Science-- there's something for everyone

Friday, March 29, 2013

Closing in on the origin of dog domestication

In 1975, the skull of an ancient canid (a member of the dog family) was discovered in Razboinichya cave within the Altai Republic, a mountainous region in southern Siberia. The skull was suspected to be that of a dog rather than a wolf or other canid. However, radiocarbon dating showed the skull to be about 33,000 years old, which is more than double the age of the oldest confirmed dog specimens. If the Altai skull was in fact a dog, that would significantly set back the date of dog domestication. The problem is that it's difficult to discriminate between early dog and wolf skulls. Researchers led by Anna Druzhkova of the Siberian Branch of the Russian Academy of Sciences solved that problem by doing mitochondrial DNA (mtDNA) analysis on the skull. They showed that it is indeed from a dog. This means that dogs have been around for a very long time, long before the invention of agriculture or the wheel.


The Razboinichya canid.
A)   aerial view, B) profile, C) palate, D) left mandible, E) left lower tooth row
(scale on ruler in cm). Sub-triangular hole in the skull is the place of initial sampling for 14C dating in 2007.

There is little doubt that dogs are the domesticated descendents of grey wolves. There is, however, a fair bit of controversy as to when those domestication events first occurred. We have archeological evidence of the existence of dogs (as a distinct species from wolves) at least 14,000 years ago, but they undoubtedly emerged much earlier. Without DNA analysis, it’s difficult to prove whether ancient specimens are really dogs rather than wolves. MtDNA, which is inherited only from the mother and hence has a less complicated provenance, has been particularly helpful in creating phylogenetic trees.

The scientists extracted mtDNA from the Altai skull and compared it to the mtDNA of 72 different dogs, 30 wolves, 4 coyotes and 35 prehistoric canids. Most importantly, three of the wolf specimens were from fragments of contemporaneous remains found within the same cave as the dog skull. If the Altai skull had belonged to a wolf, it should have most closely matched the other wolves living in the same area at the same time. This was not what the researchers found. Instead, the Altai skull mtDNA most closely matched the DNA of dogs and was not closely related to the wolves that coexisted with it. 

We still can’t say for sure when dogs first split off genetically from wolves. However, these data suggest that it happened more than 33,000 years ago, by which point they were already separate species. 

For some fascinating interviews about the origin of dog domestication, listen to this episode of Skeptically Speaking.

Druzhkova, A., Thalmann, O., Trifonov, V., Leonard, J., Vorobieva, N., Ovodov, N., Graphodatsky, A., & Wayne, R. (2013). Ancient DNA Analysis Affirms the Canid from Altai as a Primitive Dog PLoS ONE, 8 (3) DOI: 10.1371/journal.pone.0057754 

Ovodov, N., Crockford, S., Kuzmin, Y., Higham, T., Hodgins, G., & van der Plicht, J. (2011). A 33,000-Year-Old Incipient Dog from the Altai Mountains of Siberia: Evidence of the Earliest Domestication Disrupted by the Last Glacial Maximum PLoS ONE, 6 (7) DOI: 10.1371/journal.pone.0022821.

Thursday, March 28, 2013

To rant or not to rant

Who hasn’t occasionally felt like indulging in an online rant against an injustice or an example of stupidity? The good news is that there are myriad sites dedicated to just this activity. Whatever triggers your ire, there’s a website where you can pour out your vitriol to like-minded enraged compatriots. The bad news is that you may not be doing yourself a favor if you partake in this kind of venting.

Ryan Martin and his colleagues from the University of Wisconsin-Green Bay gave 91 college students a Differential Emotions Scale (DES) test to evaluate their levels of happiness, sadness, anger and/or fear on a scale of 0 to 100. Immediately after assessing their current emotions, they were asked to spend five minutes reading through the posts on a rant-site (screen shots were used so that all participants read the exact same rants). After reading the site, the subjects completed another DES. Next, the volunteers were asked to spend five minutes writing their own anonymous rant on any topic they chose. Upon completion, they filled out a final DES.

Reading the rants caused the average person’s happiness levels to decrease and sadness levels to increase. However, the difference wasn’t extreme. For both emotions, the post-reading levels were less than five points different. Remember, this was on a scale of 100 possible points. Writing their own rants affected participants more significantly. People’s happiness decreased by ten points and their anger increased by close to fourteen points after writing their screeds.

