After cardiac arrest, a final surge of brain activity could contain vivid experience, new research in rodents suggests.

sn-brain

What people experience as death creeps in—after the heart stops and the brain becomes starved of oxygen—seems to lie beyond the reach of science. But the authors of a new study on dying rats make a bold claim: After cardiac arrest, the rodents’ brains enter a state similar to heightened consciousness in humans. The researchers suggest that if the same is true for people, such brain activity could be the source of the visions and other sensations that make up so-called near-death experiences.

Estimated to occur in about 20% of patients who survive cardiac arrest, near-death experiences are frequently described as hypervivid or “realer-than-real,” and often include leaving the body and observing oneself from outside, or seeing a bright light. The similarities between these reports are hard to ignore, but the conversation about near-death experiences often bleeds into metaphysics: Are these visions produced solely by the brain, or are they a glimpse at an afterlife outside the body?

Neurologist Jimo Borjigin of the University of Michigan, Ann Arbor, got interested in near-death experiences during a different project—measuring the hormone levels in the brains of rodents after a stroke. Some of the animals in her lab died unexpectedly, and her measurements captured a surge in neurochemicals at the moment of their death. Previous research in rodents and humans has shown that electrical activity surges in the brain right after the heart stops, then goes flat after a few seconds. Without any evidence that this final blip contains meaningful brain activity, Borjigin says “it’s perhaps natural for people to assume that [near-death] experiences came from elsewhere, from more supernatural sources.” But after seeing those neurochemical surges in her animals, she wondered about those last few seconds, hypothesizing that even experiences seeming to stretch for days in a person’s memory could originate from a brief “knee-jerk reaction” of the dying brain.

To observe brains on the brink of death, Borjigin and her colleagues implanted electrodes into the brains of nine rats to measure electrical activity at six different locations. The team anesthetized the rats for about an hour, for ethical reasons, and then injected potassium chloride into each unconscious animal’s heart to cause cardiac arrest. In the approximately 30 seconds between a rat’s last heartbeat and the point when its brain stopped producing signals, the team carefully recorded its neuronal oscillations, or the frequency with which brain cells were firing their electrical signals.

The data produced by electroencephalograms (EEGs) of the nine rats revealed a highly organized brain response in the seconds after cardiac arrest, Borjigin and colleagues report online today in the Proceedings of the National Academy of Sciences. While overall electrical activity in the brain sharply declined after the last heartbeat, oscillations in the low gamma frequency (between 25 and 55 Hz) increased in power. Previous human research has linked gamma waves to waking consciousness, meditative states, and REM sleep. These oscillations in the dying rats were synchronized across different parts of the brain, even more so than in the rat’s normal waking state. The team also noticed that firing patterns in the front of the brain would be echoed in the back and sides. This so-called top-down signaling, which is associated with conscious perception and information processing, increased eightfold compared with the waking state, the team reports. When you put these features together, Borjigin says, they suggest that the dying brain is hyperactive in its final seconds, producing meaningful, conscious activity.

The team proposed that such research offers a “scientific framework” for approaching the highly lucid experiences that some people report after their brushes with death. But relating signs of consciousness in rat brains to human near-death experiences is controversial. “It opens more questions than it answers,” says Christof Koch, a neuroscientist at the Allen Institute for Brain Science in Seattle, Washington, of the research. Evidence of a highly organized and connected brain state during the animal’s death throes is surprising and fascinating, he says. But Koch, who worked with Francis Crick in the early 1980s to hypothesize that gamma waves are a hallmark of consciousness, says the increase in their frequency doesn’t necessarily mean that the rats were in a hyperconscious state. Not only is it impossible to project any mental experience onto these animals, but their response was also “still overlaid by the anesthesiology,” he says; this sedation likely influenced their brain response in unpredictable ways.

Others share Koch’s concerns. “There is no animal model of a near-death experience,” says critical care physician Sam Parnia of Stony Brook University School of Medicine in New York. We can never confirm what animals think or feel in their final moments, making it all but impossible to use them to study our own near-death experiences, he believes. Nonetheless, Parnia sees value in this new study from a clinical perspective, as a step toward understanding how the brain behaves right before death. He says that doctors might use a similar approach to learn how to improve blood flow or prolong electrical activity in the brain, preventing damage while resuscitating a patient.

Borjigin argues that the rat data are compelling enough to drive further study of near-death experiences in humans. She suggests monitoring EEG activity in people undergoing brain surgery that involves cooling the brain and reducing its blood supply. This procedure has prompted near-death experiences in the past, she says, and could offer a systematic way to explore the phenomenon.

read more here: http://news.sciencemag.org/brain-behavior/2013/08/probing-brain%E2%80%99s-final-moments

Thanks to Kebmodee for bringing this to the attention of the It’s Interesting community.

Monogamy may have evolved to keep baby-killers away

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Social monogamy – when a male and female of the species stick together for the long term, although may mate with others – is rare in mammals generally. However, it occurs in over a quarter of primate species, including humans, gibbons and many New World monkeys, such as titis.

