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 of 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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Meta-Analyses of Genetic Association Studies – PLOS ONE’s Approach

Meta-analysis can be a powerful way to reveal otherwise hidden or unclear associations, when done with care. In line with recent trends in biomedical literature (1), PLOS ONE has seen a consistent increase in submissions reporting meta-analyses of genetic association studies over the last few years. These submissions report analyses of potential associations between candidate gene variants (usually single nucleotide polymorphisms, or SNPs) and specific disease risks and outcomes in human populations, based on a search of the literature to identify published reports studying the association and statistical analyses that synthesize the results of the identified studies.

However, researchers in the community, among them members of our editorial board, have raised concerns about some of these meta-analyses, including the risk of false positives due to publication bias, incomplete searches of the literature, redundancy, and an insufficient assessment of the power and quality of the included studies. As noted a decade ago, “Meta-analysis is not a replacement for adequately powered genetic association studies” (2).  Many of these studies focus on a single gene variant, and many do not include data from relevant genome-wide association  studies (GWAS), some of which have failed to replicate previously reported associations between candidate genes and diseases.

While many meta-analyses of genetic association studies are still clinically relevant, especially those studying rare conditions where GWAS data are not available, and well-conducted meta-analyses can provide useful and valid clinical evidence, we strongly feel that meta-analyses of genetic association studies considered by PLOS ONE must have the rationale clearly explained and that authors must report their studies according to high standards.

In order to address these concerns and after consultation with PLOS ONE editorial board members, we are introducing a new process to handle meta-analyses of genetic association studies. Authors will now be asked to provide the following information:

  1. The rationale for conducting the meta-analysis;
  2. The contribution that the meta-analysis makes to knowledge in light of previously published related reports, including other meta-analyses and systematic reviews;
  3. Whether GWASs relevant to the meta-analysis have been published and whether these were included in the analysis;
  4. Full methodological details for the meta-analysis, including completion of a checklist that has been developed with reference to several published guidelines (3, 4, 5) and in consultation with members of the PLOS ONE editorial board.

The information supplied by the authors will be evaluated by the in-house editorial team as part of the checks undertaken on new submissions. Meta-analyses replicating studies in the literature without adequate justification will be rejected. For those manuscripts that proceed to review, PLOS ONE Academic Editors will be consulted on the adequacy of the methodological aspects of the study and the quality of the reporting in the manuscript.

This process underscores our commitment to maintaining high standards of quality and reporting in publications at PLOS ONE. We are grateful for the input we have received from our editorial board that led to this new process, and wish to thank the PLOS ONE Academic Editors who provided advice and guidance.

If you have any questions or feedback, or if you are an author who would like additional information about our requirements for meta-analyses of genetic association studies, please contact us at plosone@plos.org.

Posted on behalf of the in-house editors at PLOS ONE:

Associate Editors Adrian Aldcroft, Gina Alvino, Meghan Byrne, Christna Chap, Michelle Dohm, Renee Hoch, Matt Hodgkinson, Alejandra Clark and Nicola Stead; Senior Editors Eric Martens, Iratxe Puebla and Emma Veitch; and Editorial Director Damian Pattinson

  1. Ioannidis JPA, Chang CQ, Lam TK, Schully SD, Khoury MJ (2013) The Geometric Increase in Meta-Analyses from China in the Genomic Era. PLOS ONE 8(6): e65602. doi:10.1371/journal.pone.0065602
  2. Marcus R. Munafò and Jonathan Flint (2004) Meta-analysis of genetic association studies. Trends Genet. 20(9):439-44 doi:10.1016/j.tig.2004.06.014
  3. Sagoo GS, Little J, Higgins JPT (2009) Systematic Reviews of Genetic Association Studies. PLOS Med 6(3): e1000028. doi:10.1371/journal.pmed.1000028
  4. Minelli C, Thompson JR, Abrams KR, Thakkinstian A, Attia J: The quality of meta-analyses of genetic association studies: a review with recommendations. Am J Epidemiol. 2009 Dec 1;170(11):1333-43. doi: 10.1093/aje/kwp350
  5. Little J, Higgins JP, Ioannidis JP, Moher D, Gagnon F, et al. (2009) STrengthening the REporting of Genetic Association Studies (STREGA)- An Extension of the STROBE Statement. PLOS Med 6(2): e1000022. doi:10.1371/journal.pmed.1000022
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Squirrels – Nut Sleuths or Just Nuts?

