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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

As Flint was slowly poisoned, Snyder’s inner circle failed to act

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Julie Mack, Ron Fonger, and John Counts report for

A year ago, Gov. Rick Snyder was stoking rumors of a presidential bid as a metrics-driven Republican whose ability to run government like a business transformed a troubled state.

But the leadership style so lauded a year ago — the emphasis on problem-solving over politics, the laser-like focus on the bottom line, the reliance on emergency financial managers to whip troubled cities into shape — has proven to be his undoing.

Now, he is viewed as the person ultimately responsible for one of the nation’s biggest public-health disasters in memory — the lead contamination of a water system serving 100,000 people, and a possible link between the water system and an outbreak of Legionnaire’s disease that killed 12 people.

Snyder has apologized repeatedly for the crisis and has vowed to fix Flint. But, to this day, he and his administration push a storyline that diminishes their role.

It has never been fully explained how crucial information didn’t reach the governor, or why the Snyder administration allowed the people of Flint to use undrinkable water for so long.

Red flags were being waved furiously for a year before Snyder took action, as Snyder’s top aides — including his chief of staff and his legal counsel — expressed concern to the governor about Flint water quality reports.

“If they weren’t passing along those assessments to the governor, that’s a huge problem,” said Eric Rothstein, a member of the Snyder-appointed Flint Water Advisory Task Force. “But, if they were passing along those assessments and the governor wasn’t taking action, that’s a huge problem, too.”

Snyder declined requests to be interviewed for this story, but his spokesman Ari Adler submitted written answers to questions from MLive.

“The Governor isn’t going to get into playing what-ifs on what staff could have or should have told him,” Adler wrote. “His focus is on fixing the problems in Flint and on changing direction on how we are doing things in state government, all the way up to the Executive Office.”

A team of MLive reporters conducted an investigation reviewing thousands of emails and other documents and interviewing numerous key players in an attempt to get to the bottom of what exactly happened in Flint.

That investigation shows the water crisis was an unintended consequence of the state’s takeover of Flint in 2011, after which a series of four emergency managers were given near-dictatorial powers so they could cut the city’s budget and bring the books in line.

Among the cost-saving measures: Change the city’s water supply and do it on the cheap.

Snyder was aware by fall 2014 that using the Flint River for the city’s water was causing serious water-quality issues. But, for the next 12 months, he and his administration saw fixing Flint’s finances as the higher priority.

In explaining the decision to continue using the Flint River for drinking water until October 2015, the governor said he was relying on DEQ’s false assurances that the water was safe. That was despite growing evidence to the contrary in the months leading up to Snyder’s acknowledgement of widespread lead contamination. . .

Continue reading.

The Governor seems strangely eager to avoid identifying responsibility for the mess and holding people accountable. I can think of one reason for that attitude. And the next sentence of the article:

The MLive investigation also found many of Snyder’s claims downplaying his administration’s role in the crisis are contradicted by the facts.

People who say that there should be no finger-pointing usually say that because they’re aware that the fingers would point at them.

Read the whole thing, an example of excellent US journalism.

Written by LeisureGuy

7 May 2016 at 12:33 pm

Science for sale: Philip Morris uses chemical industry consultants to perpetuate ‘light cigarette’ myth

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David Heath writes at the Center for Public Integrity:

In a landmark ruling nearly a decade ago, a federal judge ordered tobacco companies to stop lying.

After listening to 84 witnesses and perusing tens of thousands of exhibits, U.S. District Judge Gladys Kessler of the District of Columbia took a year to write a1,652-page opinion detailing the companies’ elaborate strategy to deny the harmful effects of smoking.

“In short, [the companies] have marketed and sold their lethal product with zeal, with deception, with a single-minded focus on their financial success, and without regard for the human tragedy or social costs that success exacted,” Kessler wrote in United States of America v. Philip Morris USA.

Kessler noted that the Justice Department, in a racketeering lawsuit, had presented “overwhelming evidence” of a conspiracy to defraud the public. She ordered the companies to take a number of actions, including ceasing to claim there was such a thing as a low-tar cigarette that reduced the risk of disease. The evidence showed this simply was not true.

Yet in about a dozen pending lawsuits, Philip Morris continues to do just that. It routinely argues that the nation’s top-selling cigarette, once known as Marlboro Lights and now called Marlboro Gold, reduces the risk of cancer.

