Boing Boing 

Open-source human genomes

Yesterday, during a World Science Festival panel on human origins and why our species outlasted other species of Homo, geneticist Ed Green mentioned that there were thousands of sequenced human genomes, from all over the world, that had been made publicly available. Our code is open source.

But where do you go to find it? Several folks on Twitter had great suggestions and I wanted to share them here.

The 1000 Genomes Project—organized by researchers at the Wellcome Trust, the National Institutes of Health, and Harvard—is working on sequencing the genomes of 2500 individuals. The data they've already collected is available online. Read a Nature article about The 1000 Genomes Project: Data management and community access.

The Personal Genome Project is interactive. Created by a researcher at Harvard Medical School, the program is aimed at enrolling 100,000 well-informed volunteers who will have their genomes sequenced and linked to anonymized medical data. Everything that's collected will be Creative Commons licensed for public use.

The University of California Santa Cruz Genome Browser is a great place to find publicly available genomes and sequences.

Thanks to Eva Rose, Aatish Bhatia, and Edward Banatt.

How to: Collect 6,000-year-old swamp mud

Photo:Eric Niiler

I spent last weekend in the Harvard Forest, participating in hands-on science experiments as part of the Marine Biological Laboratory's science journalism fellowship. The goal was to give us an inside look at what, exactly, scientists actually do. When you're reading a peer-reviewed scientific research paper, where did all that data come from?

Sometimes, it comes from a swamp.

On Saturday, we walked into the Forest's Blackgum Swamp to take core samples out of the muck. There was no standing water in this swamp, at least not when we visited. But I wouldn't call the ground "solid", either. Instead, it was more like a moss-covered sponge. With every step, the ground beneath me would sink and smoosh. In some of the lower patches, that meant a shoe-full of water. In other spots, it was just a disconcerting sensation.

Taking core samples involves a little machine that's like a cross between a shovel and a straw. Made of heavy, solid metal, it has an extendable handle on one end. At the other, there's a hollow, cylindrical chamber that can be opened and closed by turning the handle counterclockwise. You drive the chamber into the ground, turn the handle, and then pull it back out. Once everything is back on the surface, you can open the chamber and see a perfect cylinder of earth, pulled up from below. That cylinder is removed from the chamber, wrapped in plastic wrap, labeled, and put in a long wooden box. Then you do all of that again, in 50 centimeter increments, until you hit stone. We got to about 475 centimeters—15 feet deep. By that point, you'll have collected 1000s of years of layered sediment.

This is not as easy as it sounds.

Read the rest

Enter the world of the xenopus

Every now and then, I get a glorious reminder of just how much the Internet has enriched my life. Fifteen years ago, if I had arrived at a conference center—as I did yesterday for my stint in the Marine Biological Laboratory Science Journalism Fellowship program—and seen a sign in the lobby announcing the presence of a "Xenopus Workshop" I could have, eventually, found out that a Xenopus was a frog frequently used as a model animal in medical research.

Thanks to the Internet, though, I was able to learn the following things in a remarkably short period of time:

Xenopus Fact: Xenopuses (Xenopodes? Xenopi? Freshman Latin was a really long time ago, you guys) were used in one of the earliest reliable pregnancy tests. That's because exposure even a tiny amount of the hormone human chorionic gonadotropin will cause a female Xenopus to lay eggs. Inject a female Xenopus with urine from a human female and, if the Xenopus lays eggs, it means the female human is knocked up.

Xenopus Fact: You know how some lizards can grow a new tail if you cut the old one off? Xenopuses can do that with the lenses of their eyes.

Xenopus Fact: Because Xenopuses are so widely used in laboratories, there's a whole industry of suppliers of Xenopuses and Xenopus accessories. Case in point, the "Xenopus enrichment tube" in the photo above—apparently, they like to have something to hide out in. Also, you can buy synthetic slime to replace your Xenopus' natural protective coating that is often lost through frequent handling.

More detail on what Kodak was doing with a neutron multiplier

Earlier today, David told you about a news story that's everywhere right now: The fact that the Kodak company ran a small nuclear facility at its research lab in Rochester, New York.