To investigate what originally drove us to establish such pair bonds, a team led by Kit Opie of University College London and Susanne Shultz from the University of Manchester, UK, gathered data on the mating behaviour of 230 primate species. They selected behavioural traits associated with several possible evolutionary drivers of monogamy, including the risk of infanticide, the need for paternal care and the potential for guarding female mates.

Using data on the genetic relationships between the species, the team ran millions of computer simulations of the evolution of these traits to work out which came first.

All three were linked to the evolution of monogamy but only behaviours associated with infanticide actually preceded it, suggesting that this was the driver. Suckling infants are most likely to be killed by unrelated males, in order to bring the mother back into ovulation.

With pair-bonding in place, not only would a mother have a male to help protect the infant from marauding males, but there would then be the opportunity for the male to help care for it by providing extra resources. This means the infant can be weaned earlier, again reducing the chance of it being killed.

“Until recently, reconstructing how behaviour evolves has been very tricky as there are few behavioural traces in the fossil record. The statistical approach we have used allows us to bring the fossils to life and to understand the factors that have led to the evolution of monogamy in humans and other primates,” says Shultz.

Carel van Schaik, a primatologist at the University of Zurich in Switzerland says the results are solid but questions whether they can be extrapolated to humans. He says evidence suggests that humans were never really monogamous and that the monogamy we see today in many cultures is socially imposed.

Shultz counters that there is fossil evidence pointing to monogamy in australopithecines, the hominin genus from which modern humans descended.

“Although we suggest that infanticide may help explain the evolution of monogamy in humans, we do not argue that it is the only factor nor that monogamy is universal,” Shultz says. “I would suggest that where infanticide risk is high, as it would be with our ancestors, having a father provide protection and care would facilitate the evolution of the modern human extended childhood.”

Journal reference: PNAS, DOI: 10.1073/pnas.1307903110

‘Lost’ Medieval City Discovered Beneath Cambodian Jungle

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A lost city known only from inscriptions that existed some 1,200 years ago near Angkor in what is now Cambodia has been uncovered using airborne laser scanning.

The previously undocumented cityscape, called Mahendraparvata, is hidden beneath a dense forest on the holy mountain Phnom Kulen, which means “Mountain of the Lychees.”

The cityscape came into clear view, along with a vast expanse of ancient urban spaces that made up Greater Angkor, the large area where one of the largest religious monuments ever constructed — Angkor Wat, meaning “temple city” — was built between A.D. 1113 and 1150.

In a series of archaeological mapping projects, scientists had previously used remote sensing to map subtle traces of Angkor. Even so, dense vegetation now veils much of the complex, impenetrable to conventional remote-sensing techniques, the researchers noted.

In the new study, led by the Archaeology and Development Foundation’s (ADF) Phnom Kulen program, the team relied on airborne laser scanning, or LiDAR (light detection and ranging), to survey about 140 square miles (363 square kilometers) in northwestern Cambodia in 2012.

“LiDAR provides an unparalleled ability to penetrate dense vegetation cover and map archaeological remains on the forest floor,” the researchers wrote in an accepted manuscript submitted to the journal Proceedings of the National Academy of Sciences.

The survey revealed, “with exceptional clarity,” traces of planned urban spaces hidden beneath the dense forest surrounding the major temples of Angkor, they wrote. In addition, the researchers confirmed the existence of “a vast, low-density urban periphery stretching far beyond the major Angkorian temples.”

This low-density urban area suggests that rather than Angkor Thom being the central, walled-in city that some have suggested, it is just part of a more dispersed city with a densely populated area at its center.

“It’s the same sort of configuration as Los Angeles — so, a dense middle, but it consists of huge, sprawling suburbs connected by giant roads and canals in exactly the same way as the freeways link up Los Angeles,” said Roland Fletcher, of the University of Sydney.

Lost medieval city

To the north of central Angkor, the LiDAR data revealed a previously unknown city hidden beneath the forest, its roadways, temples and other urban infrastructure, etched into the surface of the holy Phnom Kulen mountain. The newfound cityscape would have existed between the eighth and ninth centuries (well before Angkor Wat) and seems to correspond to Mahendraparvata, one of the first capitals of the Khmer Empire. Until now, Mahendraparvata was known only from written inscriptions dating to A.D. 802, the researchers said.

When the LiDAR data revealed the elevation beneath Phnom Kulen’s dense vegetation, the researchers knew they had found something big.

“With this instrument — bang — all of a sudden, we saw an immediate picture of an entire city that no one knew existed, which is just remarkable,” Damien Evans, director of the University of Sydney’s archaeological research center in Cambodia, told Australia’s The Age.

Weird landscape

The LiDAR also revealed an entirely new class of Angkorian architecture, Fletcher said.

To the south of the Angkor Wat complex and dating to the 12th century, “there is a set of absolutely unique, very strange features, which we call rectilinear coils,” Fletcher told LiveScience. “They are like enormous embankments of sand with channels between them. They have no counterpart anywhere in Angkor; we’ve never seen the design of this sort before, and they’ve never been seen before in Angkorian architecture.”

Fletcher thinks the embankments represent gardens, but their exact purpose remains unknown. The channels would have carried water to the various plants and trees growing in the gardens, he suggested.

