Science-- there's something for everyone

Friday, November 30, 2012

Selfish huddling for the common good

Emperor penguins (Aptenodytes forsteri) have perfected the art of the huddle. It’s this tight bunching of up to ten of these large birds per square meter that lets them survive the harsh Antarctic winter storms. It’s not hard to see how the birds in the center benefit. Not only is the temperature at least twenty degrees warmer in the center, but even more importantly, birds located in that region are not exposed to the grueling winds. But what about the unfortunate birds on the periphery? Do they get a turn on the inside?

You’ll be happy to hear that penguins are surprisingly egalitarian. All members get an equal chance to enjoy the shelter of the huddle’s center. What may surprise you is how the penguins achieve this fairness. According to Aaron Water, Fran├žois Blanchette and Arnold Kim from the University of California, Merced, the flow of penguins within a huddle is entirely self-centered and can be predicted mathematically.

To be clear, the authors did not observe actual penguin huddles. Their data is based on computer simulations. You can see an example below:


Temperature distribution around a huddle of 100 penguins. Here red and blue correspond to warmer and cooler temperatures, respectively. Individual penguins are shown in black, as is the boundary of the huddle, while the polygonal interior of the huddle is shown in white.

The scientists began with the assumption that each penguin’s movements are based solely on whether such movement would benefit it personally. They then threw different wind and temperature conditions at their huddle model. The ‘bird’ with the greatest virtual heat loss (which would correspond to the bird in the most exposed position of the huddle) is relocated to a new position along the edge of the huddle. This is then repeated with the next most vulnerable penguin, which eventually causes the whole group to shift. Birds on the windward side end up on the leeward side, and birds that had been in the center are gradually edged out to the windward side.

You can see a real Emperor penguin huddle in the timelapse video below.

Aaron Waters, Fran├žois Blanchette, & Arnold D. Kim (2012). Modeling Huddling Penguins PloS ONE : doi:10.1371/journal.pone.0050277

Thursday, November 29, 2012

The whipworm treatment for inflammatory bowel disease

Some parts of the world have high incidences of inflammatory bowel disease (IBD). Those regions tend to have at least one factor in common: low rates of intestinal worm infection. Doctors have been investigating this intriguing connection and finding that giving people worms can actually benefit them. For example, people with ulcerative colitis (a type of IBD) have been helped by worm treatment.  But why is this so? Researchers, led by Mara Jana Broadhurst of the University of California, San Francisco and P’ng Loke of New York University, suggest that patients suffering from IBD have compromised mucosal barriers in their intestines, and that this defect is remedied by worm infestation.

A good model for ulcerative colitis is the idiopathic chronic diarrhea often suffered by captive baby rhesus macaque monkeys. The scientists treated five baby monkeys who had this illness by infecting them with the whipworm Trichuris trichiura. The researchers performed colonoscopies on the monkeys just prior to treatment and fourteen weeks after the worm treatment.

Four of the monkeys improved after the worm treatment, as shown both by weight gain and stool consistency. In addition, the colon biopsies revealed that the monkeys had a decreased inflammatory response after being infected with the worms. The mucosal layer of the primates’ intestines was restored to almost normal. Perhaps most significantly, the monkeys’ mucosal bacterial communities were also restored.

The authors summarize their hypothesis below:


Working model of the immunologic mechanisms underlying the amelioration of colitis in the setting of Trichuris sp. treatment.
(A)  Colitis is driven by a TH1-type inflammatory response to increased bacterial attachment and dysbiosis at the mucosal epithelium as a result of compromised barrier function.
(B)  Trichuris sp. elicits a mucosal TH2-type response (including the canonical cytokines IL-4 and IL-13) that promotes mucosal wound healing and mucus production. These functions reduce bacterial attachment and restore microbial homeostasis, removing the inflammatory stimulus.

Two things about this study. First, the authors did not include any controls. That is, all five of the monkeys received the worm treatment, none were untreated or received placebo. The researchers claim that there is plenty of evidence for how untreated baby monkeys fare under similar conditions. That may be true but further experiments including controls must be conducted before any broad conclusions are reached, something the authors agree to. Second, how glad are you that it isn’t your job to catalog monkey feces for consistency and quantity?

