Getting Credit for Data

As the largest journal in the world, PLOS ONE publishes an incredible amount of data alongside its research articles, yet the article itself remains the gold standard for attributing credit. While data is the fundamental unit of research, it isn’t recognized as an important component of a researcher’s scholarly output. How can we change this?

At present, sharing data can be onerous work, but Data-Level Metrics (DLMs) can equip researchers with concrete evidence of the value of their efforts. PLOS, in partnership with UC3 and DataONE, has undertaken a project called Make Data Count to develop DLMs. This 12-month NSF-funded project is aimed at piloting a suite of metrics that track and measure data use so that it can be shared to funders, tenure & promotion committees, etc.

But first, we need to better understand the needs of researchers across disciplines and communities—how might you get credit for the data you produce? what do you want to know about how your data is used? Please take this 5-10 minute survey and help us craft data-level metrics: Feel free to share widely!

We are excited to engage the PLOS ONE community in designing a new system of crediting scholarly work on data. Please contact Jennifer Lin ( for more information or to share your feedback directly.

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Our 200,000-Year-Old Ancestors: Neanderthal Bones in Northern France

Neanderthal bones

We often make new discoveries about our ancient ancestors and how they may have behaved, and we sometimes find the evidence right in their bones. For instance, researchers recently described how the jaw and teeth of a Neanderthal might suggest that they created their own toothpicks out of sticks or used small blades of grass to remove food from their teeth and relieve the pain from gum disease.

At a rescue excavation of an open-air prehistoric site, Tourville-la-Rivière in the Seine Valley of Normandy in northern France, the authors of a study recently published in PLOS ONE were in for a surprise – the discovery of three long human arm bones. The authors detail the unearthing, description, and analysis of these three partially crushed bones: a left humerus, radius, and ulna from the same upper left limb (image above).

The authors used a spectroscopic technique (electron spin resonance, or ESR) and a radiometric dating technique (Uranium-thorium dating, or U-series dating) to determine an approximate age for the Tourville human remains. The authors then scanned the bones in an X-ray and processed them on the computer (X-ray Computerized tomography, or CT) to generate a 3D cross-sectional image of the bones, allowing the authors to examine their shapes and characterize them within the Neanderthal lineage.

As a result of the analyses, the authors estimate the bones most likely belonged to a single Neanderthal adult or older adolescent from 200,000 years ago. This discovery may be the first example of the Neanderthal lineage in northwestern Europe, and the authors suggest that it may provide insight into the relationship of the Tourville remains to other human fossils from ~781,000-126,000 years ago, a period known as the Middle Pleistocene era.

The authors also describe how the shape and other features of these bones are more similar to Neanderthals than to humans. The longest part of the humerus that connects to the deltoid muscle is closer to the length of a Neanderthal bone than a modern human bone. In addition, the attachment site where the radius and ulna meet is similar in structure to Neanderthal bones. The image below displays these similarities, showing the Tourville human remains to the left of well-preserved female Neanderthal bones.

Tourville and Neanderthal arm bones

The researchers also noted that the connective tissue between the tendon and the humerus featured a rather unusual long ridge or crest—this formation is often found in older modern humans, and is located at a section of the bone connected to the deltoid, or back shoulder muscle. Since this muscle allows for the rotation and lifting of the arm, this crest may be the result of a repetitive throwing motion. The researchers suggest that this throwing motion could be connected to activities like spear throwing.

The Tourville fossils may be the oldest found in France during a rescue excavation, and may provide new material for a limited sample of fossils from northwestern Europe. Previously discovered fossil samples from the Middle Pleistocene era mainly consist of skulls and teeth, so the discovery of three arm bones may reveal an unusual shape in the connective tissue that may provide new evidence for how Neanderthals may have behaved. While the authors concede that the precise cause of this abnormality in the connective tissue is unclear, it poses an interesting question for further research on how Neanderthals behaved and whether this change may have impacted their survival as a species.


Antoine P, Lautridou JP, Sommé J, Auguste P, Auffret JP, et al. (1998) Les formations quaternaires de la France du Nord-Ouest: Limites et corrélations. Quaternaire 9: 227–241. doi: 10.3406/quate.1998.1605

Lozano M, Subirà ME, Aparicio J, Lorenzo C, Gómez-Merino G (2013) Toothpicking and Periodontal Disease in a Neanderthal Specimen from Cova Foradà Site (Valencia, Spain). PLoS ONE 8(10): e76852. doi:10.1371/journal.pone.0076852

Faivre J-P, Maureille B, Bayle P, Crevecoeur I, Duval M, et al. (2014) Middle Pleistocene Human Remains from Tourville-la-Rivière (Normandy, France) and Their Archaeological Context. PLoS ONE 9(10): e104111. doi:10.1371/journal.pone.0104111

Images: All images are from the article.

