science

The CDC on Antibiotic-Resistant Infections in America

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A troubling new report from the CDC estimates that in the United States, more than two million people are sickened every year with antibiotic-resistant infections, with at least 23,000 dying as a result . The estimates are based on conservative assumptions and are likely minimum estimates. From the report:

Each year in the United States, at least 2 million people acquire serious infections with
bacteria that are resistant to one or more of the antibiotics designed to treat those
infections. At least 23,000 people die each year as a direct result of these antibiotic-resistant infections. Many more die from other conditions that were complicated by an antibioticresistant infection.

In addition, almost 250,000 people each year require hospital care for Clostridium difficile (C. difficile) infections. In most of these infections, the use of antibiotics was a major contributing factor leading to the illness. At least 14,000 people die each year in the United States from C. difficile infections. Many of these infections could have been prevented .

Antibiotic-resistant infections add considerable and avoidable costs to the already
overburdened U .S . healthcare system . In most cases, antibiotic-resistant infections require prolonged and/or costlier treatments, extend hospital stays, necessitate additional doctor visits and healthcare use, and result in greater disability and death compared with infections that are easily treatable with antibiotics . The total economic cost of antibiotic resistance to the U .S . economy has been difficult to calculate . Estimates vary but have ranged as high as $20 billion in excess direct healthcare costs, with additional costs to society for lost productivity as high as $35 billion a year (2008 dollars) .

Here is one important point: taking antibiotics when it they are not needed can lead to the development of antibiotic resistance. When resistance develops, antibiotics may not be able to stop future infections . Every time someone takes an antibiotic they don’t need, they increase their risk of developing a resistant infection in the future.

The New York Times raises this point:

One point of contention has been the extent to which industrial-scale animal farming contributes to the problem of antibiotic-resistant infections in humans. The government has estimated that more than 70 percent of antibiotics in the United States are given to animals. Companies use them to prevent sickness when animals are packed together in ways that breed infection. They also use them to make animals grow faster, though federal authorities are trying to stop that.

A note on MRSA (page 77 in the report):

Infections from one of the most pervasive types of drug-resistant bacteria tracked in the report, MRSA, have been declining. Invasive MRSA infections in hospitals went down by more than half from 2005 to 2011, according to a paper published Monday in the journal JAMA Internal Medicine. However, the number of invasive MRSA infections picked up outside health care settings has not changed much, and researchers pointed out that the number of those types of infections has for the first time outstripped the number acquired in hospitals.

Beauty is in the Eye of the Beer Holder

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These are always fun: the Ig Nobel Prizes. The winners for 2013 were announced yesterday. The big winner is a study on our perception of our own attractiveness after drinking. People have long observed that drunk people think others are more attractive but the Ig Nobel winner was the first study to find that drinking makes people think they are more attractive themselves.

The full list of 2013 Ig Nobel winners, per BBC:

Medicine Prize: Masateru Uchiyama, Gi Zhang, Toshihito Hirai, Atsushi Amano, Hisashi Hashuda (Japan), Xiangyuan Jin (China/Japan) and Masanori Niimi (Japan/UK) for assessing the effect of listening to opera on mice heart transplant patients.

Psychology Prize: Laurent Bègue, Oulmann Zerhouni, Baptiste Subra, and Medhi Ourabah, (France), Brad Bushman (USA/UK/, the Netherlands/Poland) for confirming that people who think they are drunk also think they are more attractive.

Joint Prize in Biology and Astronomy: Marie Dacke (Sweden/Australia), Emily Baird, Eric Warrant (Sweden/Australia/Germany], Marcus Byrne (South Africa/UK) and Clarke Scholtz (South Africa), for discovering that when dung beetles get lost, they can navigate their way home by looking at the milky way.

Safety Engineering Prize: The late Gustano Pizzo (US), for inventing an electro-mechanical system to trap airplane hijackers. The system drops a hijacker through trap doors, seals him into a package, then drops the hijacker through the airplane’s specially-installed bomb bay doors through which he is parachuted to the ground where police, having been alerted by radio, await his arrival.

