Determining appearance from ancient skeletal remains

Forensic scientists can tell an amazing amount about what a person looked like by examining his skeletal remains. Even heavily decomposed bodies can allow scientists to reconstruct the appearance of the diseased person with a fair amount of precision. In particular, we now have highly predictive DNA markers for hair and eye color. Researchers from the Institute of Forensic Research in Poland and from Erasmus MC University Medical Center Rotterdam decided to use the same techniques to determine the eye and hair color of long dead people.

First, the researchers perfected the IrisPlex system, a compilation of six snippets of DNA known to be involved in eye color. When tested on close to 4,000 modern Europeans, the IrisPlex system accurately predicted whether the person had blue or brown eyes 94% of the time. They combined this test with markers for hair color to create the HIrisPlex system. The accuracy rate of this system in identifying the hair color of over 300 modern people was 69.5% for blonds, 78.5% for brunettes, 80% for gingers and 87.5% for people with black hair (is there a name for such individuals? Leave me a comment if you know of one!).

Next, the scientists collected DNA from twenty-six tooth and bone samples. Most were from people who had died within the last century, but a few were from people known to have lived over 700 years ago. The HIrisPlex system successfully yielded eye and hair color results for all these individuals.

Unfortunately, because the actual appearance of all but one of the individuals was not known, this set of experiments did not independently verify the accuracy of the HIRisPlex system. The authors assumed that the error rate for the skeletal remains was the same as for the living Europeans mentioned above. Instead, this study simply demonstrated that it is possible to use the HIrisPlex system on ancient bones from which only degraded fragments of DNA can be obtained.

If this system is in fact just as accurate for ancient bones as for modern ones, the next obvious usage for this technology is to determine the hair and eye color of far older specimens. I’m looking at you, Neanderthals and Denisovans!


Draus-Barini, J., Walsh, S., Pospiech, E., Kupiec, T., Glab, H., Branicki, W., & Kayser, M. (2013). Bona fide colour: DNA prediction of human eye and hair colour from ancient and contemporary skeletal remains Investigative Genetics, 4 (1) DOI: 10.1186/2041-2223-4-3.

Just for fun: The Earth at night

Recently, NASA and NOAA (the National Oceanic and Atmospheric Administration) produced this short film of the Earth at night. They used the Suomi National Polar-orbiting Partnership (NPP) satellite, which can detect the light coming from a single street light, to scan the night side of the Earth and then superimposed those images over prior Blue Marble ones. 

As Chris Elvidge, NOAA scientist, states:

Nothing tells us more about the spread of humans across the Earth than City lights.

Ultimatum game demonstrates chimpanzee sense of fairness

Ever play ‘the ultimatum game’? There are many variations, but basically it involves two players dividing a pot of goodies. The first person proposes how to split the pot, and the second can either accept or refuse the split. If the division is accepted, they each get the agreed upon amount, but if refused, neither player gets anything. This simple game has been used to illustrate complex economical principals. It also tells us something about psychology. Consider that if person A is given $100 to divvy up, he should be able to offer person B one penny. After all, if B refuses, he gets nothing. Isn’t a penny better than nothing? Not according to almost everyone who plays the game. If A wants to end up with anything, he has to offer B a minimum amount of the pot, usually at least 20%. Fairness is valued over absolute gain by both participants, as evidenced by the fact that many player As will offer 50%.

Researchers from Georgia State University and from Emory University found a way to make chimpanzees play the ultimatum game. One chimp (A) is offered a choice of two tokens, one of which represents an equal split of a pile of bananas and the other an unequal split. A passes the token to chimp B, who can choose whether to return it to the human experimenter. If B returns the token, the food is divided as indicated (either three bananas each or five for A and one for B).

Like humans, the chimp As chose the fair division token most of the time. When playing a version of the game called ‘the dictator game’ in which person or chimp B must accept whatever A decides, the chimp As were far less likely to choose the equitable token. This was interesting because when given the choice, no chimp Bs ever refused any offer, making the ultimatum game effectively equivalent to the dictator game. Yet, the chimp As treated the two versions completely differently. Again, this is similar to typical reactions in human populations. Apparently, the chimpanzees' sense of fairness is not unlike that of humans.