The facility closed down in 2007, but I can totally understand why this story interests people. It's nuclear! And it is really weird for a corporation to be sitting on 3.5 pounds of uranium. Like David said, this is unusual today. David did a good job covering this in a sane way. The TV news I saw this morning at the airport ... not so much. That's why I like the detail provided the Physics Buzz blog, where Bryan Jacobsmeyer explains, better than I've seen elsewhere, just what exactly Kodak was doing with their nuclear system. Turns out, it's really not all that odd for this specific company to own this specific piece of equiptment when they did. That's because of what Kodak was. We're not just talking about a corporation in the sense of middle managers and salesmen. We're talking about original research and development—a job for which a californium neutron flux multiplier is quite well suited.

In fact, these research reactors can be found on several university campuses, and they are operated under strict guidelines without any nefarious intentions.

Researchers working at Kodak wanted to detect very small impurities in chemicals, and Neutron Activation Analysis (NAA) proved to be one of the best techniques to find these impurities. During NAA, samples are bombarded with neutrons, and elemental isotopes from the sample will absorb a small fraction of these neutrons.

Many of these stable elemental isotopes will become radioactive after gaining a new neutron; consequently, they will emit gamma rays. With the right equipment, researchers can measure the precise energy levels of this radiation and narrow down which elements are in the sample.

Basically, it provided a way to sift through the components of a sample at a molecular level, and spot the things that shouldn't be there. Originally, the lab used just californium. Later, it added uranium plates that helped make the system more powerful.

Read the full Physics Buzz post

Via Jennifer Ouellette

Image: IMG_7391.jpg, a Creative Commons Attribution (2.0) image from jameskarlbuck's photostream

Curiosity in the desert

Last week, scientists used ice caves in Austria as a stand-in for Martian caves, testing spacesuits and rovers in the freezing chambers. This week: We go to the desert near Baker, California, where NASA is testing out its Curiosity rover. Curiosity is 86 days away from landing on the real Martian surface.

Gene Blevins / Reuters

Testing spacesuits beneath the Earth's surface

The Eisriesenwelt—the "World of the Ice Giants"—is an Austrian cave that stays cold enough year-round to freeze any water that gets into it. As a result, the cave is full of massive ice formations. On April 28th, it was also full of people like physicist Daniel Schildhammer (seen above) who came to the cave to test out a wide array of space technologies, from protective suits to roving robots. It's all part of an international effort to prepare for a mission to Mars. Caves on Mars are likely place where bacteria and other forms of microbial life might be hiding out—the temperatures stay steady underground and the cave would protect those microbes from cosmic rays. Below: Another scientist tests out a rover meant to scale cliffs.

Images: REUTERS/Lisi Niesner

Why we still don't totally understand how diseases spread

 

When I was little, I read a Reader's Digest book of great disasters, which included a segment on the Black Death. One of the things the book tried to do was explain, on a child's level, why it wasn't easy to figure out that rats and fleas were the source of the plague. You couldn't just look for patterns, because there seemed to be no pattern. Half a household might drop dead while the other half only got a little sick, or remained entirely healthy. Plague doctors who handled the sick every day lived another 20 years. The real spread of disease wasn't like the movies, where one person coughing means everyone in close proximity is doomed.

One reason for the emergence of strange non-patterns like this is something called "super spreaders"—basically, some people spread disease more effectively than others. The infamous Typhoid Mary is the poster child for super spreaders, but the effect has been well-documented in a range of infectious diseases and it goes beyond the simple story of one woman who infected thousands. In fact, what makes the super spreader phenomenon so fascinating is that it isn't an anomaly at all. Super spreaders are the primary way some diseases spread. The Contagions blog—which is all about the history of infectious disease—has a great post up about this.

Eventually new models arose like the “20/80″ rule that says that 20% of cases are responsible for 80% of the transmission and formed a core ‘high risk’ group. This model works well for some diseases but not all.

For pathogens that do rely on super-spreaders, the majority of cases will not transmit the infection to anyone. This can lead to a sense of false security because it seems poorly communicated. As Galvani and May assert, “heterogeneously infectious emerging disease will be less likely to generate an epidemic, but if sustained, the resulting epidemic is more likely to be explosive”. Super-spreaders tend to beget more super-spreaders, although most of the cases they generate will still not transmit the infection to anyone. For example, a super-spreader begets 30 cases, 3 (10%) of which become new super spreaders. The rest may transmit to 0-1 people.

