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Editor's Note: Life and Death

Let me say up front: I am a registered organ donor. I joined the ranks just a few weeks ago when I renewed my driver’s license and discovered—much to my surprise—that I had forgotten to check the donor box when I got my first New York license years ago. This time I signed up without a moment’s hesitation. Organ transplants save thousands of lives in the United States every year, and if I had a fatal accident or disease I would certainly want my death to assist someone else’s life. Enlisting as a donor is one of the easiest forms of altruism around.

So it was with some trepidation that I agreed to publish Dick Teresi’s cover story, “The Beating Heart Donors.” 
Not because of its actual thesis, which I find fascinating and powerful, but because of the way the piece could be easily 
misconstrued. Many people already feel queasy about signing up to donate their organs; anything that increases those anxieties could have unfortunate consequences...

discovermagazine.com | 17-May-2012 18:25

To Disinfect Water Cheaply, Just Add Sunlight (and Salt or Lime Juice) | 80beats

The cheapest and easiest way to disinfect water? Sunlight. Just leave a clear glass or plastic bottle out in the sun for six hours. SODIS, or solar water disinfection, is an age-old method touted by the World Health Organization for areas where access to clean water is limited. UV rays in the sunlight tear apart the microbes to make water safe. Drink up!

SODIS is quite effective, but scientists have found two hacks that make the technique even better. One problem is that the water may be cloudy from sediment, which can be fixed with a dash of salt. NPR’s Salt blog explains:

Pierce and his colleagues discovered that by adding a little table salt to this murky water, they could get the particles of clay to stick together and settle to the bottom, making the water clear enough to purify using the solar disinfection method. They also found that the addition of salt works best for certain kinds of clay soils, namely bentonite, and not so well with others. But when they added a little bentonite along with salt to water that contained other types of clay soils, it worked just as well.

Pierce says the method works because bentonite clays have ...

discovermagazine.com | 16-May-2012 16:41

Sleeper viruses explain why HIV evolves more slowly between people than within them | Not Exactly Rocket Science

HIV – the virus behind AIDS – is the most diverse of all viruses. Once it infects someone new, it mutates so rapidly that it can spawn a million genetically different strains in just a few months. This evolutionary onslaught overwhelms the host’s immune system, and creates big problems for any scientist trying to create a cure or a vaccine. By evolving so quickly, HIV turns itself into a million moving targets.

But when HIV jumps from one individual to another, something odd happens. The virus still mutates at a breakneck speed, but it does so 2 to 6 times more slowly than within any single person. Unexpectedly, the virus seems to evolve faster in a single host, than in a population.

There are three possible explanations for this puzzling trend, but Katrina Lythgoe and Christophe Fraser from Imperial College London think that only one is correct. They think that the ancestral strain – the one that kicked off someone’s infection – is more likely to spread to other people than its millions of descendants.

The progeny of the ancestral virus quickly evolve to avoid their host’s immune system and ...

discovermagazine.com | 16-May-2012 01:00

Big Picture Science: Antivaxxers (and updates) | Bad Astronomy

I do a roughly monthly segment with astronomer Seth Shostak on Big Picture Science, a radio show/podcast done by The SETI Institute. This month, Seth and I talked about the American Airlines dustup when they were planning to run an interview with reality-impaired antivaxxer Meryl Dorey. This story is a great victory for reality, and I’ve already written about the back story.

Never forget: this antivax issue is more than important: it is literally life and death. Because of lowering vaccine rates, pertussis outbreaks are so prevalent health officials in the state of Washington have declared it to be an epidemic. The governor has had to dip into emergency funds to the tune of $90,000 to finance an information campaign to get the word out.

But the money is secondary to the idea that babies and people with immune deficiencies are at risk of dying from a disease that is essentially totally preventable if everyone got their vaccinations and boosters.

I cannot state that any more simply. The antivax crowd says vaccines cause autism, vaccines cause neurological problems, vaccines hurt your immune ...

discovermagazine.com | 15-May-2012 19:15

What’s in Spam with Bacon? Tasty, Tasty Chemistry | 80beats

You’d be surprised what’s in your lunch. When you look closer at what makes your American cheese melt well and your hotdog so delicious, you might cringe for a few minutes, but hopefully you also get curious about what other characteristics we like in our food and how food manufacturers have, for better or for worse, given our taste buds what they want.

Over at Wired, they’ve dissected Spam with Bacon, and what they find runs the gammut from “Hey, it’s cool that science can do that!” to “Maybe canned meat was a really bad idea.”

This description of bacon captures the balance nicely:

“The cured belly of a swine carcass,” says the USDA. “Mmmm, bacon,” says most of America. Large-scale curing is usually done by injecting a brine solution into the belly of a butchered swine. The brine contains sodium erythorbate, an antioxidant that’s chemically similar to vitamin C. But it’s not here to prevent scurvy; instead it boosts the conversion of the sodium nitrite in bacon into nitric oxide, which minimizes the production of carcinogens when the pork belly is fried up. The brining increases the meat’s weight by 12 percent, but a ...

discovermagazine.com | 15-May-2012 18:26

The Brain: Hidden Epidemic: 
Tapeworms Living Inside People's Brains | DISCOVER

Theodore Nash sees only a few dozen patients a year in his clinic at the National Institutes of Health in Bethesda, Maryland. That’s pretty small as medical practices go, but what his patients lack in number they make up for in the intensity of their symptoms. Some fall into comas. Some are paralyzed down one side of their body. Others can’t walk a straight line. Still others come to Nash partially blind, or with so much fluid in their brain that they need shunts implanted to relieve the pressure. Some lose the ability to speak; many fall into violent seizures.

Underneath this panoply of symptoms is the same cause, captured in the MRI scans that Nash takes of his patients’ brains. Each brain contains one or more whitish blobs. You might guess that these are tumors. But Nash knows the blobs are not made of the patient’s own cells. They are tapeworms. Aliens.

A blob in the brain is not the image most people have when someone mentions tapeworms. These parasitic worms are best known in their adult stage, when they live in people’s intestines and their ribbon-shaped bodies can grow as long as 21 feet. But that’s just one stage in the animal’s life cycle. Before they become adults, tapeworms spend time as larvae in large cysts. And those cysts can end up in people’s brains, causing a disease known as neurocysticercosis.