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The Rights Stuff: Copyright, Scientific Debate, and Reuse

We’ve all monkeyed around trying to sort out the ownership of published content. In the scientific community, copyright and its (mis)application in publishing has authors, publishers, and readers grappling with questions of what is legally possible, what is desirable, and what is “allowable” by any particular party.

The most recent example of these challenges can be found in a PLOS ONE article published yesterday by Stirling et al., which focuses on a re-analysis of images used by other research groups as evidence for the creation of “striped nanoparticles”. The scientific controversy is fascinating and has been covered on blogs and in social media, but the copyright issues that cropped up during the paper’s publication process are also noteworthy.

In the study, the authors re-analyzed key results from previous work written up in the literature by other researchers and wanted to share their findings by publishing them, formally adding to the scientific literature on nanoparticles. To provide context and more effectively discuss the data, the authors of the re-analysis included figures (images) from previous studies in their own paper. However, the original figures were published in journals that owned the copyright of all the written content. And here is where we ran into a problem, and one that was far from simple.

Clearing rights for republication

These journals generally hold a copyright status of “all rights reserved”. With this restriction, there are three possible ways that these figures could be incorporated into a newly published article.

1) The authors could declare that the reproduction is “fair use” or “fair dealing”:

Traditionally, this hasn’t been done for reproduction of single images from papers. The problem from a publisher’s (and author’s) perspective with this approach is that it isn’t totally clear whether it applies in this case. Publishers are pretty risk averse about this kind of claim (as fair use is a defense against infringement rather than a license itself), so we usually prefer to ask permission.

2) The copyright holder could authorize a specific use under a limited license:

This is the traditional approach—the author would be responsible for negotiating a single use license from the rights holder. This will be a familiar experience to many authors who have written reviews that incorporate figures from other papers. It’s common enough that there are online tools to speed up this kind of transaction.

3) The rights holder could authorize the image to be republished under an open license that allows extensive reuse, with the authors as the copyright holder:

PLOS uses a Creative Commons Attribution License (CC BY 4.0) specifically to cover this issue. With the Stirling, et al. paper, we worked with the authors and the publishers on taking this approach, and we want to say thank you to The Royal Society of Chemistry, Nature Publishing Group (NPG), Wiley Blackwell, and the American Chemical Society for working with us to enable the republication of the material. NPG has a standing policy that they will authorize re-publication of images under the same license as the rest of the article, something they’ve done for us in the past. The other publishers worked hard to make it possible on this occasion, giving approval a few weeks ago. We are very grateful for their efforts.

Why the fuss?

So why did PLOS push for option three when the second was more traditional? As Kevin Smith at Duke has pointed out, it’s not a legal question or a problem with the Creative Commons licenses. It is perfectly possible to mark part of an article as being made available under a different copyright license. But as a question of policy, we make every effort to avoid mixing different licenses within articles.

We do this because, at the heart of PLOS’s work on Open Access, is enabling re-use. Every day people grab newly published articles for various kinds of processing. Some are mining text for information, some are collecting images for use in other projects, and some are working on new forms of display and article presentation. Each of these depends on the downstream user having the rights to copy, store, and transmit the articles. All the articles. And all the pieces of the articles.

On any given day, PLOS might publish a few hundred articles. It is certainly possible in principle to add a copyright statement to a single image. But downstream users would need to check every figure legend of every paper by hand to identify single images they aren’t allowed to use. By insisting on a uniform CC BY license throughout, we give the downstream users clarity and confidence in their rights.

In a perfect world, there would be a clear and consistent machine-readable way of designating sections of an article and differing copyrights within them. But such a standard doesn’t yet exist, and even if it did, there is still a clear advantage to the downstream user to have a uniform policy that grants largely unrestricted reuse.