Super-spreading has been documented for HIV, SARS (Sudden Acute Respiratory Syndrome), measles, malaria, smallpox and monkeypox, pneumonic plague, tuberculosis, Staphylococcus aureus, typhoid fever, and a variety bacterial sexually transmitted diseases.

And that brings us back to medical mysteries because, the Contagion blog explains, we don't know exactly why some people are super spreaders and others aren't—or why some people are more vulnerable to infection than others. So far, what we have to go on is a list of well-established correlations.

Read about what makes a super-spreader at the Contagions blog.

Image: Thomas Bartholini's illustration of beak doctor from 1661. Via Wikipedia.

Moon boxes and mystery men

See the box in this photo? It's more interesting than it looks. This is a box that went to the Moon.

Astronauts used the boxes to collect and bring back to Earth nearly 50 pounds of moon rocks and soil ... Each of the boxes was machined from a single piece of aluminum, "seamless except for the lid opening, which had a metalized gasket that firmly sealed when closed."

The photo comes from the Y-12 National Security Complex in Oak Ridge, Tenn.—a research facility that participated in the Manhattan Project and later was involved in designing equipment for the Apollo Project. Journalist Frank Munger writes about Y-12 and other parts of the Oak Ridge National Laboratory for the Knoxville News Sentinel.

This photo, which he posted on his blog, is also interesting because nobody knows who the three guys in the photo are. Munger was hoping that Boingers might be able to offer some leads.

Read Frank Munger's blog post

How long does food poisoning last?

I recently had what I am pretty sure was foodborne illness. It arrived in the middle of a friend's birthday party, a sudden onslaught of misery that lasted for the next 8 hours, reminding me, horribly, of a similar scene in The Mask of the Red Death. It was followed by two days of pretty much constant sleep. I don't recommend it.

But if a growing body of research is right, that 48-hours of grossness might not be the end of your body's interaction with a foodborne bug. In fact, some people seem to have otherwise unexplained symptoms persisting for years after they thought they'd recovered from food poisoning. This is best documented in people whose food poisoning experience was much worse than mine—folks who ended up in the hospital or the doctor's office and were, thus, accurately diagnosed, so we know they had a foodborne illness and not, say, a stomach flu. But it's an interesting hypothesis.

Maryn McKenna, my favorite Scary Disease Girl, has a story about this at Scientific American, plus some extra information at her Wired blog, where she explains why this phenomenon is so difficult to study.

I start the story with the tale of a Florida teen named Dana Dziadul, who 11 years ago was hospitalized with Salmonella and now at 14 has what is called “reactive” arthritis. Her mother Colette struggled for years to figure out why this was happening to her daughter, but didn’t put the pieces together until she was asked to complete a survey of foodborne illness survivors, and spotted a list of possible after-effects — sequelae, technically — that the surveyors were curious about. That caused her to go back into Dana’s medical chart, where she realized that her daughter’s joint problems actually began while she was hospitalized as a 3-year-old.

The challenge of proving this connection is that our system for investigating foodborne illness is not set up for tracking victims long afterward. That’s first because state health departments, which bear the burden of identifying outbreaks, are most concerned with finding people at the time, not keeping track of them; and second, because many outbreaks are spread across multiple states, with only a few victims in each state — so that maintaining contact with former victims would require a shared effort that no one is set up, or funded, to do. (That’s not even to mention the complication of people moving from one jurisdiction to another. Myself, for instance, I’ve moved five times in the past 10 years.)

Read the full story at Scientific American.

Read Maryn's summary of the research, and extra info, at her Wired blog.

Image: X.L.D. Agar 1 - detail, a Creative Commons Attribution (2.0) image from nathanreading's photostream

Historic Apollo 11 rocket engines found on ocean floor by Jeff Bezos and team

Amazon founder and space entrepreneur Jeff Bezos announces on his blog that the Apollo 11 rocket engines which propelled Neil Armstrong and Buzz Aldrin to the moon in 1969—making them the first humans on the moon—have been found on the bottom of the Atlantic ocean by Bezos' research team. Next step? Finding a way to safely recover the long-lost engines, and bring them back to the surface.

Snip:

Millions of people were inspired by the Apollo Program. I was five years old when I watched Apollo 11 unfold on television, and without any doubt it was a big contributor to my passions for science, engineering, and exploration. A year or so ago, I started to wonder, with the right team of undersea pros, could we find and potentially recover the F-1 engines that started mankind's mission to the moon?