Mara Jana Broadhurst, Amir Ardeshir, Bittoo Kanwar, Julie Mirpuri, & et al. (2012). Therapeutic Helminth Infection of Macaques with Idiopathic Chronic Diarrhea Alters the Inflammatory Signature and Mucosal Microbiota of the Colon PloS ONE Pathogens : doi:10.1371/journal.ppat.1003000

Wednesday, November 28, 2012

Just for fun: Soaring around the Earth

James Drake put together this time lapse video from the perspective of the International Space Station.

Hat tip and explanation:  Bad Astronomy.

Tuesday, November 27, 2012

The smell of white

You’ve heard of white noise, and you’re certainly familiar with the color white. Now meet ‘olfactory white’, courtesy of researchers from the Weizmann Institute of Science led by Tali Weiss. Yes, they’ve identified white odors.

First, what is meant by white? When it relates to color or noise, white is what you get when you mix equal proportions of many wavelengths or frequencies. Despite being individually extremely varied, the disparate elements cancel each other out to produce a sensation we refer to as ‘whiteness’. The scientists were interested in whether you could create the same effect with smells.

To that end, the researchers started with 86 monomolecular odorants (chemically pure single smells) and diluted them to be of equal intensity. They then mixed the smells in various combinations. Mixtures contained anywhere from one to forty-three components. 56 volunteer sniffers compared 191 pairs of mixtures. Except for identity controls (both sniff-jars contained the exact same components), there were no component scents in common between the pairs of mixtures. In other words, if jar one contained elements 5, 13, 27 and 76, jar two did not contain any of those odorants.

The scientists found that the more components in each mixture, the more alike the two smells were judged to be. Jars with thirty or more component smells were rated as nearly identical despite having no scents in common. This is a clear analog for the color or sound we call ‘white’.

So why don’t complex foods and perfumes all smell alike? After all, many things contain more than thirty separate scents. Apparently, you need two conditions to achieve white smell. First, all the components have to be equally intense. This clearly isn’t the case for items like coffee. Second, the thirty plus individual aromas have to be from very different regions of the olfactory spectrum. You can’t get to white by mixing a bunch of smells that are already fairly similar. Taken together, this may mean that unlike the color white, white smells are a purely manufactured phenomenon. 

Weiss, T., Snitz, K., Yablonka, A., Khan, R., Gafsou, D., Schneidman, E., & Sobel, N. (2012). Perceptual convergence of multi-component mixtures in olfaction implies an olfactory white Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1208110109

Monday, November 26, 2012

Do animals get bored?

When I was a kid, I had a hamster that spent an inordinate amount of time climbing to the top of her cage and falling off, bouncing into her wheel multiple times on the way down. Thanks to the work of Rebecca Meagher and Georgia Mason from the University of Guelph I now think I know why. They found that caged animals get bored if they don't have enough variety in their environments. At least, that's true for mink.

Mink are small carnivores from the same family as weasels, ferrets and otters. The researchers divided 29 mink into two groups. All the mink were housed in identical wire cages with nest boxes. However, the mink fortunate enough to be in the enriched group (E) could access a second, much larger cage full of a variety of interesting objects and running water. The non-enriched group (NE) had no such tunnel access to goodies.

After seven months of acclimating to their respective living conditions, the mink were presented with some novel stimuli. These could be aversive (like a puff of air), neutral (a scented candle) or pleasant (for male mink, female feces made the list—go figure). Interest in food treats was also evaluated. The NE mink were far less reluctant to investigate even negative stimuli than the E mink, who presumably had better things to do with their time. The non-enriched mink also ate considerably more treats. All in all, the NE mink showed classic signs of boredom.

Although it can be dangerous to extrapolate across species, I wouldn’t be at all surprised if this result held true for other caged mammals. I guess we should be mixing it up a little more for our small pets.

Rebecca K. Meagher, & Georgia J. Mason (2012). Environmental Enrichment Reduces Signs of Boredom in Caged Mink PloS ONE : doi:10.1371/journal.pone.0049180

Wednesday, November 21, 2012

Just for fun: Capuchin equality

The title of this YouTube video says it all: Capuchin monkeys reject unequal pay.

Hat tip: Pam Dowling, who also coined the phrase 'throwing cucumbers'.

Tuesday, November 20, 2012

On the trail of chronic pain

NaV1.7 is a voltage-gated sodium channel. This means that it’s a group of transmembrane proteins that together form a tunnel through which sodium ions can pass. The passage isn’t open all the time though. Only a localized difference in electrical potential (voltage) will open the gate, allowing sodium ions to enter the cell from the outside. This, in turn, alters the microenvironment of the next stretch of membrane. In this way, a signal is rapidly propagated along the length of the cell. Each type of ion can only enter a cell through a matching ion channel (sodium ions through sodium channels, potassium ions through potassium channels, etc). What makes NaV1.7 special is that it’s associated with the sensation of pain.

