Just for fun: Subway maps!

Have you ever considered the subway map? It needs to give information about stops and transfer points so clearly that even someone as directionally challenged as myself can figure it out. This is typically done with a little creative license about the actual geography of the location serviced. And it doesn't hurt if the result is a work of art. 

Recently, the Massachusetts Bay Transportation Authority (MBTA) held a contest to redesign their current subway map:




And this was the contest winner:
 
It's based on the gold standard of subway map beauty and functionality, the Vignelli New York City subway map of the 1970's:

Massimo Vignelli’s 1972 NYC subway map uses geographic distortions to accommodate subway lines

You can read more about the science that goes into subway map design here and here.

Let's take a tour of Stochastic Scientist

In honor of the Thanksgiving holiday, I thought I'd give you guys a tour of the Stochastic Scientist website. You've been reading the main articles (thank you!) but you may not have noticed the other goodies on the website.

First of all, why 'stochastic scientist'? Although my training is in molecular biology, I didn't want to narrow my focus for this blog. You can read more about my motivations in the side bar on the left.

Also on the left, you can see that there's a Stochastic Scientist Facebook page. I put a lot more stuff on the Facebook page than I do on this website, including extra videos, amazing photographs and amusing cartoons. If you enjoy this blog, you should 'like' Stochastic Scientist on Facebook.

Further down in the left panel, you'll find updated lists of science podcasts, science blogs and science youtube channels. A simple click will take you to the latest post or episode. If you have a favorite site that's not on any of my lists, please send it to me!

You can also find lists of the most popular Stochastic Scientist posts and an archive of all Stochastic Scientist posts, in case you missed one.

Finally, at the bottom you can find contact information to follow me on twitter.

Now enjoy your Thanksgiving!

Wag to the left, I’m bereft, wag to the right, out-a-sight!

The next time you see a dog wagging its tail, look a little more closely. You may be able to detect that the tail sweeps slightly more toward one side of the dog’s body. This asymmetry isn’t random. When dogs see something they want to approach (like their owners) they wag to their right. When they see something that makes them wary, like a strange dog, they wag to their left.

Most of the time, you’re not going to notice the difference. Humans don’t usually place that much importance on the nuances of tail wagging. However, dogs might have a different perspective. Scientists led by Marcello Siniscalchi of the University of Bari Aldo Moro found that dogs do indeed pay attention to other dogs’ wagging habits.

The scientists showed dogs video clips of other dogs, wagging either to the left or to the right.

The test dogs’s heart rates were elevated when they watched another dog wagging to the left. They also exhibited more anxious behavior when seeing a left-wagging dog compared to a right-wagging dog. In fact, dogs were more relaxed when viewing a dog wagging its tail to the right than when watching a motionless dog. 

While the observing dogs may have been picking up other cues besides just the tail wags, these data do suggest that dogs pay attention to other dogs' tails, and that they can communicate their emotion state via the direction of their tail wags.

Siniscalchi M, Lusito R, Vallortigara G, & Quaranta A (2013). Seeing Left- or Right-Asymmetric Tail Wagging Produces Different Emotional Responses in Dogs. Current biology : CB PMID: 24184108

Reindeers’ color-changing eyes

If you live above the Arctic Circle (or if you became the first permanent resident of Antarctica), you have to cope with seasons of light and dark. Humans haven’t evolved to handle these extreme environments, but Arctic reindeer have, and the way they’ve adapted to long stretches of day and night may amaze you.

Like many animals, reindeer have a tapetum lucidum (TL), essentially a mirror that reflects light forward from the retina, giving neurons a second chance to capture that light. It’s the TL that gives cats their eerie glowing stare. However, there’s something unusual about these particular TLs, as shown by Karl-Arne Stokkan from the University of Tromsø. Reindeer TLs are not the same in winter as they are in summer.

Left: eye taken from a reindeer in winter
Right: eye taken from a reindeer in summer
Credit: Glen Jeffery.

During the summer, the reindeers’ TLs appear to be golden, which is how most ungulates’ TLs look. The golden TL reflects almost all the light out of the eye. In contrast, the blue TL reflects 60% less light. Experiments with live animals showed that winter adapted reindeer were far more sensitive to light.

To be clear, we’re not talking about two subsets of reindeer. The same reindeer have golden eyes in summer and blue eyes in winter. What’s causing them to change? The answer seems to be eyeball pressure and collagen spacing. During the winter, the intra-ocular pressure is greater, probably due to pupil dilation, leading to more tightly spaced collagen in the TL.

The scientists tested this by putting heavy clear coverslips on top of sections of the golden summer TL. As you can see, the compressed TL is now blue.