The subjects were each asked whether they’d like their own rant posted onto the site they had been reading (though none were actually posted regardless of preference). Those who wished to publish had experienced more anger while reading posts than those who did not want their own vents published. On the other hand, the people who were ready to publish their own rants had less decrease in happiness while writing those rants than people who didn’t want to publish. Interestingly, the subset of participants (7%) who said they would go back to the rant site on their own time actually experienced an increase in happiness while reading the site.

This data suggests that for most people, reading and writing rants is counterproductive. They were more angry and sad and less happy after engaging in these activities. However, for the people who looked forward to publishing their own rants, reading and writing rants seemed to be somewhat enjoyable. I should point out that this was a small, highly subjective study with no controls, and that the body of evidence about the value of catharsis is mixed. I think the bottom line is that if you find that reading diatribes makes you angry or anxious, it’s probably not the best activity for you. Personally, I’m very selective about reading the comments on YouTube channels or blogs (except mine, I love the comments on The Stochastic Scientist!). 

Martin, R., Coyier, K., VanSistine, L., & Schroeder, K. (2013). Anger on the Internet: The Perceived Value of Rant-Sites Cyberpsychology, Behavior, and Social Networking, 16 (2), 119-122 DOI: 10.1089/cyber.2012.0130.

Wednesday, March 27, 2013

Just for fun: Iron Egghead Video Contest

Scientific American sponsors the ‘Iron Egghead Video Contest’. The goal of this contest is to explain an aspect of human anatomy or a biological function using only the following props: paper (or other writing surface), writing implement, rubberbands, paper clips, string, cups, balls and yourself/yourselves in a two minute video. 

Below, the grand prize winners explain our adrenal glands in a way you won't forget.

You can see another entry here.

Tuesday, March 26, 2013

The temporal Doppler effect makes the future seem closer

We’ve all experienced the Doppler effect. This is what causes the change in sound we hear as a siren approaches and then passes us. The sound waves shift in frequency as each crest takes first shorter and shorter and then longer and longer to reach us. According to researchers led by Eugene Caruso of the University of Chicago, there is also a ‘temporal Doppler effect’ that makes events in the future seem closer to us than events in the past.

In one set of experiments, the scientists asked volunteers to think ahead a specific amount of time in the future (a week, a month or a year) and to think back the same amount of time in the past. The subjects reported that the future seemed closer than the past. You can try this yourself and see if you agree. We’re about equidistant from Christmas and the end of the school year right now. Which seems closer?

One possible reason for this observation is that we perceive time as moving, just like objects or sounds waves. We feel as if the past is actually receding and the future approaching. If so, our own physical movements might affect that perception. To test this, the researchers submersed undergraduates in a virtual reality environment in which they moved either forward or backward and then asked the students about their time perceptions. Participants felt that the future was closer than the past when they were moving forward but not when moving backward.

This is yet another example of how our brains fool us about the world around us. And of course, I can’t end a story about time without my favorite quotation, usually (but probably wrongly) attributed to Groucho Marx:

Time flies like an arrow,
Fruit flies like a banana.
Thank you, I'll be here all week.

Caruso, E., Van Boven, L., Chin, M., & Ward, A. (2013). The Temporal Doppler Effect: When the Future Feels Closer Than the Past Psychological Science DOI: 10.1177/0956797612458804.

Monday, March 25, 2013

How to get people to donate blood

If you want people to do something, is it better to tell them what wonderful things will happen if they do as you ask, or what terrible things will happen if they don’t? In other words, should you entice or threaten? That’s a question Eileen Chou from the University of Virginia and Keith Murnighan of Northwestern University set out to answer, at least with respect to blood donation.

There are chronic shortages in the supply of blood available for transfusions. Hopefully, the need for donated blood will someday be eliminated by the development of artificial blood. In the meantime, however, the Red Cross is working on getting more people to donate blood. To that end, they took a close look at the messaging used to encourage people to donate blood.

The authors sent 3500 undergraduates one of five different emails soliciting blood donations. One email merely stated the time and place at which the recipient could donate blood. The other four were framed as either saving lives (gains to be made if the subject accedes to the request) or preventing deaths (losses to be suffered if the person doesn’t comply). In addition, each version was presented either as being urgent or moderately important.