Diagram of ion channel.
Credit Sandwalk.

If your NaV1.7 channels are inactive (permanently closed) you might not feel any pain at all (which is a lot worse than it seems). If the channels are overactive (unable to close) you’ll have chronic pain. This is the case for the unfortunate sufferers of a condition called inherited erythromelalgia, a.k.a. ‘Man on Fire Syndrome’. You can guess how that feels. To make things worse, some varieties of NaV1.7 channels do not respond well to medicines designed to stabilize ion channels.

Yang Yang and her colleagues from Yale University School of Medicine were able to study the effects of specific mutations within the NaV1.7 channels that render them more or less sensitive to pain medicines. Apparently, genotype does make a significant difference in how well people will respond to treatment. The scientists suggest that chronic pain patients routinely have their ion channels screened for subtype as a part of their treatment regimens. This may lead to the illusive cure for at least some types of chronic pain.

Yang, Y., Dib-Hajj, S., Zhang, J., Zhang, Y., Tyrrell, L., Estacion, M., & Waxman, S. (2012). Structural modelling and mutant cycle analysis predict pharmacoresponsiveness of a Nav1.7 mutant channel Nature Communications, 3 DOI: 10.1038/ncomms2184

Monday, November 19, 2012

Comet collisions at 49 CETI

Early in their history, stars are surrounded by a cloud of dust and gas. Although the dust may persist, the gas is usually lost fairly quickly (within a few million years). That isn’t the case for the star 49 CETI, which still has an extremely gassy orbit some forty million years after its formation. Cosmologists were at a loss to explain why all that gas was still in orbit around the star. Recently, Benjamin Zuckerman from the University of California, Los Angeles and Inseok Song from the University of Georgia came up with the solution. It seems that the gas is constantly being replenished from comet collisions.

In our solar system, there’s a disk of space known as the Kuiper Belt that begins just past the orbit of Neptune. This region of space is home to at least 70,000 objects, including the dwarf planet Pluto. Astronomers say that the total mass of these objects, currently one tenth that of the Earth, was once 400 times larger. Remember that our solar system is over a hundred times older than 49 CETI. If 49 CETI has its own, much younger, version of the Kuiper Belt, that band of comets could be far larger than ours. This is exactly what Zuckerman and Inseok found.

In fact, according to the researchers, there are hundreds of trillions of comets circling 49 CETI, so many that two of them collide about every six seconds. This constant barrage releases a steady stream of carbon monoxide into the surrounding space—enough to keep the orbit of 49 CETI well supplied with gas.

Zuckerman, B., & Song, I. (2012). A 40 Myr OLD GASEOUS CIRCUMSTELLAR DISK AT 49 CETI: MASSIVE CO-RICH COMET CLOUDS AT YOUNG A-TYPE STARS The Astrophysical Journal, 758 (2) DOI: 10.1088/0004-637X/758/2/77

Friday, November 16, 2012

Brute force cancer drug testing

There are different ways of finding effective anti-cancer drugs. You can carefully select the likeliest drugs based on their mode of action. Or you can throw everything you have at tumor cells and see what works. Susan Holbeck of the National Cancer Institute and her colleagues chose the latter route. Their results were presented at the 24th EORTC-NCI-ACCR (don’t ask) Symposium on Molecular Targets and Cancer Therapeutics.

There are currently a hundred approved anti-cancer drugs. Holbeck and her colleagues were interested in whether any of these drugs would be more effective against specific types of tumor if the drugs were used in combination. To that end, they tested all 5000 different drug combinations in 60 cell lines over the course of 300,000 experiments. The cell lines were chosen both because they were derived from nine distinct types of cancer and because they are well characterized (gene expression and other parameters are well understood in these cells).

As hoped, some of the drug combinations showed great promise in a few or many of the cell lines. A couple of the combinations have since been tested in mice and seem to be more effective than single drug regimens. Because all the drugs have already been approved for use in humans as single agents, the researchers hope that they can fast track any promising combinations into clinical trials.