For more on animal cooperation, see my post on the elephants and parrots.



Proctor, D., Williamson, R., de Waal, F., & Brosnan, S. (2013). Chimpanzees play the ultimatum game Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1220806110.

Barefoot running doesn’t guarantee strain reduction

Many studies have shown that barefoot running is both more energetically efficient and better for one’s joints. If it weren’t for hot pavements and gravel, more people would probably take it up. However, thanks to the work of Kevin Hatala from George Washington University and his colleagues, it now seems that barefoot running isn’t necessarily a cure-all for running problems. This is because, contrary to conventional wisdom, running barefoot doesn’t guarantee a more healthful foot strike pattern.

It was thought that during a normal stride, an unshod runner would strike first with the fore or midfoot whereas a person wearing running shoes would tend to land first on the back of the foot. Among other factors, it’s this impact on the heel that causes the greater foot and joint strain associated with shod running. Prior studies with habitually barefoot runners such as the Kalenjin people of Kenya showed that they did land on their forefeet as they ran.

Hatala and his colleagues looked at a different barefoot community: the Daasanach of northern Kenya. The scientists recruited 38 habitually unshod adult Daasanachs (half men and half women) and asked them to run at varying speeds along a 15 meter trackway containing a pressure pad at the midpoint. Each volunteer ran across the pad at least three times for a total of 133 trials.

At endurance speed, the barefoot runners landed each stride on their forefeet only 4% of the time. 72% of the time, they used a rearfoot or heel strike as they ran. Avoiding the heel strike was supposed to be the unshod runner’s claim to fame, and yet these normally barefoot people were using the same stride as people wearing Nikes. A few of the subjects did revert to a forefoot strike as they increased speed, but most people landed on the middle or back of their feet regardless of speed.

This doesn’t mean that it isn’t better to land on your toes than on your heels as you run, but it does seem to indicate that landing on one’s toes is not necessarily the way that humans evolved to run. I should note that the Daasanach people do not spend as much time running as other barefoot populations that have been studied. For example, the Kalenjin, who do land on their toes, spend a lot more time running than the Dassanach do. So, it could be that the Daasanach have lost the knack of injury-free long distance running.

In any case, I've decided to give those minimalist five-toed running shoes a try. Wish me luck!

Kevin G. Hatala, Heather L. Dingwall, Roshna E. Wunderlich, & Brian G. Richmond (2012). Variation in Foot Strike Patterns during Running among Habitually Barefoot Populations PloS ONE : doi:10.1371/journal.pone.0052548.

Laser communication with satellites

Satellites are only useful to us if we can communicate with them. Until now, that communication has been via radio signals. However, the good folks at NASA have successfully used lasers to send an image from the Goddard Space Flight Center in Greenbelt, MD to the Lunar Reconnaissance Orbiter (LRO), which, as the name implies, is currently orbiting the moon. In an appealing mix of art and science, the chosen image was the Mona Lisa.

We already track satellites using lasers, but we hadn’t previously been able to send information to those satellites via lasers. To send the image, the picture of the Mona Lisa was first broken down into individual gray-tone pixels, each of which was represented by number from zero to 4,095. Each pixel was transmitted as a single laser pulse at a rate of about 300 bits per second, and reassembled by the Lunar Orbiter Laser Altimeter (the instrument aboard the LRO which received the image, aka the LOLA). Defects caused by the Earth’s atmosphere were corrected as shown below.

To clean up transmission errors introduced by Earth's atmosphere (left), Goddard scientists applied Reed-Solomon error correction (right), which is commonly used in CDs and DVDs. Typical errors include missing pixels (white) and false signals (black). The white stripe indicates a brief period when transmission was paused.

Image courtesy: Xiaoli Sun, NASA Goddard

As verification of the success of the test, the image was returned to Earth by the LRO’s radio telemetry system. 

To be clear, this system wouldn't work with currently existing satellites that have launched without the equipment aboard to receive laser communications. The LOLA was already set up to receive such information for tracking purposes. However, going forward, new satellites and spacecraft will undoubtedly have this capability. David Smith from the Massachusetts Institute of Technology and principal investigator of the LOLA said this about the mission:

In the near future, this type of simple laser communication might serve as a backup for the radio communication that satellites use. In the more distant future, it may allow communication at higher data rates than present radio links can provide.

