESSW showed that a photon could pass through the left slit and yet, in the Bohmian view, still end up being recorded as having passed through the right slit. This seemed impossible; the photons were deemed to follow “surreal” trajectories, as the ESSW paper put it.

The ESSW argument “was a striking philosophical objection” to the Bohmian view, said Aephraim Steinberg, a physicist at the University of Toronto. “It damaged my love for Bohmian mechanics.”

But Steinberg has found a way to rekindle that love. In a paper published inScience Advances, Steinberg and his colleagues — the team includes Wiseman, in Australia, as well as five other Canadian researchers — describe what happened when they actually performed the ESSW experiment. They found that the photon trajectories aren’t surrealistic after all — or, more precisely, that the paths may seem surrealistic, but only if one fails to take into account the nonlocality inherent in Bohm’s theory.

The experiment that Steinberg and his team conducted was analogous to the standard two-slit experiment. They used photons rather than electrons, and . . .

Continue reading.

Written by LeisureGuy

19 May 2016 at 10:15 am

Posted in Math, Science

Making velcro on metal

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More in this Motherboard article by John Wenz.

Written by LeisureGuy

16 May 2016 at 11:44 am

The psychology of public bathrooms

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Fascinating column by Nick Haslam, the author of “Psychology in the Bathroom” and  a professor of psychology and head of the Melbourne School of Psychological Sciences at the University of Melbourne, in the Washington Post:

Sigmund Freud didn’t think much of American public restrooms. During his 1909 visit to the United States, he grumbled that they lacked the refinement of European conveniences — when he could find one at all. Writing to a German friend years later, Freud’s lasting bitterness was obvious: “Is it not sad that we are materially dependent on these savages?”

It’s not surprising that a latrine could provoke such strong feelings: We’re seeing a version of these tensions play out today. This week, the White House ordered schools to provide trans students with bathrooms and locker rooms that match their gender identity. Meanwhile, lawmakers in states such as South Carolina, North Carolina, Tennessee and Virginia are trying to legislate which bathrooms transgender people can use, arguing that they should stick to facilities that match their birth certificate sex. Proponents argue that the laws are about privacy and public safety. “I think it’s just inappropriate,” said North Carolina state Sen. David Curtis (R), of trans people choosing a facility based on their gender identity. “We have rules in our society, and that’s just one of the rules.” Conservative blogger Matt Walsh put it more bluntly: “If you have a daughter in public school, you should certainly be concerned that boys now have a ‘civil right’ to follow your daughter into the locker room or the bathroom.”

These fears reflect both the vulnerability we feel in bathrooms and our expectation that these spaces are, and should be, strictly divided by sex. That’s nothing new. Public restrooms have always been riddled with anxiety and conflict. They’ve been sites of panic over contagious diseases, scandalous revelations about lewd behavior and political struggles over “potty parity” between men and women. The current controversy is only the latest saga.

One reason public restrooms provoke such strong reactions: They’re hotbeds of anxiety already. They’re places where private behavior becomes shared, where taboo subjects cannot be escaped, where intimate body parts are exposed. We’re taught from an early age that excretion should be secret, spoken of euphemistically, if at all. (Bathroom shame ran so high in the 1950s that CBS refused to air the pilot for “Leave It to Beaver” until the show was scrubbed of a shot of a closed toilet bowl.) As the psychologist Erik Erikson argued, childhood toilet accidents humiliate us, making us feel defective and infantile. In public facilities, then, we are violating something we learned early and deeply. Of course we feel awkward, embarrassed or vulnerable.

To understand how deeply that anxiety runs, look at how many people are unable to even use public bathrooms. A surprisingly large proportion of us — as high as 15 percent, according to some studies — suffer an aversion to public urination or defecation. For some, it’s so bad that sufferers remain housebound; others carefully plan their days around their excretory schedule.

Milder forms of bashful bladder are also common. In a 1976 investigation, researchers observed how long men stood at a urinal before urinating. It depended, they found, on the proximity of a fellow user. The closer the peer, the longer the wait.

Public restrooms also force us to confront the disgusting reality of others. Psychological studies have shown that people find their own fecal smells less offensive than those of others. People exposed to these smells — one study employed fart spray, a staple of pranksters — were harsher in their moral judgments. Gut feelings of revulsion turn into a primal rejection that can be transferred to other people in the vicinity. Public lavatories are places where disgust is rife and people are primed to distrust one another.

The fight over trans bathrooms is also explained by another tenet of bathroom psychology: Public restrooms, segregated by gender, make people highly aware of the sexual divide. Look at toilet graffiti, known among scholars as “latrinalia.” Men’s toilet scribblings are often graphic and tend to be sexual, aggressive, insulting and bigoted. Women’s tend to be longer, and more grammatical, romantic and supportive. Virtually unique to female restrooms is the tradition of extended exchanges of advice and encouragement. Sisterhood has its limits, though, as one well-punctuated Texas graffito reveals: “Keep him, Donna, you whore.”

Things get particularly interesting when . . .

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Written by LeisureGuy

15 May 2016 at 5:11 pm

GPS tracking device catches major US recyclers exporting toxic e-waste

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Elizabeth Grossman reports in The Intercept:

A two-yea investigation of electronics recycling using GPS tracking devices has revealed that policies aimed at curtailing the trade in toxic e-waste have been unsuccessful, with nearly one third of the devices being exported to developing countries, where equipment is often dismantled in low-tech workshops — often by children — endangering workers, their families, and contaminating the surrounding environment.

A report from the Basel Action Network (BAN), a Seattle-based non-profit devoted to ending the trade in toxic waste, raises major questions about U.S. government e-waste policies and oversight as well as the voluntary programs the electronics recycling industry relies on to ensure that this equipment is handled responsibly. BAN’s early data has already resulted in one major recycler losing an important certification as a responsible e-waste handler and launched state investigations into possible hazardous waste violations. The data BAN obtained with these tracking devices also shows equipment left at Goodwill, with whom Dell partners for recycling, was also exported.

Knowing that e-waste exports were ongoing and frustrated by recent federal government commissioned reports suggesting that these exports had dropped dramatically, BAN decided to physically track devices sent for recycling. “In our view those reports underestimated the export flows,” said BAN’s executive director Jim Puckett. “So we decided if the government is not going to use tracking devices, we will.”

BAN installed 200 GPS tracking devices into “used, non-functional computer equipment that its research team delivered to publicly accessible e-waste recycling drop-off sites around the U.S.” This equipment was left for recycling in more than a dozen states across the country between July 1, 2014 and December 31, 2015; 149 devices went to recyclers, 49 to thrift stores (mainly Goodwill) and 2 to retailers.

“What we found out is that quite a large percentage of this equipment is flowing offshore,” said Puckett. “These are like little lie detectors that we put out there. They tell their story and they tell it dispassionately.”

As of this month, BAN has found that 65 of all those devices (or 32.5 percent of the equipment tracked) has been exported. Of that equipment, BAN estimates that 62 devices (or 31 percent of all the tracked equipment) were likely to be illegal shipments based on the laws in the countries or regions where the electronics ended up. Of the equipment left with commercial recyclers, 39 percent of the tracked equipment was exported. Of the 46 tracked devices sent to Goodwill stores, 7 (or 15 percent) were exported. This includes 6 (or 21 percent) of the 28 delivered to Dell Reconnect stores.

Most of this equipment went to Hong Kong. But others were tracked to 10 different countries that include . . .

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Written by LeisureGuy

11 May 2016 at 9:55 am


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