October 03, 2013

Some Online Journals Will Publish Fake Science, For A Fee

Many online journals are ready to publish bad research in exchange for a credit card number.

That's the conclusion of an elaborate sting carried out by Science, a leading mainline journal. The result should trouble doctors, patients, policymakers and anyone who has a stake in the integrity of science (and who doesn't?).

The business model of these "predatory publishers" is a scientific version of those phishes from Nigerians who want help transferring a few million dollars into your bank account.

To find out just how common predatory publishing is, Science contributor John Bohannon sent a deliberately faked research article 305 times to online journals. More than half the journals that supposedly reviewed the fake paper accepted it.

"This sting operation," Bohannan writes, reveals "the contours of an emerging Wild West in academic publishing."

Online scientific journals are springing up at a great rate. There are thousands out there. Many, such as PLoS One, are totally respectable. This "open access" model is making good science more accessible than ever before, without making users pay the hefty subscription fees of traditional print journals.

(It should be noted that Science is among these legacy print journals, charging subscription fees and putting much of its online content behind a pay wall.)

But the Internet has also opened the door to clever imitators who collect fees from scientists eager to get published. "It's the equivalent of paying someone to publish your work on their blog," Bohannan tells Shots.

These sleazy journals often look legitimate. They bear titles like the American Journal of Polymer Science that closely resemble titles of respected journals. Their mastheads often contain the names of respectable-looking experts. But often it's all but impossible to tell who's really behind them or even where in the world they're located.

Bohannan says his experiment shows many of these online journals didn't notice fatal flaws in a paper that should be spotted by "anyone with more than high-school knowledge of chemistry." And in some cases, even when one of their reviewers pointed out mistakes, the journal accepted the paper anyway — and then asked for hundreds or thousands of dollars in publication fees from the author.

A journalist with an Oxford University PhD in molecular biology, Bohannan fabricated a paper purporting to discover a chemical extracted from lichen that kills cancer cells. Its authors were fake too — nonexistent researchers with African-sounding names based at the fictitious Wassee Institute of Medicine in Asmara, a city in Eritrea.

With help from collaborators at Harvard, Bohannan made the paper look as science-y as possible – but larded it with fundamental errors in method, data and conclusions.

For starters, the purported new cancer drug was tested on cancer cells – but not healthy cells. So there's no way to tell whether its effect was cancer-specific, or if it's simply toxic to all cells.

A graph in the paper purports to show that the more lichen drug that was added to test tubes of cancer cells, the more effective it was at killing. But in fact the actual data show no such difference.

Bohannan says it wasn't easy to write a convincing fake. Initially he made the data "too crazy," he says. His Harvard collaborators worried it made the paper look too interesting. "So we rewrote it, making boring rookie mistakes," he says.

The final touch was to make the paper read as though it had been written by someone whose first language is not English. To do that, Bohannan used Google Translate to put it into French, then translated that version back into English.

In the end, the paper's fictitious authors got 157 acceptance letters and 98 rejections – a score of 61 percent. "That's way higher than I expected," Bohannan says. "I was expecting 10 or 15 percent, or worst case, a quarter accepted."

For the privilege of being published, the paper's authors were asked to send along a publishing fee of up to $3,100.

The highest density of acceptances was from journals based in India, where academics are under intense pressure to publish in order to get promotions and bonuses.To learn the location of online journals that accepted or rejected Bohannan's paper, see this interactive global map.

Bohannan says the exercise is a damning indictment of the way peer review works (or doesn't) at many online journals. Peer review is the time-honored system of having outside experts comb through submissions to identify flaws in method, data or conclusions. It's the way scientific journals do quality control.

"Peer review is in a worse state than anyone guessed," he says.

Bohannan says he doesn't mean to suggest that the whole business model of online open-access journals is a failure. "You can't conclude that from my experiment, because I didn't do the right control – submitting a paper to paid-subscription journals," he says.

As he acknowledges, it's not as if peer review is always up to snuff at subscription journals – even the top subscription journals have been embarrassed by lapses in their peer review processes. But he says online publishing makes poor-quality journals easier to set up. And the sheer volume of online publications these days makes it harder to distinguish between legitimate and shady journals.

Jeffrey Beall of the University of Colorado wasn't surprised in the least by the outcome of Bohannan's sting. "He basically found what I've been saying for years," he tells Shots.

A growing number of online open-access journals "are accepting papers just to earn publishing fees, and as a result science is being poisoned by a lot of bad articles," Beall says.