The research also involved French archaeologist and ADF program director Jean-­Baptiste Chevance, Christophe Pottier of the French School of the Far East (EFEO), and other scientists.

http://www.livescience.com/37520-lost-medieval-city-discovered-beneath-cambodian-jungle.html

As the Earth warms, 400 year old frozen plants are being revived

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Plants that were frozen during the “Little Ice Age” centuries ago have been observed sprouting new growth, scientists say. Samples of 400-year-old plants known as bryophytes have flourished under laboratory conditions. Researchers say this back-from-the-dead trick has implications for how ecosystems recover from the planet’s cyclic long periods of ice coverage. The findings appear in Proceedings of the National Academy of Sciences.

They come from a group from the University of Alberta, who were exploring an area around the Teardrop Glacier, high in the Canadian Arctic. The glaciers in the region have been receding at rates that have sharply accelerated since 2004, at about 3-4m per year. That is exposing land that has not seen light of day since the so-called Little Ice Age, a widespread climatic cooling that ran roughly from AD 1550 to AD 1850.

“We ended up walking along the edge of the glacier margin and we saw these huge populations coming out from underneath the glacier that seemed to have a greenish tint,” said Catherine La Farge, lead author of the study.

Bryophytes are different from the land plants that we know best, in that they do not have vascular tissue that helps pump fluids around different parts of the organism. They can survive being completely desiccated in long Arctic winters, returning to growth in warmer times, but Dr La Farge was surprised by an emergence of bryophytes that had been buried under ice for so long.

“When we looked at them in detail and brought them to the lab, I could see some of the stems actually had new growth of green lateral branches, and that said to me that these guys are regenerating in the field, and that blew my mind,” she told BBC News. “If you think of ice sheets covering the landscape, we’ve always thought that plants have to come in from refugia around the margins of an ice system, never considering land plants as coming out from underneath a glacier.”

But the retreating ice at Sverdrup Pass, where the Teardrop Glacier is located, is uncovering an array of life, including cyanobacteria and green terrestrial algae. Many of the species spotted there are entirely new to science.

“It’s a whole world of what’s coming out from underneath the glaciers that really needs to be studied,” Dr La Farge said.

“The glaciers are disappearing pretty fast – they’re going to expose all this terrestrial vegetation, and that’s going to have a big impact.”

http://www.bbc.co.uk/news/science-environment-22656239

Children with older fathers and grandfathers live longer

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Delaying fatherhood may offer survival advantages, say US scientists who have found children with older fathers and grandfathers appear to be “genetically programmed” to live longer.

The genetic make-up of sperm changes as a man ages and develops DNA code that favours a longer life – a trait he then passes to his children. The team found the link after analysing the DNA of 1,779 young adults. Their work appears in Proceedings of the National Academy of Sciences.

Experts have known for some time that lifespan is linked to the length of structures known as telomeres that sit at the end of the chromosomes that house our genetic code, DNA. Generally, a shorter telomere length means a shorter life expectancy. Like the plastic tips on shoelaces, telomeres protect chromosomal ends from damage. But in most cells, they shorten with age until the cells are no longer able to replicate.

However, scientists have discovered that in sperm, telomeres lengthen with age. And since men pass on their DNA to their children via sperm, these long telomeres can be inherited by the next generation. Dr Dan Eisenberg and colleagues from the Department of Anthropology at Northwestern University studied telomere inheritance in a group of young people living in the Philippines.

Telomeres, measured in blood samples, were longer in individuals whose fathers were older when they were born. The telomere lengthening seen with each year that the men delayed fatherhood was equal to the yearly shortening of telomere length that occurs in middle-aged adults. Telomere lengthening was even greater if the child’s paternal grandfather had also been older when he became a father. Although delaying fatherhood increases the risk of miscarriage, the researchers believe there may be long-term health benefits.

Inheriting longer telomeres will be particularly beneficial for tissues and biological functions that involve rapid cell growth and turnover – such as the immune system, gut and skin – the scientists believe. And it could have significant implications for general population health. “As paternal ancestors delay reproduction, longer telomere length will be passed to offspring, which could allow lifespan to be extended as populations survive to reproduce at older ages.”

Prof Thomas von Zglinicki, an expert in cellular ageing at Newcastle University, said more research was needed.

“Very few of the studies that linked telomere length to health in late life have studied the impact, if any, of paternal age. It is still completely unclear whether telomere length at conception (or birth) or rate of telomere loss with age is more important for age-related morbidity and mortality risk in humans. “The authors did not examine health status in the first generation offspring. It might be possible that the advantage of receiving long telomeres from an old father is more than offset by the disadvantage of higher levels of general DNA damage and mutations in sperm,” he said.

http://www.bbc.co.uk/news/health-18392873

Thanks to Kebmodee for bringing this to the attention of the It’s Interesting community.

Have scientists rendered the final word on penis size?

sn-penis

No man is an island, and it turns out neither is his penis. New research suggests that size does matter (sorry, guys), but the penis is only one (sometimes) small contributor to manly allure. A man’s overall attractiveness to a woman, researchers have found, depends in part on the trio of height, body shape, and penis size.

Although the assault of penis pill spam in your inbox might make you think that “bigger is better,” scientific research has returned mixed results. Some findings say that women prefer longer penises, others say they like wider ones, and still others report that size doesn’t matter at all.

