Fun(d) with Science

Many researchers will tell you that financing their work–writing grants, securing funding, and budgeting for varying funding levels year to year–is the least rewarding part of life in academia, but there’s no escaping the simple fact that science costs money. … Continue reading »

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Does Urbanization Always Drive Economic Growth? Not Exactly…

City

We often think of cities as major drivers of economic development and growth. Big cities expand our access to infrastructure like public transit and public education. They allow for more efficient distribution of social services such as government assistance and … Continue reading »

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Magnifying Power to the People with the Foldscope

The microscope holds a place on the short list of inventions that have changed the world and revolutionized our understanding of science. Microscopes are crucially important public health tools, allowing workers to identify pathogens and correctly diagnose the cause of illnesses. As educational tools, they can excite and engage students, revealing a world invisible to the naked eye. And, as many people who’d love a microscope but don’t have one can tell you, they are also expensive. Millions of doctors, health workers, and patients worldwide lack the resources to benefit from this vital tool, and millions of students have never seen a microscope before. In a dramatic step to address this problem, researchers from Stanford University have designed ultra-low-cost microscopes built from an inexpensive yet durable material: paper. They recently published their designs and data in PLOS ONE.

Foldscope template

Meet the Foldscope. Borrowing from the time-honored tradition of origami, the Foldscope is a multi-functional microscope that can be assembled much like a paper doll. Users cut the pieces from a pattern of cardstock, fold it according to the printed lines, and add the battery, LED, and lens, and?voilà?a microscope. Foldscope schematicClick here to watch a video of how one is assembled. Some of their coolest features are as follows:

  • Foldscopes are highly adaptable and can be configured for bright-field and dark-field microscopy, to hold multiple lenses, or to illuminate fluorescent stains (with a special LED).

Foldscope Configurations

  • They can be designed for low or high powers and are capable of magnifying an image more than 2,000-fold.
  • They accept standard microscope slides, and the viewer can move the lens back and forth across the slide by pushing or pulling on paper tabs.
  • Users can focus the microscope by pushing or pulling paper tabs that change the lens’ position.
  • Foldscopes are compact and light, especially when compared with conventional field microscopes. They also weigh less than 10 grams each, or about the weight of two nickels.
  • They are difficult to break. You can stomp on them without doing much damage, and they can survive harsh field environments and encounters with children.

Stepping on FoldscopeWhat’s the total cost, you ask? According to authors, it’s less than a dollar.  At that price, it’s easy to imagine widespread use of Foldscopes by many who previously could not afford traditional microscopes. In this TED Talk, Manu Prakash demonstrates the Foldscopes and explains his hopes for them. The authors envision mass producing them and distributing different designs optimized for detecting the pathogens that cause specific diseases, such as Leishmaniasis and E. coli.  They could even include simple instructions for how to treat and prepare slides for specific diagnostic tests or provide pathogen identification guides to help health workers in the field make diagnoses.  This is just one way in which the ability to see tiny things could make a huge difference in the world.

Related links:

Low-Cost Mobile Phone Microscopy with a Reversed Mobile Phone Camera Lens

Community Health Workers and Mobile Technology: A Systematic Review of the Literature

Citation: Cybulski JS, Clements J, Prakash M (2014) Foldscope: Origami-Based Paper Microscope. PLoS ONE 9(6): e98781. doi:10.1371/journal.pone.0098781

Images: Images are from Figures 1 and 2 of the published paper

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Awl be Darned: Metal Arrived in the Southern Levant Long Before Previously Thought

The Copper Age, sometimes referred to as the Chalcolithic period, was a time of technological transition for humans. As stone tools gave way to metal ones, the Levant—which includes parts of modern-day Israel, Palestine, Jordan, Lebanon, and Syria—emerged as a significant hub of copper crafting. Important archaeological finds, like the cache of copper artifacts found in the Nahal Mishmar Cave, are testaments to a robust copper-working tradition in the region, dating back to at least 4500-3800 BC. Although little is known about the origin and proliferation of metallurgy, or metal-working, in the Near East, a recent study published in PLOS ONE may offer new evidence of the earliest known use of copper in the southern Levant.