(a) Central TL from summer animals, revealing a golden appearance.
(b) The same specimen after coverslipping with an 8 g weight. 

This is the first documentation of a color-changing eye strategy for coping with extreme environments. 

Stokkan KA, Folkow L, Dukes J, Neveu M, Hogg C, Siefken S, Dakin SC, & Jeffery G (2013). Shifting mirrors: adaptive changes in retinal reflections to winter darkness in Arctic reindeer. Proceedings. Biological sciences / The Royal Society, 280 (1773) PMID: 24174115.

The unpublished trial problem

© 2013 - William Reed Business Media SAS

People enter clinical trials for a variety of reasons. Subjects may volunteer because they hope to be cured of whatever ails them, or they may be altruistically hoping to advance the state of medical knowledge. Either way, they endure inconvenience at the very least, and often some degree of pain or discomfort. Whatever motivates them to participate in a study, it’s certainly not in order to let the study languish unpublished after completion. Yet, according to researchers from the University of North Carolina, that’s exactly what happens a quarter of the time.

First author Christopher Jones from Cooper Medical School of Rowan University and his colleagues collected data on clinical trials that had been registered with ClinicalTrials.gov between 2005 and 2009. They found 585 randomized trials that had included at least 500 people.

The scientists then used a variety of search techniques to match these trials with publications, including in non-peer reviewed venues like conferences. They even contacted study investigators to see whether their results had ever been published. For 250,000 trial participants, there were no results available anywhere. It was as if all those people had never been in a clinical trial at all.

It’s not clear what’s preventing these studies from being published. There is an unfortunate bias against publishing negative results, either because the investigators and their sponsors don’t like them or because journals and their readers don’t find them interesting. Jones and his colleagues were hoping to circumvent that bias by restricting their analysis to large trials that require too much expense and effort to be casually discarded. Yet a quarter of the trials still didn’t get published.

According to US Federal Policy for the Protection of Human Subjects  and the Declaration of Helsinki:

Authors have a duty to make publicly available the results of their research on human subjects and are accountable for the completeness and accuracy of their reports.

That’s certainly what volunteers expect when they agree to participate in a trial. Anything else could be considered a breech of ethics, if not of contract.

Jones CW, Handler L, Crowell KE, Keil LG, Weaver MA, & Platts-Mills TF (2013). Non-publication of large randomized clinical trials: cross sectional analysis. BMJ (Clinical research ed.), 347 PMID: 24169943.

The Sauropod collection

The journal PLoS ONE has an entire collection dedicated to understanding our giant friends, the sauropods. This body of works answers a number of pressing questions about these enormous creatures.

Why did they get so big?

Well, we still don't know for sure, but there is one prevailing idea that links food quality to size. The idea is that as animals get bigger, they require more food. This means they have to accept poorer quality (nutritionally speaking) food, and larger bodies are better equipped to cope with low quality food than smaller bodies. 

Obviously, this reasoning has limited explanatory power, being completely circular, and, according to Marcus Clauss from the University of Zurich and his colleagues, has the added disadvantage of probably not being true.

There are other factors besides browse quality that could have led to giganticism. Martin Sander from the University of Bonn examined a number of possible ‘evolutionary cascade models’, including size and number of newly hatched babies, lack of food processing (no chewing capability), and even the type of lungs sauropods had to explain why they grew so large. Most likely a combination of many factors was ultimately responsible for the enormous bulk of these creatures.

What did sauropods do with those long necks?

Giraffes have long necks, but like nearly every other mammal, they only have seven neck vertebrae. Some birds also have long necks, but they can have over twenty neck vertebrae. This is why swans have far more flexible necks than giraffes. Despite their large number of neck vertebrae, sauropods were not nearly as flexible as birds.

Kent Stevens from the University of Oregon has found that the ‘neutral’ position of the head and neck (when the animal is resting comfortably) is most likely represented by position E in the graphic below.

doi:10.1371/journal.pone.0078572.g004.

While not as flexible as birds, they could sweep out fairly large swaths from ground level to high above their bodies, as shown in the next picture.

Apatosaurus and Diplodocus are shown reaching down to ground level (A and B), and reaching as high as possible (C and D). While both necks sweep out a huge surface area, Apatosaurus could reach higher despite having a somewhat shorter neck than Diplodocus.

doi:10.1371/journal.pone.0078572.g007.

How fast could these giants move? 

Probably, not very. Here's a handy infographic, courtesy of the University of Manchester:

Even better, here's an animation.