Most of these studies had either asked women directly about their preferences or had them rate the attractiveness of different male figures that varied only in penis length. The penis doesn’t exist in a vacuum, though, and biologists led by Brian Mautz, who was then at the Australian National University in Acton, wondered how penis size interacts with other body traits that are usually considered attractive or manly.

Using data from a large study of Italian men, the researchers created 343 computer-generated male figures that varied in penis size, as well as in height and shoulder-to-hip ratio—traits that other research has linked to attractiveness and reproductive success. Mautz and colleagues turned the figures into short video clips and projected them, life-sized, onto a wall for viewing by 105 women. Each woman watched a random set of 53 figures and rated their attractiveness as potential sexual partners on a scale of 1 to 7.

“The first thing we found was that penis size influences male attractiveness,” Mautz says. “There’s a couple of caveats to that, and the first is that the relationship isn’t a straight line.” Rather than the attractiveness rating consistently improving with each jump in penis size, the team found what Mautz calls “an odd kink in the middle.” Attractiveness increased quickly until flaccid penis length reached 7.6 centimeters (about 3 inches) and then began to slow down, the team reports online today in the Proceedings of the National Academy of Sciences.

The reason, Mautz says, is that penis size isn’t the only thing that matters. It interacts with other traits, and its effect depends on whether those other traits are already attractive to begin with. If one of the model men was tall and had a masculine, V-shaped torso with broad shoulders and narrower hips, for example, he was considered more attractive than his shorter, stockier counterparts, regardless of penis size.

An increase in penis size was also a bigger benefit to attractiveness, and a smaller penis was less of a detriment, to the taller, fitter figures than it was to shorter or potato-shaped ones. For example, a model that was 185 cm tall (about 6 ft) with a 7-cm-long (about 3-in-long) penis got an average score for attractiveness. To get that same score, a model that was 170 cm (about 5’6″) needed a penis of about 11 cm (about 4.5 in) in length. Boost the taller guy’s penis by just about centimeter, and the shorter guy needs double that to keep up and get the same attractiveness score. After that, the shorter male pretty much can’t continue to compete. To really reap the benefits of a big penis, a guy needs to be attractive in the first place, Mautz says. If he isn’t, even the biggest penis in the world won’t do him that much good.

So have women been responsible for the male penis getting larger—at least over the course of evolution? That’s a distinct possibility, the researchers say. Women may have selected for larger penises because they’re linked to higher rates of female orgasm and sexual satisfaction, which may explain why the human penis is proportionally larger than those of our evolutionary cousins.

That size matters, and that it matters in the context of other traits, makes sense, because proportionate features are attractive, says Adam Jones, a biologist who studies sexual selection and mate choice at Texas A&M University in College Station and who was not involved in the work. But he cautions that projections on a wall are no substitute for real life. Just because a woman prefers a man with a large penis doesn’t mean that she’s going to find one. Outside the lab, there’s greater variation and more traits to consider, so penis size might not be as important. That’s good, Jones says, because hurdles like competition with other women and her own perceived attractiveness could place her with a man who comes up a little short.

http://news.sciencemag.org/sciencenow/2013/04/the-final-word-on-penis-size.html?ref=em

Thanks to Dr. Rajadhyaksha for bringing this to the attention of the It’s Interesting community.

Doubts about Johns Hopkins research have gone unanswered, scientist says

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Daniel Yuan, pictured at his home in Laurel, raised doubts for years about the work of his colleagues in a Johns Hopkins medical research lab. “The denial that I am hearing from almost everyone in the group as a consensus is troubling to me,” he wrote in one e-mail. In December 2011, after 10 years at the lab, he was fired.

By Peter Whoriskey
The Washington Post Published: March 11
The numbers didn’t add up.

Over and over, Daniel Yuan, a medical doctor and statistician, couldn’t understand the results coming out of the lab, a prestigious facility at Johns Hopkins Medical School funded by millions from the National Institutes of Health.

He raised questions with the lab’s director. He reran the calculations on his own. He looked askance at the articles arising from the research, which were published in distinguished journals. He told his colleagues: This doesn’t make sense.

“At first, it was like, ‘Okay — but I don’t really see it,’ ” Yuan recalled. “Then it started to smell bad.”

His suspicions arose as reports of scientific misconduct have become more frequent and critics have questioned the willingness of universities, academic journals and the federal government, which pays for much of the work, to confront the problem.

Eventually, the Hopkins research, which focused on detecting interactions between genes, would win wide acclaim and, in a coup for the researchers, space in the pages of Nature, arguably the field’s most prestigious journal. The medical school even issued a news release when the article appeared last year: “Studies Linked To Better Understanding of Cancer Drugs.”

What very few readers of the Nature paper could know, however, was that behind the scenes, Yuan’s doubts seemed to be having profound effects.

In August, Yu-yi Lin, the lead author of the paper, was found dead in his new lab in Taiwan, a puncture mark in his left arm and empty vials of sedatives and muscle relaxants around him, according to local news accounts — an apparent suicide.