squirrel2

Crazed squirrels: we’ve all seen them. Some dashing toward you only to stop short long enough to glare with beady eyes before fleeing, others dive-bombing the dirt, coming up with their heads waving back and forth. They’re the butt of many a joke on college campuses, providing endless amusement with their antics. Some UC Berkeley students even think that the resident campus squirrels may have gobbled up substances left over from the wilder moments of Berkeley’s past, leaving them permanently crazed. However, according to a recently published PLOS ONE article from UC Berkeley, these squirrels’ seemingly odd behavior may actually have a purpose. We’ve long known that scatter-hoarders will store food they find to prepare for periods when it’s less abundant, but there is little information on the hoarding process. Turns out these squirrels might actually have a refined evaluation method based on economic variables like food availability and season. To eat now, or cache for later?

Researchers interacted with 23 fox squirrels, a species well-habituated to humans, in two sessions during the summer and fall of 2010 on the Berkeley campus, evaluating food collection behavior during both lean (summer) and bountiful (fall) seasons. The authors engaged the squirrels with calls and gestures to attract their attention, and the first squirrel to approach was the focus of that round of testing.

Each squirrel was given a series of 15 nuts, either peanuts or hazelnuts, in one of two sequences. Some were offered five peanuts, followed by five hazelnuts, then five more peanuts (PHP). Others were given five hazelnuts, five peanuts, then five hazelnuts (HPH). The purpose of this variation was to evaluate how squirrels would respond to offers of nuts with different nutritional and “economic” values at different times. Hazelnuts are, on average, larger than peanuts, and their hard shell prevents spoiling when stored long term, but peanuts tend to have more calories and protein per nut.  Researchers videotaped and coded each encounter to calculate variables, like the number of head flicks per nut, time spent pawing a nut, and time spent traveling or caching nuts. See the video below for a visual example of these behaviors.

The results showed that season and nut type significantly affected the squirrel’s response, and the squirrel’s evaluation of the nut could forecast its course of action. Predictably, the fall trial showed squirrels quickly caching most of their nuts, likely taking advantage of the season’s abundance. Squirrels ate more nuts in the summer, though they still cached the majority of hazelnuts (76% vs. 99% cached in the fall) likely due to their longer “shelf life”.

The squirrels who head-flicked at least one time in response to a nut cached it nearly 70% of the time, while those who spent more time pawing the nut tended to eat it (perhaps searching for the perfect point of entry?). The time spent caching and likelihood of head flicking were clearly linked to the type of nut received and to the trial number, with time spent evaluating a nut decreasing as the trials continued for a squirrel. The authors suggest that the changes in food assessment strategies in response to resource availability provide an example of flexible economic decision making in a nonhuman species.

So, now that squirrels are possibly making economically prudent decisions when evaluating nuts, I guess we have to give them a break when we see them running around like crazy on campus. Doesn’t mean we’ll stop laughing.

Citation: Delgado MM, Nicholas M, Petrie DJ, Jacobs LF (2014) Fox Squirrels Match Food Assessment and Cache Effort to Value and Scarcity. PLoS ONE 9(3):e92892. doi:10.1371/journal.pone.0092892

Image: Squirrel by likeaduck

Video: Video S1 from the article

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A Disease of Considerable Antiquity: Cancer Detected in a Nubian Skeleton

Figure 11

New bone formation in a lesion of the pelvis.