Beall, a research librarian, is a self-appointed watchdog over open-access publishing. He maintains a list of what he calls "predatory publishers" – those who "exploit the open-access model of publishing for their own profit."

He points out that online publishers operate under an incentive that's just the opposite of traditional scientific journals. Print journals have rigid constraints on how many articles they can publish, so they have to screen out all but the best. And they have subscribers to keep happy, so they have to cultivate reputations as curators of high-quality research.

But online journals don't have to worry about subscribers; they make their money by charging contributors – who have a strong incentive to get published. So "the more papers they publish the more money they make," Beall says.

Two big questions arise out of all this: What damage is done by publish-anything journals? And what can be done about it?

The potential damage is both far-reaching and difficult to quantify. Bohannan points out that universities and government agencies, particularly in developing countries, may hire researchers based on resumes packed with sleazy citations. Determining which of those CV entries is high-quality and which aren't is no easy task.

Beall notes that lawyers often use scientific citations in briefs and trials. Government officials draw on published research to set policy. Drug companies have a strong incentive to manipulate research to bolster their claims. And researchers may be led down futile paths on the basis of poor research.

As to what can be done, Beall says poor-quality research can probably only be driven out by naming and shaming.

Bohannan thinks there might be a sort of Consumer Reports to survey the quality of online journals and call out those that fall short. And he thinks maybe such an enterprise might regularly carry out stings like his to keep everyone in the field on their toes.


Cellist Matt Haimovitz made it big in the classical music scene as a little kid.
(Stephanie Mackinnon)
October 03, 2013

Studying The Science Behind Child Prodigies

Matt Haimovitz is 42 and a world-renowned cellist. He rushed into the classical music scene at age 10 after Itzhak Perlman, the famed violinist, heard him play.

"By the time I was 12, 13 years old I was on the road playing with Israel Philharmonic, New York Philharmonic and some of the great orchestras. So it was pretty meteoric," Haimovitz says. "I grew up with a lot of classical music in the household. My mother is a pianist and took me to many concerts."

But nothing in his family history explains where Haimovitz got his extraordinary talent. And that's typical, Ellen Winner, a psychology professor at Boston College who has studied prodigies, tells NPR's David Greene.

"People are fascinated by these children because they don't understand where it came from. You will see parents who say, 'I wasn't like this, my husband wasn't like this.' It seems to sometimes just come out of the blue," Winner says.

 

It's not clear whether a prodigy's brain is any different from the brain of other children, in part because there have been no studies comparing the brains of prodigies to those of average people.

"But I believe that anything that shows up so early, without training, has got to be either a genetic or some other biological basis," Winner says. "If a child suddenly at age 3 goes to the piano and picks out a tune and does it beautifully, that has to be because that child has a different brain."

Children who are extremely gifted tend to be socially different, too, Winner says. "They feel like they can't find other kids like themselves, so they feel kind of weird, maybe even like a freak, and feel like [they] don't have anybody to connect with."

Gifted children are more likely to be introverted, Winner says, and spend more time alone. "On the other hand, they also long to connect with other kids, and they can't find other kids like themselves."

For his part, Haimovitz says he didn't have many friends as a child, mainly because he was so focused on the music.

"There was no time afterwards to party. I would at the time practice four or five hours a day and I'd have to get my homework done, but I didn't feel like I was missing anything because this is what I wanted," he says. "I chose it. But certainly in terms of friendships, they've been few and intense."

As Haimovitz got older, his friendship with his best friend – his music – began to change. He became frustrated creatively. He wanted to play other kinds of music but felt constricted by the image and the expectations of the boy prodigy who played classical music and filled concert halls.

"When you start that early, you suddenly start to grow up in public, and I wanted to experiment," Haimovitz says.

So he took his cello into punk rock clubs and coffee houses. He played Bach and Haydn and Hendrix.

"My teacher, Leonard Rose, we never played any 20th-century music. He didn't like it. But once I was exposed to Jimi Hendrix, Miles Davis and others, I couldn't really turn back. I wanted to know more," he says.

Bow in hand, he even took a stab at Led Zeppelin.

What Haimovitz did may have been exceptional, even for a prodigy. Winner says as prodigies grow up, they struggle to advance their talents.

"The skill of being a child prodigy is the skill of mastering something that's already been invented – whether it's Western math, classical music or realistic drawing," Winner says. But adult creators actually do something in a new way. "That's a very different skill, and most prodigies do not make that leap."