Physics Prize: Alberto Minetti (Italy/UK/Denmark/Switzerland), Yuri Ivanenko (Italy/Russia/France), Germana Cappellini, Francesco lacquaniti (Italy) and Nadia Dominici (Italy/Switzerland), for discovering that some people would be physically capable of running across the surface of a pond – if those people and that pond were on the Moon.

Chemistry Prize: Shinsuke Imai, Nobuaki Tsuge, Muneaki Tomotake, Yoshiaki Nagatome, Hidehiko Kumgai (Japan) and Toshiyuki Nagata (Japan/Germany), for discovering that the biochemical process by which onions make people cry is even more complicated than scientists previously realised.

Archaeology Prize: Brian Crandall (US) and Peter Stahl (Canada/US), for observing how the bones of a swallowed dead shrew dissolves inside the human digestive system

Peace Prize: Alexander Lukashenko, president of Belarus, for making it illegal to applaud in public, and to the Belarus State Police, for arresting a one-armed man for applauding.

Probability Prize: Bert Tolkamp (UK/the Netherlands), Marie Haskell, Fritha Langford. David Roberts, and Colin Morgan (UK), for making two related discoveries: First, that the longer a cow has been lying down, the more likely that cow will soon stand up; and second, that once a cow stands up, you cannot easily predict how soon that cow will lie down again.

Public Health Prize: Kasian Bhanganada, Tu Chayavatana, Chumporn Pongnumkul, Anunt Tonmukayakul, Piyasakol Sakolsatayadorn, Krit Komaratal, and Henry Wilde (Thailand), for the medical techniques of penile re-attachment after amputations (often by jealous wives). Techniques which they recommend, except in cases where the amputated penis had been partially eaten by a duck.

Thank you, science!

On Compatibility Genes: Can You Smell the Perfect Partner?

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The Guardian on whether humans have the ability to smell out suitable partners/mates, based on an upcoming book by Daniel M. Davis, The Compatibility Gene: How Our Bodies Fight Disease, Attract Others, and Define Our Selves:

The basis for this notion is the so-called smelly T-shirt experiment, first performed by a Swiss zoologist called Claus Wedekind in 1994. He analysed a particular bit of the DNA of a group of students, looking specifically at the major histocompatibility genes (MHC). The students were then split into 49 females and 44 males. The men were asked to wear plain cotton T-shirts for two nights while avoiding anything – alcohol, cologne etc – that might alter their natural odour. After two days the shirts were placed in cardboard boxes with holes in them, and the women were asked to rank the boxes by smell using three criteria: intensity, pleasantness and sexiness.

Wedekind’s results appeared to show that the women preferred the T-shirts worn by men with different compatibility genes from themselves, raising the possibility that we unconsciously select mates who would put our offspring at some genetic advantage. The experiment was controversial, but it did alter scientific thinking about compatibility genes. And while the mechanism behind this phenomenon is poorly understood, that hasn’t stopped dating agencies from employing MHC typing as a matchmaking tool.

Of course, there are labs out there taking advantage of this science:

One lab offering such testing to online agencies (you can’t smell potential partners over the internet; not yet), a Swiss company called GenePartner, claims: “With genetically compatible people we feel that rare sensation of perfect chemistry.”

But take all this with a big grain of salt, as the research is still preliminary and no one really understands how all this works:

It is not completely understood how all this works at the molecular level, but it is at this forefront that Davis toils. “My research is in developing microscopes that look with better resolution at immune cells and how they interact with other cells,” he says. This interaction is “reminiscent of the way neurons communicate” in the brain, raising the possibility that your compatibility genes are responsible for more than just fighting infection, and could even influence how your brain functions. I confess to Davis that I don’t really understand this part. “None of us do,” he says. “I just happened to write a book about it.”

But how does the smelling thing work – if it works? It has been shown that mice can, and do, detect compatibility genes by smell, and that stickleback fish also choose mates by their odour, but in humans, Davis admits, the jury is out. “How it works on the olfactory level is basically not understood at all,” he says.