“Nobody knows exactly how many people there are with it in the United States,” says Nash, who is the chief of the Gastrointestinal Parasites Section at NIH...

Image: A human brain overrun with cysts from Taenia solium, a tapeworm that normally inhabits the muscles of pigs. Courtesy of Theodore E. Nash , M.D.

discovermagazine.com | 15-May-2012 17:00

Ready, set, trial: why pandemics catch us out and how to prepare for them | Not Exactly Rocket Science

When we think about preparing for pandemics, we think about vaccines, stockpiles of drugs, and surveillance. We rarely think about research. This oversight means that when big epidemics hit, like the swine flu pandemic of 2009, scientists lose valuable chances to find more about these illnesses. A new consortium is out to change that. I wrote about their work, and the problem of slow clinical research in a new feature for the BMJ, which I’m reprinting here.

 *****

While viruses are fast and adaptable, clinical research is lumbering and cumbersome. Epidemics tend to arrive with little warning, spread quickly, and end abruptly. By contrast, clinical trials can take months to plan. Forms must be designed to record the right data and ethical approval must be sought. By the time would-be researchers can vault over these obstacles the epidemic is history.

This explains why, during the 2009 A/H1N1 influenza pandemic, virtually no patients were enrolled in a randomised controlled trial designed to identify the best ways of treating the infection. Such trials are the gold standard of medicine and the best way of getting rigorous evidence for a treatment’s effectiveness. During the ...

discovermagazine.com | 14-May-2012 15:00

Why Preserved Food is So Bad: “Retort Flavor” | 80beats

Autoclaves—would you cook a turkey in this?

At Popular Science is a profile of food scientists given an impossible task: make year-old mashed potatoes taste good. Food that lasts a year on the shelf needs to be sterilized, and that is a battle against extremophiles. Our most effective weapon is a very blunt one—heat. 252 degrees Fahrenheit to be exact.

Writer Paul Adams tours a food science lab and gets a taste of “retort flavor” in his sterilized mashed potatoes. The unappetizing term refers to the retort, a machine that obliterates microbes and flavor in one fell (and very hot) swoop:

The potatoes look right, once we’ve fluffed them up a bit, but the wholesome earthy taste and smell of fresh potatoes is almost gone from the dish. In its place there’s a tired, wet-paper flavor with notes of old steam pipe. This side effect of confined high-heat cooking is known in the trade as “retort flavor.” Stuckey’s theory is that it’s just underlying parts of the flavor coming through. Before food is retorted, she says, the dank base notes present in it are masked in part “by the beautiful aromatic volatile notes that we ...

discovermagazine.com | 14-May-2012 14:29

Why Are 90% of Asian Schoolchildren Nearsighted? From Doing What You’re Doing Now | 80beats

With glasses, contacts, and LASIK surgery, most of us nearsightedness folks don’t have to worry about squinting at the blackboard anymore. But the sheer prevalence of nearsightedness, or myopia, among Asian schoolchildren (in Singapore, China, Taiwan, Hong Kong, Japan, and Korea) is stunning: 80 to 90% according to a recent review in the journal Lancet. In comparison, that number is just 20 to 30% in the UK. Myopia has also been on the rise in both Asia and Europe over the past few years.

While there are genes linked to myopia, its rising prevalence in both continents points to environmental causes. Namely, kids are spending more time hunched over screens and books instead of playing outdoors. In myopia, light coming into the eye can no longer focus at the retina because the eyeball has become too long. A body of research in humans and animals suggest that reading at close distances and lack of bright sunlight could cause elongated eyeballs.

In Singapore, myopia has shot up in the last 30 years among all three major ethnic groups—Chinese, Indian, and Malay—which highly suggests a environmental cause. Singaporean schoolchildren who read more than two books per week were also more likely ...

discovermagazine.com | 12-May-2012 14:40

Now *This* Is a Cell Phone: Using Radio Waves to Control Specific Genes in Mice | 80beats

With some clever genetic engineering but without ever touching a cell or an animal, scientist can remotely control cells using ultrasound, light, and, now, also radio waves. The electromagnetic waves can be used to selectively heat up parts of cells and activate a gene to make insulin in mice, according to a recent study published in Science.

But why care about radio waves if we have light and ultrasound? Radio waves have a couple distinct advantages over existing techniques.

In the current study, the radio waves didn’t heat up a whole patch of tissue or even a whole cell—it only affected specific pores in the cell, called TRPV1, that open in response to heat. To get this specificity, the scientists made special iron oxide nanoparticles attached to an antibody that only sticks to TRPV1. When they turned on the radio waves, the iron oxide particles warmed up and opened the TRPV1 channel, minimally affecting the rest of the cell or surrounding cells. Ultrasound, on the other hand, heats up a whole patch of tissue to 42° Celsius, which could have damaging or confounding effects on the cells.

Radio waves, unlike light, can also penetrate deep into tissue. To show ...

discovermagazine.com | 11-May-2012 19:25

Discover Interview: The World's Most Celebrated Virus Hunter: Ian Lipkin | DISCOVER

When Ian Lipkin chose a career in infectious diseases, he envisioned hunting for pathogens in daring treks around the world. Though disappointed to learn that modern-day virus hunters work largely from the lab, he still wound up a pioneer. At the Scripps Research Institute in La Jolla, then at the University of California, Irvine, and since 2001 as director of the Center for Infection and Immunity at Columbia University’s Mailman School of Public Health, Lipkin has developed groundbreaking techniques that have helped a new generation of disease detectives sleuth out the infectious roots of mystery ills, chronic disease, and neuropsychiatric disorders like autism and OCD. Lipkin’s signature invention is a technology called Mass Tag PCR, which searches through large numbers of known viral and bacterial genomes to identify a culprit in a few hours. He often complements this test with others, including microbial detection microchips (GreeneChips) and gene sequencers that can complete an exhaustive search for known and unknown pathogens within a tissue sample in less than a day.