Thursday, November 15, 2012

Beware of clean sheets

Ever find yourself struggling to pull an overly tight sheet onto a mattress? If so, you could be setting yourself up for a type of nerve damage. Francis Walker, Mary Lyles and Zhongyu Li of Wake Forest University School of Medicine document a case of a 73 year-old woman developing this condition after spending over an hour wrestling with her sheets.

You may be familiar with carpal tunnel syndrome, in which repetitive motions, such as the wrist flexing required for typing, cause pressure on the median nerve in the wrist. People with this syndrome may have pain or numbness in their hands or arms. However, overuse of the wrist can also result in blood clots that block those critical nerves. These clots impair the functioning of the hand and may need to be surgically repaired. Yanking on so-called fitted sheets is apparently a possible, though rather unusual cause of this problem. The woman in the case study developed clots in her wrist that prevented her from performing normal actions with her hand. Luckily, surgery and a year of physical therapy reversed the problem.

I knew there was a good reason not to change my sheets that often. Now to convince my family that we should all be using sleeping bags.

Walker, F., Lyles, M., & Li, Z. (2012). Sheet Fitting Palsy Journal of Clinical Neuromuscular Disease, 14 (1), 48-50 DOI: 10.1097/CND.0b013e31826506ff

Wednesday, November 14, 2012

Just for fun: Who would Attenborough save?

If you get BBC channels, then you may already know which ten species superstar naturalist Sir David Attenborough would save if he were in charge of an ark. For the rest of us, here's the list complete with pictures. You can read more about his rationale for choosing these particular creatures here.

1. The black lion tamarin
Image by Stavenn.

2. The Sumatran Rhino
Image by AlanB, May 18, 2007.

3. The Solenodon

Image by Frank Wouters, 2/4/2008.

4. The Olm salamander (a blind cave dweller than can live for a hundred years and go a decade without eating)
Image by Ranko, 7/13/2008.

5. The Marvellous Spatuletail hummingbird
Image by Roger Ahiman.

6. Darwin’s frog

Image by Mono Andes 7/28/2006.

7. The Sunda pangolin
Image by Stephen Hogg/WWF Malaysia.

A Sunda pangolin, not putting up much of a fight (Image: Stephen Hogg/WWF Malaysia)

8. Priam’s birding butterfly
Image by Barbara Stmadova, 2003.

9. The Northern Quoll (a marsupial)
Image by Wildlife Explorer 12/9/2009.

10. Venus’s flower basket (a sponge).

external image Venus-Flower-Basket.jpg

Tuesday, November 13, 2012

Good news for recovering addicts

Conventional wisdom says that drug or alcohol addicts can only kick their habits by abstaining from ever consuming their drug of choice again. It seems that addiction counselors aren’t getting that memo. Alan Davis and Harold Rosenberg of Bowling Green State University interviewed 913 members of the National Association of Alcoholism and Drug Addiction Counselors, and found that roughly half of them would feel comfortable telling some of their clients that it’s okay to imbibe now and then.

First, it’s important to note that the counselors distinguished between levels of addiction. For example, there’s a distinction between ‘abuse’ and ‘dependence’. People who abuse drugs may get into trouble with their bosses or loved ones, but they usually don’t suffer from withdrawal symptoms like dependent people. Second, the counselors took into consideration which particular drug or drugs were being abused.

Overall, about half the counselors were somewhat or completely comfortable telling at least some of their clients that strict abstinence was not necessary. The percentage depended on the degree of addiction, the drug or drugs of choice and whether the continued drug use was to be considered temporary or permanent. About 15% of counselors felt that even drug-dependent people could safely view non-abstinence as a final goal.

One important caveat is that this study did not evaluate outcomes. In other words, we don’t know from these results whether the counselors were right or wrong in allowing their clients to continue to use their substances. On the other hand, the authors suggest that telling drug addicts that they may not have to completely abstain from drug usage could make treatment more palatable. Just getting more people into treatment programs may be a net benefit even if some people relapse. 

Davis, A., & Rosenberg, H. (2012). Acceptance of Non-Abstinence Goals by Addiction Professionals in the United States. Psychology of Addictive Behaviors DOI: 10.1037/a0030563

Monday, November 12, 2012

The avian family tree

Walter Jetz of Yale University and his colleagues have put together the definitive molecular map of birds. They collected fossil and DNA data to determine how each of the 9,993 extant (living) species of birds is related to every other type of bird. They were able to see how both time and geographical location affected bird evolution.