Marcus Clauss, Patrick Steuer, Dennis W. H. Müller, Daryl Codron, & Jürgen Hummel (2013). Herbivory and Body Size: Allometries of Diet Quality and Gastrointestinal Physiology, and Implications for Herbivore Ecology and Dinosaur Gigantism PloS ONE DOI: 10.1371/journal.pone.0068714.

P. Martin Sander (2013). An Evolutionary Cascade Model for Sauropod Dinosaur Gigantism - Overview, Update and Tests PloS ONE, 8 (10) : doi:10.1371/journal.pone.0078573.

Kent A. Stevens (2013). The Articulation of Sauropod Necks: Methodology and Mythology PloS ONE DOI: 10.1371/journal.pone.0078572.

William Irvin Sellers, Lee Margetts, Rodolfo Aníbal Coria, & Phillip Lars Manning (2013). March of the Titans: The Locomotor Capabilities of Sauropod Dinosaurs PloS ONE, 8 (10) DOI: 10.1371/journal.pone.0078733

Just for fun: Veritasium explains the kilogram

Behold! The roundest object in the world, and the savior of the kilogram.

Veritasium gives a fascinating history of the kilogram on his YouTube channel.

T. rex, bigger than ever

Photo taken at Universal Studios "Jurassic Park" 4/12/07 by Scott Kinmartin.

While Tyrannosaurus rex wasn't the largest of all meat-eating dinosaurs, it holds a special place in the hearts and minds of school children everywhere. No other animal symbolizes 'huge fearsome predator' like T. rex. It turns out that the kids may have been thinking too small. According to Jack Horner and his colleagues from the Museum of the Rockies, all the T. rex specimens we know about may have been still growing.

Earlier this month, Horner presented his findings at the Society of Vertebrate Paleontology. Upon cutting open a variety of bones in the museum's collection, he found evidence of blood vessels and osteocytes, hallmarks of bones that are still growing. This was true not only for bones previously labelled as 'juvenile' but also in bones thought to have come from adults.

To be clear, the 'adult' specimens may well have been sexually and behaviorally mature. There are species alive today that continue to grow throughout their lifetimes, and this may have been true of dinosaurs. Horner speculates that, had they lived, the larger T. rex specimens would have continued to grow thicker and bulkier, rather than longer or taller.

On the other hand, perhaps there are T. rex giants waiting to be discovered. Think about that, all you future paleontologists. 

Extinction event affected bees

The meteor that took out the non-avian dinosaurs at the end of the Cretaceous period (at the K-T boundary) also decimated many other life forms. According to Sandra Rehan of the University of New Hampshire, Remko Leys from Flinders University of South Australia and Michael Schwarz from the University of Adelaide, those extinctions included bees.

Bees have been around since the mid-late Cretaceous. Not coincidentally, so have a group of flowering plants called eudicots. The scientists used DNA sequence data to map the evolutionary history of 229 species in the long-tongued bee family (Xylocopinae). This family is unevenly divided into four tribes as you can see below.

doi:10.1371/journal.pone.0076683.g001

This pattern of divergence is best explained by a model where 92% of bee lineages died out 65 million years ago, and the few remaining species rapidly diverged soon afterwards. 

I like to think of this as good news. If we can halt the current decimation of our modern honeybees, maybe they too can bounce back from the brink. Of course, it might take a few million years.

Sandra M. Rehan, Remko Leys, & Michael P. Schwarz (2013). First Evidence for a Massive Extinction Event Affecting Bees Close to the K-T Boundary PloS ONE DOI: 10.1371/journal.pone.0076683.

Good news for children: parents benefit if you're the center of the family

We all have our opinions on whether children are best served by ‘helicopter parents’, who hover over them keeping them safe from physical or emotional harm, or by ‘tiger parents’ who insist on early and exceptional achievement. We also differ on how much nurturing or discipline children need. But the bigger question is, what’s better for the parents? Children everywhere can rejoice to hear that, according to Claire Aston-James of VU University Amsterdam and her colleagues, parents who center their lives around their children are the happiest.

The researchers asked 136 parents with at least one child to self-rank themselves on a child-centrism scale. The parents were asked whether and how much they agreed with statements such as ‘the happiness of my children is more important to me than my own happiness’. 

Parents next filled out detailed surveys on how much time they spent with their children, thinking about their children, talking about their children, driving their children around, participating in activities with their children, etc. More to the point, they were asked how often they had changed their own plans to accommodate the needs of their kids.

Finally, the parents filled out questionnaires on how much enjoyment they got from their children. 

Child-centric parenting correlated with happier parenting. 