This case has been both interesting and challenging for us and the authors (who we thank for their patience while we have addressed the licensing issues!). It has highlighted the need for publishers to be willing to authorize onward publication rights with reasonable flexibility as to the licensing arrangements. As the industry moves away from copyright assignment to “license to publish” arrangements, it is important that we get the details of those licenses right. There could be immense value in shared model “license to publish” agreements that would help consistency and support smaller publishers. Most importantly, we have learned the need for clear presentation of our legal and policy obligations when it comes to copyright and reuse.

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Next Steps in Reproducibility

In last week’s Nature and Science, the outcome of a meeting convened by NIH, Nature, and Science to discuss the issue of lack of reproducibility in the basic science research literature was published. This meeting, which brought together representatives from publishers (including PLOS), and many representatives from the NIH and other funders, produced a series of principles, Proposed Principles and Guidelines for Reporting Preclinical Research, which were endorsed by a large and diverse group of publishers, associations, and societies including ourselves. The main principles are as follows:

  • Rigorous statistical analysis
  • Transparency in reporting
  • Data and material sharing
  • Consideration of refutations
  • Consider establishing best practice guidelines for image based data and descriptions of biological data.

Everyone who works in research, as scientist, editor or funder knows that trust is a critical component of having confidence in scientific advances. It would be fair to say that until quite recently it was accepted that the somewhat unstructured narrative style of journal articles with no or little associated data along with few other accepted standard practices was considered sufficient reporting. However, both an increasing number of high profile articles which were found to be unreliable, together with a more general unease, for example around a lack of availability of data, has led journals to conclude that it is now imperative to be much more specific about what an article needs to contain in order for it to be reproducible.

These issues have long been discussed in the medical publishing world and are the rationale behind two long standing initiatives – the ICMJE’s Recommendations for the Conduct, Reporting, Editing and Publication of Scholarly Work in Medical Journals and the many reporting guidelines collected together by the EQUATOR initiative,

Hence, these new principles build on the momentum within the medical literature and are to welcomed as a baseline that all biomedical journals should now be able to adhere to in the basic science literature; they will be a concrete move towards increasing the reproducibility of papers.

However, as with all principles that are put together by committees made up of different groups with their own agenda, they do not go as far as any one party might like. As a publisher that straddles science and medicine, PLOS’s own editorial policies already go some way beyond what is currently being suggested. In two specific areas – data availability and publication of refutations – we hope that other journals move rapidly toward more robust requirements.

Availability of the data underlying a published study is probably the most significant way in which journals can, now, ensure reproducibility of the published literature. A more robust position on data availability, as PLOS has recently pushed for with its data policy, which requires deposition of data in a publicly available repository at the point of publication, would seem possible now.

On refutations, PLOS ONE has been leading the charge to get these papers published for many years. The ICMJE requirements have long noted in the need for medical journals to publish refutations, but in practice getting refutations, failed replications or negative findings published is hard. Although the reasons for this are complex, there is no doubt that in a subscription-based world there were very specific disincentives for journals doing so. In Open Access publishing by contrast, these financial disincentives disappear and journals potentially are much freer to consider such papers. It will be interesting to see whether journals do in practice follow this recommendation.

What’s next? It will be critical that journals move now to operationalize the recommendations made in this document into their workflows. This is no small feat. It will require creating tools for reviewers and editors to assess papers in a systematic, consistent fashion – for example structured review would be a good step in the right direction, although we know that reviewers are not keen on having to tick boxes and justify decisions in any kind of structured way – so journals need to figure out how to bring reviewers with them on this. Furthermore, implementing at scale is even more difficult for large publishers/journals.

We applaud the work that has been done in the recent meeting.  These principles and attributes of sound science reporting will serve as critical cornerstones for long term change for the entire industry and will require deep adoption across the industry.


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Fecal Matters: A Stepping Stool to Understanding Indigenous Cultures

Humans differ by opinions, traits, and baseball team preferences. But one constant factor unifies all humans–we excrete feces, and scientists have recognized that number 2 is number 1 in terms of material for ancient population studies. Humans expel hundreds of grams of feces each day, and prehistory versions of this abundant matter may provide insight into the lives of ancient humans.

Human feces contain DNA from bacteria, fungi, parasites, and even from the human herself. Suspecting that this excrement is rich in biological clues, a group of researchers conducted experiments to investigate fecal microbiomes and published a study in PLOS ONE detailing insights into the diets and lifestyles of two ancient indigenous cultures of Puerto Rico: the Saladoid and Huecoid.