It's also hard for prodigies to grow up and suddenly not be so special, she says.

Haimovitz says he's been able to navigate all of this. He has a very full life – a wife, two children and music.

"I rarely look back, honestly, because there's so much going on in the present and the future. But those moments when I am in the car and I happen to hear an old broadcast or recording, occasionally I am struck and say 'Wow, I did some good things back then,'" he says.

Winner says that it's often the adults in a prodigy's childhood who determine how they'll fare when they grow up.

"I think it all has to do with how many expectations were put on you as a child: You're a genius. You're going to be a genius when you grow up. That is really dangerous," she says.

"But if you say 'You're terrifically musical and you're going to have a wonderfully musical life,' that's a very different kind of message to give to kids, and a much more positive one."

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Dr. Kathleen Campbell
(SIU School of Medicine)
September 17, 2013

SIU Researcher Promotes Treatment For Hearing Loss

A researcher at Southern Illinois University is working on a pill that could restore hearing loss.

Dr. Kathleen Campbell, director of audiology research at SIU's School of Medicine, said the treatment involves a drug that "donates" electrons to make sure the hearing loss is not permanent. She said the U.S. Army is interested in her research and is involved in the clinical trial.

“The military is spending over $2 billion dollars a year for noise induced hearing loss and tinnitus,” Campbell said. “So, we would really like to reduce that so that these people who do serve our country do have good hearing in the long-run, but also from a financial standpoint for the U.S. government. The other thing is that hearing loss for the soldier on the battlefield increases their risk of mortality.”

Campbell noted that the treatment would not be a substitute for hearing protection, like earmuffs or earplugs.  If all goes well, she said the treatment could be widely available in five-to-six years.

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This may look like a mad scientist's garage sale, but it's actually the most precise clock ever built.
(Jim Burrus/NIST)
August 22, 2013

The World's Most Precise Clock Could Prove Einstein Wrong

What a makes a good clock? Andrew Ludlow, a physicist at the National Institute of Standards and Technology, says one of the most important criteria is stability.

"If you could imagine a grandfather clock and see the pendulum swinging back and forth, ideally that pendulum would swing back and forth very uniformly," Ludlow says. "Each swing would take exactly the same amount of time."

That's stability. But what if something perturbs the system, like a mischievous toddler?

"Imagine that toddler shaking the grandfather clock itself — that oscillation period could vary quite a bit," Ludlow says. "How much that ticking rate varies determines the precision with which you can measure the evolution of time."

Ludlow is a clockmaker, but his clocks don't have pendulums or gears. They are atomic clocks that rely on what Ludlow calls "the natural internal ticking of the atom."

Every atom of a given element has its own characteristic resonant frequency. The speed of that vibration is very consistent and very fast — there are quadrillions of "ticks" every second. Atomic-clock makers use the regularity of these vibrations to keep time with extreme accuracy.

Toddlers can't mess up these clocks, but there's still a little instability. Atoms move around, and that makes their vibrations slightly harder to measure. So Ludlow and his team used a lattice of lasers to trap the atoms and then cool them down. With the atoms frozen in place, the scientists could more accurately measure their vibration.

Ludlow's clock is 10 times more accurate than the last model. It's the most precise atomic clock ever built.

"Obviously getting to a meeting on time doesn't require this type of precision," Ludlow says. "But believe it or not, there's a number of both scientific and technical applications."

Better atomic clocks will facilitate more precise GPS and faster telecommunication networks. And some physicists are excited about another application: testing Einstein's Theory of Relativity.

"Today many scientists believe that the theory of relativity is incompatible with other physical theories," Ludlow says.

Einstein predicted that certain physical properties, like the strength of the interaction between photons and electrons, or the ratio of the mass of electrons and protons, should never change. But competing theories say that those "fundamental constants" might actually fluctuate and such changes would slightly influence the ticking speed of atomic clocks.

"As clocks become better and better, they become more and more useful tools to explore this possible variation," Ludlow says.

Einstein also predicted that clocks in different gravitational fields would tick at different speeds. For example, a clock in Boulder, Colo., which is a mile above sea level, would feel a slightly weaker gravitational pull than a clock at sea level in Washington, D.C. As a result, it would tick just a bit faster — and after 200,000 years it would be a full second ahead.

That's not much of an effect, but it's big enough for most atomic clocks to measure. And Ludlow's clock can register the change in gravity across a single inch of elevation. That kind of sensitivity will allow scientists to test Einstein's theories with greater precision in the real world.