To find scientists willing to make this claim, Philip Morris turned to consultants for the chemical industry. The experts Philip Morris hired work for firms whose scientists regularly contend in medical journals, courtrooms, and regulatory arenas that their clients’ chemical products pose little or no health risks to the public. The firms have been instrumental in delaying new regulations by criticizing the work of other scientists, and emphasizing the doubt inherent in health science. The resultant uncertainty has helped delay attempts by the U.S. Environmental Protection Agency to crack down on ubiquitous chemicals with known dangers, such as formaldehyde, arsenic, and hexavalent chromium.

The irony in this arrangement is that the tobacco industry pioneered such tactics. “The tobacco industry wrote the playbook for the rest of the industries,” said Matt Myers, president of the Campaign for Tobacco-Free Kids. “Whether it’s the chemical industry, whether its climate change … you see it in industry after industry.” Now, it’s hiring consultants who took its techniques and pushed them further in other industries, relying on their experience to contest the scientific consensus on the dangers of low-tar cigarettes.

The industry’s tactics continue to have catastrophic consequences. The Centers for Disease Control and Prevention attribute 480,000 deaths each year to smoking, equal to one in every five deaths. Since 1964, when the U.S. Surgeon General warned that smoking caused cancer, the government estimates that tobacco has killed more than 20 million Americans. That is 15 times the number of Americans who have perished in all wars combined. . .

Continue reading.

Do read the entire article. The degree of dishonesty is astonishing.

Written by LeisureGuy

5 May 2016 at 1:09 pm

Lead Water Pipes in 1900 Caused Higher Crime Rates in 1920

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Kevin Drum has an interesting post at Mother Jones:

Last year I wrote about a paper that looked at the relationship between childhood lead poisoning and violent crime rates in a whole new way. James Feigenbaum and Christopher Muller compared cities from the early 20th century that installed lead water pipes with those that installed iron pipes, and found that cities with lead pipes had higher homicide rates. Today, Josh Marshall alerts me to the fact that Feigenbaum and Muller have now published a final draft of their paper. The basic results are below:


As you can see, the effect is consistently positive. “Based on the lowest and highest point estimates,” the authors conclude, “cities that used lead pipes had between 14 and 36 percent higher homicide rates than cities that did not.” They present further versions of this chart with various controls added, but the results are largely the same. Overall, they estimate that cities with lead pipes had homicide rates 24 percent higher than cities with iron pipes.

As a check, they also examine the data to see if lead pipes are associated with higher death rates from cirrhosis and infant diarrhea, both of which have been linked with lead poisoning:

As expected, we observe large, positive, and statistically significant relationships between a city’s use of lead pipes and its rates of death from cirrhosis and infant diarrhea. Unexpectedly, we find that . . .

Continue reading.

Written by LeisureGuy

3 May 2016 at 3:32 pm

One minute a day of strenuous exercise has same health and fitness benefit as 45 minutes of moderate exercise

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Very interesting article in the NY Times by Gretchen Reynolds. The core:

. . . One group was asked to change nothing about their current, virtually nonexistent exercise routines; they would be the controls.

A second group began a typical endurance-workout routine, consisting of riding at a moderate pace on a stationary bicycle at the lab for 45 minutes, with a two-minute warm-up and three-minute cool down.

The final group was assigned to interval training, using the most abbreviated workout yet to have shown benefits. Specifically, the volunteers warmed up for two minutes on stationary bicycles, then pedaled as hard as possible for 20 seconds; rode at a very slow pace for two minutes, sprinted all-out again for 20 seconds; recovered with slow riding for another two minutes; pedaled all-out for a final 20 seconds; then cooled down for three minutes. The entire workout lasted 10 minutes, with only one minute of that time being strenuous.

Both groups of exercising volunteers completed three sessions each week for 12 weeks, a period of time that is about twice as long as in most past studies of interval training.

By the end of the study, published in PLOS One, the endurance group had ridden for 27 hours, while the interval group had ridden for six hours, with only 36 minutes of that time being strenuous.

But when the scientists retested the men’s aerobic fitness, muscles and blood-sugar control now, they found that the exercisers showed virtually identical gains, whether they had completed the long endurance workouts or the short, grueling intervals. In both groups, endurance had increased by nearly 20 percent, insulin resistance likewise had improved significantly, and there were significant increases in the number and function of certain microscopic structures in the men’s muscles that are related to energy production and oxygen consumption.

There were no changes in health or fitness evident in the control group. . .

The research was done by scientists at McMaster University in Hamilton, Ontario.

Written by LeisureGuy

27 April 2016 at 4:18 pm


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