The recently discovered awl

The recently discovered copper awl

In the study, archaeologists from institutions in Israel and Germany describe a copper awl they discovered at an archaeological dig in Tel Tsaf, Israel, that they estimate dates back to 5100-4600 BC. An awl is a sharp spike, generally attached to a handle, that can be used to pierce holes in leather or textiles. Residue at the base of the spike indicates that it initially was connected to a wooden handle.  Researchers found the awl at a complex of mud brick buildings, rectangular rooms, and large circular grain silos. In addition, a multitude of beads, intricately decorated pottery, obsidian objects, and more were also found on site, and they appear to have originated from locations as far away as Armenia, Syria, Mesopotamia, and Egypt.  The presence of objects from other regions suggests that the site was connected to far-reaching trade networks.  The awl in question was found in an elaborate burial with a woman of about forty years of age, along with an ornate necklace made from over 1,500 ostrich eggshell beads. Its favored place as part of a burial indicates that it would have been a highly prized item.

The awl was discovered in this burial of a woman of about 40

The awl was discovered in this burial of a woman of about 40. A necklace of ostrich eggshell beads is visible in the bottom left corner.

The estimated age of the awl may make it the first known copper artifact in the Levant. Its presence at the excavation site shows that metal tools and objects may have arrived in the southern Levant via long-distance trade networks hundreds of years earlier than previously thought, long before the technology to make it locally was widely understood and adopted in the region.

The authors of this study used X-ray spectroscopy, or the bombarding of a sample with a beam high-energy particles, to determine the awl’s chemical composition by analyzing the unique signal that different elements emit in response. The spectroscopy revealed significant amounts of tin in the awl, an additive that creates bronze when mixed with copper. Bronze, like copper, is so important that it also gets its own Age (the Bronze Age). However, because this awl predates the advent of bronze by thousands of years, the authors speculate that the tin may have actually been incidental and naturally occurring.  Copper with traces of tin is known to occur naturally in the Caucuses, a range of mountains stretching between the Caspian and Black Seas, and the awl may have originated there and made its way through trade networks to where it was finally discovered in Tel Tsaf. Copper-working know-how may have proliferated along the same networks, paving the way for widespread local production of copper artifacts, and followed closely, no doubt, by the ever-present scourge of copper theft.

Related Links:

What Early Neolithic People Left Behind: Levantine Arrowheads Found in Saudi Arabia

Dressed-Up Donkey Discovered at Religious Burial Site

Citation: Garfinkel Y, Klimscha F, Shalev S, Rosenberg D (2014) The Beginning of Metallurgy in the Southern Levant: A Late 6th Millennium CalBC Copper Awl from Tel Tsaf, Israel. PLoS ONE 9(3): e92591. doi:10.1371/journal.pone.0092591

Images: Images are Figures 4 and 5 of the published article

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There is No Real but the Real You Feel: New “Marble-Hand” Illusion Changes Perception of Body

It behooves us for our brains to have a solid working knowledge of our bodies: to know where our limbs are, what they feel like, and how they’ll interact with objects in the world. Even as you perform the simple act of lifting a glass of water to your mouth, you rely on the assumptions your brain makes about your body to know how hard your muscles should pull to move your arm, where your fingers end, and how hard you should grip the glass. But can these assumptions about your body ever change? A new study from PLOS ONE by researchers in Italy and Germany uses a powerful illusion to show just how fast our brains can update our perceptions of our bodies, given the right sensory cues.

Participants in the experiment first completed a questionnaire about how their right hand felt: its stiffness, heaviness, hardness, temperature, naturalness, and sensitivity. Next, they donned headphones and placed one hand behind a screen. Researchers then repeatedly tapped each participant’s hand with a small hammer for five minutes, and every time they did, they played the sound of a hammer striking stone. To maximize the illusion, the stone-hammer sound started at a very low volume and became louder over time. After the hammer session, participants filled out the same survey about their hand. Survey results showed that test subjects felt their hand was harder, heavier, stiffer, and less natural than before. In other words, as the brain started perceiving a strong auditory indication that the arm was hard and stone-like, it seems it also started updating its assumptions about the arm’s properties very quickly.