Here’s the urgent, loss prevention message:
Don’t delay. Help prevent someone from dying! Each year, 4.5 million Americans would die without blood transfusions. Every second, 2 people could die waiting for blood. Every pint that you donate can help them avoid dying. Don’t delay! Help prevent unnecessary deaths.
And the moderate need, gain message: 
Act now. Help save someone’s life! Every day, many people could be saved by donated blood. Every pint that you donate can help them stay healthy. Act now! Promote healthy lives.
I haven’t included the other two variations, but you get the idea. Which message would be more likely to drive you to the donation site? It turns out that the ‘prevent a death’ message was far more successful than the ‘save a life’ message. More than three times as many people showed up to donate blood after receiving the ‘loss’ message than did for the ‘gain’ message. Interestingly, the degree of need did not seem to matter very much. Perhaps, people already have a sense of how essential it is to donate blood.

This greater desire to prevent loss versus to achieve gain has been documented in other arenas. The authors of this study performed a second study in which they tested whether requests to prevent a charity from no longer being able to provide services would elicit more or fewer contributions than requests to increase that charity’s services. Again, people were more charitable to prevent losses.

I guess the lesson from this data is that if you want someone to do something, give them the doomsday scenario and not the possible utopia their actions could create.

Chou, E., & Murnighan, J. (2013). Life or Death Decisions: Framing the Call for Help PLoS ONE, 8 (3) DOI: 10.1371/journal.pone.0057351.

Friday, March 22, 2013

For better viral transmission, have a defective partner

We have extensive correction and repair mechanisms in our cells to keep our DNA error free. Viruses, being minimalists, tend to skip such extraneous functions. For better or worse (and it works both ways for them), viruses tend to accumulate mutations at a high rate. This also means that a fair number of new viruses are altered to the point of being ‘defective’. That is, they lack the necessary equipment to complete their life cycle (for the sake of argument, I’ll consider viruses to be alive). Are these defects ejected from the gene pool? Not so fast, say Ruian Ke of UCLA and his colleagues.

While it is true that defective viruses are useless on their own, if they happen to co-infect a cell with a functional virus, they can use the working genes from the second virus to complement whatever capabilities they lack. But that’s not the interesting bit. It turns out that for Dengue viruses, the presence of defective viruses helps the normal viruses spread more effectively.

Image of a Dengue virus.
Source: Virusworld.

This was a surprise because defective viruses were thought to hinder their normal counterparts by depleting the resources of the infected cell. A cell infected with both defective and normal viruses should make enough defective viruses that can’t infect other cells to cause the infection to wind down. Instead, the defective Dengue viruses significantly increased the transmissibility of the normal virus. In fact, Ke and his colleagues traced the start of some Dengue epidemics to the appearance of specific defective virus strains.

So how does this work? That’s still unknown. However, one intriguing possibility is that the defective viruses do interfere with normal viruses and decrease the number of infectious agents just as suspected. As a consequence, the infected individuals don’t feel as sick and are that much more likely to interact with other people and spread the infection. In this scenario, there are fewer functional viruses made, but the virus wins anyway because it still gets circulated.

If these findings prove true for other viruses, they could have broad-ranging implications for the study of infectious viruses. To be clear, defective viruses can only cause trouble if they co-infect a cell with a complementary intact virus. We don't know how often this happens. In any case, researchers and doctors will no longer be able to dismiss defective viruses as unimportant to epidemiology. 

Ke, R., Aaskov, J., Holmes, E., & Lloyd-Smith, J. (2013). Phylodynamic Analysis of the Emergence and Epidemiological Impact of Transmissible Defective Dengue Viruses PLoS Pathogens, 9 (2) DOI: 10.1371/journal.ppat.1003193.

Thursday, March 21, 2013

To avoid weight gain, get enough sleep

Who hasn't suffered from inadequate sleep? Whether because of overscheduling or insomnia, we all face a bleary-eyed day from time to time. 

Insufficient sleep has a number of drawbacks, including irritability and inability to think or function. Interestingly, people who don’t get enough sleep often also succumb to weight gain. University of Colorado researchers led by Rachel Markwald investigated this link by limiting the sleep of some in-patient volunteers.