Below is a video describing the experiment.

Adélie penguins have their moment on camera

Ever wonder what penguins do when they’re under the waves? So did Yuuki Watanabe and Akinora Takahashi of the National Institute of Polar Research, Tokyo, who attached video cameras to free-swimming Adélie penguins. This allowed the researchers to address the question of just how these birds forage for food.

Besides the cameras on the penguins’ backs, which lasted just under one and a half hours, each bird was also fitted out with two tiny accelerometers. These had a lifetime of about 50 hours and were attached to the head and back of the animals. By using the devices in combination, the scientists were able to see exactly how the birds proceeded to capture their prey.

The movie cameras showed when each animal’s activities culminated in an actual meal so that unrelated movements could be screened out. Next, the scientists were able to subtract the birds’ whole body movements from their head alone movements by comparing data from the accelerometers in those two positions. In this way, they could determine the exact technique the birds used to subdue different types of prey.

I’m not sure how groundbreaking it is to know whether Adélie penguins sweep their heads to the side or keep their necks stiff when foraging for food. On the other hand, I do think this combination of video and movement detectors is pretty ingenious. I’m sure many more interesting discoveries will come of it. 

You can see footage from the 'penguin-cam' below:



Watanabe, Y., & Takahashi, A. (2013). Linking animal-borne video to accelerometers reveals prey capture variability Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1216244110.

Just for fun: The lovely bones

In 1952, LIFE magazine published an amazing collection of pictures of bones taken by photographer Andreas Feininger. The images were part of a 'Lovely Bones: the Art of Evolution' feature and included mole, bat and armadillo skeletons, to name just a few. Here's my favorite, a 'jumping mouse'.

The virtual bystander effect

Ever hear of the ‘bystander effect’? In essence, it’s the observation that the more people present to witness a violent incident, the less likely it is that any one of them will intervene to help the victim. Mel Slater of University College London and his colleagues used immersive virtual reality to study this phenomenon.

The authors hypothesized that the bystander effect would be minimized if the victim were a member of the same group as the witness. Since actually mugging people in order to study the reactions of bystanders would be unethical, the researchers resorted to virtual attacks. They recruited 40 ardent supporters of the Arsenal Football Club, a football (or soccer) club based in Holloway London, and immersed them in a life-sized virtual bar. Within that environment, each participant was approached by a virtual human (V for victim) who spent a few minutes talking to the subject about football. In some cases, V was also a huge Arsenal fan. Next, a second virtual person (P for perpetrator) started an argument with V that ended violently.

Four combinations of factors were recorded: whether V was a fellow Arsenal fan (in group versus out group) and whether V made eye contact with the volunteers during the attack. Ten participants were tested for each of these combinations. Any attempt by the volunteers to intervene verbally or physically was recorded. As expected, there were more intervention attempts on the part of the test subjects when V was part of the same in-group. Whether or not V looked to the subjects for help did not seem to make much difference.

I’m not sure this says all that much about human psychology. It’s telling that the number one thing the participants said would have gotten them more involved would have been if the virtual characters had been more reactive to them. In other words, it was probably clear that the little vignette was going to be played out regardless of what the test subjects did. Besides, the bystander effect is supposed to involve multiple witnesses not just one. That said, I still think this was an interesting experiment. With a little fine-tuning, virtual environments might very well turn out to be excellent ways to study human behavior.


Mel Slater, Aitor Rovira, Richard Southern, David Swapp, Jian J. Zhang, Claire Campbell, & Mark Levine (2012). Bystander Responses to a Violent Incident in an Immersive Virtual Environment PloS ONE : doi:10.1371/journal.pone.0052766.

Touchless surgical interfaces

It won’t surprise you to know that computers and electronic imagery are nearly ubiquitous in today’s operating rooms (ORs). But have you thought about the problems involved in keeping such devices sufficiently sterile? Mithun Jacob, Juan Wachs and Rebecca Packer from Purdue University certainly have. The researchers are testing ‘non-contact gesture-controlled human-computer interfaces’, adopted from gaming consoles. Rather than touching controls, images can be accessed via hand gestures.