Cancer, the transformation of normal cells into malignant tumor cells, reigns among diseases as one of the leading causes of death around the world. In 2012, cancer claimed 8.2 million lives, and numbers continue to increase each year. While our understanding of cancer is far from complete, we’ve been able to attribute some of the killer’s virulence to increased environmental risk: Increased pollutants and other environmental carcinogens, coupled with an average increase in tobacco and alcohol use and added to a concurrent decrease in daily exercise, cumulatively represent significant risk factors directly related to an increasingly modern world. Ironically, we humans also live a lot longer than we used to, which increases the disease’s chances of occurring.

However, we have identified far fewer examples of the disease in the archaeological record compared to its current frequency in the current population, which has led to the idea that cancer was much less widespread in antiquity. As a result, very little is known about its evolutionary history.

As part of a larger research project undertaken by the British Museum in the city of Amara West, Sudan, the authors of a PLOS ONE paper dug a little deeper into the dark, early history of cancer. Their subject of interest was an over 3,000 year-old skeleton of a young man from ancient Nubia, then part of Egypt, whose remains were excavated at this site, designated on the map below.

Figure 1

Map of modern Sudan showing the archaeological site of Amara West.

When the researchers uncovered skeleton 244-8, as he has been cataloged, they were presented with the difficulties of examining a less-than-complete body. Parts of the skeleton had been broken, highlighted as fragmentary in the image below. In addition, salt in the surrounding soil had slowly damaged the skull over time. The soft tissue of the over 3,000-year-old skeleton, was also long gone.

Figure 3

Hatched areas show areas of bone affected by lesions.

On top of these difficulties, damages to the body incurred over time, both before and after death, can look very similar to the eye. Cancer, in particular, is notoriously hard to diagnose in human remains; its similarities to other pathologies combined with natural damages sustained after burial made the researchers’ task of properly diagnosing skeleton 244-8 a complicated one. The earliest signs of cancer in bone are also only visible via methods like X-ray that allow us to visualize the inner parts of bone where the disease begins, which the naked eye cannot see.

The researchers assessed the condition of skeleton 244-8, using digital microscopes, scanning electron microscopes (SEM), and radiography (X-rays), and by examining the visual markers on the bone. They looked for evidence of sustained lesions, or damage on the bone, which they found on his vertebrae, ribs, sternum, pelvis, and other parts of the skeleton.

Figure 8

Lesions of the left first rib.

In the X-ray and photo image above of a rib, we can see the damage as noted by the arrows. The parts of the skeleton most affected by lesions were sections of the spine. The image below depicts an especially damaged thoracic vertebra.

Figure 9

Lesions of the 7th thoracic vertebra. The inset shows a close-up of new bone growth.

The authors discussed four possible causes for the skeleton’s bone damage:

  • Metastatic organ cancer, or the rapid creation of abnormal cells that spread from the original site in the organs to other parts of the body
  • Multiple myeloma, a cancer of the plasma cells in bone marrow
  • Fungal infection
  • Taphonomic damage, or natural decay after death

Although very similar, the visual markers on bone differ slightly depending on the malady causing the damage. We can see in the image below of a tibia that taphonomic damage caused by insects is slightly more uniform in shape than lesions caused by cancer, and the holes continue straight through to the other side of the affected bone.

Figure 13

Tibia of a skeleton from Amara West showing post-mortem damage caused by insects.

Based on the shape, size, and appearance of the lesions under X-ray, the authors surmised that the man suffered from metastatic cancer, originating in the man’s organs. However, since no soft tissue was preserved over time, it is nearly impossible to ascertain the exact location of skeleton 244-8’s primary tumor, which would have affected soft tissue like his organs.

Considering the decay caused by time, salt, and insects, the researchers were able to ascertain quite a lot about skeleton 244-8 based on their examinations of the skeleton. In addition to diagnosing him with metastatic cancer, researchers suggest that skeleton 244-8 was a young man between the ages of 25 to 35 who belonged to a middle-class Nubian family at the time of his death, based on the context of his burial.