The scientists recruited sixteen healthy volunteers who all ordinarily get about eight hours sleep per night. The subjects gave up coffee and maintained a nine-hour per night sleep schedule for one week prior to the start of the study. Over the next five days, half the participants were only allowed to sleep five hours per night whereas the other half were given nine hours in which to sleep. The subjects were allowed to eat as much as they liked. After those five days, the two groups switched sleep patterns for another five days. Thus, everyone experienced a stretch of five days getting five hours sleep and another stretch getting nine hours sleep. Each person’s energy expenditure was monitored 24 hours/day.

People who only slept five hours/night used about 5% more energy than those allowed to sleep for nine hours. However, when given free reign, they consumed about 6% more calories, resulting in a net weight gain. After dinner snacking was the main source of additional calories during the five-hour sleep nights. This could have been due to changes in the circadian timing of meals, as evidenced by a delay in melatonin onset.

The order of the sleep conditions turned out to be significant. Subjects who slept nine hours first were already eating more than they needed (perhaps because of the novelty of being allowed unlimited food) and continued that practice after switching to five hours of sleep. In contrast, the people who started with five hours sleep gained weight during those five days but reduced their caloric intake after switching to nine hours of sleep per night. In particular, women gained weight during the five-hour regimens but lost it after switching to nine hours. Unfortunately, men overate during both phases. 

This suggests that if you do have to go through an interval of shortened sleep, you should follow it up by getting plenty of sleep for a few days. This study didn't address what would happen if you underslept for a prolonged period of time. It would be interesting to know whether you'd need an equal period of regular sleep hours to reverse any weight gain.

Getting enough sleep each night is probably not all you’ll have to do to shed a few pounds, but it might make things easier. Since adequate sleep is important for other reasons, it’s an easy recommendation to make.

Rachel R. Markwald, Edward L. Melanson, Mark R. Smith, Janine Higgins, Leigh Perreault, Robert H. Eckelb, & Kenneth P. Wright, Jr (2013). Impact of insufficient sleep on total daily energy expenditure, food intake, and weight gain Proceedings of the National Academy of Sciences of the United States of America : doi:10.1073/pnas.1216951110.

Wednesday, March 20, 2013

Just for fun: The Great Brain Experiment

I don't usually talk about holidays on this blog. My friend Cathy Earle already has them beautifully covered over at Every Day Is Special. In this case, however, I'll make an exception because it happens to be Brain Awareness Week. In commemoration of this momentous week, the folks at Wellcome Trust Centre for Neuroimaging at University College London have developed a free mobile phone app: The Great Brain Experiment.

iPhone Screenshot 2
Screen shot of The Great Brain Experiment

As you play the games, your data is sent back to the Wellcome Trust Centre and becomes part of a (hopefully) huge citizen science project. 

I tried the games myself and I think I did OK…once I figured out how to play them.

Tuesday, March 19, 2013

Distractions during driving affect brain activity

By now, we all know that talking on the phone can diminish our ability to drive safely. Our brains simply aren’t equipped to do more than one thing well at a time. Researchers, led by Tom Schweizer of the University of Toronto, were interested in capturing that difference between distracted and regular driving at the level of brain activity. Traffic statistics show that distracted driving is particularly problematic while making left turns (right turns for those of you in the United Kingdom, Australia, or other left-driving countries). Therefore, the scientists used complex left turns for their comparison.

The researchers put sixteen volunteers in a virtual reality enhanced driving simulator that was located within a functional magnetic resonance imaging (fMRI) machine. The subjects were given a variety of ‘routes’ ranging from traffic-free right turns to left turns through busy intersections. While ‘driving’, the subjects were given audio tasks designed to mimic either conversing with passengers or talking on a hands-free phone. For example, they were asked true or false questions, which they answered by pressing buttons on the steering wheel.

I’m no cognitive scientist, but even I can see that different parts of the brain are being activated during distracted driving. The top panel shows the regions of the brain activated during normal, non-distracted driving. It’s mostly the posterior of the brain, containing regions critical for visual-spatial orientation that is engaged. This is especially true while making challenging left turns (bottom row). In contrast, the lower panel shows that when distracted, there’s a shift in activation to the anterior of the brain where regions involved in problem solving predominate.