And within hours of this discovery, a note was sent from Lin’s e-mail account to Yuan. The e-mail, which Yuan saved, essentially blamed him for driving Lin to suicide. Yuan had written to Nature’s editors, saying that the paper’s results were overstated and that he found no evidence that the analyses described had actually been conducted. On the day of his death, Lin, 38, the father of three young daughters, was supposed to have finished writing a response to Yuan’s criticisms.

The subject line of the e-mail to Yuan, sent by an unknown person, said “your happy ending.”

“Yu-yi passed away this morning. Now you must be very satisfied with your success,” the e-mail said.

Yuan said he was shocked by the note, so much so that he began to shake.

But in the seven months since, he has wondered why no one — not the other investigators on the project, not the esteemed journal, not the federal government — has responded publicly to the problems he raised about the research.

The passions of scientific debate are probably not much different from those that drive achievement in other fields, so a tragic, even deadly dispute might not be surprising.

But science, creeping ahead experiment by experiment, paper by paper, depends also on institutions investigating errors and correcting them if need be, especially if they are made in its most respected journals.

If the apparent suicide and Yuan’s detailed complaints provoked second thoughts about the Nature paper, though, there were scant signs of it.

The journal initially showed interest in publishing Yuan’s criticism and told him that a correction was “probably” going to be written, according to e-mail rec­ords. That was almost six months ago. The paper has not been corrected.

The university had already fired Yuan in December 2011, after 10 years at the lab. He had been raising questions about the research for years. He was escorted from his desk by two security guards.

More recently, a few weeks after a Washington Post reporter began asking questions, a university spokeswoman said that a correction had been submitted to Nature and that it was under review.

“Your questions will be addressed with that publication,” a spokeswoman for the Hopkins medical school, Kim Hoppe, wrote in an e-mail.

Neither the journal nor the university would disclose the nature of the correction.

Hoppe declined an opportunity to have university personnel sit for interviews.

In the meantime, the paper has been cited 11 times by other published papers building on the findings.

It may be impossible for anyone from outside to know the extent of the problems in the Nature paper. But the incident comes amid a phenomenon that some call a “retraction epidemic.”

Last year, research published in the Proceedings of the National Academy of Sciences found that the percentage of scientific articles retracted because of fraud had increased tenfold since 1975.

The same analysis reviewed more than 2,000 retracted biomedical papers and found that 67 percent of the retractions were attributable to misconduct, mainly fraud or suspected fraud.

“You have a lot of people who want to do the right thing, but they get in a position where their job is on the line or their funding will get cut, and they need to get a paper published,” said Ferric C. Fang, one of the authors of the analysis and a medical professor at the University of Washington. “Then they have this tempting thought: If only the data points would line up . . . ”

Fang said retractions may be rising because it is simply easier to cheat in an era of digital images, which can be easily manipulated. But he said the increase is caused at least in part by the growing competition for publication and for NIH grant money.

He noted that in the 1960s, about two out of three NIH grant requests were funded; today, the success rate for applicants for research funding is about one in five. At the same time, getting work published in the most esteemed journals, such as Nature, has become a “fetish” for some scientists, Fang said.

In one sense, the rise in retractions may mean that the scientific enterprise is working — bad work is being discovered and tossed out. But many observers note that universities and journals, while sometimes agreeable to admitting small mistakes, are at times loath to reveal that the essence of published work was simply wrong.

“The reader of scientific information is at the mercy of the scientific institution to investigate or not,” said Adam Marcus, who with Ivan Oransky founded the blog Retraction Watch in 2010. In this case, Marcus said, “if Hopkins doesn’t want to move, we may not find out what is happening for two or three years.”

The trouble is that a delayed response — or none at all — leaves other scientists to build upon shaky work. Fang said he has talked to researchers who have lost months by relying on results that proved impossible to reproduce.

Moreover, as Marcus and Oransky have noted, much of the research is funded by taxpayers. Yet when retractions are done, they are done quietly and “live in obscurity,” meaning taxpayers are unlikely to find out that their money may have been wasted.

Johns Hopkins University typically receives more than $600 million a year from NIH, according to NIH figures.

For someone who has taken on a battle with Johns Hopkins and Nature, Yuan is strikingly soft-spoken.

He grew up in Gainesville, Fla., and attended MIT and then medical school at Johns Hopkins. He worked briefly as a pediatrician and an assistant professor of pediatrics before deciding that he preferred pure research. He has a wife and two kids and is an accomplished violinist.

In 2001, he joined the lab of Jef Boeke, a Hopkins professor of molecular biology and genetics. Boeke’s work on the yeast genome is, as academics put it, “highly cited” — that is, other papers have used some of his articles numerous times for support. Last year, he was named a member of the prestigious American Academy of Arts and Sci­ences.

The lab’s research focused on developing a methodology for finding evidence of genes interacting, primarily in the yeast genome and then in the human genome. Genetic interactions are prized because they yield insights into the traits of the genes involved.

During Yuan’s time there, the lab received millions in NIH funding, and according to internal e-mails, the people in the lab were under pressure to show results. Yuan felt the pressure, too, he says, but as the point person for analyzing the statistical data emerging from the experiments, he felt compelled to raise his concerns.