Traditionally, there are two ways to control an OR computer workstation. The surgeon can manipulate it himself, in which case the workstation must be sterilized, a nearly impossible task. I suppose the surgeon could change gloves before and after each data entry, but that would greatly increase the length of surgeries and provide multiple opportunities for contamination. Alternatively, the surgeon could verbally instruct a nurse or assistant to manipulate the computer, but that can also lead to delays as miscommunications are straightened out. The Purdue University researchers had a better idea.

To begin with, the researchers asked ten surgeons to come up with a gesture command lexicon. For example, facing the palms toward each other and moving them closer or farther apart would signify zooming in or zooming out, respectively.  They paired these gestures with special 3D-sensing cameras that could interact with the computer workstations. They next set about designing algorithms to let the camera system distinguish between motions intended to manipulate the computer and unrelated gestures. Body position and direction of gaze proved critical for ensuring that the interface was interpreting the surgeons’ movements correctly. In trials, volunteers got the result they were looking for about 93% of the time, definitely good enough to continue testing.

You can see a test example below:

Jacob MG, Wachs JP, & Packer RA (2012). Hand-gesture-based sterile interface for the operating room using contextual cues for the navigation of radiological images. Journal of the American Medical Informatics Association : JAMIA PMID: 23250787.

Other stars have asteroid and comet belts

You’re familiar with the eight planets in our solar system (sorry, Pluto), but that list is far from a complete inventory of the objects orbiting our sun. We also have two regions, or belts, full of asteroids and comets. It turns out that at least two nearby stars have the same swath of objects in proportionately the same places. This may mean that they also have planets in about the same places as the sun does.

To put things in perspective, let’s take a tour of our solar system. By definition, the Earth orbits the sun at a distance of one astronomical unit (1 AU). Mars is a little further out at 1.5 AU. Next comes the asteroid belt, which contains millions of objects, mostly tiny, swirling around the sun at 2.3 to 3.3 AU. Then comes Jupiter at 5.2 AU, followed by Saturn, Uranus and finally Neptune at 30 AU. The Kuiper belt begins just at the edge of Neptune’s orbit and spreads from 30-50 AU. Like in the asteroid belt, most of the Kuiper objects are small, though this time they tend to be frozen comets rather than rocky asteroids.

University of Arizona astronomer Kate Su and her colleagues have discovered that the stars Vega and Formalhaut have asteroid belts in the same places. These are extremely bright stars only about 25 light years from the Earth. Like our sun, they each have an inner ‘warm’ (negative 190 ^oF) asteroid belt and an outer ‘cool’ (negative 370 ^oF) comet belt. You can see from the diagram, that if our solar system were the same size as that of Vega’s these belts would be in the same positions (the actual size of the solar system at the scale of Vega’s system is shown in the middle).

Image: NASA/JPL-Caltech.

What makes this particularly interesting is that it strongly implies that there are planets between the two bands, just as there are in our solar system. Otherwise, what would have swept away the debris dividing those two regions? Because of the larger scale of those systems (Vega and Formalhaut are each about twice the size of our sun), there’s about a hundred AU between the inner and outer belts. According to the researchers, multiple planets are probably responsible for tidying up that section of space. The next task is to find them.

Getting men to wash their hands

The bad news is that only 77% of men regularly wash their hands after using a public restroom (93% of women do so). The good news is that according to Maria Knight Lapinski from Michigan State University and her colleagues from the University of Pennsylvania, West Chester University and North Central College, those numbers can be improved upon with a little messaging.

The researchers observed the hand-washing behavior of 252 men who entered a university bathroom alone. Confederates outside the bathroom prevented other men from entering and disrupting the experiment by hanging ‘Out of Order’ signs on the door. Inside the bathroom, each subject was presented with one of six different combinations of messaging and privacy. Posters on the walls indicated either that four out of five students wash their hands after using the restroom (high prevalence) or that only one out of five do so (low prevalence). There was also a no poster control. Some of the time, the observer was hidden (private), whereas in other tests the observer was clearly visible (public). To be clear, in either case, the observer was watching the sinks, not the stalls or urinals so it wasn't at all creepy.

The observers noted both whether or not the subject washed his hands at all (liquid hitting the subject’s hands for one or more seconds was counted as a ‘yes’) and how thorough the washing had been (duration, use of soap, etc).