I think the more interesting point from Davis’s research is this: since each human responds slightly differently to any particular disease, in the not-too-distant future vaccines and other medications may be tailored to match our compatibility genes.

Why and How Jellyfish are Taking Over the World’s Oceans

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Tim Flannery provides an excellent review of Lisa-ann Gershwin’s new book Stung!: On Jellyfish Blooms and the Future of the Ocean in this New York Review of Books piece. It’s such a good, thorough review that I am disinclined to read the book.

From the Arctic to the equator and on to the Antarctic, jellyfish plagues (or blooms, as they’re technically known) are on the increase. Even sober scientists are now talking of the jellification of the oceans. And the term is more than a mere turn of phrase. Off southern Africa, jellyfish have become so abundant that they have formed a sort of curtain of death, “a stingy-slimy killing field,” as Gershwin puts it, that covers over 30,000 square miles. The curtain is formed of jelly extruded by the creatures, and it includes stinging cells. The region once supported a fabulously rich fishery yielding a million tons annually of fish, mainly anchovies. In 2006 the total fish biomass was estimated at just 3.9 million tons, while the jellyfish biomass was 13 million tons. So great is their density that jellyfish are now blocking vacuum pumps used by local diamond miners to suck up sediments from the sea floor.

This particular examples notes the collapse of the fishing economy in Bulgaria, Romania, and Georgia:

Would you believe, Gershwin asks, that “a mucosy little jellyfish, barely bigger than a chicken egg, with no brain, no backbone, and no eyes, could cripple three national economies and wipe out an entire ecosystem”? That’s just what happened when theMnemiopsis jellyfish (a kind of comb jelly) invaded the Black Sea. The creatures arrived from the east coast of the US in seawater ballast (seawater a ship takes into its hold once it has discharged its cargo to retain its stability), and by the 1980s they were taking over. Prior to their arrival, Bulgaria, Romania, and Georgia had robust fisheries, with anchovies and sturgeon being important resources. As the jellyfish increased, the anchovies and other valuable fish vanished, and along with them went the sturgeon, the long-beloved source of blini toppings.

By 2002 the total weight of Mnemiopsis in the Black Sea had grown so prodigiously that it was estimated to be ten times greater than the weight of all fish caught throughout the entire world in a year. The Black Sea had become effectively jellified. 

Some of the reasons for jellyfish growth are downright frightening;

One of the fastest breeders of all is Mnemiopsis. Biologists characterize it as a “self-fertilizing simultaneous hermaphrodite,” which means that it doesn’t need a partner to reproduce, nor does it need to switch from one sex to the other, but can be both sexes at once. It begins laying eggs when just thirteen days old, and is soon laying 10,000 per day. Even cutting these prolific breeders into pieces doesn’t slow them down. If quartered, the bits will regenerate and resume normal life as whole adults in two to three days.

Jellyfish are voracious feeders. Mnemiopsis is able to eat over ten times its own body weight in food, and to double in size, each day.

So what exactly is causing the jellyfish to thrive and take over the oceans? The reasons are numerous, and the review elucidates a few of them:

Our waste, such as plastic bags, and fishing methods like drift nets and long lines are busy destroying the few jellyfish predators, such as sea turtles. We are also creating the most splendid jellyfish nurseries. From piers to boat hulls, oil and gas platforms and industrial waste and other floating rubbish, we’re littering the oceans with the kind of artificial hard surfaces that jellyfish polyps love.

Then there is the amount of oxygen dissolved in seawater. Oxygen is created by plants using photosynthesis, and high oxygen levels allow fish and other complex creatures to compete successfully with jellyfish. But the oxygen in water can be depleted far more quickly that it can be replaced. Where humans add nutrients to seawater (such as fertilizer runoff from farms), areas with depleted oxygen, known as eutrophied zones, form. They can occur naturally, but are spreading quickly as the oceans become filled with excess phosphorus and nitrogen derived from a variety of agriculture and industrial human activities. In river estuaries, and in confined waters such as the Baltic, the Black Sea, and the Gulf of Mexico, eutrophied zones have spread to a frightening extent, and they appear to be permanent. Nothing that needs even moderate amounts of oxygen, including fish, shellfish, prawns, and crabs, can survive in them. But the jellyfish thrive.