I'm excited to report that, using state-of-the-art deep sea sonar, the team has found the Apollo 11 engines lying 14,000 feet below the surface, and we're making plans to attempt to raise one or more of them from the ocean floor. We don't know yet what condition these engines might be in - they hit the ocean at high velocity and have been in salt water for more than 40 years. On the other hand, they're made of tough stuff, so we'll see.

Read more at his Bezos Expeditions blog.

Your brain, your food, and obesity

We recently hosted an article by scientist and guest blogger Stephan Guyenet that explained how certain foods—those with a high calorie density, fat, starch, sugar, salt, free glutamate (umami), certain textures (easily chewed, soft or crunchy, solid fat), certain flavors, an absence of bitterness, food variety, and drugs such as alcohol and caffeine—could trip reward systems in the human brain. Those reward systems, then, encourage people to eat more of the foods that trigger the reward. The result, says Guyenet, is a cycle that could be the link between the American obesity epidemic and the rise of highly processed convenience foods, designed specifically to trip those neural reward systems.

This theory, and several related theories, are increasingly popular in the scientific community. This week, there's an opinion piece in the journal Nature Reviews Neuroscience that looks at the strengths and weaknesses of these theories and talks about what research needs to be done going forward. It's kind of a space for researchers to step back and say, "Okay, here's what we know, here's what's not lining up with what we think we know, and here's what we have to do if we want to understand this better." In the context of science, an article like this isn't really a slam against the ideas it analyzes. Instead, it's meant to summarize the state of the science and share ideas that could either strengthen the case, or lead down entirely new roads.

Sadly, you can't read this article unless you have a subscription to Nature Reviews Neuroscience (or pay them $32 for single article access).

Luckily, Scicurious, a neuroscientist and an excellent blogger, has read the article, and has a nice run-down of what it's saying and what you should know. Some of the ideas being discussed here overlap with Stephan Guyenet's research. Some don't. But this is connected enough that I thought you guys would be interested in reading more and getting more perspectives on this issue. Let me make this clear, though: Guyenet isn't doing bad science. As with a lot of scientific research, there's often more than one way to look at the same data. Scientists can disagree without one person having to be all-wrong and another all-right. In fact, having different scientists working on the same subject is a key part of getting the facts right.

As you read, you'll notice that an important place where Scicurious' perspective really differs from Guyenet's is in terms of connecting the idea of "addiction" to certain foods back to the idea of an obesity epidemic.

...is there a place for food addiction? The authors think so, and I am inclined to agree. However, it needs to be much more stringent than the current model of food addiction that many people want to embrace (the idea that sugar makes you addicted or that being overweight means you have a problem). Changes need to be made.

First off, it's important to separate food addiction from obesity. Binge eating does not necessarily mean you are overweight, and being overweight does not necessarily mean that you binge eat. Ranking by BMI is not going to work.

Read Scicurious' full post.

(Via the illustrious Ed Yong. Image: Fabio Berti, Shutterstock)

Dosing cats with Uncle Sam

Over on Submitterator, frycook keeps finding these amazing/horrible old U.S. Army newsreels. He or she has posted some great stuff, including this gem, in which the chemical corps tests psychoactive substances on a cat while the narrator cheerfully natters about the strategic military benefits of hallucinogens.

Video Link

Quick! Apply to taste Mars mission food during 120-day study in Hawaii

Yes, the deadline is tomorrow. But I know this is the perfect opportunity for at least one of you, so hop to it! Cornell and the University of Hawaii are putting together a series of studies aimed at finding out what it's going to take to keep people well-fed (both in the physical and psychological sense) during a trip to Mars. The research culminates in a 120-day analogue mission, during which subjects will live in a "Mars-like habitat", where they will eat nothing but rehydratable and instant space foods and will record data on factors like bodily odors and emotional well-being. If you've got a bachelor's degree in the sciences or engineering, a desire to contribute to the future of space travel, and a strong stomach, this might be the study for you! Here's the information on how to apply. (Via Paleofuture)

AIDS research done by 17-year-olds: Day 2 at AAAS 2012

It's that time again. Maggie is back at the largest science convention in the Western Hemisphere for four days of wall-to-wall awesomeness.