With increasing advances in the technology used to examine subjects like skeleton 244-8, the inner secrets and pathologies held in places like the inside of bone become less of a mystery. With further study, we’ll be able to understand a little more about the environmental risk factors of skeleton 244-8’s own world: for instance, the possible use of fires in poorly ventilated mudbrick houses, or possible infectious diseases spread by parasites. By taking a closer look at human remains like skeleton 244-8, it may eventually be possible to see the effects of a disease not only of our time, but of considerable antiquity.

Citation: Binder M, Roberts C, Spencer N, Antoine D, Cartwright C (2014) On the Antiquity of Cancer: Evidence for Metastatic Carcinoma in a Young Man from Ancient Nubia (c. 1200BC). PLoS ONE 9(3): e90924. doi:10.1371/journal.pone.0090924

Image 1: pone.0090924

Image 2: pone.0090924

Image 3: pone.0090924

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Image 5: pone.0090924

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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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3000 Years Ago, We Were What We Ate

Efate, VanuatuFor many of us, moving to a new house means recruiting a couple good friends to help pack and haul boxes. After a day or two of work, everyone shares a pizza while resting tired muscles at the new home. But 3000 years ago, enjoying a post-move meal may have required a little more planning. Early settlers of remote tropical islands in the Pacific had to bring along all resources needed for survival, including food, from their original homes overseas.

The Lapita people were early settlers of islands in the Pacific, called Remote Oceania (pictured below). When these people, whose culture and biology links to Southeast Asian islands, first decided to sail to the island Vanuatu, they brought domestic plants and animals—or what you might call a ‘transported landscape’—that allowed them to settle this previously uninhabited, less biodiverse (and less resource-available) area. However, the extent to which these settlers and their domestic animals relied on the transported Remote Oceanialandscape at Vanuatu during the initial settlement period, as opposed to relying on the native flora and fauna, remains uncertain.

To better understand the diet and lives of the Lapita people on Vanuatu, archaeologist authors of a study in PLOS ONE analyzed the stable carbon, nitrogen, and sulfur isotopes from the bones of ~ 50 adults excavated from the Lapita cemetery on Efate Island, Vanuatu.

Why look at isotopes in human remains? Depending on what we eat, we consume varying amounts of different elements, and these are ultimately deposited in our bones in ratios that can provide a sort of “dietary signature”; in this way, the authors can investigate the types of plants, animals, and fish that these early people ate.

For instance, plants incorporate nitrogen into their tissue as part of their life cycle, and as animals eat plants and other animals, nitrogen isotopes accumulate. The presence of these different ratios of elements may indicate whether a human or animal ate plants, animals, or both. Carbon ratios for instance differ between land and water organisms, and sulfur ratios also vary depending on whether they derive from water or land, where water organisms generally have higher sulfur values in comparison to land organisms.

Scientists used the information gained about the isotopes and compared it to a comprehensive analysis of stable isotopes from the settlers’ potential food sources, including modern and ancient plants and animals. They found that early Lapita inhabitants of Vanuatu may have foraged for food rather than relying on horticulture during the early stages of colonization. They likely grew and consumed food from the ‘transported landscape’ in the new soil, but appear to have relied more heavily on a mixture of reef fish, marine turtles, fruit bats, and domestic land animals.

The authors indicate that the dietary analysis may also provide insight into the culture of these settlers. For one, males displayed significantly higher nitrogen levels compared to females, which indicates greater access to meat. This difference in food distribution may support the premise that Lapita societies were ranked in some way, or may suggest dietary differences associated with labor specialization.  Additionally, the scientists analyzed the isotopes in ancient pig and chicken bones and found that carbon levels in the settlers’ domestic animals imply a diet of primarily plants; however, their nitrogen levels indicate that they may have roamed outside of kept pastures, eating foods such as insects or human fecal matter. This may have allowed the Lapita to allocate limited food resources to humans, rather than domestic animals.

Thousands of years later, the adage, “you are what you eat” or rather, “you were what you ate” still applies. As the Lapita people have shown us, whether we forage for food, grow all our vegetables, or order takeout more than we would like to admit, our bones may reveal clues about our individual lives and collective societies long after we are gone.