The Huecoid and the Saladoid populations originated from the East Andes and present-day Venezeula, respectively. However, it is believed that they coexisted on the Puerto Rican Island of Vieques for a thousand years, beginning in 5 AD. Although previous studies and artifacts have shown religious and cultural differences between the two populations, notable biological differences had yet to be discovered until now.


The authors of this study gathered ancient fossilized poop samples, called coprolites, from Vieques and Guayanilla, Puerto Rico, as shown in the image above. Using the excavated samples, the researchers performed DNA sequencing and parasite egg and larva extractions to evaluate the differences in the microbial communities between the two ancient cultures. Contrary to prior belief that a coprolite could not preserve ancient DNA, scientists successfully sequenced the fossil microbes contained in the coprolite core. They found that the bacterial distribution varied significantly between the two cores (as seen in the image above) but most notably, sequencing indicated that the Saladoid population had a 10% higher relative abundance of the bacteria, Bacteroidetes, overall, which may mean that the Saladoid people had a higher protein diet.


Using the remaining coprolite core, the researchers identified parasites based on the shape and presence of dehydrated eggs or larva. According to the authors, the rates of parasite abundance may be double in Saladoid feces as compared to Huecoid. Additionally, the Saladoid core consistently contained hookworms, fish parasites, and dog parasites, providing evidence that the Saladoid people may have eaten raw fish regularly, and may have had dogs as pets. Perhaps sushi and puppies have long been staples in human life?

Researchers also found quite a different diet in the fecal remains of the Huecoid people. The presence of freshwater parasites and evidence of maize may suggest that the Huecoid ate aquatic plants or freshwater invertebrates, and that they may have helped introduce a grain diet to the island.


As the first image shows, the Saladoid and Huecoid populations lived quite close to each other, making these biological differences in the feces appear even more noteworthy. The authors attribute the distinct microbiotas and parasitism composition to diet and cultural differences such as living arrangements, the way food was handled, and human contact with pets.

Although this is a relatively new field of research, analyzing ancient fossilized fecal matter may be useful for scientists trying to characterize indigenous diets and lifestyles. What was previously disregarded as waste may now be considered a trove of historical and scientific data; the clue is in the poo.

Related Content:

Citation: Cano RJ, Rivera-Perez J, Toranzos GA, Santiago-Rodriguez TM, Narganes-Storde YM, et al. (2014) Paleomicrobiology: Revealing Fecal Microbiomes of Ancient Indigenous Cultures. PLoS ONE 9(9): e106833. doi:10.1371/journal.pone.0106833

Images: Images are from Figure 1, Figure 4, and Table 5 of the published paper.

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PLOS ONE’s Spookiest Images of 2014


As we take a look back at research articles published so far in PLOS ONE in 2014, we realize we have no shortage of images to terrify our readers, or at least sufficiently creep them out long enough to last through Halloween and possibly the whole weekend. Without further ado, we present our staff picks for figures in PLOS ONE articles that we felt were eerie, ghostly, spine-chilling, corpselike, gross, nightmarish, or just plain weird!

If you enjoy these, we encourage you to comment down below with any of your other favorite, spooky PLOS ONE images from this year.

Click on any one image to see a larger version.


Where else would we begin? Those with phobias, look away!




We started off easy and only slightly creepy. The above is actually just a neat 3D model of a bug, specifically a granary weevil.




Okay, this one is definitely creepier than the last image. This is a female (top) and male (bottom) leafcutter bee at the pupal stage…just waiting to come out and say hello.




Eek. This is a fossil millipede embedded in amber, with a close dorsal view of the first segments and mid-body rings. For an overload of creepiness, check out the other figures in the paper.




What’s this?! If spiders can catch fish—they can, as this paper describes, on all continents except Antarctica—what can’t they do? Also, if spiders don’t need webs, are they all set to take over the world?




Here we have more insects in amber. In this image, an ant and a termite hang out together in the same piece of Mexican amber.




This image might look slightly unbelievable, but it shows a new species of spider wasp that may sometimes use dead ants to protect its nest. Obviously…dead ants always add a certain something to the décor, in addition to being excellent home protection!


Other species that give us the creeps




Okay, not so bad, a creepy mushroom-lookalike. What’s slightly freaky about it is that it may be a multicellular organism that does not fit into our current phylogenetic tree, which means that it may be part of a new branch of life.




Yuck. Unlike other baby animals, baby coral? Not as adorable.




Slimey goodness in the form of a vocalizing Indian purple frog.