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Academic database "imprisons" research

Laura McKenna excoriates JSTOR, the online database of academic journals that has universities and the public paying thousands of dollars to read their own taxpayer-funded research. [The Atlantic]

I will not put a pun in this headline

You may be pleased to know that there is an International Forum for the Study of Itch. And it has a regular conference, which just leads to inevitable jokes.

Open medical knowledge saves lives: Oppose H.R. 3699

Here's a terrific article by Gilles Frydman at e-patients.net advocating for opposition to H.R. 3699, aka The Research Works Act (RWA). The bill before Congress would seriously impede "the ability of patients and caregivers, researchers, physicians and healthcare professionals to access and use critical health-related information in a timely manner." (@timoreilly via @epatientdave)

Inside NASA's Venus machine

This chamber, currently under construction at NASA Glenn Research Center in Cleveland, will be able to reproduce the temperature, pressure, and chemical conditions on the surface of Venus. Scientists will use it to find materials and lander designs that can withstand the 1,000 degrees Fahrenheit temperatures on that planet.

In a story on the chamber for WIRED, Dave Mosher points out that a similar chamber already exists. The trouble is, it's too small to fit a life-size model of a Venusian lander. The new chamber will be big enough to test out equipment at the size it will be used. Better yet, the new chamber could also be used to replicate conditions on other moons and planets, as well.

Thanks to its thick walls, it can simulate all conditions experienced during a trip to Venus: launch, the cold vacuum of space and even atmospheric entry.

In the future, operators could simulate conditions found in Jupiter’s outer atmosphere, the Martian equator and even vents near volcanoes on Jupiter’s moon Io. Seven- and 10-foot-wide additions to the first chamber (below) could also make room for prototypes designed for ultra-cold conditions on the moons Europa, Ganymede and Titan.

A scientific conference presentation no one will ever forget

"He stepped around the podium, and pulled his loose pants tight up around his genitalia in an attempt to demonstrate his erection." — You really, really, really must read the story of Professor G.S. Brindley, the 1983 Urodynamics Society meeting, and the first public demonstration of the first effective medical therapy for erectile dysfunction. NSFW. (Thank you, Miriam Goldstein. I think.)

TV, video games, or Internet: Which activity makes teenagers fat?

I talk a lot about the importance of context in understanding science. The results of one, single research paper do not tell you everything you need to know on a given subject. Instead, you have to look at how those results fit into the big picture. How do they compare to the results of other studies on the same subject? Have the results been independently verified? How do the specific experiments being done influence what you can and cannot say about the results? What questions aren't answered by the study, and what new questions does it bring up?

You should be thinking about that every time you see anybody talk about the results of a single, new study. Without context, you get situations like this one, described by Travis Saunders on the Obesity Panacea blog:

Earlier this year my friend and colleague Valerie Carson published an interesting paper examining the health impact of various types of sedentary behaviour in a sample of 2500 children and adolescents. They created a clustered risk score (CRS) which took into account a child’s waist circumference, blood pressure, cholesterol, and inflammation, and then examined whether it was associated with 3 different measures of sedentary behaviour – accelerometry (an objective measure of movement), self-reported TV watching, and self-reported computer use.

Here is what they found (emphasis mine): For types of sedentary behavior, high TV use, but not high computer use, was a predictor of high CRS after adjustment for MVPA and other confounders. Here is what the Daily Mail had to say: Watching TV most damaging pastime for inactive children, increasing risk of heart disease.

Last month, our group in Ottawa published another paper (led by Dr Gary Goldfield) looking at different types of sedentary behaviour and heart disease risk factors in a cohort of overweight and obese teens (in contrast, the earlier study was on a sample of nationally representative youth). Interestingly, we found that neither TV time nor computer time was associated with increased risk in this group - in our dataset it was video games that were by far the most important sedentary behaviour.

Why is this a problem? Put yourself in the shoes of someone who just read the Daily Mail article, and who now believes that TV viewing is the single most damaging sedentary behaviour for kids to engage in. What reaction are you going to have when you read a similar article about our new study, suggesting that TV viewing and computer use aren’t important at all, but that video games are actually “the most damaging activity an inactive child can indulge in”?