Interestingly, 88% of men who saw the low prevalence posters washed their hands, but only 81% of men in bathrooms with high prevalence posters washed their hands. Either poster was better than nothing, because only 70% of the men who weren’t exposed to any of the posters washed their hands. The no poster group also washed for one third less time than the people who saw posters (though almost everyone fell well short of CDC guidelines). The men were more virtuous when they thought someone might be watching. 86% washed in front of a visible observer whereas only 75% washed when they thought they were alone.

Putting up posters is a lot less expensive, not to say antagonistic, than installing sink monitors in every public restroom. The tactic also seems to be surprisingly effective. When queried, male college students believe that only about half their cohorts regularly wash their hands after using the bathroom, even though they themselves do wash their hands. Apparently, hygiene posters remind people to continue using good bathroom practices.

Lapinski, M., Maloney, E., Braz, M., & Shulman, H. (2013). Testing the Effects of Social Norms and Behavioral Privacy on Hand Washing: A Field Experiment Human Communication Research, 39 (1), 21-46 DOI: 10.1111/j.1468-2958.2012.01441.x.

Just for fun: Explore the Universe with NASA

Want to take a virtual tour of the universe from the comfort of your home? The helpful folks at NASA have made that possible with a suite of incredible programs called 'Eyes on...'. My family and I attended a lecture by Kevin Hussey, one of the producers of these tour de force visualizations, and we were blown away with the possibilities.

You can start with Eyes on the Earth to explore Earth’s life signs (carbon monoxide levels, temperature, etc) or to watch our many satellites traveling around us. Move on to Eyes on the Solar System to see any part of our solar system from any vantage point. Finally, move way out across the universe with Eyes on Exoplanets.

Everything is accurate for both scale and time. Satellites and planets move at their actual speed (you can speed them way up if you like, but then everything else is speeded up by the same amount). No matter where you look, you’ll see a real time visualization with everything in the correct position and of the right size relative to your vantage point. You can move forward or backward in time to see how things looked at precise moments in history.

I could go on and on without scratching the surface or doing these incredible programs justice, but this is really something you should play with yourself. I will leave you with one more thing: you can make your own 3D effects with the Spacecraft 3D app. on your phone or tablet. Here's the Hubble floating above my carpet:

A negative study on Bisphenol A

In science, it's critical to repeat experiments. Unless you can replicate results, you can't be sure that you're seeing a true effect. A new agouti mouse study about the effects of Bisphenol A is a prime example of why this is so. 

Agouti mice can produce offspring with colors varying from black through brown to yellow. These differences are not genetic, the baby mice can look completely different despite being genetically identical. Rather, the coat color differences are caused by epigenetic changes. There are two interesting things about this. First, the environment of the pregnant mother (what she eats or is exposed to) affects the coat color of her young, and second, the yellowest pups are the sickest, exhibiting ‘metabolic syndrome’ (obesity and diabetes) as they age. I think you can see where this is going. Researchers can expose the mommy mice to different conditions and directly observe how these conditions will affect the future health of the babies.

Among the environmental conditions of current interest is exposure to Bisphenol A (BPA). BPA is an endocrine disrupter. It mimics estradiol by binding to estrogen receptors and has been implicated in a variety of health issues. Prior studies with agouti mice have shown that giving mother mice BPA causes more of her offspring to have yellow coats. In other words, the maternal exposure was predisposing the fetuses to later illness. 

University of Missouri researchers, led by Cheryl Rosenfeld, repeated these experiments with three different concentrations of BPA and found that the chemical had no effect. Let me repeat that. In this new study, maternal exposure to BPA did not set off the baby mouse color-coded biohazard alarm.

To be clear, this study does not prove that BPA is safe for people and certainly not that it’s safe for pregnant women to consume. There are many studies showing that BPA is in fact harmful. This new data does, however, demonstrate the necessity for repeating experiments, particularly when health claims are being made. It also shows that we do not yet understand everything about BPA.

Rosenfeld CS, Sieli PT, Warzak DA, Ellersieck MR, Pennington KA, & Roberts RM (2012). Maternal exposure to bisphenol A and genistein has minimal effect on Avy/a offspring coat color but favors birth of agouti over nonagouti mice. Proceedings of the National Academy of Sciences of the United States of America PMID: 23267115.