What on Earth is happening in panel D? Lucky for him, the bioluminescent viper dogfish shark has protruding jaws it uses to capture his prey.




This is an Eurasian brown bear breaking the bones of a deer in different ways—such talent! If she could just focus all her efforts on deer and not other species (cough, cough) that would be fantastic.


Carcasses under the sea




Above is a set of carcasses, including a whale shark in the panel on the top left, is being devoured by fish in the deep sea.




What we see here, for as long as we can bear to look, are dead pigs in the deep sea, showing carcass decomposition assisted by shrimp and crab that eat them and drag them around. Yum.


Let’s put the past behind us




The first eerie image above compares the footprint of an early limbed vertebrate, a temnospondyl (right), with that of a salamander (left). Researchers showed that his walk, shown as a hypothetical in the second image, was probably a lot different from that of a salamander, with a forelimb-driven gait as opposed to the hindlimb-driven one of the latter species.




Yikes. The “ripper” behavioral model is illustrated above for a non-avian theropod dinosaur, known for having a “killing claw” used for slashing and eating prey that are still alive!




Behold a rare “bone bed” containing remnants from a newly discovered species of pterosaur. This mess of bones may indicate that the species was fairly social, outgoing, and lived in groups.


Mummies and the like


Saving the best for last, no scary image list is complete without some totally stomach-wrenching mummy pics. Enjoy!




This South American mummy was likely suffering from a disease, hit in the head, and murdered.




While not a mummy, this young individual may have suffered traumatic brain injury and was buried with two red deer antlers on its chest, a possibly unique funerary practice.




A clothes-wrapped body was found inside this coffin, which is a possible case of cherubism in a 17th-century Korean mummy.




And lastly, the above depicts three plastered skulls dating to a pre-pottery period, with the plastering process a possible representation of the shift from hunter-gathering to food-producing strategies. Scary stuff!

Happy Halloween from PLOS ONE!



Image 1: Slon V, Sarig R, Hershkovitz I, Khalaily H, Milevski I (2014) The Plastered Skulls from the Pre-Pottery Neolithic B Site of Yiftahel (Israel) – A Computed Tomography-Based Analysis. PLoS ONE 9(2): e89242. doi:10.1371/journal.pone.0089242

Image 2: Nguyen CV, Lovell DR, Adcock M, La Salle J (2014) Capturing Natural-Colour 3D Models of Insects for Species Discovery and Diagnostics. PLoS ONE 9(4): e94346. doi:10.1371/journal.pone.0094346

Image 3: Holden AR, Koch JB, Griswold T, Erwin DM, Hall J (2014) Leafcutter Bee Nests and Pupae from the Rancho La Brea Tar Pits of Southern California: Implications for Understanding the Paleoenvironment of the Late Pleistocene. PLoS ONE 9(4): e94724. doi:10.1371/journal.pone.0094724

Image 4: Riquelme F, Hernández-Patricio M, Martínez-Dávalos A, Rodríguez-Villafuerte M, Montejo-Cruz M, et al. (2014) Two Flat-Backed Polydesmidan Millipedes from the Miocene Chiapas-Amber Lagerstätte, Mexico. PLoS ONE 9(8): e105877. doi:10.1371/journal.pone.0105877

Image 5: Nyffeler M, Pusey BJ (2014) Fish Predation by Semi-Aquatic Spiders: A Global Pattern. PLoS ONE 9(6): e99459. doi:10.1371/journal.pone.0099459

Image 6: Coty D, Aria C, Garrouste R, Wils P, Legendre F, et al. (2014) The First Ant-Termite Syninclusion in Amber with CT-Scan Analysis of Taphonomy. PLoS ONE 9(8): e104410. doi:10.1371/journal.pone.0104410

Image 7:  Staab M, Ohl M, Zhu C-D, Klein A-M (2014) A Unique Nest-Protection Strategy in a New Species of Spider Wasp. PLoS ONE 9(7): e101592. doi:10.1371/journal.pone.0101592

Image 8:  Just J, Kristensen RM, Olesen J (2014) Dendrogramma, New Genus, with Two New Non-Bilaterian Species from the Marine Bathyal of Southeastern Australia (Animalia, Metazoa incertae sedis) – with Similarities to Some Medusoids from the Precambrian Ediacara. PLoS ONE 9(9): e102976. doi:10.1371/journal.pone.0102976