When DISCOVER features editor Pamela Weintraub interviewed Lipkin last year, he had to cut his workday short because his dog, Koprowski—a gift from Polish virologist Hilary Koprowski—was desperately sick. Lipkin had a treatment plan: not an antiviral drug or chemotherapy, but red meat. “It has antibiotics, it has growth hormone, it has everything. Koprowski’s my best friend in the world,” he explained before descending into the subway and heading home.

You were in the first class of men at Sarah Lawrence, where you studied anthropology, even shamanism. Yet you are known for hunting pathogens. How did that come about?

I felt that if I went straight into cultural anthropology after college I’d be a parasite. I’d go someplace, take information about myths and ritual, and have nothing to offer. So I decided to become a medical anthropologist and try to bring back traditional medicines. Suddenly I found myself in medical school.


But you didn’t become a medical anthropologist. Instead you studied neurological disease and infection. Why?

By 1977 I had gotten a fellowship at the Institute for Neurology in London, where a professor named John Newsom-Davis was working on myasthenia gravis, a neuromuscular disorder characterized by weakness often so profound that people lose their ability to breathe. Back then, nobody really understood what the disorder was. John was trying something new, treating it with plasmapheresis...

discovermagazine.com | 11-May-2012 18:05

Cancer evolution at TEDMED | The Loom

Earlier this year, TEDMED took place in Washington DC, showcasing people doing innovative research in medicine. This year’s talks are now being loaded online, and today I was happy to see that cancer and evolution got their due. Franziska Michor of Harvard explained how the threat of cancer is a legacy of our evolution into multicellular animals, and how every case of cancer is a miniature unfolding of evolution within our own bodies. What makes Michor’s work particular exciting is that she is bringing the mathematical precision of population genetics and other aspects of evolution to the treatment of cancer.

I wrote about some of Michor’s work in my 2007 Scientific American article, “Evolved for Cancer?” (carlzimmer.com, sciam.com) I’ve also explored cancer evolution here on the Loom: “Inside Darwin’s Tumor” and “The Mere Existence of Whales.”  And you can find lots of Michor’s papers as free pdf’s on her publication page.

discovermagazine.com | 11-May-2012 15:00

How Microbes & Plants Around Us Might Prevent Allergies | 80beats

Crawling my way to a healthier immune system.

Bacteria are practically everywhere around us, including on and inside you, but that is in many ways a good thing. For instance, having a diverse set of microbes living on your skin might help prevent allergies. A new study published in PNAS links two factors related to how microbes might affect our health: the observation that diversity of microbes on a person is related to the diversity of microbes in their environment, and the hygiene hypothesis, which suggests that the modern uptick in allergies and autoimmune diseases is caused by childhood under-exposure to bacteria.

For a while now, scientists have known that kids living on farms are less likely to have allergies or asthma. Being around livestock means the farm kids are also around a more diverse set of bacteria than city kids living in an apartment. In this new study, scientists swabbed the skin bacteria of 118 Finnish kids, some who lived in rural areas and some who lived in urban areas. They also tested the kids for levels of an antibody called IgE, high levels of which indicate hypersensitivity to allergens, or what is ...

discovermagazine.com | 10-May-2012 17:16

What does it mean to say that something causes 16% of cancers? | Not Exactly Rocket Science

A few days ago, news reports claimed that 16 per cent of cancers around the world were caused by infections. This isn’t an especially new or controversial statement, as there’s clear evidence that some viruses, bacteria and parasites can cause cancer (think HPV, which we now have a vaccine against). It’s not inaccurate either. The paper that triggered the reports did indeed conclude that “of the 12.7 million new cancer cases that occurred in 2008, the population attributable fraction (PAF) for infectious agents was 16·1%”.

But for me, the reports aggravated an old itch. I used to work at a cancer charity. We’d get frequent requests for such numbers (e.g. how many cancers are caused by tobacco?). However, whenever such reports actually came out, we got a lot confused questions and comments. The problem is that many (most?) people have no idea what it actually means to say that X% of cancers are caused by something, where those numbers come from, or how they should be used.

Formally, these numbers – the population attributable fractions (PAFs) – represent the proportion of cases of a disease that could be avoided ...

discovermagazine.com | 10-May-2012 15:00

Flame Retardants Are Toxic & Haven’t Been Shown to Save Lives. Why Are They Ubiquitous? | 80beats

“The average American baby is born with 10 fingers, 10 toes and the highest recorded levels of flame retardants among infants in the world.” So begins the Chicago Tribune’s damning four-part series about spin and science, or lack thereof, in the flame retardants industry. Flame retardant chemicals have become so ubiquitous–there’s two pounds of the stuff in just the cushions of a large couch—because we’ve accepted the health dangers are worth the protection they provide against fire. Except, there is no scientific basis for the claim that flame retardants save lives.

Part three in the series, published today, is a systematic debunking of the few studies the industry has continuously cited as evidence for the efficacy of flame retardants. One obscure Swedish study, available only in Swedish, relied on flimsy evidence from just eight electrical fires caused by TVs. The peer-reviewed paper also lists a PR specialist among its authors. The lead scientist of another study has disavowed what he calls the industry’s “grossly distorted” flogging of his work, which looked at levels of flame retardants far above industry standard in household furniture. These examples and many more show how scientific authority has been manipulated for profit:

Industry has disseminated ...

discovermagazine.com | 09-May-2012 21:49

16% of Cancers Are Caused by Viruses or Bacteria | 80beats

Where viruses and bacteria cause cancer

Strictly speaking, cancer is not contagious. But a fair number of cancers are clearly caused by viral or bacterial infections: lymphomas can be triggered by the Epstein-Barr virus, which also causes mononucleosis. Liver cancers can be caused by Hepatitis B and C. Cervical cancers can be caused by human papillomavirus, the major reason behind the development of a vaccine against it.  For some of these cancers, nearly 100% of the cases have an infectious link—when researchers check to see if a virus or bacterium is working in the tumor or has left signs of its presence in a patient’s blood, the answer is nearly always yes.

A new paper in The Lancet takes a look at the very best data on the prevalence of infection-caused cancers and comes up with some striking numbers. Overall, 16.1% of cancer cases worldwide in 2008 had an infectious cause—2 million out of 12.7 million.