As far back as 2007, as the group was developing the methodology that would eventually form the basis of the Nature paper, Yuan wrote an anguished e-mail to another senior member of the lab, Pamela Meluh.

“I continue to be in a state of chronic alarm,” he wrote in August 2007. “The denial that I am hearing from almost everyone in the group as a consensus is troubling to me.”

Meluh quickly wrote back: “I have the same level of concern as you in terms of data quality, but I have less basis to think it can be better. . . . I’m always torn between addressing your and my own concerns and being ‘productive.’ ”

Then Boeke weighed in, telling Yuan that if he could improve the data analysis, he should, but that “the clock is ticking.”

“NIH has already given us way more time than we thought we needed and at some point we’ve got to suck it up and run with what we have,” Boeke wrote to Meluh and Yuan.

A few years later, another deadline was looming, and Elise Feingold, an NIH administrator, wanted to know what the lab had accomplished.

“I do need some kind of progress report on what you have been doing the past two years . . . and what you think you can accomplish with these funds,” she wrote to Boeke.

Citing Feingold’s message, ­Meluh wrote to Yuan, asking for help in explaining what the lab had produced. Its members had worked diligently, Yuan says, but hadn’t arrived at the kind of significant findings that generally produce scientific papers.

“I want to make it look like we’ve been busy despite lack of publications,” Meluh wrote.

Meluh did not respond to a request for an interview. Boeke referred questions to the university’s public relations team, which declined to comment further. An NIH official declined to comment.

While Yuan was growing increasingly skeptical of the lab’s methodology, Yu-yi Lin, who was also working at the lab, was trying to extend it. In the past, it had been applied to the yeast genome; Lin would extend it to the human genome — and this would become the basis of the Nature paper.

Lin, who was from Taiwan, was an up-and-comer. As a graduate student at Johns Hopkins just a few years before, he’d won an award for his work in cell metabolism and aging. He was also arranging for a prestigious spot at National Taiwan University.

At one point, when he was still at the Boeke lab at Hopkins, Lin asked Yuan to help analyze the data that would become the basis for the Nature paper, Yuan says. Yuan said he declined to get involved because he thought the methodology still had deep flaws.

Interactions between Lin and Yuan at the lab were few, Yuan said, and at any rate, Yuan had other things to worry about. He was slowly being forced out. He was demoted in 2011 from research associate to an entry-level position. A disagreement over whether Yuan should have asked Boeke if he wanted a byline on a paper erupted into further trouble, e-mail and other records show.

The Johns Hopkins spokeswoman, Hoppe, declined to discuss Yuan’s job termination.

On Dec. 15, 2011, Yuan was forced to leave the lab. He wasn’t allowed to make copies of his cell collection. He spent the next month trying to keep his mind busy. He read books about JavaScript and Photoshop, which he thought would enrich his research abilities. As he looked for other research jobs, he sensed that he had been blackballed.

Then, in February 2012, the Nature paper was published.

The research was a “profound achievement” that would “definitely be a great help to solve and to treat many severe diseases,” according to a news release from National Taiwan University, where Lin was now working.

Upon reading it, Yuan said, he was astonished that Lin had used what he considered a flawed method for finding genetic interactions. It had proved troublesome in the yeast genome, he thought. Could it have possibly been more reliable as it was extended to the human genome?

Lin, Boeke and their co-authors reported discovering 878 genetic interactions, or “hits.”

But Yuan, who was familiar with the data and the statistics, reanalyzed the data in the paper and concluded that there was essentially no evidence for any more than a handful of the 878 genetic interactions.

One of the key problems, Yuan wrote to the Nature editors, was that the numerical threshold the investigators used for determining when a hit had arisen was too low. This meant they would report far more hits than there actually were.

Yuan also calculated that, given the wide variability in the data and the relative precision required to find a true hit, it would have been impossible to arrive at any conclusions at all. By analogy, it would be like a pollster declaring a winner in an election when the margin of error was larger than the difference in the polling results.

“The overwhelming noise in the . . . data and the overstated strength of the genetic interactions together make it difficult to reconstruct any scientific process by which the authors could have inferred valid results from these data,” Yuan wrote to the editors of Nature in July.

His analysis attacks only the first portion of the paper; even if he is correct, the second part of the paper could be true.

Nevertheless, Yuan wanted Nature to publish his criticism, and following instructions from the journal, he forwarded his letter to Boeke and Lin, giving them two weeks to respond.

Just as the two weeks were to elapse, Boeke wrote to Nature asking for an extension of time — “a couple weeks or more” — to address Yuan’s criticism. Boeke explained that end-of-summer schedules and the multiple co-authors made it difficult to respond on time.

A day later, Lin was discovered dead in his office at National Taiwan University.

“Renowned scientist found dead, next to drug bottles,” the headline in the Taipei Times said.

Even in his death, the Nature paper was a kind of shorthand for Lin’s scientific success.

“A research team [Lin] led was featured in the scientific journal Nature in February for their discovery of the key mechanism for maintaining cell energy balance — believed to be linked to cellular aging and cancer,” the newspaper said.

If there was a suicide note, it has not been made public, and it is difficult to know what went through Lin’s mind at the end of his life. The apparent suicide and the e-mail to Yuan suggest only that Lin may have been distraught over the dispute; they do not prove that he acted improperly.