In a second experiment, 186 parents were asked to reconstruct their previous day: getting up, having breakfast, getting kids ready for school, etc. For each activity, the parents assessed what their mental and emotional state had been, and whether they had felt any sense of purpose in their lives. Only after this detailed introspection was completed, did the parents fill out the child-centrism survey.

While caring for their children, the parents who rated high for child-centrism felt much more positive about themselves, their day, and their lives. Non-child related activities were not influenced by how child-centric the adults were. Thus, overall, child-centric parents had greater feelings of well being throughout the day. Everyone felt the same during their 'adult time', but the child-centric parents got a boost of pleasure while caring for their kids.

It’s well known that investing in others makes one happier. If this is true for strangers, how much more likely is it to be true for one’s own children? Still, while perfectly believable, these results are also highly subjective. And of course, the data says nothing about what parenting styles are most beneficial for the kids. Nevertheless, I have the feeling that most children would be willing to be the center of family life. For their parents’ sake.



Claire E. Ashton-James, Kostadin Kushlev, & Elizabeth W. Dunn (2013). Parents Reap What They Sow: Child-Centrism and Parental Well-Being SAGE Journals DOI: 10.1177/1948550613479804.

A fifth of Sun-like stars may have Earth-like planets

How many Earth-like planets could there be in our galaxy? According to Erik Petigura and Geoffrey Marcy from the University of California Berkeley and Andrew Howard from the University of Hawaii, lots. It looks like up to 20% of all Sun-like stars have at least one Earth-like planet.

There are two criteria for determining that a planet is ‘Earth-like’. First, the planet must have a rocky surface and be more or less the same size as the Earth. Gas giants like Jupiter need not apply. Second, the planet has to orbit its star within the ‘habitable zone’. That is, the planet must orbit under conditions that allow for liquid water on the surface. If a planet is too far away from its star (too cold) all liquids are permanently frozen solid. If a planet is too near (too hot), any water will evaporate out into space.

For four years, the Kepler Space Telescope scoured the skies, using the ‘transit method’ to find exoplanets. Although the telescope can no longer continue that mission, it has provided an enormous amount of information and cosmologists are still pouring over the data. So far, 603 planets have been confirmed from Kepler, ten of which are Earth-like. That sounds like a ratio of 1 in 60. How did the astronomers get to 1 in 5 stars having an Earth-like planet?

As good as it was, Kepler was never going to find all the planets that are out there. After all, the transit method works by detecting the periodic dimming of light that occurs when a planet passes in front of its star. If, from our vantage point, there is no transit, then there is no planet detection. Even if a planet does eclipse its star, there’s still a chance that the Kepler failed to spot it. 

The scientists created computer models to correct for these missed planets. According to their algorithm, they calculate that about 22% of Sun-like stars have a rocky planet between one and two times the size of the Earth that receives between one and four times as much light as we do. 

At first glance, this seems like an unreasonably high percentage. However, keep in mind that many if not most stars have more than one planet. Among the planets in a star’s orbit, there very well could be at least one smallish, rocky one. That’s certainly the case in our solar system. 

If the predictions are accurate, the nearest Earth-like planet might be as close as twelve light years from Earth, a distance that a highly advanced civilization might one day traverse. But probably not us, at least not anytime soon. The fastest rockets we have today would take over ten thousand years to get there.



Petigura EA, Howard AW, & Marcy GW (2013). Prevalence of Earth-size planets orbiting Sun-like stars. Proceedings of the National Academy of Sciences of the United States of America PMID: 24191033.

Just for fun: Gimball, the flying robot

If you were designing a flying robot and you didn't want it to break every time you set it loose in an obstruction-filled environment, you could fill it with avoidance sensors to keep it from crashing.

Or you could design it with no sensors whatsoever and let it blunder its way from obstacle to obstacle. 

Adrien Briod and Mariusz Kornatowski from Ecole Polytechnique Fédérale de Lausanne chose the latter tactic, taking inspiration from insects like bumblebees and carpenter beetles.

Their 'Gimball' robot contains only a gyroscopic stabilization system, a compass and an altitude sensor within a carbon-fiber ring.

You can see the result below:

Closed captions for the win

Example of closed captioning

Recently, my family decided to turn on the closed captions feature for our TV. We’re not deaf or English language learners, but we still don’t always catch everything that’s said. Apparently, we’re not alone. Robert Keith Collins from San Francisco State University has shown that adding captions to educational films helps students learn and retain the material better.

Captions can be a transcript of the dialogue in a scene, a translation of that dialogue, or a visual narration. The first type (transcript) are usually ‘closed captions’. These can be turned on or off at the discretion of the viewer. The second two types are ‘open captions’, and these are permanently on display as the film plays.