Citation: Kinaston R, Buckley H, Valentin F, Bedford S, Spriggs M, et al. (2014) Lapita Diet in Remote Oceania: New Stable Isotope Evidence from the 3000-Year-Old Teouma Site, Efate Island, Vanuatu. PLoS ONE 9(3): e90376. doi:10.1371/journal.pone.0090376

Image 1: Efate, Vanuatu by Phillip Capper

Image 2: Figure 1

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PLOS’ New Data Policy: Part Two

The past couple of weeks have led to an extraordinary outpouring of discussions on open data and its place in scientific publishing. We are grateful to everyone who took the trouble to tweet, blog or email about this and are heartened that so many people care as passionately as we do about open science. However, much of the discussion has centered on a misunderstanding in a previous blog post and we want to correct that now.

We apologize for causing confusion

In the previous post, and also on our site for PLOS ONE Academic Editors, an attempt to simplify our policy did not represent the policy correctly and we sincerely apologize for that and for the confusion it has caused. We are today correcting that post and hoping it provides the clarity many have been seeking. If it doesn’t we’d ask you once again to let us know – here on the blog, by email at data@plos.org, and via all the usual channels.

Two key things to summarize about the policy are:

  1. The policy does not aim to say anything new about what data types, forms and amounts should be shared.
  2. The policy does aim to make transparent where the data can be found, and says that it shouldn’t be just on the authors’ own hard drive.

Correction

We have struck out the paragraph in the original PLOS ONE blog post headed “What do we mean by data”, as we think it led to much of the confusion. Instead we offer this guidance to authors planning to submit to a PLOS journal.

What data do I need to make available?

We ask you to make available the data underlying the findings in the paper, which would be needed by someone wishing to understand, validate or replicate the work. Our policy has not changed in this regard. What has changed is that we now ask you to say where the data can be found.

As the PLOS data policy applies to all fields in which we publish, we recognize that we’ll need to work closely with authors in some subject areas to ensure adherence to the new policy. Some fields have very well established standards and practices around data, while others are still evolving, and we would like to work with any field that is developing data standards. We are aiming to ensure transparency about data availability.

An example

We are happy to answer questions about specific fields in detail. A generalized example of the type of question we have received recently, and our answer, is as follows.

Question sent to data@plos.org:

When I do an experiment taking a number of different measurements from cells, I usually report them in bar graphs as means from different experiments with their corresponding standard deviations, and the details of statistical analysis are provided in the methods section. Under this new policy is this information enough? Or does the new policy require that I upload the excel files with all the data underlying the graphs? And do I need to include every reading from the cells in raw form or can I provide just the summary in the excel files?

 
Answer:

There is no specific requirement with the new policy concerning the type of data that you make available – our focus at this stage is on making transparent where the data can be found. It has always been the case that different fields have different types of data that need to be provided – and indeed such requirements change over time, too. In the case of sensational claims, editors and reviewers frequently ask for more data than in other cases – as ‘extraordinary claims need extraordinary evidence’.

 

So, as was always the case, if you are providing graphs, it would indeed be helpful to provide the spreadsheet from which you generated the graph. If you think some other form of the data would be useful to other researchers who might want to understand, replicate or build on your work, please do include it. Conversely, if it is usual in publications in this field to provide only the summary information, then that remains sufficient now. As ever, reviewers and editors will tell you if they feel more data is needed to support your findings, as this is one of the key functions of peer review.

 
Where to go for more information

Data sharing policy: http://www.plosone.org/static/policies#sharing

FAQs: http://www.plosone.org/static/policies#faqs

Contact: data@plos.org

Image Credit: jonathangray.com

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The Science of Snakeskin: Black Velvety Viper Scales May be Self-Cleaning

West African Gaboon Viper

West African Gaboon viper

Whether you love them or hate them, snakes have long captivated our interest and imagination. They’ve spurred countless stories and fears, some of which may have even affected the course of human evolutionary history. We must admit, there is something a little other-worldly about their legless bodies, willingness to swallow and digest animals much bigger than them, and fangs and potentially fatal (or therapeutic?) venomous bites.