Compelling read.

Theranos and the Future of Diagnostic Medicine

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Elizabeth Holmes is a 29-year-old chemical and electrical engineer and entrepreneur who dropped out of Stanford as an undergraduate after founding a life sciences company called Theranos in 2003. Her inventions, which she is discussing in detail for the first time in this Wall Street Journal interview, could upend the industry of laboratory testing and might change the way we detect and treat diseases:

The secret that hundreds of employees are now refining involves devices that automate and miniaturize more than 1,000 laboratory tests, from routine blood work to advanced genetic analyses. Theranos’s processes are faster, cheaper and more accurate than the conventional methods and require only microscopic blood volumes, not vial after vial of the stuff. The experience will be revelatory to anyone familiar with current practices, which often seem like medicine by Bram Stoker.

This is the future of diagnostic medicine. Theranos’s technology will eliminate multiple lab trips because it can “run any combination of tests, including sets of follow-on tests,” at once, quickly, and with just one microsample.

A microsam

A microsample of blood used by Theranos

Another goal is transparency:

Ms. Holmes says her larger goal is increasing access to testing, including among the uninsured, though she might also have a market-share land grab in mind. For instance, she says Theranos will publish all its retail prices on its website. The company’s X-ray of self-transparency also includes reporting its margins-of-error variations online and on test results and order forms, which few if any labs do now.

Worth the read. Don’t miss who’s on the board of directors of Theranos: Henry Kissinger, Sam Nunn (ex-senator from Georgia), and Richard Kovacevich (who served as the CEO of Wells Fargo & Company).

The Role of Sleep in Brain Repair and Growth

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The purpose of sleep is not very well understood. I’ve been fascinated with the topic for a number of years, so I am pretty excited when there’s new developments in the field of sleep research.

A new study sheds light on the role sleep plays in the the ability of the brain’s cells to grow and repair themselves. Preliminary research suggests that sleep replenishes a type of brain cells that go on to make an insulating material known as myelin, which protects our brain’s circuitry.

The research, published in The Journal of Neuroscience, was conducted in mice that were either allowed to sleep, or forced to stay awake. Researchers looked particularly at how sleep affected gene activity of cells called oligodendrocytes, which play a role in the production of myelin. Myelin covers brain and spinal cord nerve cell projections as a sort of “insulation”; researchers explained that it is integral to the movement of electrical impulses from cell to cell.

The study shows that sleep seems to turn on genes known to play a part in the formation of myelin. Conversely, lack of sleep was linked with the activation of genes associated with cell stress and death.

Dr Chiara Cirelli and colleagues from the University of Wisconsin, where the study was conducted, explained:

For a long time, sleep researchers focused on how the activity of nerve cells differs when animals are awake versus when they are asleep.

Now it is clear that the way other supporting cells in the nervous system operate also changes significantly depending on whether the animal is asleep or awake.

 

Men of Science, Men of Faith

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In a must-read op-ed piece in The New York Times titled “Welcome to the State of Denial,” Adam Frank, a professor of physics and astronomy at the University of Rochester, laments on the decline of people’s perception of science in our society.

Today, however, it is politically effective, and socially acceptable, to deny scientific fact. Narrowly defined, “creationism” was a minor current in American thinking for much of the 20th century. But in the years since I was a student, a well-funded effort has skillfully rebranded that ideology as “creation science” and pushed it into classrooms across the country. Though transparently unscientific, denying evolution has become a litmus test for some conservative politicians, even at the highest levels.

Meanwhile, climate deniers, taking pages from the creationists’ PR playbook, have manufactured doubt about fundamental issues in climate science that were decided scientifically decades ago. And anti-vaccine campaigners brandish a few long-discredited studies to make unproven claims about links between autism and vaccination.