Hepatitis B and C, HPV, and Helicobacter pylori, a bacterium that triggers stomach cancer, caused the lion’s share of those cases, about 1.9 million together. Eighty percent of all infection-caused cancers were in less developed regions, where vaccines and ...

discovermagazine.com | 09-May-2012 21:03

Unstoppable | Bad Astronomy

My willingness to fight has seen some major impediments in the past few weeks. The increase in antireality nonsense seems like a growing tsunami. Antivax health threats. Global warming denial on a major (and heavily funded) scale. The ugliness yesterday in North Carolina.

And even though we’ve had some great victories, it’s still an endless road, always uphill, always against the wind. Despair seems inevitable.

But then, but then, this:

Made for the Canadian Paralympic Committee, that may be the single greatest ad ever made. I suddenly find myself able to stand, dust myself off, and get back on the road.

Unstoppable. As we must be.

Tip o’ the starting gun to Laughing Squid.

discovermagazine.com | 09-May-2012 16:49

Vital Signs: "We Can Take His Heart Out, Remove the Tumor, and Put It Back In"

I was in the middle of a normal clinic day, seeing candidates for surgery, when a nurse told me that one of them had arrived with a diagnostic video. When I had a free moment, I walked over to a computer and put the CD into the drive. As the program booted up, I noticed that the video was a cardiac MRI (magnetic resonance imaging) study. I clicked through the images, and what I saw was frightening. A large mass was growing in the patient’s heart, in the back wall of the left atrial chamber, perhaps the worst possible place to have a problem like this. The right atrium and both ventricles

are somewhat accessible to the surgeon’s knife. But the left atrium at the back of the heart next to the spine is a difficult, if not impossible, area to reach.

As I watched the video, more details emerged. As the left atrium attempted to pump blood, the wall opposite the growth ballooned out awkwardly instead of contracting with the rest of the chamber, its movement altered by the growth. The mass also took up a lot of space and was impeding blood flow. If it got just 5 percent larger, the chamber would be almost completely obstructed, resulting in a high risk of sudden death...

discovermagazine.com | 09-May-2012 15:35

Thick, 1,000-Year-Old Dental Plaque Is Gross, Useful to Archaeologists | Discoblog

What big plaque deposits you have!

A dentist will tell you to floss everyday, but an archeologist might, well, have different priorities. Turns out the nitrogen and carbon isotopes in dental plaque can give archeologists a look at 1,000-year-old diets.

The buildup of plaque on this set of teeth is, um, impressive. (Cut the skull some slack though, this was before we had dentists to chide us about daily flossing.) Without the benefit of modern dental hygiene, the plaque built up over a lifetime, layer upon layer like a stalagmite. In a paper recently published in the Journal of Archeological Science researchers exhumed 58 medieval Spanish skeletons and scraped off their dental plaque to test carbon and nitrogen isotopes. When they compared the isotope profiles of the Spaniards to that of plaque from an Alaskan Inuit, the scientists found the ratio of nitrogen-15 to be quite different. That makes sense, as the Intuit ate a predominantly marine diet, and there is more nitrogen-15 in the protein molecules of organisms living in sea than on land.

Another benefit of plaque is that it’s easier to test than bone, which has to be dissolved in acid to extract from ...

discovermagazine.com | 08-May-2012 20:46

20 Things You Didn't Know About... Science 
Fraud

1. What evil lurks in the hearts of scientists? Behavioral ecologist Daniele Fanelli knows. In a meta-analysis of 18 surveys of researchers, he found only 2 percent ’fessed up to falsifying or manipulating data...but 14 percent said they knew a colleague who had.

5  If caught stealing someone else’s ideas, scientists have a handy defense: cryptomnesia, the idea that a person can experience a memory as a new, original thought.

8  Even geniuses succumb to temptation. Researchers have found that Isaac Newton fudged numbers in his Principia, generally considered the greatest physics text ever written.

9  Other legends who seem to have altered data: Freud, Darwin, and Pasteur.

10  And Austrian monk Gregor Mendel’s famous pea-breeding experiments—the foundation of modern ideas of heredity—are suspiciously good, matching his theory of genetic inheritance a little too well.

18  Write what you know: Harvard evolutionary psychologist Marc Hauser resigned last year after he was found guilty of eight counts of scientific misconduct. Now he’s working on a book, reportedly titled Evilicious: Explaining Our Evolved Taste for Being Bad.

discovermagazine.com | 08-May-2012 16:50

Gross But Cool: Weaving Blood Vessels with Threads of Human Tissue | 80beats

This machine is weaving 48 strands of human connective tissue together into a tube.

Growing fresh blood vessels is a much fantasized-about goal of biomedical engineers. It sounds vaguely vampiric, but the idea is to replace the veins in the arms of dialysis patients, which are a mess from being breached several times a week to be hooked up to a blood-cleaning machine. From there, engineers hope to provide off-the-shelf replacements for heart valves and such.

Most approaches involve getting human cells—either donor cells or cells from the patient—to manufacture rubbery connective tissue made of proteins, from which the cells are stripped away to avoid an immune reaction in patients. Some companies start with flat sheets of this tissue and roll them into tubes, while others have the cells make the stuff around a tubular mold. One company, though, is trying out a technique that made us look twice. They’re weaving the vessels from thread spun with thin strips of cultured connective tissue, Technology Review reports.

The hope is that given manufacturers’ copious experience with machine weaving, these woven structures could be easier to mass-produce than the tubes made with other techniques. Though there isn’t much ...

discovermagazine.com | 07-May-2012 19:14

Will we ever have an HIV vaccine? | Not Exactly Rocket Science

Here’s the seventh piece from my new BBC column

For around 30 years we have lived under the spectre of HIV. In the early 1980s, the mysterious appearance of symptoms that would later be known as AIDS led to unprecedented efforts to unmask the cause. On 23 April 1984, Margaret Heckler, the US Secretary of Health and Human Services, told the world that scientists had identified the virus that was the probable cause of AIDS. She was correct. She also said that a vaccine would be “ready for testing in approximately two years.” She was wrong.