Shortly after the Nature paper appeared, Yuan hired lawyer Lynne Bernabei to challenge the way he was terminated at Hopkins.

In late August, Yuan asked the Nature editors again whether they would publish his criticism. Lin was dead, but Boeke and the others had had a month to respond, and Yuan hadn’t heard a thing.

On Sept. 28, a Nature editor informed Yuan by e-mail that the journal was still waiting on a fuller response from Boeke and that “experiments are being done and probably a Correction written.”

Such a correction has not appeared.

So as a last attempt, he figured he’d try the federal government, which paid for much of the research. But the government suggested that the threat to the federal research, if there was any, ended with Lin’s death.

“It is our understanding that these allegations are being investigated by Johns Hopkins University,” said the letter from the Office of Research Integrity.

Besides, it noted, the person responsible for the paper was Lin.

“Deceased respondents no longer pose a risk,” the letter said.

http://www.washingtonpost.com/business/economy/doubts-about-johns-hopkins-research-have-gone-unanswered-scientist-says/2013/03/11/52822cba-7c84-11e2-82e8-61a46c2cde3d_story_4.html

Thanks to Kebmodee for bringing this to the attention of the It’s Interesting community.

Microbes discovered to be thriving high in the atmosphere

sn-atmosphere

Each year, hundreds of millions of metric tons of dust, water, and humanmade pollutants make their way into the atmosphere, often traveling between continents on jet streams. Now a new study confirms that some microbes make the trip with them, seeding the skies with billions of bacteria and other organisms—and potentially affecting the weather. What’s more, some of these high-flying organisms may actually be able to feed while traveling through the clouds, forming an active ecosystem high above the surface of the Earth.

The discovery came about when a team of scientists based at the Georgia Institute of Technology in Atlanta hitched a ride on nine NASA airplane flights aimed at studying hurricanes. Previous studies carried out at the tops of mountains hinted that researchers were likely to find microorganisms at high altitudes, but no one had ever attempted to catalog the microscopic life floating above the oceans—let alone during raging tropical storms. After all, it isn’t easy to take air samples while your plane is flying through a hurricane.

Despite the technical challenges, the researchers managed to collect thousands upon thousands of airborne microorganisms floating in the troposphere about 10 kilometers over the Caribbean, as well as the continental United States and the coast of California. Studying their genes back on Earth, the scientists counted an average of 5100 bacterial cells per cubic meter of air, they report in the Proceedings of the National Academy of Sciences. Although the researchers also captured various types of fungal cells, the bacteria were over two orders of magnitude more abundant in their samples. Well over 60% of all the microbes collected were still alive.

The researchers cataloged a total of 314 different families of bacteria in their samples. Because the type of genetic analysis they used didn’t allow them to identify precise species, it’s not clear if any of the bugs they found are pathogens. Still, the scientists offer the somewhat reassuring news that bacteria associated with human and animal feces only showed up in the air samples taken after Hurricanes Karl and Earl. In fact, these storms seemed to kick up a wide variety of microbes, especially from populated areas, that don’t normally make it to the troposphere.

This uptick in aerial microbial diversity after hurricanes supports the idea that the storms “serve as an atmospheric escalator,” plucking dirt, dust, seawater, and, now, microbes off Earth’s surface and carrying them high into the sky, says Dale Griffin, an environmental and public health microbiologist with the U.S. Geological Survey in St. Petersburg, Florida, who was not involved in the study.

Although many of the organisms borne aloft are likely occasional visitors to the upper troposphere, 17 types of bacteria turned up in every sample. Researchers like environmental microbiologist and co-author Kostas Konstantinidis suspect that these microbes may have evolved to survive for weeks in the sky, perhaps as a way to travel from place to place and spread their genes across the globe. “Not everybody makes it up there,” he says. “It’s only a few that have something unique about their cells” that allows them survive the trip.

The scientists point out that two of the 17 most common families of bacteria in the upper troposphere feed on oxalic acid, one of the most abundant chemical compounds in the sky. This observation raises the question of whether the traveling bacteria might be eating, growing, and perhaps even reproducing 10 kilometers above the surface of Earth. “That’s a big question in the field right now,” Griffin says. “Can you view [the atmosphere] as an ecosystem?”

David Smith, a microbiologist at NASA’s Kennedy Space Center in Florida, warns against jumping to such dramatic conclusions. He also observed a wide variety of microbes in the air above Oregon’s Mount Bachelor in a separate study, but he believes they must hibernate for the duration of their long, cold trips between far-flung terrestrial ecosystems. “While it’s really exciting to think about microorganisms in the atmosphere that are potentially making a living, there’s no evidence of that so far.”

Even if microbes spend their atmospheric travels in dormancy, that doesn’t mean they don’t have a job to do up there. Many microbial cells are the perfect size and texture to cause water vapor to condense or even form ice around them, meaning that they may be able to seed clouds. If these microorganisms are causing clouds to form, they could be having a substantial impact on the weather. By continuing to study the sky’s microbiome, Konstantinidis and his team hope to soon be able to incorporate its effects into atmospheric models.

http://news.sciencemag.org/sciencenow/2013/01/microbes-survive-and-maybe-thriv.html

Sunlight stimulates release of carbon dioxide in melting permafrost

la-sci-sn-carbon-sunlight-permafrost-20130211-001

By Monte Morin, Los Angeles Times

Ancient plant and animal matter trapped within Arctic permafrost can be converted rapidly into climate-warming carbon dioxide when melted and exposed to sunlight, according to a new study.