As the source of this problem, Saunders rightly calls out journalists for pushing every individual study as a "GROUNDBREAKING NEW FINDING". It is, unfortunately, rare to find TV and newspaper coverage that treats new studies in context, rather than as the final word. But to that, I'd add university PR people. The sad truth is, with newspaper layoffs, many of the people writing about science aren't specialists. They cover city council one day, school board the next, and a new research finding after that. The press releases they get (and I know, because I get those press releases, too) push GROUNDBREAKING NEW FINDINGS not research that fits into a larger context. It's the journalists job to know better. But it's also the university's job to not manipulate journalists.

A hole in the ground: Storing carbon dioxide thousands of feet below Illinois

One blazing hot afternoon in August of 2010, I stood on a mountain top in Alabama, staring at a styrofoam beer cooler upended over the top of a metal pole.

Read the rest

Sad story about a chimp in space

The life story of Enos, the second primate to orbit Earth, is extremely depressing. In fact, it's significantly more depressing than the life story of Yuri Gagarin, the first primate to orbit Earth. Which is saying something.

Otzi the Iceman and life after death

In Science Ink, Carl Zimmer's new book collecting photos of cool science tattoos and the stories behind them, there's a photo of a guy who got tattoos to match those found on Otzi, aka The Iceman, who died more than 5,000 years ago in the Italian Alps.

Mike Goldstein, the guy who got the tattoo, said the series of 10 simple lines arranged in groups of four, three, and three served to remind him that you don't have to be incredibly important during your lifetime in order to be important. "It reminds me that I can live however I want," he says in the book. "I don't have to work in an office or wear a tie, as are the expectations of our culture. I can walk across the Alps and die in a swamp, and that's OK."

I was reminded of that quote today, while reading my news stream. There's no evidence that Otzi was a particularly important figure to his culture. But here we are, thousands of years later, still debating the minutia of how he died. Emily Sohn writes about new Otzi research for Discover News:

...new analyses have revealed that a deep cut likely led to heavy bleeding in the man's eye. In the cold, high-altitude conditions where he was found, that kind of injury would have been tough to recover from.

The official opinion remains that an arrow in his left shoulder was the cause of death for Ötzi. But the new study raises the possibility -- for some, at least -- that he fell over after being shot by an arrow. And, at higher than 10,000 feet in elevation, his alpine fall may have made the situation much worse.

"Maybe he fell down or maybe he had a fight up there, nobody knows," said Wolfgang Recheis, a physicist in the radiology department at the University of Innsbruck in Austria. "With this cut alone, at 3,250 meters, it would have been a deadly wound up there. Bleeding to death in the late afternoon when it was getting cold up there, this could be really dangerous."

Granted, most of us have a better chance of making an impact after our deaths by helping other people during our lives. Or by donating our bodies to science. But it's still interesting to think about all that could happen to you thousands of years after you're gone.

The trouble with lab mice

You've probably seen this caveat pretty often: Just because a study that uses mice as subjects produces a specific result, doesn't mean you'd get the same result using human subjects. Mice are handy research animals, but they aren't perfect analogues to humans. A mouse study is a stepping stone towards better evidence. It is something we do because there are potentially useful ideas that we should not try out on humans first. But mouse studies should not count as incontrovertible proof of anything.

Usually, when that caveat comes up, the person giving it is talking about fundamental differences between mouse biology and human biology. For instance, a mouse might only need one copy of a genetic factor to grow normally. Meanwhile, a human needs to have both copies or risk altered sexual development.

But there are other problems with mice, problems that have more to do with how we select, breed, and raise mouse models. In a fascinating three-part series on Slate.com, Daniel Engber looks at how we undermine the usefulness of our own lab mice, and the risks we take when we do so.

If you put a rat on a limited feeding schedule—depriving it of food every other day—and then blocked off one of its cerebral arteries to induce a stroke, its brain damage would be greatly reduced. The same held for mice that had been engineered to develop something like Parkinson's disease: Take away their food, and their brains stayed healthier.

But Mattson wasn't so quick to prescribe his stern feeding schedule to the crowd in Atlanta. He had faith in his research on diet and the brain but was beginning to realize that it suffered from a major complication. It might well be the case that a mouse can be starved into good health—that a deprived and skinny brain is more robust than one that's well-fed. But there was another way to look at the data. Maybe it's not that limiting a mouse's food intake makes it healthy, he thought; it could be that not limiting a mouse's food makes it sick. Mattson's control animals—the rodents that were supposed to yield a normal response to stroke and Parkinson's—might have been overweight, and that would mean his baseline data were skewed.