Despite 28 years of research, there is still no vaccine that provides effective protection against HIV, and in that time around 25 million people have died of HIV-related causes. To understand why creating a vaccine is so hard, you need to understand HIV. This is no ordinary virus. Scientists who study it speak of it with a mix of weary frustration and awed reverence.

The virus is the most diverse we know of. It mutates so rapidly that people might carry millions of different versions of it, just months after becoming infected. HIV’s ...

discovermagazine.com | 07-May-2012 15:00

The Mystery of the Melanesian Blondes | 80beats

A blond boy from the island of Vanatu

In many places, blond hair usually goes with white skin and European ancestry. But in the islands of Melanesia and among the Aborigines of Australia, blond hair crops up on dark-skinned people with no known European heritage. Scientists have long wondered, is it because they have some (very, very) long-lost European ancestors? Or did blond hair arise from a genetic mutation in the population there?

A paper published in Science this week lays that question to rest. The researchers found that blond Solomon Islanders in Melanesia have a single amino acid difference in the tyrosinase-related protein 1 (TYRP1) gene, which codes for an enzyme involved in the production of the pigment melanin. Other mutations in TYRP1 can give people albinism; this one gives them light-colored hair. The mutation is recessive, so only people who have two mutant copies of the TYRP1 gene are blond.

This mutation is not responsible for European blondness, which hammers home the fact that pale hair didn’t arrive on a boat with early European explorers—it’s definitely native to the islands.

For the full story and lots of tasty genetics, head over to Discover’s Gene ...

discovermagazine.com | 04-May-2012 22:28

Mutant flu paper is finally published, reveals pandemic potential of wild viruses | Not Exactly Rocket Science

It’s finally out. After months of will-they-won’t they and should-they-shouldn’t-they deliberations, Nature has finally published a paper about a mutant strain of bird flu that can spread between mammals.

The strain was produced by Yoshihiro Kawaoka from the University of Wisconsin-Madison, who was trying to understand whether wild bird flu viruses have the potential to start a pandemic. These viruses can occasionally infect humans, but so far, they’ve been contained by their inability to efficiently jump from human to human. Kawaoka’s work makes it clear that they can evolve that ability.

Kawaoka’s study, along with a similar one from Ron Fouchier, has been the subject of intense debate for the last several months (catch up on the backstory here). What are the benefits of the research, and do they outweigh the risks? Now that the paper is finally out, we can start to answer those questions.

I’ve written about the paper for Nature News, focusing very heavily on the science rather than the politics. Head over there for a tighter version of this story. In this post, I’m going to highlight four important themes from the paper.

One: H5N1 can evolve to spread ...

discovermagazine.com | 02-May-2012 19:00

E. Coli That Cause Urinary Tract Infections are Now Resistant to Antibiotics | 80beats

Thanks to antibiotics, we tend to think of urinary tract infections as no big deal. Pop some cipro, and you’re done. A good thing, too—if the E. coli that usually cause UTIs crawl up the urinary tract, they can cause kidney failure and fatal blood poisoning.

But antibiotics may not be saving us from UTIs for very much longer. Scientists tracking UTIs from 2000 to 2010 found a dramatic uptick in cases caused by E. coli that do not respond to the drugs that are our first line of defense. In examining more than 12 million urine analyses from that people, they found that cases caused by E. coli resistant to ciprofloxacin grew five-fold, from 3% to 17.1% of cases. And E. coli resistant to the drug trimethoprim-sulfame-thoxazole jumped from 17.9% to 24.2%. These are two of the most commonly prescribed antibiotics used to treat UTIs. When they are not effective, doctors must turn to more toxic drugs, and the more those drugs are used, the less effective they in turn become. When those drugs stop working, doctors will be left with a drastically reduced toolkit with which to fight infection.

Some of this growing resistance in ...

discovermagazine.com | 02-May-2012 17:46

The Beating Heart Donors

in 1968, thirteen men gathered at the Harvard Medical School to virtually undo 5,000 years of the study of death. In a three-month period, the Harvard committee (full name: the Ad Hoc Committee of the Harvard Medical School to Examine the Definition of Brain Death) hammered out a simple set of criteria that today allows doctors to declare a person dead in less time than it takes to get a decent eye exam. A good deal of medical language was used, but in the end the committee’s criteria switched the debate from biology to philosophy. Before many years went by, it became accepted by most of the medical establishment that death wasn’t defined by a heart that could not be restarted, or lungs that could not breathe. No, you were considered dead when you suffered a loss of personhood.

But before we see what substituting philosophy for science actually means to real patients, let’s look at the criteria the Harvard authors believed indicated that a patient had a “permanently nonfunctioning brain”:

• Unreceptivity and unresponsivity. “Even the most intensely painful stimuli evoke no vocal or other response, not even a groan, withdrawal of a limb or quickening of respiration,” by the committee’s standard.

• No movements or spontaneous breathing (being aided by a respirator does not count). Doctors must watch patients for at least one hour to make sure they make no spontaneous muscular movements or spontaneous respiration. To test the latter, physicians are to turn off the respirator for three minutes to see if the patient attempts to breathe on his own (the apnea test).

• No reflexes. To look for reflexes, doctors are to shine a light in the eyes to make sure the pupils are dilated. Muscles are tested. Ice water is poured in the ears.

• Flat EEG. Doctors should use electroencephalography, a test “of great confirmatory value,” to make sure that the patient has flat brain waves.

The committee said all of the above tests had to be repeated at least 24 hours later with no change, but it added two caveats: hypothermia and drug intoxication can mimic brain death. And since 1968, the list of mimicking conditions has grown longer.

Although the Harvard criteria were based on zero patients and no experiments were conducted either with humans or animals, they soon became the standard for declaring people dead in several states, and in 1981, the Uniform Determination of Death Act (UDDA) was sanctioned by the National Conference of Commissioners on Uniform State Laws. The UDDA is based on the Harvard Ad Hoc Committee’s report. That a four-page article defining death should be codified by all 50 states within 13 years is staggering...

discovermagazine.com | 02-May-2012 17:45

Do Gut Microbes Travel From Person to Person? | 80beats

It’s an exciting time for ecologists who study microbes. DNA sequencing has grown so cheap and fast that they can run around identifying bacteria living just about anywhere they can reach with a cotton swab. Turns out, bacteria are everywhere, even in the cleanest houses, and scientists are starting to wonder: do those bacteria in the home reflect the bacteria that live inside the inhabitants?