In a report published Monday in the Proceedings of the National Academy of Sciences, a team of environmental and biological scientists examined 27 melting permafrost sites in Alaska and found that bacteria converted dissolved organic carbon materials into the greenhouse gas CO2 40% faster when exposed to ultraviolet light.

Study authors said that while it remained unclear just how much CO2 would be released as Arctic permafrost continues to melt, the findings were cause for concern. High latitude soils currently store twice the amount of carbon than is found in the atmosphere.

“What we can say now is that regardless of how fast the thawing of the Arctic permafrost occurs, the conversion of this soil carbon to carbon dioxide and its release into the atmosphere will be faster than we previously thought,” senior author George Kling, a University of Michigan ecologist and aquatic biogeochemist, said in a statement.

“That means permafrost carbon is potentially a huge factor that will help determine how fast the Earth warms,” Kling said.

Plant and animal matter has remained locked in frozen Arctic soils for thousands of years. When those soils begin to thaw, however, the organic matter begins to decay. As that matter decays, it is eaten by microbes, which produce either methane or CO2 as a byproduct. Methane — an even more powerful greenhouse gas than CO2 — occurs when the decaying matter is not exposed to oxygen.

Study authors examined melt water in so-called thermokarst impacted areas. Thermokarsts occur when long-frozen earth melts and the soil collapses into a sink-hole or causes a landslide.

As the permafrost melts, organic matter is dissolved in the melt water and exposed to sunlight in streams or pools.

Authors found that the rate of CO2 conversion slowed at night, or during cloudy conditions.

“Although no estimates exist for what percentage of now-frozen carbon will be released to the surface as the Arctic warms, the alteration and fate of this carbon will depend on its susceptibility to coupled photobiological processing and the available light,” wrote study lead author Rose Cory, an assistant professor of environmental sciences and engineering at the University of North Carolina.

http://www.latimes.com/news/science/sciencenow/la-sci-sn-carbon-sunlight-permafrost-20130211,0,5550833.story

Thanks to Ray Gaudette for bringing this to the attention of the It’s Interesting community.

Adelie penguins: cool, efficient killing machines

Handout of an Adelie penguin carrying a video camera on its back stands in Langhovde
An Adelie penguin carrying a video camera on its back stands in Langhovde, Antarctica January 7, 2012, in this handout photo released by Japan’s National Institute of Polar Research’s Assistant Professor Yuuki Watanabe on January 23, 2013. REUTERS/Yuuki Watanabe/National Institute of Polar Research/Handout

Fish of the Antarctic, be very afraid. There’s an unlikely stealth predator on the loose – Adelie penguins.

Forget their ungainly waddling on land or comical bobbing at the ocean’s surface. As soon as these penguins dive into the icy Antarctic ocean, they become calculating, efficient killing machines, say Japanese researchers.

“You could say the penguins have an amazing stealth mode,” said Yuuki Watanabe, a researcher at Japan’s National Institute of Polar Research. “They’re great at sneaking up on their prey and taking them unaware.”

Watanabe this week released footage recorded in December 2010 showing a bird’s eye view of a hunt for fish and small crustaceans called krill, captured using a small video camera strapped to the backs of more than a dozen penguins.

“The krill wiggle their bodies about, they clearly make an attempt to swim off at full speed and escape,” Watanabe said of his findings, published in the U.S.-based Proceedings of the National Academy of Sciences this week.

“But that doesn’t make the slightest difference to the penguins. They just gobble up the krill that are trying to get away and swallow them whole.”

Using the “penguin cams,” which were set to automatically switch on when a penguin entered the water and shoot for 90 minutes, Watanabe and his team were able to capture the secrets of penguins on the hunt.

Additional information came from two accelerometers strapped to each bird that measured its head and body movements to calculate how fast it devoured its prey.

“We didn’t really know if the penguins caught krill one-by-one. I’d thought that maybe they just got into their stomachs when they were after some other prey,” Watanabe said. “But when we saw the footage it turned out the penguins were doing just that, eating these tiny little creatures one after the other.”

Not only that, the penguins didn’t swim randomly but hung poised on the edge of the ice until a thick swarm neared, then swooped into the water. Footage showed a penguin zooming under the ice and then deeper, its head snapping rapidly up as it fed.

The krill killing-rate was both fast and efficient. The penguins gobbled an average of two krill per second when the krill were clustered in swarms, a much faster rate than under general hunting conditions when the penguins consumed about 244 krill in roughly 90 minutes.

“I was so happy when I got the footage of a penguin going straight into a swarm of krill and gorging itself,” Watanabe said.

Penguin research completed, Watanabe now aims to repeat the same exercise with sharks.

http://www.newsdaily.com/stories/bre90n04i-us-japan-penguins-stealth/