Part 1: The unhealthy lives of industrialized lab mice
Part 2: The trouble with focusing so much research on one single mouse species
Part 3: Why the naked mole rat (and the Burmese python) can help

A tour of McMurdo Station, Antarctica

This video was made by Henry Kaiser, a musician and research diver who guest blogged here yesterday about the problems caused by thinning sea ice in Antarctica. The film takes you on a tour of McMurdo Station and the research being done there by Gretchen Hoffman of the University of California Santa Barbara.

Kaiser dives for different researchers every year. This year, he's working with Hoffman's team, helping them study the effects of climate change on ocean life. Specifically, Hoffman has Kaiser out collecting Antarctic sea urchins so that her team can extract the animals' sperm and eggs to test the development of sea urchin zygotes in differing conditions of PH and temperature.

There's great footage in here of human life above the ice, and animal life below. It's a bit long, but I recommend taking the time to watch the whole thing.

Video Link

Once more, with feeling

A repeat of the faster-than-light neutrino experiment turned up the same result. Bear in mind, this was performed by the same group of researchers that performed the original experiment. So it's not quite the same thing as if the results had been reproduced by an entirely different team of scientists. But it is a step forward in what will be a long process. So far, we still can't rule out that neutrinos can travel faster than the speed of light.

The problem with fecal transplants

Over the past few years, we've linked to a couple of stories about fecal transplants—a real medical procedure where doctors take a donor stool sample, dilute it, and inject it into the colon of a patient. It sounds gross. But it appears to be incredibly effective at treating certain intestinal issues.

Basically, the fecal transplant is really a bacteria transplant. A fresh set of healthy bacteria can fix problems that aren't reliably treatable any other way. On the other hand, most of this information comes from anecdotal evidence. Fecal transplants haven't gone through any large-scale, randomized clinical trials. Until that happens, most doctors won't offer the procedure and insurance won't cover it. That makes sense. We rely on clinical trials to separate treatments that work from treatments that just appear to work. The problem with fecal transplant, though, is that it doesn't fit into any of the bureaucratic categories necessary to get a trial like that approved.

Over on Scientific American, Maryn McKenna has a great feature about fecal transplants—their promise, what we don't know about them, and what's keeping them from becoming a mainstream treatment.

Marion Browning of North Providence, R.I., was at her wit’s end. The 79-year-old retired nurse had suffered from chronic diarrhea for almost a year. It began after doctors prescribed antibiotics to treat her diverticulitis, a painful infection of small pouches in the wall of the colon. The regimen also killed friendly bacteria that lived in Browning’s intestines, allowing a toxin-producing organism known as Clostridium difficile to take over and begin eating away at the entire lining of her gut ... In the fall of 2009 Browning performed the bowel-cleansing routine that precedes a colonoscopy, while her son took an overnight laxative. Kelly diluted the donation, then used colonoscopy instruments to squirt the solution high up in Browning’s large intestine. The diarrhea resolved in two days and has never recurred.

Browning is not alone in being a success story. In medical journals, about a dozen clinicians in the U.S., Europe and Australia have described performing fecal transplants on about 300 C. difficile patients so far. More than 90 percent of those patients recovered completely, an unheard-of proportion. “There is no drug, for anything, that gets to 95 percent,” Kelly says. Plus, “it is cheap and it is safe,” says Lawrence Brandt, a professor of medicine and surgery at the Albert Einstein College of Medicine, who has been performing the procedure since 1999.

So far, though, fecal transplants remain a niche therapy, practiced only by gastroenterologists who work for broad-minded institutions and who have overcome the ick factor. To become widely accepted, recommended by professional societies and reimbursed by insurers, the transplants will need to be rigorously studied in a randomized clinical trial, in which people taking a treatment are assessed alongside people who are not. Kelly and several others have drafted a trial design to submit to the National Institutes of Health for grant funding. Yet an unexpected obstacle stands in their way: before the NIH approves any trial, the substance being studied must be granted “investigational” status by the Food and Drug Administration. The main categories under which the FDA considers things to be investigated are drugs, devices, and biological products such as vaccines and tissues. Feces simply do not fit into any of those categories.