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August 08, 2013

Study Ties Higher Blood Sugar To Dementia Risk

New research suggests a possible way to help prevent Alzheimer's disease, by keeping blood sugar at a healthy level. A study found that higher glucose levels, even those well short of diabetes, seemed to raise the risk for dementia.

Alzheimer's disease is the most common form of dementia, and doctors have long known that diabetes makes dementia more likely. The new study tracked blood sugar over many years in people with and without diabetes. Researchers found that the higher the blood sugar, the greater the chance that people would develop dementia, regardless of whether they had diabetes.

The work involved more than 2,000 people 65 and older in a Seattle-area health care system. Results are in Thursday's New England Journal of Medicine.


July 16, 2013

University of Illinois Researchers Build 'Vanishing' Tech Gear

Imagine this: There's no need to throw out your old cellphone, because it will self-destruct.

That's the idea behind a project at the University of Illinois at Urbana-Champaign, where researchers are investigating how to build electronics that vanish in water.

John Rogers is a professor of Materials Science and Engineering at the university. Rogers says the goal of the "born to die" program is to design transient technology that can dissolve at the end of its useful life, thus saving space in landfills and reducing waste.

The research team isn't there yet. But it has designed a chip built on a thin film of silk that dissolves when hit with water.

 


Crop consultant Dan Steiner inspects a field of corn near Norfolk, Nebraska.
(Dan Charles/NPR)
July 09, 2013

As Biotech Seed Falters, Insecticide Use Surges In Corn Belt

Across the Midwestern corn belt, a familiar battle has resumed, hidden in the soil.

On one side are tiny, white larvae of the corn rootworm. On the other side are farmers and the insect-killing arsenal of modern agriculture.

We've reported on earlier phases of this battle: The discovery of rootworms resistant to one type of genetically engineered corn, and an appeal from scientists for the government to limit the use of this new corn to preserve the effectiveness of its protection against rootworm.

It appears that farmers have gotten part of the message: Biotechnology alone will not solve their rootworm problems. But instead of shifting away from those corn hybrids, or from corn altogether, many are doubling down on insect-fighting technology, deploying more chemical pesticides than before. Companies like Syngenta or AMVAC Chemical that sell soil insecticides for use in corn fields are reporting huge increases in sales: 50 or even 100 percent over the past two years.

This is a return to the old days, before biotech seeds came along, when farmers relied heavily on pesticides. For Dan Steiner, an independent crop consultant in northeastern Nebraska, it brings back bad memories. "We used to get sick [from the chemicals]," he says. "We'd dig [in the soil] to see how the corn's coming along, and we didn't use the gloves or anything, and we'd kind of puke in the middle of the day. Well, I think we were low-dosing poison on ourselves!"

For a while, biotechnology came to his rescue. Biotech companies such as Monsanto spent many millions of dollars creating and inserting genes that would make corn plants poisonous to the corn rootworm but harmless to other creatures.

The first corn hybrids containing such a gene went on sale in 2003. They were hugely popular, especially in places like northeastern Nebraska where the rootworm has been a major problem. Sales of soil insecticides fell. "Ever since, I'm like, hey, we feel good every spring!" says Steiner.

But all along, scientists wondered how long the good times would last. Some argued that these genes — a gift of nature — were being misused. (For a longer explanation, read my post from two years ago.)

Those inserted genes, derived from genes in a strain of the bacterial Bacillus thuringiensis, worked well for a while. In fact, the Bt genes remain a rock-solid defense against one pest, the European corn borer.

In parts of Illinois, Iowa, Minnesota and Nebraska, though, farmers are running into increasing problems with corn rootworms.

"You never really know for sure, until that big rain with strong wind, and you get the phone call the next morning: 'What's going on out there?'" says Steiner.

Entire hillsides of corn, with no support from their eaten-away roots, may be blown flat.

Monsanto has downplayed such reports, blaming extraordinary circumstances. But in half a dozen universities around the Midwest, scientists are now trying to figure out whether, in fact, the Bt genes have lost their power.

At the University of Nebraska, entomologist Lance Meinke is turning colonies of rootworms loose on potted corn plants that contain different versions of the anti-rootworm gene, to see how well they survive.

The larvae get to feed on the corn roots for about two weeks. The soil from each pot then is dumped into a kind of steel container. If the larvae are still alive, a bright light will drive them into little glass jars filled with alcohol. "They try to escape from the heat," says David Wangila, a graduate student who is managing this experiment.