Gene position affects gene activity

Thanks to work on epigenetics, we now know that there's more to genes than just the underlying DNA sequence. In fact, according to University of California, San Diego researchers led by Menzies Chen, epigenetics may be used to tease out whether the location of a gene within the genome can affect that gene's expression.

Epigenetics involves the modification of not only DNA itself, but also of protein complexes associated with DNA. For example, the histones that wrap up DNA into chromatin can be methylated, and these modifications are correlated with changes in transcription activity. It just isn’t clear which is the cause and which the effect. In other words, do transcription levels alter histone modification patterns, or do the histones cause the changes in gene expression? If the former, the activity level of a gene shouldn't change if the gene were moved to a new site. On the other hand, if the latter possibility is true, the gene activity would depend on the local histones at its new location.

This might be extremely tricky to elucidate if it weren't for the genome deletion library of the yeast Saccharomyce scerevisiae. For nearly every gene (over 90% of them anyway), there exists a strain of yeast in which that gene is deleted. In place of each missing gene is a recorder gene. The UCSD researchers were able to use this deletion library to test how the activity of the recorder gene was influenced by its position within the genome.

Because some genes are obviously essential for life, even for a yeast, the researchers used heterozygous organisms. This means that each yeast cell had one normal gene and one gene replaced by the recorder. Thus, the scientists could determine the transcription levels of the recorder in a more or less normally functioning yeast cell.

The genomic environment (modification of histones) was not altered by the substitution of the recorder for the original gene. On the other hand, about 35% of the difference in recorder expression was due to its position within the genome. This suggests that the histones affect transcription and not the other way around. This question is far from settled yet, though, as other studies have found differing results. Even in this study, one particular type of modified histone had a different effect on the recorder gene than on the normal genes that the recorder replaced. It’s not clear why that would be.

If nothing else, this gene replacement study serves as a proof of concept for studying genome location questions.

Chen, M., Licon, K., Otsuka, R., Pillus, L., & Ideker, T. (2013). Decoupling Epigenetic and Genetic Effects through Systematic Analysis of Gene Position Cell Reports DOI: 10.1016/j.celrep.2012.12.003.

Will long space missions make us lethargic?

What kind of effects would a prolonged space mission have on people? To date, only four people have spent more than a year in space. Six people have, however, spent 520 days enclosed in the Mars500 simulator. During that time, they were isolated from all outside contact, except by means that would be accessible in space (including communication delays).

Among the things lacking during their seventeen-month mission was any degree of privacy. The six men had their movements, activity level and wakefulness continuously monitored by wrist devices. In addition, each person was given an alertness test twice a week and a questionnaire about workload, tiredness and sleep quality once a week.

• Diego Urbina looking out from the hatch inside Mars500 facility.
  Credit ESA, 9/11/2010.
  
  
  

Four of the six crewmembers experienced some type of sleep problem, such as poor sleep quality or disruptions of their wake/sleep cycles. As the mission progressed, the volunteers spent less and less time in ‘active wakefulness’. The rest of the time, they were either asleep or sedentary. The drop in activity level was precipitous during the first three months, but continued to fall until the last twenty days of the mission, at which time everyone seemed to perk up. On the plus side, the extra sleep seemed to help the crew maintain alertness when they were awake, because their scores on those tests improved as their sleep time increased. This might be a lesson for all of us.

This mission highlighted a number of issues, as far as sleep goes. For one thing, it’s clear that different people have different reactions to prolonged isolation. Two of the crewmembers developed such skewed sleep rhythms that they were offset (asleep when the other four were awake or vice versa) twenty percent of the time. For another, the increasing amounts of inactivity as the mission progressed could be problematic in a real mission, especially if that quiescence reflects boredom or apathy.

You can see the crew’s triumphant 'return' below:

Basner M, Dinges DF, Mollicone D, Ecker A, Jones CW, Hyder EC, Di Antonio A, Savelev I, Kan K, Goel N, Morukov BV, & Sutton JP (2013). Mars 520-d mission simulation reveals protracted crew hypokinesis and alterations of sleep duration and timing. Proceedings of the National Academy of Sciences of the United States of America PMID: 23297197.