Brain activations from the bottom to the top of the brain (left to right figures) of participants when performing various simulated driving conditions.
(A)         The right-turn condition showed minimal activation in the brain
(B)         Left-turn showed more activation in the posterior brain regions;
(C)         The left-turns with oncoming traffic.
DOI: 10.3389/fnhum.2013.00053.


Brain activations associated with distracted driving.
(A)   Straight driving with a cognitive-distraction, audio task.
(B)   The demanding, left-turn condition with oncoming traffic plus the cognitive distraction.
Despite these changes in brain usage, there were no great performance differences between distracted and undistracted driving. Participants maintained similar speeds and lane positions during both. This is not to say that it’s perfectly safe to talk on the phone and drive. Numerous studies have indicated the opposite, and that even hands-free calling causes people to be less attentive to their surroundings. This study did not evaluate those dangers. Instead, it simply demonstrated the clear changes that occur in brain activity between distracted and non-distracted driving. How these changes correlate with behavior requires another study.

Schweizer, T., Kan, K., Hung, Y., Tam, F., Naglie, G., & Graham, S. (2013). Brain activity during driving with distraction: an immersive fMRI study Frontiers in Human Neuroscience, 7 DOI: 10.3389/fnhum.2013.00053.

Monday, March 18, 2013

Animals help children with autism

Among the common symptoms of children with autism spectrum disorder (ASD) are diminished communication and/or social interaction. There have been many treatments proposed to alleviate this problem, including animal therapies. Studies testing animal-assisted interactions for kids with ASD have had generally positive results. However, those studies did not specifically compare the benefits of animals to those of equally engaging toys. In other words, perhaps it was the stimulation rather than anything particular about animals that helped the kids. Marguerite O’Haire of the University of Queensland and her colleagues set the record straight: it's the animals all right.

The scientists recruited 99 children aged 5 to 13, one third of whom were diagnosed with ASD. The kids were divided into groups of three, with one ASD child and two neurotypical kids in each group. After signing up, the children had an eight-week waiting period followed by the eight-week study period during which two guinea pigs lived in their classroom. Before and after the waiting period and after the study period, the kids were given unstructured time to play with a variety of toys. Twice each week during the eight-week study, the guinea pigs were brought out and handled by the threesome.

Three of those sixteen animal sessions (the first, last and one in the middle) were videotaped, as were the three toy sessions. Experienced behavior coders who did not know the aims of the study watched the tapes and evaluated the kids’ behavior. As an aside, they used a coding system that was specifically designed for this study, the full name of which is ‘Observation of Human Animal Interaction for Research’. The researchers refer to it as OHAIRE, but I’m sure that’s just a coincidence.

Anyway, the children with ASD showed more prosocial behaviors of nearly every kind (approaching others, speaking to or looking at others, smiling) during the guinea pig sessions than they did during the toy sessions. The only exception was that the kids with ASD spoke to their peers more during the toy sessions (they spoke to adults more when animals were present). Interestingly, the kids with ASD handled the toys much more than they did the animals. Apparently, the children didn’t have to have the guinea pigs in their laps, the animals just had to be around. This was born out by the fact that 82% of the kids said they preferred the guinea pigs to the toys.

No one is suggesting that having animals around is a panacea for the problems faced by children with ASD. However, this is one more study showing that animal therapy does help. It’s nice that in this case, the helpers were small animals that nearly any household or classroom could maintain. 

O'Haire, M., McKenzie, S., Beck, A., & Slaughter, V. (2013). Social Behaviors Increase in Children with Autism in the Presence of Animals Compared to Toys PLoS ONE, 8 (2) DOI: 10.1371/journal.pone.0057010.

Friday, March 15, 2013

Life in subglacial Antarctic lakes

Did you know there are hundreds of lakes underneath the Antarctic ice sheet? These bodies of water, which were detected by ground penetrating radar, are about 800 meters under the ice and are totally isolated from the outside world. This means that anything living in those lakes has had no contact with the outside world since the lakes’ formation. This is a treat that’s too good to pass up for either biologists or astrobiologists. So far it looks like they won’t be disappointed.