If the rootworm-fighting genes in the corn are working well, no larvae should emerge.

But some have. Wangila points to one of the little glass jars. Inside, there are three nice plump corn rootworm larvae.

This is not good. Those insects, originally collected from a cornfield in Nebraska, were feeding on corn that contained the first rootworm-fighting gene that Monsanto introduced ten years ago. Technically, it's known as the Cry 3Bb gene.

Meinke and Wangila will compare the survival rate of these rootworms with others that have never been exposed to Bt. They're looking for signs that rootworms in the corn fields of Nebraska have evolved resistance to genetically engineered crops.

An identical experiment in Iowa, carried out more than a year ago, found corn rootworms resistant to the Cry 3Bb gene.

Nobody knows how widely those insects have spread, but farmers aren't waiting to find out. Some are switching to other versions of biotech corn, containing anti-rootworm genes that do still work. Others are going back to pesticides.

Steiner, the Nebraska crop consultant, usually argues for another strategy: Starve the rootworms, he tells his clients. Just switch that field to another crop. "One rotation can do a lot of good," he says. "Go to beans, wheat, oats. It's the No. 1 right thing to do."

Insect experts say it's also likely to work better in the long run.

Meinke, who's been studying the corn rootworm for decades, tells farmers that if they plant just corn, year after year, rootworms are likely to overwhelm any weapon someday.

The problem, Meinke says, is that farmers are thinking about the money they can make today. "I think economics are driving everything," he says. "Corn prices have been so high the last three years, everybody is trying to protect every kernel. People are just really going for it right now, to be as profitable as they can."

As a result, they may just keep growing corn, fighting rootworms with insecticides — and there's a possibility that those chemicals will eventually stop working, too.

 
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July 03, 2013

Tiny Stem-Cell Livers Grown In Laboratory

Tiny functioning human livers have been grown from stem cells in the laboratory by scientists in Japan.

They said they were "gobsmacked" when liver buds, the earliest stage of the organ's development, formed spontaneously.

The team, reporting their findings in Nature, hope that transplanting thousands of liver buds could reverse liver failure.

Experts welcomed the findings, describing them as "exciting".

Scientists around the world are trying to grow organs in the lab to overcome a shortage of organ donors.

Some patients already have bladders made from their own cells, but dense solid organs such as the liver and kidneys are much harder to produce.

Grow your own

The team at the Yokohama City University were reproducing the earliest stages of liver development - similar to that in an embryo.

They had mixed three types of cells - two types of stem cells and material taken from the umbilical cord.

Unexpectedly, the cells began to organise themselves and appeared to curl up to form a liver bud.

These buds were transplanted into mice, where they hooked themselves up with the blood supply and began to function as little livers.

The transplants increased the lifespan of mice with liver failure.

Prof Takanori Takebe said: "We just simply mixed three cell types and found that they unexpectedly self-organise to form a three-dimensional liver bud - this is a rudimentary liver.

"And finally we proved that liver bud transplantation could offer therapeutic potential against liver failure."

He told the BBC that he was "completely gobsmacked" and "absolutely surprised" when he first witnessed the buds forming.

Treatment hope

It is thought that other organs such as the pancreas, kidneys and even the lungs could be developed in the same way. However, turning this into a treatment is still a distant prospect.

The buds are 4-5mm in length but the researchers say they would need to develop buds that are much smaller and could be injected into the blood.

The buds would not grow to be a whole new liver, but would embed themselves in the failing one and restore it.

Dr Varuna Aluvihare, a liver transplant physician at King's College Hospital in London, told BBC News: "This a great piece of work and as a proof of concept, very interesting.

"The real highlight is that such simple mixtures of cells can differentiate and organise themselves into highly complex tissue structures that function well in an animal model."

He said the liver was very damaged in chronic liver disease so there were still questions about where the buds were transplanted and how they would function.

The risk of a tumour developing after the transplant would also need to be assessed.

Dr Dusko Ilic, a stem cell scientist at King's College London, said: "The strategy is very promising, and represents a huge step forward.

"Although the promise of an off-the-shelf-liver seems much closer than one could hope even a year ago, the paper is only a proof of concept. There is much unknown and it will take years before it could be applied in regenerative medicine."

Prof Chris Mason, the chair of regenerative medicine at University College London, said there might be more immediate benefits for drug testing.

New medicines can be toxic to the human liver in a way which does not show up in animal tests. He said using liver buds might be a better way to test for toxicity.


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