And if so, can they travel from person to person?

A small insight into this question came at one of the presentations at the International Human Microbiome Congress (covered by New Scientist in a short piece here). James Scott, who studies molecular genetics at the University of Toronto, reported that the gut microbes of babies, as found in their poop, were also in the dust in the babies’ homes. It’s not clear whether this means that bacteria in the dust are colonizing the babies or vice versa—or both—but it’s still something of a surprise. Gut microbes don’t seem like the sort to thrive outside the body, as they tend to require an oxygen-free environment. But maybe the gut bacteria in the dust are in a dormant form, waiting to be absorbed into ...

discovermagazine.com | 01-May-2012 17:04

Followup: Antivaxxers, airlines, and ailments | Bad Astronomy

Reality recently scored a major win when American Airlines agreed not to run an interview with notorious antivaxxer Meryl Dorey. An American living in Australia, Dorey runs the Orwellian-named Australian Vaccine Network, where she dispenses horrifically bad and outright false information about vaccines. Read the link above to see details about her shenanigans.

After AA decided not to run the interview, Dorey pulled a lot of tired and clearly silly claims out of her playbook, saying it’s denying her free speech — which it obviously isn’t, since this isn’t a free speech issue! — and that we’re all part of a global cabal funded by Big Pharma blah blah blah. I’ve yet to see a check from Big Pharma, so her making this claim is at best paranoid and at worst a lie. You can read more about her nonsensical claims in an ABC article about this.

As usual, I have a very, very hard time feeling any sympathy for Dorey, especially when measles is roaring back into the population. Measles is easy to prevent with a simple vaccination, but due in large part to the antivax effort (and I include religious exemptions ...

discovermagazine.com | 01-May-2012 14:15

Why We Should Not Worry about the Mad Cow Case in California | 80beats

A phrase like “mad cow” is sure to whip up a media frenzy. When the USDA confirmed last week the first case of bovine spongiform encephalopathy (BSE) in six years, news headlines were splashed with reports of “mad cow disease,” the informal and scarily evocative term for BSE. What got lost in these initial reports is that this case of BSE involves a different protein than previous epidemics in Europe, and there’s no evidence that this type is transmissible to humans.

Nature News has a solid and thorough explanation of the science behind this case of BSE, known as L-type. As it happens in nature, mutations arise spontaneously, and L-type BSE is caused by a spontaneous mutation in a particular protein. A lot is still unknown about L-type, but we have never seen it spread through cow populations (or jump to humans) through ingestion. Previous BSE epidemics in Europe were spread by the admittedly gruesome practice of grinding up leftover cow parts and feeding them back to cows, but this has been long banned in the United States because of BSE. Critics have argued that there may still be indirect sources of cow protein ...

discovermagazine.com | 30-Apr-2012 18:38

This Scientist Endures 15,000 Mosquito Bites a Year | Discoblog

The things we do for science.

Researchers who study mosquitoes and other blood-sucking insects sometimes use themselves as skeeter chow. In some cases, it’s because certain species of mosquitoes seem to prefer human blood to animal blood. In others, though, it’s a cheap, convenient alternative to keeping animals around for the insects to feed on or buying blood. And as it turns out, once you’ve been bitten a certain number of times you develop a tolerance to mosquito saliva.

Entomologist Steve Schutz, seen above paging through a magazine while the bloodsuckers go to work on his arm, feeds his mosquito colony once a week. He has welts for about an hour, but after that the bites fade, occasionally leaving a few red spots. That’s good, because at 300 bites a week, he averages about 15,000 a year. That’s dedication.

discovermagazine.com | 27-Apr-2012 19:35

New Study That Allegedly Found the Fabled G-Spot Is Deeply Flawed | 80beats

You may have heard the G-spot buzz today: a gynecological surgeon claims to have discovered an actual structure in a vagina that corresponds to this reputed female pleasure center. Just by itself, any invocation of the G-spot should set off alarms; it has been called a “gynecologic UFO: much searched for, much discussed, but unverified by objective means.”

There is much about this particular study, though, that is deeply troubling, as best exposed by Ricki Lewis, who has authored textbooks on human physiology, at Scientific American. Here is a quick sum-up of what is so wrong about this situation.

Big Problem #1

Adam Ostrzenski, the surgeon behind the paper, has made this claim on the basis of dissecting a single corpse. As Lewis points out, a single data point does not really mean anything in science, especially when you’re claiming to have found an organ that supposedly exists in 50% of people. Many, many such dissections, all revealing the same thing, would be required to make this claim plausible.

Big Problem #2

In this single corpse, he found a structure that looks like a string of grapes, which he says is erectile tissue that swells during arousal. He ...

discovermagazine.com | 25-Apr-2012 18:54

Will we ever correct diseases before birth? | Not Exactly Rocket Science

Here’s the sixth piece from my new BBC column

Every year, millions of people are born with debilitating genetic disorders, a result of inheriting just one faulty gene from their parents. They may have been dealt a dud genetic hand, but they do not have to stick with it. With the power of modern genetics, scientists are developing ways of editing these genetic errors and reversing the course of many hard-to-treat diseases.

These gene therapies exploit the abilities of viruses – biological machines that are already superb at penetrating cells and importing genes. By removing their ability to reproduce, and loading them with the genes of our choice, we can transform viruses from causes of disease into vectors for cures.

After a few shaky starts, some of these approaches are beginning to hit their stride. Thirteen children with SCID, an immune disorder that leaves people fatally vulnerable to infections, now have working immune systems. Several British patients with haemophilia, which prevents their blood from clotting properly, can now produce a clotting protein called factor IX, which they once had to inject. A British man and ...

discovermagazine.com | 25-Apr-2012 15:00

How ‘superspreader’ viruses invaded our genes by hanging up their coats | Not Exactly Rocket Science

Around 8 to 10 per cent of your DNA comes from viral ancestors. These sequences are the remains of prehistoric viruses that inserted their DNA into the genes of our ancestors, hundreds of millions of years ago. Some of them became permanent residents, and were passed down from parent to child. These endogenous retroviruses, or ERVs, are a legacy of epidemics past.