Image: Toilet Roll, a Creative Commons Attribution (2.0) image from smemon's photostream

Can cows sense magnetism? The debate continues

In 2008, some scientists proposed that cows can sense magnetism and actually line up in fields along Earth's magnetic lines. It's the sort of paper that everybody in the media wants to talk about for, roughly, two weeks ... and then never mention again.

But that's not how science works. One research paper does not an unquestionable fact make. Luckily Discover's Discoblog has been kind enough to update us on the current state of magnetic cow research. Shorter version: This issue is far from settled, with a second research team attempting to poke holes in the original study. Nevertheless, outside researchers say, the original findings still look strong. There is evidence that herds of cows stand along magnetic lines, and fail to stand along those lines in the presence of magnetic-field distorting high-voltage power lines. Whether this is absolutely the case and, if so, why, remains a bit of a mystery. Needs moar research.

... an analysis of Google Earth images by another team finds no such lining up. In a back-and-forth over the last year in scientific journals, the first team reanalyzed the second’s data and said that half of the images were useless, since they were near high-voltage power lines or contained hay bales or sheep instead of cows. Plus, the first team points out that the second team looked at single cows within herds instead of herds as a whole, and it’s pretty clear at this point that animals in herds and flocks aren’t operating as independent entities. The second team retorts that their images were too okay to use, and the first team may have been looking at the wrong pictures.

Image: Cows, a Creative Commons Attribution (2.0) image from 35463710@N06's photostream

How autistic adults can contribute to science

The downside to having a brain disorder: Your brain works differently than the majority of humans'. That can make it difficult to participate in society. It puts people at risk for poverty, abuse, and exclusion.

The benefit to having a brain disorder: Your brain works differently than the majority of humans'. That means that you could have something really valuable to contribute to society, if society will make a space for you.

Back in September, Amy Harmon wrote a great long feature for the New York Times Magazine about efforts to integrate autistic adults into the larger community. Now, the journal Nature has published an interesting commentary about how autistic adults can aide the cause of science as researchers. A commentary is basically like an editorial. In this case, a scientist combined several published research papers and his own experience to make a point. The Canadian Globe and Mail had this to say:

Over the past seven years, eight people with autism have been associated with Laurent Mottron’s research group, including Michelle Dawson, who has become a close collaborator. Some of the team members have exceptional memories, while others have an ability to see patterns in data, or other skills, and contribute because of their autism, not despite it, Dr. Mottron said.

... Individuals with autism tend to fare poorly on a standard IQ tests that require verbal instructions, but can do much better on non-verbal tests that measure reasoning and creative problem-solving. They are faster on these kinds of tests than normal volunteers and use a different part of the brain to solve the problems.

Other studies suggest people with autism are also better in a wide range of perception tasks, such as spotting a pattern in a distracting environment or mentally manipulating complex three-dimensional shapes.

...He said that people with autism in the workplace may need mediators to help settle situations that trigger anxiety, giving occasions when Ms. Dawson’s computer crashes as an example.

The new Nature paper is locked, unfortunately. But you can read a 2006 research paper by Laurent Mottron on the same subject.

Via Annie Murphy Paul

Help crowdfund scientific research!

Over the next two months, you can fund scientific research through Rockethub.

The SciFund challenge runs from November 1 through December 15. Essentially, it's an experiment by a group of scientists who think that they might be able to use crowdfunding to fuel their research. Forty-nine different projects, in a wide variety of disciplines, have signed on to the challenge.

You can browse the projects, decide which ones you'd like to help support, and make a donation. As a bonus, many of the projects are offering nice little gifts for crowdfunders. For instance, if you donate $75 to help researchers at the University of Massachusetts, Amherst study the biology and physics of duck sex, you'll earn a pass code to access a regularly updated research blog, a collection of duck postcards, a "Duck Force!" mug, and a USB flash drive loaded with videos of explosive duck ejaculations that the scientists filmed for their research. (Naturally, this is one of the projects that have currently raised the most money.)

Not interested in duck sex? You're a rarity on the Internet, but there are plenty of other options. There are studies on depression, urban butterflies, cellulosic biofuels, and the mathematics of direct democracy.

Check out all 49 projects. And pledge your support to science!

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