Scientists have discovered that under the massive Antarctic ice sheets there lies a vast hydrological system of liquid water.  This water exists because geothermal heat flow from below, coupled with pressure, movement, and the insulating nature of the ice sheet above, is great enough to maintain some areas at the base of the ice sheet above the freezing point, even in the extreme cold of Antarctica.  In topographic depressions there are hundreds of lakes, both large and small; some are isolated, but many are interconnected by water channels and large areas of saturated sediments, the water eventually running out into the Southern Ocean as the ice sheet becomes a floating ice shelf.
WISSARD Project.

Of course, we first have to find out what’s down there. To that end, NASA is funding the Whillans Ice Stream Subglacial Access Research Drilling (WISSARD) project. The goal of this project is to drill a hole through the ice and see what’s in the lake beneath it. This is vastly more complicated than it sounds for several reasons. To begin with, the team had to drill a hole all the way to Lake Whillans, half a mile down through the ice. Next, the instruments had to be threaded down that long hole and then brought back up with samples and without scraping along the sides and becoming damaged. Also, the instruments had to be completely sterile so as not to contaminate any findings. And lastly, did I mention this was Antarctica? This is not the most hospitable place in which to stand around doing fieldwork.

Alberto Behar, co-investigator of the WISSARD project, gives us a tour:

Although the findings are preliminary, there do appear to be microbes in the subglacial lake water. This is good news for people hoping to find life under the ice sheets of other worlds, such as Europa or Enceladus. The next step is to see how closely these samples resemble other forms of life on Earth.

You can hear interviews with Helen Fricker (discoverer of Lake Whillans), microbiologist Jill Mikucki and planetary scientist Chris McKay on this Feb. 11, 2013 Big Picture Science podcast

Thursday, March 14, 2013

Recycled fodder for the 3D printer

You may remember Joshua Pearce of Michigan Technological University from a story I wrote five months ago. He’s the scientist who is encouraging everyone to make their own lab equipment using 3D printers. He and his colleagues, Christian Baechler and Matthew DeVuono of Queen's University, Ontario, have now done themselves one better. They’ve found a way to make plastic filament (the ‘ink’ with which the printers make things) out of discarded milk jugs.

If you have your own 3D printer, you know that you can make an endless supply of cool and useful items. However, like Pearce, you will undoubtedly have realized that the limiting step is keeping your printer supplied with plastic filament. Thanks to the researchers proof of concept designs, which they are providing for free, you too can make your own filament.

The researchers chose discarded items made of high-density polyethylene (HDPE), not because it makes the best filament (it doesn’t), but because such items are prevalent in household waste. A variety of plastic items including bottles made for milk, detergent and shampoo are made of HDPE. These plastic items are washed, stripped of labels, cut into pieces and fed through an office shredder. The shreds are melted and then passed through a homemade extruder to make the filament, which was successfully used in 3D printers.

The process does take some time. To make about 18 meters of filament (about enough for five coffee mugs), you’d need to process 100 grams of plastic. Just extruding that amount of melted plastic took over three hours, and that was after washing and shredding it. Needless to say, some work needs to be done to make the system more practical. Also, there were some consistency issues in the diameter of the resulting filament that need to be addressed. Plus, there's the fact that HDPE isn't usually used in 3D printing. The inks of choice are PLA (Polylactic Acid) and ABS (Acrylonitrile Butadiene Styrene).

But make no mistake, Pearce and his colleagues foresee widespread usage of this new technology. For one thing, the process is far cheaper. You could recycle your own HDPE trash into 3D printer filament for about a dollar a kilogram. Compare that to the current price of commercially available filament of around $40/kg. From start to finish, the recycling process also uses about half the energy that goes into making virgin filament. And of course, these numbers will get much better as the process goes large-scale and becomes automated. Finally, we’d be doing something useful with all that HDPE trash. Saving energy and money and shrinking our landfills: a win for everyone.

By the way, Pearce isn’t the only one with this idea. The makers of Filabot have a shredder/extruder ready for purchase if you’re so inclined.

Baechler, C., Matthew DeVuono, & Joshua M. Pearce (2013). Distributed recycling of waste polymer into RepRap feedstock Rapid Prototyping Journal, 19 (2), 118-125 DOI: 10.1108/13552541311302978.