We understand how ERVs got into our DNA in the first place. But why have they been such successful invaders, to the point where they fill around a tenth of our genome? Gkikas Magiorkinis from the University of Oxford has an answer. By comparing the ERVs of 38 mammals, from humans to dolphins, he has found that the critical step in these invasions was the moment when the viruses hung up their coats.

Retroviruses, such as HIV, can copy their genetic material by inserting it into the DNA of their host. That way, whenever the host copies its own genes, it also makes more viruses. But to infect a new cell, the viruses need to package their duplicated DNA in a protein coat. This process depends on ...

discovermagazine.com | 24-Apr-2012 16:18

Gallery | Our Wonderful Age of Abundance, in 9 Striking Infographics | DISCOVER
Click through to view gallery

discovermagazine.com | 24-Apr-2012 15:40

Bug becomes instantly resistant to insecticide by swallowing the right bacteria | Not Exactly Rocket Science

Many insects eventually evolve to resist insecticides. This process typically takes many generations and involves tweaks to the insect’s genes. But there is a quicker route. Japanese scientists have found that a bean bug can become instantly resistant to a common insecticide by swallowing the right bacteria.

The bug forms an alliance with Burkholderia bacteria, and can harbour up to 100 million of these microbes in a special organ in its gut (see arrow above). Some strains of Burkholderia can break down the insecticide fenitrothion, detoxifying it into forms that are harmless to insects. In fields where the chemical is sprayed, these pesticide-breaking bacteria rise in number. And if bugs swallow them, they become immune to the otherwise deadly chemical.

I’ve written about this story for The Scientist, so head over there to read the details of the study.

To me, the alliance is fascinating because the bug is coping with a new environmental challenge by bolstering its own genome with that of a microbe.

Many creatures rely on microscopic partners to safeguard their health. Insects inherit beneficial bacteria from their mothers, which help them to resist other bacteria that would cause disease, ...

discovermagazine.com | 24-Apr-2012 15:00

UPDATE: partial success with American Airlines! | Bad Astronomy

Good news: I just received a tweet from the American Airlines Twitter feed:

Yay! They have decided to not air the audio version of the antivax interview. That’s excellent, and I thank American Airlines for that.

However, as far as I can tell, the interview is still slated to run in their in-flight magazine. I will hopefully have more news about that soon as well.

Remember: we have the power to make sure good, accurate science gets told, and bad, inaccurate misinformation does not spread. Never rest, never tire, and never forget that the price of freedom is eternal vigilance.

discovermagazine.com | 23-Apr-2012 23:36

American Airlines to air dangerous antivax propaganda | Bad Astronomy

[UPDATE: American Airlines has agreed not to run the audio version of the interview! I'm waiting to hear if they will still run the print version in their magazine or not.]

[Note: This post contains numerous links to articles showing antivax claims are misleading at best, and pose a huge health risk. I strongly urge you to read those links before leaving a comment.]

In May 2011, an unvaccinated infant was brought on board American Airlines flight 3965. Measles is a highly contagious, dangerous, and potentially fatal disease, and because of this public health emergency officials had to track down 100 passengers and quarantine quite a few of them.

This event was not American Airlines’ fault. However, it’s hard to see what they learned from it, since they plan on printing and airing an interview with a notorious antivaxxer who makes provably false and incredibly dangerous claims about vaccines and vaccine-preventable diseases.

The antivaxxer in question is Meryl Dorey, an American living in Australia who has made it her life’s work to spread misinformation about vaccines. Her ability to distort the truth — to phrase it kindly — is nothing short of ...

discovermagazine.com | 23-Apr-2012 14:30

Gallery | 6 Creepy-Crawlies We Hate But Couldn't Do Without
Click through to view gallery
discovermagazine.com | 18-Apr-2012 19:55

I | Not Exactly Rocket Science

In an act of transformation worthy of any magician, scientists have converted scar tissue in the hearts of living mice into beating heart cells. If the same trick works in humans (and we’re still several years away from a trial), it could lead us to a long-sought prize of medicine – a way to mend a broken heart.

Our hearts are made of several different types of cell. These include muscle cells called cardiomyocytes, which contract together to give hearts their beats, and connective cells called cardiac fibroblasts, which provide support. The fibroblasts make up half of a heart, but they become even more common after a heart attack. If hearts are injured, they replace lost cardiomyocytes with scar tissue, consisting of fibroblasts. In the short-term, this provides support for damaged tissue. In the long-term, it weakens the heart and increases the risk of even further problems.

Hearts can’t reverse this scarring. Despite their vital nature, they are terrible at healing themselves. But Deepak Srivastava from the Gladstone Institute of Cardiovascular Disease can persuade them to do so with the right chemical cocktail. In 2010, he showed that just ...

discovermagazine.com | 18-Apr-2012 19:00

Climbing Everest is So Much Like Aging That the Mayo Clinic is Headed There To Do Research | 80beats

Mount Everest is often the site of impressive physical feats, as climbers brave brutal conditions to scale the tallest peak in the world. But the extreme altitude takes quite a toll on the body, causing hypoxia, muscle loss, sleep apnea, and other ill effects. Many of the same symptoms are more commonly found in elderly patients suffering from heart conditions or other chronic ailments—meaning Everest provides a natural laboratory for researchers to gain a better understanding of these diseases.