To validate these findings, researchers also took physical measurements of skin sensitivity on a subset of the group, both before and after the hammer hits. Our skin conducts electricity, and as it responds to stimuli—a painful prick, a change in temperature, or even an emotion—its conductivity varies. Measuring the resistance between electrodes connected to two points on the skin gives us a physiological measure of skin sensitivity and arousal, which is sometimes called the Galvanic skin response. The authors found that after the hand-hammering illusion, participants’ physiological response to a threatening stimulus (in this case, watching a needle approach their hand) increased significantly.

The authors conducted several other control experiments to better understand the mechanism behind the illusion. They repeatedly struck the hands of participants in a control group with a hammer and played the same hammer-on-stone sound, but did not time the hammer hits and the sound to sync up perfectly. This group did not report the same change in hand feeling or perception that the experimental group did, nor did it display a change in Galvanic skin response. The team also tested the effect of playing a pure tone with each hammer tap, rather than a hammer-and-stone sound, and found that this also had no significant effect on hand perception or Galvanic skin response. Finally, participants who heard the natural, unaltered sound of the hammer hitting their skin did not report any changes in their hand perception after their hand was hammered.

Control is not an Illusion

Control is not an illusion:  In one control, the hammer sounds and hammer hits were staggered

The authors state that these controls help demonstrate how the illusion works. When incoming signals do not appear related—for instance, when the hammer hits and sounds don’t come at the same time—our brains can easily keep them separate. It is only when signals come at the same time and seem to be related that the illusion occurs. Rather than using static information about your body, your brain can take the extraordinary step of updating its understanding of the body to match the incoming signals, even when the new body perception is at odds with what we know to be true.  Seeing is believing, and so too, it seems, is hearing and feeling.

Related links:

A Sense of Embodiment Is Reflected in People’s Signature Size

Out-of-Body Experiences Make It Harder To Encode Memories

Citation: Senna I, Maravita A, Bolognini N, Parise CV (2014) The Marble-Hand Illusion. PLoS ONE 9(3): e91688. doi:10.1371/journal.pone.0091688

Images: Figures are panels A and B of Figure 1 of the full manuscript

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Falcon Physics: The Science of Diving Peregrine Falcons

Peregrine falcons, the world’s fastest-moving animal, are found on six continents around the world. Once an endangered species in the United States, their population comeback has been attributed to the widespread ban of DDT and other pesticides in the 1970s, and is a great success story in conservation. It is easy to see why these remarkable birds are so charismatic. Peregrine falcons hunt unknowing prey by diving from above at speeds of up to 200 miles per hour, maintaining an astounding degree of maneuverability and precision.  However, conducting in-depth analysis of the aerodynamic properties of peregrine falcons is no easy task. Dives are infrequent in the wild, we usually only see them from a distance, and their blistering speeds make the birds difficult to film. Nevertheless, that is exactly what a team of researchers in Germany managed to do, and they recently published the results in PLOS ONE.

Peregrine falcon in flight

Peregrine falcon in flight

Researchers first trained several peregrine falcons to dive from the top of a dam to the bottom, following a specific and predictable flight path. A trainer at the top of the dam released a falcon from the same spot each time, and a second trainer at the base used a lure to attract the bird’s attention. High-speed cameras facing the dam wall filmed falcon dives from different angles. The authors used the dam in the background of the video footage as a frame of reference to precisely and accurately recreate the peregrine’s diving trajectory, something that is nearly impossible to do filming peregrines in the wild against the sky.

Stages of a Peregrine Falcon's dive

Stages of a peregrine falcon’s dive

Back at the lab, the scientists positioned the wings and body of a stuffed peregrine falcon to resemble a falcon diving at maximum speed, and then used it to create a life-sized plastic version. The plastic falcon was analyzed in a wind tunnel using two different methods of analysis:  oil-painting-based flow visualization and particle image velocimetry.  A brief description of both techniques:

  • Surface flow visualization: By coating an object in a thin layer of paint or oil and putting it in a wind tunnel, we can examine the streaking patterns left in the paint or oil to reveal flow lines.
Peregrine falcon surface flow

Peregrine falcon model after  oil-painting-based flow visualization, showing the air flow across the body

  • Particle image velocimetry: By introducing tiny tracer particles into the wind tunnel, illuminating them with a laser, and photographing them rapidly, we can use computers to track the movement of individual particles through a sequence of photographs, calculate the particles’ trajectories and velocities, and then use this data to build an accurate model of the wind flow.