Interestingly, there has been more rapid speciation in birds in the western hemisphere than in the eastern hemisphere. In contrast, speciation did not vary much between northern and southern hemispheres. Australia, Southeast Asia, Africa and Madagascar experienced counterintuitively low rates of diversification. Overall, the diversification rate has increased over the past 50 million years, contrary to what researchers expected to find.

The best part of this study is this lovely cladogram, courtesy of the University of Sheffield.

Diversification across the avian tree. 

W. Jetz, G.H. Thomas, J.B. Joy, K. Hartmann, & A. O. Mooers (2012). The global diversity of birds in space and time Nature : doi:10.1038/nature11631

Friday, November 9, 2012

Advances in science thanks to monsters and kids

How many scientific papers did you publish in high school? If the answer is none, then you’re one behind Julian Levy of Lord Byng Secondary School in Vancouver, British Columbia. He and his father, Alan Kingstone of the University of British Columbia, investigated whether it’s specifically the eyes or more generally the middle of the face that attracts our attention when we follow someone’s gaze. The results were published in the journal Biology Letters.

Many animals will follow another creature’s gaze. People certainly do this, and you can even induce a dog into looking where you’re looking. However, Kingstone wasn’t convinced that we’re really looking into each other’s eyes. Perhaps we’re simply focusing on the middle of the face, and the eyes just happened to be positioned there. How could you tell the difference? Enter Kingstone’s twelve year old son Levy, and the Monster Manual for Dungeons and Dragons. Humans may invariably have their eyes in the centers of their faces, but monsters have no such restrictions. 

So, if confronting a monster like the one above, where would a person spend most of his time looking? To answer this, Levy fitted 22 student volunteers with some eye-tracking equipment and had them watch video images of humans, humanoids with eyes in the centers of their faces, and creatures with eyes in completely different and unexpected places. Subjects quickly fixated on the eyes in each image regardless of where on the creature those eyes happened to be.

It seems obvious that we must be tracking eye-movements rather than facial postions when you consider that we can easily follow a gaze even if the indicator doesn’t move his head at all. Still, it was possible that we were wrong about this. Levy got a first authorship for coming up with a way to test the eye versus face problem and for doing the bulk of the experiments.

More from Ed Yong at Not Exactly Rocket Science.

Levy, J., Foulsham, T., & Kingstone, A. (2012). Monsters are people too Biology Letters DOI: 10.1098/rsbl.2012.0850

Thursday, November 8, 2012

Graduated driver license decals mean fewer crashes

Over the past few years, all U.S. states have passed graduated driver licensing (GDL) laws. These laws restrict teenaged drivers during their first months or years of having a license. For example, teens may not be allowed to carry passengers or to drive alone late at night. While this may seem like a good idea, it’s very difficult to enforce these laws. Police can’t tell whether a driver is under the jurisdiction of the GDL laws unless they stop him and examine his license. Some other countries with similar laws also require novice drivers to display decals on their cars. Police in these locations can clearly see if a car with a novice driver sticker is carrying a load of teenagers.

Would having a GDL decal affect crash rates within the U.S.? I’m glad you asked. It turns out that, thanks to New Jersey having implemented the first GDL decal law in the nation, we now have some data on the subject. Allison Curry from the Center for Injury Research and Prevention, The Children’s Hospital of Philadelphia, and her colleagues compared the number of citations and crashes given to teens both before and after the law was passed.

a New Jersey license plate.

The red decal required by the New Jersey law.

The New Jersey law requires all drivers under age 21 to display decals on the front and back license plates of any car they are driving. Citations increased by about 14% after the law went into effect on May 1, 2010. This isn’t surprising, since the decals made it much easier for police to pick out obvious violators. More importantly, there was a 9% decrease in the number of car crashes involving teen drivers after the GDL decal requirement became law. Police may be watching teen drivers more carefully or teens may only perceive that they’re being watched, but in any case, the law seems to be contributing to a safer driving environment for young people.

The decal law is not without controversy. Many teens and their parents would like to see it repealed, not least because they say it could allow predators to target young drivers. Those fears might change once information on the decrease in crash rates is disseminated among the public. In that case, perhaps other states will pass GDL decal laws as well.

Allison Curry, Melissa Pfeiffer, Russell Localio, & Dennis Durbin (2012). Graduated Driver Licensing Decal Law Effect on Young Probationary Drivers American Journal of Preventive Medicine.