Collins gave about a hundred students two sets of educational films, the first with closed captioning off and the second with the captions on. After each set of films, the students were given an exam on the material covered by the films. For each film, the students were provided with written supplementary materials including lists of people and events.

Using closed captions significantly improved the students’ academic performances. They had much better recall of names and dates after watching films with the captions on. This doesn’t surprise me at all. Not only does seeing and hearing something help reinforce it in one’s memory, but seeing things written out can also help clarify what was said.

What was surprising was that with the captions on, the students were far more engaged with what they were watching. They were more apt to draw analogies between the events depicted in the films and their own lives, leading to livelier discussions. They also remembered more of the specific elements within the films. 

This was a small study. However, the results corroborate other studies which show that closed captioning can be extremely helpful as a learning tool. Which makes me a little sad I didn’t turn my captions on sooner. Think how much more I would have learned from Breaking Bad.


Robert Keith Collins (2013). Using Captions to Reduce Barriers to Native American Student Success American Indian Culture and Research Journal , 37 (3).

Just for fun: The anatomy artist

What do you get when a talented artist barters a commission to draw biomedical illustrations for a spot in a gross anatomy class? Only the most beautiful and accurate anatomical body paintings you've ever seen.

Danny Quirk produces his 'living lectures' with permanent marker and latex body paint.

You can read about Quirk here, or see more of his work here, here (includes one 'not safe for work' picture) or on his Facebook page.

Whistle while you work

Researchers from the Universities of Ghent and Leipzig and from the Max Planck Institute for Human Cognitive and Brain Sciences have been investigating why music can make strenuous physical activities seem less exhausting. No one who brings their iPod along for a run will be surprised that listening to music can decrease the perception of exertion. What’s more controversial is that the scientists believe that there’s something specific about music that goes beyond merely being a distraction or motivator.

Sixty-three volunteers who were neither professional musicians nor athletes were asked to operate three different fitness machines (a tower, a stomach trainer and a stepper) while listening to music. Under condition A, the subjects could only listen passively to music while they worked out, but under condition B, the subjects could control the music with their movements on the machines. A force meter on the tower determined the amount of pressure participants were using and oxygen consumption determined how much aerobic energy they were expending.

First author Tom Fritz of the Max Planck Institute shows how it's done.

The subjects' perceived exertion levels were much lower under condition B even though they were actually applying more force. They also consumed less oxygen when in control of the music. Because the participants had to hold specific positions to make particular musical notes, the music couldn't have simply been distracting them from their efforts. They were able to exert more force even while concentrating on their muscles.

While this study confirms that music can be helpful during exercise and that actively making music is better than just listening, I’m not so sure this says anything special about music. I personally like to listen to audiobooks while I exercise. I’ll have to see if making up a story while I run will make the exercise even more palatable. 

More on this story at Only Human.


Fritz TH, Hardikar S, Demoucron M, Niessen M, Demey M, Giot O, Li Y, Haynes JD, Villringer A, & Leman M (2013). Musical agency reduces perceived exertion during strenuous physical performance. Proceedings of the National Academy of Sciences of the United States of America PMID: 24127588.

Why is the sun’s corona so hot?

The sun is hot. It’s literally blazing hot. Nothing surprising there. Yet, one solar feature, the corona, is much hotter than it should be. For seven decades, physicists have been trying to understand this ‘coronal heating problem’. Thanks to work by Michael Hahn and Daniel Savin from Columbia University, we may have finally cracked it.

The sun’s core clocks in at 15 million degrees Kelvin. As you move outward, the temperature cools down until it’s a mere 6000 degrees at the surface. However, the temperature of the gas in the corona above the solar surface is over a million degrees. This is counterintuitive, to say the least. What could possibly be heating up the corona like that?

There were two leading contenders for the solution, both involving energy transfer via magnetic waves. In one hypothesis, magnetic fields loop across the solar surface, in the other, waves carry energy up from below the surface. Hahn and Savin showed that the latter explanation is most likely correct. Not only do these waves contain enough energy to heat the corona to high temperatures, but they also deposit that energy in the lower reaches of the corona where the solar wind can spread the heat around the entire sun.

There are still mysteries to be solved, including why these waves (known as Alfvén waves) dissipate at such low heights. Hahn and Savin plan to work on that next.

Michael Hahn, & Daniel Savin (2013). Observational Quantification of the Energy Dissipated by Alfvén Waves in a Polar Coronal Hole: Evidence that Waves Drive the Fast Solar Wind The Astrophysical Journal. DOI: 10.1088/0004-637X/776/2/78.