Scientists from the Mayo Clinic are making their way from Minnesota to Everest base camp, where they’ll set up an ersatz lab to monitor the vital signs of nine climbers making the ascent (the scientists’ 1,300 pounds of equipment will be carried to camp by yaks). The team will gather data on the mountaineers’ heart rate, oxygen levels, and sleep quality, as well as taking samples of their blood and urine. Among the questions the scientists will investigate are whether muscle loss, common in heart disease patients and the elderly, is related to lack of oxygen, especially during sleep, and why fluid gathers in the lungs of both ...

discovermagazine.com | 18-Apr-2012 17:37

Fresh Air interview: links to information on viruses, antivirals, the microbiome, and more | The Loom

Yesterday my Fresh Air interview was broadcast. You can listen to it here. I’ve been lots of emails with follow-up questions, and it occurred to me that I really ought to gather up some links to more information about the topics I discussed.

If I haven’t addressed a question you had listening to the show, leave a comment to this post and I’ll add a link.

Antivirals:
My feature in Wired on the search for antiviral drugs

The “virome”–the viruses that live in our body:
A Loom post about the swarms of viruses in the mouth, where they kill off bacteria
An article in Nature about a study of the viruses in identical twins

The microbiome
My article in the New York Times
My essay on the Loom about medical ecology
My Wired atlas of the human ecosystem
An example of microbiome research: extreme navel gazing
Maryn McKenna’s story in Scientific American on the struggle to mainstream fecal transplants to treat deadly infections
Ed Yong’s oeuvre on the microbiome at Not Exactly Rocket Science
Mayrn McKenna on her blog at Wired writing on the link between beneficial ...

discovermagazine.com | 18-Apr-2012 16:16

Numbers: The Majority of Minors Have Faced Mental Illness | DISCOVER

82.5: The percentage of children and young adults who exhibit significant symptoms of mental illness at some point between the ages of 9 and 21. The startling statistic comes from a collaborative study conducted by Duke University and the North Carolina Department of Health and Human Services, which surveyed 1,420 children over 12 years beginning in 1993. Investigators checked in up to nine times to test for anxiety, depression, addiction, obsessive-compulsive 
disorder, and more. The results...

discovermagazine.com | 17-Apr-2012 21:35

None dare call it eugenics! | Gene Expression

Well, almost no one:

“The unspoken central reason for the societal taboo and the penal ban on incest is the possibility of hereditary defects — a factor that Strasbourg only hinted at. But the intention behind the eugenic argument is one that is indefensible, and not just in Germany with its terrible Nazi past: The increased risk of hereditary defects does not justify a legal ban. Otherwise you would have to legally ban other risk groups, like women over 40 or people with genetic diseases, from having children. Does anyone truly want to prevent predictable disabilities using penal measures and thus deny disabled children the right to life in 2012? That’s absurd. And yet such fears of genetic damage are precisely what shape the punishibility of sexual intercourse between siblings.”

There are a set of arguments against near relation incest which strike me as generally ad hoc. And there’s social science to back that up. Incest is reflexively disgusting to most people (depending on how it is categorized). But disgust alone is not a sufficient grounds for banning a practice in educated circles today, so people create rationales after the fact. ...

discovermagazine.com | 17-Apr-2012 06:37

Could Bird Flu Be a Weapon? Dutch Law May Keep Flu Research Bottled Up | 80beats

Publication of the controversial mutant avian flu papers have hit yet another roadblock. In March, a US advisory panel reversed its prior decision to take out experimental details from two reports about research that seemed to turn the H5N1 bird flu virus into a more virulent and deadly form. Under the original decision, some redacted information would have been available only to accredited researchers.

But in a new, international twist, one of the papers is encountering another obstacle: NPR reported that the Netherlands-based team behind one of the studies is being stifled by Dutch law, which limits the export of technology that could be weaponized. So now there are two main questions about whether the flu research would be published for all to see: how dangerous the virus is, and whether the Dutch law would apply to this research.

Humans, This Mutant H5N1 Virus Will Not Kill You

Last year, two research teams submitted papers that showed how H5N1 could be made contagious between ferrets, which are the best stand-in for humans when it comes to flu research. (The wild H5N1 virus only spreads from bird to human, so an airborne human-to-human virus could be much deadlier in the hands of bioterrorists.) ...

discovermagazine.com | 16-Apr-2012 21:00

Dog Ate My Experiment—And Now Dog Is My Experiment | Discoblog

Please don’t make me eat thallium.

If you’re an average normal person and your dog eats thallium-tainted agar plates from the trash, you’d probably take Rover to the vet. If you’re a vet and your dog eats thallium-tainted agar plates, you start taking notes—and blood and hair samples too.

That’s the backstory to a recent paper published in the Journal of Veterinary Diagnostic Investigation. A poor, overly curious one-year-old shepherd mix broke into the laboratory trash and gobbled up 15 agar plates containing thallium. The poisonous compound is used in labs to isolate Mycoplasma fungi because it pretty much kills everything else that could grow on agar. Known as “the poisoner’s poison,” thallium has also been implicated in a number of famous murders and was a favorite of Saddam Hussein. (So if you are a non-scientist with thallium in your trash, it is kind of suspect…)

The dog’s owner, a vet, knew immediately the thallium was bad news. At the onset, the dog refused to eat and lost weight. And then things only got worse over several weeks as she lost control of her muscles, seized, caught pneumonia twice, and lost a ...

discovermagazine.com | 16-Apr-2012 18:39

How to Treat Drug Addition With Videos of Drug Use | 80beats

What’s the News: Retrieving a memory in your brain is a bit like taking an old keepsake off the shelf. If you get startled while holding grandma’s old vase in your hands, you could drop and break it. Memory retrieval is just as vulnerable to disruption, and scientists have tried to exploit this fact to erase PTSD-associated memories with drugs.

A new study in Science tries a different tack, using a behavioral approach to rid people of addictions to drugs. Addiction is sometimes treated with “extinction,” which means showing patients drug-related images while they’re off drugs, so that, for example, they stop associating needles with a high. The researchers found that retrieving drug memories right before an extinction session—basically, giving them a short exposure to drug-related stimulus, followed by a similar but longer exposure session—made the treatment more effective in both rats and humans.

How the Heck:

The researchers got rats addicted to either cocaine or morphine and gave them a short memory-retrieval session 10 minutes, one hour, or six hours before the longer extinction session. Memory retrieval was done by giving the rats a light and sound cue they had previously learned to associate with getting high. ...

discovermagazine.com | 16-Apr-2012 17:39