Not least of all, their scaly skin is quite mesmerizing and often laden with intricate and beautifully geometric patterns just perfect for camouflaging, regardless of whether they live high up in a tree, deep in murky waters, or on the forest floor. Snakeskin was the focus of recent research by the authors of this PLOS ONE study who sought to determine whether it has any special properties less obvious to the naked eye.

Please meet the West African Gaboon viper, Bitis gabonica rhinoceros (pictured above). Native to the rainforests and woodlands of West Africa, these large, white-brown-and-black snakes can be identified by large nasal horns and a single black triangle beneath each eye—nevermind that, because they also lay claim to titles for the longest fangs and most venom volume produced per bite. The pattern of their skin is intricate and excellent for camouflage, and the black sections have a particularly velvety appearance. These eye-catching characteristics intrigued zoology and biomechanics researchers from Germany, who decided to take a closer look.

In a previously published paper, the authors analyzed the Gaboon viper’s skin surface texture by using scanning electron microscopy (SEM), as well as its optical abilities by shining light on the snakeskin in different ways to see how it’s reflected, scattered, or transmitted. They found that only the black sections contained leaf-like microstructures streaked with what they call “nanoridges” on the snake scales, a pattern that has not been observed before on snakeskin. What’s more, the black skin reflects less than 11% of light shone on it—a lot less than other snakes—regardless of the angle of light applied. The authors concluded from the previous study that both of these factors may contribute to the viper’s velvet-like, ultra-black skin appearance.

Scanning electron microscopy (SEM) of viper scales

Scanning electron microscopy (SEM) of viper scales

In their most recent PLOS ONE paper titled “Non-Contaminating Camouflage: Multifunctional Skin Microornamentation in the West African Gaboon Viper (Bitis rhinoceros),” the authors conducted wettability and contamination tests in hopes of further characterizing the viper skin’s properties, particularly when comparing the pale and black regions.

To test the wettability of the viper scales, the authors sprayed droplets of water, an iodide-containing compound (diiodomethane), and ethylene glycol on the different scale types shown above, on both a live and dead snake, and then measured the contact angle—the angle at which a liquid droplet meets a solid surface. This angle lets us know how water-friendly a surface is; in other words, the higher the contact angle, the less water-friendly the surface.

Contact angle (A) and snake skin with water droplet on light and dark areas (B)

Contact angle (A) and snake skin with water droplet on light and dark areas (B)

As you can see in the graph above, the contact angle was different depending on the liquid applied and the type of scale; in particular, the contact angle on the black scales was significantly higher than the others, in a category that the authors refer to as “outstanding superhydrophobicity,” or really, really, really water-repelling. This type of water-repelling has been seen in geckos, but not snakes.

Water droplet appearance on live snake skin

Water droplet appearance on live snake skin

The authors then took some of the snake carcass and dusted it with a sticky powder in a contamination chamber, after which they generated a fog for 30 minutes and took pictures.

Skin before dusting (A), skin under black light after dusting (B), skin under black light after fogging (C), section of SEM, showing light and dark skin (D)

Skin before dusting (A), skin under black light after dusting (B), skin under black light after fogging (C), section of SEM, showing light and dark skin (D)

After 30 minutes of fogging, the black areas were mostly free of the dusting powder, while the pale areas were still completely covered with dust. The powder itself was also water-repelling, and so the authors showed that despite this, the powder rolled off with the water rather than sticking to the black areas of snake skin. Therefore, as suggested by the authors, this could be a rather remarkable self-cleaning ability. The authors suspect that the “nanoridges,” or ridges arranged in parallel in the black regions, may allow liquid runoff better than on the paler areas of the snake.