By combining their wind tunnel analysis with the data from the video footage, the researchers created the most comprehensive analysis of a peregrine falcon dive to date, including factors such as lift, drag, acceleration, and trajectory. In particular, the high-speed footage revealed that small feathers pop up during the dive in key locations on the peregrine falcon’s body. The authors say that the feather position and wind tunnel analysis support the explanation that these feathers help keep air flowing smoothly over the bird’s body to reduce drag, similar to flaps on an airplane wing.

As if you needed someone to tell you that this bird is aerodynamic!

Diving peregrine and model

Diving peregrine and 3D computer model

Related links:

Having trouble calibrating your own particle image velocity experiments? This video may help, but be careful: lasers are dangerous!

Love fluid dynamics and tunnels? Whisker Shape and Orientation Help Seals and Sea Lions Minimize Self-Noise

And, this is just plain fun: Peregrine falcon chases a mountain bike

Citation: Ponitz B, Schmitz A, Fischer D, Bleckmann H, Brücker C (2014) Diving-Flight Aerodynamics of a Peregrine Falcon (Falco peregrinus). PLoS ONE 9(2): e86506. doi:10.1371/journal.pone.0086506

Images: Picture of flying falcon from Mike Baird. 2nd, 3rd, and 4th pictures taken from Figures 7, 15, and 4 of the published paper, respectively.

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Watch Where I’m Going: Predicting Pedestrian Flow

Pedestrian traffic flow

Pedestrian traffic flow

At last check, the population of the world was around 7.1 billion and counting.  As we all know, the sheer number of people on the planet presents a host of new challenges and exacerbates existing ones.  The overarching population problem may seem daunting, but there’s still plenty we can do to make a crowded, urbanized world livable.  A new study in PLOS ONE focuses on the specific issue of pedestrian traffic and how to accurately model the flow of people through their environment.

Researchers with Siemens and the Munich University of Applied Sciences examined video recordings of commuters walking through a major German train station on a weekday, during both the morning and evening peak commute times. Scientists analyzed the videos to determine individual pedestrians’ paths and walking speeds, and used the resulting data to set the parameters for a simulation of pedestrian traffic flow.  According to the authors, this kind of calibration of theoretical models using real-world data is largely missing from the most pedestrian flow models, which are under-validated and imprecise.

Footage from train station

Footage from train station

The authors utilized a cellular automaton model to form the basis of this simulation. Cellular automatons are models in which cells in a grid evolve and change values through steps based on specific rules. In this instance, the authors used a hexagonal grid and a few simple rules about pedestrian movement:

  • Pedestrians know and will follow the shortest path to their destination unless pedestrians or other obstacles are in the way.
  • Pedestrians will walk at their own individual preferred speeds, so long as the path is unobstructed.
  • Individuals need personal space, which acts like a repelling force to other pedestrians and objects.
  • Walking speeds decrease as crowds get denser.
  • Factors like age and fitness are all captured by setting a range of individual walking speeds.
Pedestrian traffic flow model

Pedestrian traffic flow model (Settlers of Catan Pedestrian Expansion?)

This model also borrowed from electrostatics by treating people like electrons. As the authors write:

“Pedestrians are attracted by positive charges, such as exits, and repelled by negative charges, such as other pedestrians or obstacles.”

Add to this model rules about when and where pedestrians appear, the starting points and destinations, and the relative volume of traffic from each starting point to different destinations, and you’ve got a basic model of pedestrian traffic.

Next, the authors calibrated this model by setting parameters using real-world, observational data from the train station videos:  where people at each starting point were going, distance kept from walls, the distribution of walking speeds, and so on.  To test their model and parameters, the authors validated it by running predictive simulations and comparing it to real-world scenarios. Based on the results, the authors suggest that this kind of model, which includes parameters based on real-world observation, more accurately represents pedestrian flow than other models of walkers that do not incorporate observational data.