The list goes on. North Carolina has banned state planners from using climate data in their projections of future sea levels. So many Oregon parents have refused vaccination that the state is revising its school entry policies. And all of this is happening in a culture that is less engaged with science and technology as intellectual pursuits than at any point I can remember.

He goes on to write:

We face many daunting challenges as a society, and they won’t all be solved with more science and math education. But what has been lost is an understanding that science’s open-ended, evidence-based processes — rather than just its results — are essential to meeting those challenges.

My professors’ generation could respond to silliness like creationism with head-scratching bemusement. My students cannot afford that luxury. Instead they must become fierce champions of science in the marketplace of ideas.

As some comments note, the effort to denigrate science is strong and insidious. I agree with this:

The push by religious institutions to have creationism and intelligent design taught alongside evolution in schools as legitimate competing theories, as well as the suppression of data linking man-made atmospheric discharges to climate change by industry are designed to preserve the status quo. Science, as a catalyst of change, has always upended institutions as it ushers in new ideas. We are on the verge of discoveries that may forever change the way we look at the universe and our place in it. It’s clear that those with a vested interest in the institutions of today fear what this means for their futures. Science can make oil and bishops largely irrelevant rather quickly if left unchecked. You bet they’re scared.

If I am not being clear: this perverse social acceptability of the denial of scientific fact must be fought with vigor. I fear for our future generation in America otherwise.

Your Thoughts Can Release Abilities beyond Normal Limits

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This is an interesting piece at Scientific American on how our thoughts may expand/better our cognitive and physical limits:

Our cognitive and physical abilities are in general limited, but our conceptions of the nature and extent of those limits may need revising. In many cases, thinking that we are limited is itself a limiting factor. There is accumulating evidence that suggests that our thoughts are often capable of extending our cognitive and physical limits.

Can our thoughts improve our vision? We tend to believe that an essentially mechanical process determines how well we see. Recent research by Ellen Langer and colleagues suggests otherwise. It is a common belief that fighter pilots have very good vision. The researchers put people in the mindset of an Air Force pilot by bringing them into a flight simulator. The simulator consisted of an actual cockpit including flight instruments. The cockpit was mounted on hydraulic lifts that mimic aircraft movement and performance. People were given green army fatigues; they sat in the pilot’s seat, and performed simple flight maneuvers. They took a vision test while “flying” the simulator. A control group took the same vision test in the cockpit while the simulator was inactive. People’s vision improved only if they were in the working simulator.

To rule out the possible effect of motivation, the researchers brought another group of people into the cockpit and asked them to read a brief essay on motivation. After people finished reading, they were strongly urged to be as motivated as possible and try hard to perform well in the vision test. The test was conducted while the simulator was inactive. They did not show a significant improvement.

In an eye exam, we are used to start experiencing problems at the bottom third of the eye chart, where letters start to get small. In another experiment, Ellen Langer and colleagues showed people a shifted chart. At the top, it included letters equivalent to the medium-size letters on the normal eye chart and the chart progressed to letters of very small size at the bottom. Because people were expecting to read the top two thirds of the shifted chart as well, they were able to read much smaller letters.

Here is the paper in which this premise is made clear: vision can be improved by manipulating mind-sets.

This reminds me of this adage I first encountered in high school: “If you believe you can or can’t, you’re right.”

The Sports Gene and the New Science of Athletic Excellence

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Katie Drummond interviews David Epstein, the author of the recently released The Sports Gene: Inside the Science of Extraordinary Athletic Performance.

The context is fascinating: whether you’re a gym rat or just starting out with an exercise routine, you typically follow the advice you read in magazines, from friends/coworkers, or personal trainers. But in the future, however, you might be able to develop a training plan that has nothing to do with external edicts, generalized principles, or even trial and error. Instead, you’d be training according to your own genetic athletic profile — a sequence of genes that determine what kind of exercise, done for how long and how often, your body will best respond to.