How does this texture variation help the snake, you ask? The authors posit that all these properties basically contribute to a better form of camouflage. If the snake were completely covered in one color, it may stand out against a background of mixed colors (or “disruptive coloration”), like that of a forest floor. If the black regions have fairly different properties from the paler regions, mud, water, or other substances would rub off in these areas and continue to provide the light-dark color contrast and variation in light reflectivity that helps the snake do what it does best: slither around and blend in unnoticed.

Citations

Spinner M, Kovalev A, Gorb SN, Westhoff G (2013) Snake velvet black: Hierarchical micro- and nanostructure enhances dark colouration in Bitis rhinoceros. Scientific Reports 3: 1846. doi:10.1038/srep01846

Spinner M, Gorb SN, Balmert A, Bleckmann H, Westhoff G (2014) Non-Contaminating Camouflage: Multifunctional Skin Microornamentation in the West African Gaboon Viper (Bitis rhinoceros). PLoS ONE 9(3): e91087. doi:10.1371/journal.pone.0091087

Images

First image, public domain with credit to TimVickers

Remaining images from the PLOS ONE paper

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Infectious Earworms: Dealing with Musical Maladies

earworm - record playing This menace may leap out at you in the subway or find you when you’re tucked away, safe in your bed; it might follow you when you’re driving down the street or running at the gym. Hand sanitizer can’t protect you, and once you’re afflicted, the road to recovery can be a long one. However, this isn’t the Bubonic plague or the common cold—instead, the dreaded earworms!

Derived from the German word ohrwurm, which translates literally to “ear-worm,” an earworm commonly refers to a song, or a snippet of a song, that gets stuck in your head. Earworms can occur spontaneously and play in our heads in a seemingly infinite loop. Think of relentlessly catchy tunes, such as “Who Let the Dogs Out?,” “It’s a Small World,” or any Top 40 staple. An estimated 90% of people fall prey to an earworm at least once a week and most are not bothersome, but some can cause distress or anxiety. And yet, despite the earworm’s ubiquity, very little is known about how we react to this phenomenon. With the assistance of BBC 6 Music, the authors of a recent PLOS ONE study set out to connect the dots between how we feel about and deal with these musical maladies.

Researchers drew upon the results of two existing surveys, each focusing on different aspects of our feelings about earworms. In the first, participants were asked to reflect on whether they felt positively or negatively toward earworms, and whether these feelings affected how they responded to them. The second survey focused on how effective participants felt they were in dealing with songs stuck in their heads. Responses to both surveys were given free form.

To make sense of the variety of data each survey provided, the authors coded participant responses and identified key patterns, or themes. Two researchers developed their own codes and themes, compared notes and developed a list, as represented below.

earworm - Finnish study

Survey responses. Participants either chose to “cope” with their earworms or “let it be.”

The figure above represents responses from the first survey, in which participants assigned a negative or positive value to their earworm experiences and described how they engaged with the tune. The majority didn’t enjoy earworms and assigned a negative value to the experience. These responses were clustered by a common theme, which the researchers labelled “Cope,” and were associated with various attempts to get rid of the internal music. A significant number of participants reported using other music to combat their earworms.

Participants in the second survey, which focused on the efficacy of treating earworms, responded in a number of different ways. Those whose way of dealing was effective often fell into one of two themes: “Engage” or “Distract.” Those that engaged with their earworms did so by, for example, replaying the song; those that wanted distraction often utilized other songs. Most opted to engage.

Ultimately, the researchers concluded that our relationships with these musical maladies can be rather complex. Yet, whether you embrace these catchy tunes or try to tune them out, the way we feel about earworms is often connected to how we deal with them.

Want to put in your two cents? You can tell the authors how you deal with earworms at their website, Earwormery. For more on this musical phenomenon, listen to personal anecdotes on Radiolab, read about earworm anatomy at The New Yorker, or dig deeper in the study.

 

Citation: Williamson VJ, Liikkanen LA, Jakubowski K, Stewart L (2014) Sticky Tunes: How Do People React to Involuntary Musical Imagery? PLoS ONE 9(1): e86170. doi:10.1371/journal.pone.0086170

 

Images: Record playing by Kenny Louie

Figure 1 from the paper.

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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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