The authors also changed multiple parameters to determine which ones had the largest impact on the simulation. The parameter that had the largest effect when altered was the source-target distribution (the destinations of people coming from specific starting points), so the authors note that this is critical to measure accurately and precisely.

The ability to precisely predict the flow of traffic has many clear applications, from the design of buildings and public spaces to the prediction and prevention of unsafe crowd densities during large events or emergencies.

Next research question: when it’s crowded, does pushing really not make it go faster?

Related papers:

Citation: Davidich M, Köster G (2013) Predicting Pedestrian Flow: A Methodology and a Proof of Concept Based on Real-Life Data. PLoS ONE 8(12): e83355. doi:10.1371/journal.pone.0083355

Images: All images come from the manuscript

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Reptilian Sibling Rivalry

Do you ever fight with your siblings? Unless you’re regularly biting, head-butting, and threatening each other all night long, things could probably be worse. The authors of a new PLOS ONE study investigate how well crocodilians get along with each other as youngsters.

Researchers observed seven species of hatchling and juvenile captive-raised crocodilians in Darwin, Australia and Chennai, India. The animals were divided into small groups and then introduced into new mixed water and land enclosures. The scientists counted, classified, and analyzed instances of aggressive interactions, postures and behavior among the animals. Because crocodilians are at their most active in the evenings and during the night (and at their most amiable during the day), the authors analyzed footage from 4pm until 8am the next morning.

Siblings aren’t always so bad: juvenile Siamese crocodiles socializing

Siblings aren’t always so bad: juvenile Siamese crocodiles socializing

Some but not all of the awesome aggressive behaviors the authors observed during the study included:

  • Biting: “Jaws closed shut on an opponent.” Bites range from light mouthing to prolonged bites.
  • Head pushing: “Head is pushed into an opponent.”
  • Inflated posture: The crocodilian extends upward on its legs and arches its back downward to appear large and dominant. Other species also modify their posture in a similar fashion when challenged—two classic examples are cats and puffer fish.

  • Tail wagging: Crocodilians (like cats and many other animals) wag their tails as a way to signal and respond to aggression. They also sometimes tail wag as a windup to increase the force of a bite or a side head strike.
  • Side head strikes: One individual thrusts his or her head sideways into another’s.

Based on the observed behaviors, the authors classified the seven species according to levels of aggression. The authors suggest that the significant overall differences in relative temperament likely arise from each species’ unique ecological environment and adaptations. Some species, like the American alligator, the gharial (native to India), and the freshwater crocodile, were highly tolerant of one another and had relatively few aggressive interactions. When these species did display aggressive behavior, the vast majority of aggressive incidents appeared to be accidental and low-intensity. Other more aggressive species, like the saltwater crocodile and the New Guinea crocodile, displayed pronounced dominance patterns and had a higher incidence of deliberate, intense aggression.  These species used direct challenges like biting to establish dominance, and submissive behaviors such as raising the head into the air to yield.  Bites and head pushes were the most common forms of aggressive contact across all the species, although many behaviors were species-specific. For example, slender-snouted crocodilians tended to avoid aggressive interactions and the most potentially damaging behaviors, perhaps due to a relatively higher risk of injury.

The researchers suggest that aggressive behavior in young crocodilians could be a survival strategy to help them learn social queues and minimize their chances of being injured in social settings. The extent of the hatchling’s aggression may affect how long it takes them to abandon their initial family groups. Babies will spend anywhere from a few weeks to a few years with siblings and a small number of adults, until (like so many humans) they leave their families and strike out on their own “due to a growing intolerance of each other.”

The authors indicate that this research may have implications for effectively rearing multiple species in captivity and may also inform the planning, management, and success of effective reintroduction and conservation programs worldwide.

Related Content:

Determinants of Habitat Selection by Hatchling Australian Freshwater Crocodiles

Why the Long Face? The Mechanics of Mandibular Symphysis Proportions in Crocodiles

Citation: Brien ML, Lang JW, Webb GJ, Stevenson C, Christian KA (2013) The Good, the Bad, and the Ugly: Agonistic Behaviour in Juvenile Crocodilians. PLoS ONE 8(12): e80872. doi:10.1371/journal.pone.0080872

Images: Siamese crocodiles picture by chem7, other pictures taken from Figure 1 of the published paper.