According to Drummond,

Epstein offers a fascinating look at how genetic research is already transforming sports science. Along the way, he digs into controversial questions about gender and race, examines the latest in genetic testing that purports to spot athletic traits, and unravels how some of the world’s best athletes — from Usain Bolt to Michael Jordan — attained the pinnacle of sporting success.

On to the interview questions:

Q: You don’t shy away from controversial topics in the book, including gender and ethnic differences where athletic ability is concerned. You also mention how scientific progress has been hindered because of concerns about sexism or racism creeping into cultural discussions about findings. To what extent, do you think, have those fears held back research on genetics and athleticism?

A: You know, when I went into the book I figured that scientists worked in bubbles to some extent, and that they didn’t decide what to publish based on any external force. In a sense, that they published their data so long as they maintained academic rigor. But in this field, that hasn’t been the case at all: scientists have literally told me that they have data, really great data, that they won’t publish because of how it might be perceived or construed by the public.

The primary instance of this is related to race. Namely, scientists are concerned that data suggesting that black people are predisposed to some athletic superiority will get wound up into this bigoted misconception that athletic ability means someone lacks intellect. That might sound ridiculous, but it’s been a prejudice for some time, and it has really reached deeply into the psyches of some scientists. Where gender is concerned, I had one researcher who has published a huge amount on sex and gender differences tell me that he didn’t publish any findings until he got tenure, because it just threatened to be too controversial. From my perspective, the best way to move the field forward and to help athletes is to collect sound data and then publish it — I was disappointed to see that this hasn’t happened.

Q: As you point out, the relationship between athletics and genetics is really complicated. But where do you see research going in the future, and what will it mean for athletes — elite or otherwise?

A: It is complicated, but we’re already seeing genetic tests trickling out that can hint at different aspects of someone’s athletic ability. Namely we’re seeing gene tests that relate to injury risk — one example is a test for the ApoE gene, which helps determine your vulnerability to brain damage from the hits you take during boxing or playing football, for example. That test is already out there, and it might really make a difference for athletes, how they compete, and what kind of medical treatment they get.

Where research is concerned, the most progress we’re seeing now is in studies that look at genes related to responses to endurance training — genetic pathways that determine who responds well to cardiovascular exercise, and who doesn’t. That has obvious appeal for athletes, or even people who wish they were athletes: the takeaway is that just because you don’t seem to have this innate, amazing talent, you might have an underlying predisposition to respond much better than you’d expect. The idea of figuring out someone’s training routine based on what they do and don’t respond to is really appealing, and I’d say we’re maybe five or ten years away from getting into that.

And it might also play an important role in personalized medicine: if someone with heart problems can respond well to aerobic activity, then maybe we can prescribe an exercise program instead of medicating them.

Fascinating. I’ve placed The Sports Gene in my to-read queue.

Are Selfish Traits Favored by Evolution?

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A recently published paper in Nature argues that it doesn’t pay to be selfish, in terms of maintaining or gaining evolutionary advantage. From the abstract, they used the famous Prisoner’s Dilemma to come to their conclusion:

Zero-determinant strategies are a new class of probabilistic and conditional strategies that are able to unilaterally set the expected payoff of an opponent in iterated plays of the Prisoner’s Dilemma irrespective of the opponent’s strategy (coercive strategies), or else to set the ratio between the player’s and their opponent’s expected payoff (extortionate strategies). Here we show that zero-determinant strategies are at most weakly dominant, are not evolutionarily stable, and will instead evolve into less coercive strategies. We show that zero-determinant strategies with an informational advantage over other players that allows them to recognize each other can be evolutionarily stable (and able to exploit other players). However, such an advantage is bound to be short-lived as opposing strategies evolve to counteract the recognition.

More interestingly, this latest finding is in direct contradiction the findings in a paper published in The Proceedings of the National Academy of Sciences last year, which posited that selfish people could get ahead of more co-operative partners…

The reason that being selfish wouldn’t work in an evolutionary environment is that knowing your opponent’s decision would not be advantageous for long because your opponent would evolve the same recognition mechanism known to you.

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(via BBC News)