Image 9: Toh TC, Ng CSL, Peh JWK, Toh KB, Chou LM (2014) Augmenting the Post-Transplantation Growth and Survivorship of Juvenile Scleractinian Corals via Nutritional Enhancement. PLoS ONE 9(6): e98529. doi:10.1371/journal.pone.0098529

Image 10: Thomas A, Suyesh R, Biju SD, Bee MA (2014) Vocal Behavior of the Elusive Purple Frog of India (Nasikabatrachus sahyadrensis), a Fossorial Species Endemic to the Western Ghats. PLoS ONE 9(2): e84809. doi:10.1371/journal.pone.0084809

Image 11: Claes JM, Partridge JC, Hart NS, Garza-Gisholt E, Ho H-C, et al. (2014) Photon Hunting in the Twilight Zone: Visual Features of Mesopelagic Bioluminescent Sharks. PLoS ONE 9(8): e104213. doi:10.1371/journal.pone.0104213

Image 12: Arilla M, Rosell J, Blasco R, Domínguez-Rodrigo M, Pickering TR (2014) The “Bear” Essentials: Actualistic Research on Ursus arctos arctos in the Spanish Pyrenees and Its Implications for Paleontology and Archaeology. PLoS ONE 9(7): e102457. doi:10.1371/journal.pone.0102457

Image 13: Higgs ND, Gates AR, Jones DOB (2014) Fish Food in the Deep Sea: Revisiting the Role of Large Food-Falls. PLoS ONE 9(5): e96016. doi:10.1371/journal.pone.0096016

Image 14: Anderson GS, Bell LS (2014) Deep Coastal Marine Taphonomy: Investigation into Carcass Decomposition in the Saanich Inlet, British Columbia Using a Baited Camera. PLoS ONE 9(10): e110710. doi:10.1371/journal.pone.0110710

Image 15: Marsicano CA, Wilson JA, Smith RMH (2014) A Temnospondyl Trackway from the Early Mesozoic of Western Gondwana and Its Implications for Basal Tetrapod Locomotion. PLoS ONE 9(8): e103255. doi:10.1371/journal.pone.0103255

Image 16: Fowler DW, Freedman EA, Scannella JB, Kambic RE (2011) The Predatory Ecology of Deinonychus and the Origin of Flapping in Birds. PLoS ONE 6(12): e28964. doi:10.1371/journal.pone.0028964

Image 17: Manzig PC, Kellner AWA, Weinschütz LC, Fragoso CE, Vega CS, et al. (2014) Discovery of a Rare Pterosaur Bone Bed in a Cretaceous Desert with Insights on Ontogeny and Behavior of Flying Reptiles. PLoS ONE 9(8): e100005. doi:10.1371/journal.pone.0100005

Image 18: Panzer S, Peschel O, Haas-Gebhard B, Bachmeier BE, Pusch CM, et al. (2014) Reconstructing the Life of an Unknown (ca. 500 Years-Old South American Inca) Mummy – Multidisciplinary Study of a Peruvian Inca Mummy Suggests Severe Chagas Disease and Ritual Homicide. PLoS ONE 9(2): e89528. doi:10.1371/journal.pone.0089528

Image 19: Coqueugniot H, Dutour O, Arensburg B, Duday H, Vandermeersch B, et al. (2014) Earliest Cranio-Encephalic Trauma from the Levantine Middle Palaeolithic: 3D Reappraisal of the Qafzeh 11 Skull, Consequences of Pediatric Brain Damage on Individual Life Condition and Social Care. PLoS ONE 9(7): e102822. doi:10.1371/journal.pone.0102822

Image 20: Hershkovitz I, Spigelman M, Sarig R, Lim D-S, Lee IS, et al. (2014) A Possible Case of Cherubism in a 17th-Century Korean Mummy. PLoS ONE 9(8): e102441. doi:10.1371/journal.pone.0102441

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You Live in What Kind of Home? A-nem-mo-ne-men… me-ne-mo-nee!

Clownfish Find Refuge among the Toxic Tentacles of Sea Anemones

pone.0098449 First Image

As we’ve seen in the movies, the world is a dangerous place for a clownfish far away from home. This is all the more reason to ensure that their homes provide adequate protection. What makes a good home for a clownfish, you might ask? Sea anemones. The toxic venom that anemones produce to kill intruders and prey alike provides clownfish with a safe haven. It’s fairly effective too. Clownfish can live for 35 years or more, which is more than three times the lifespan of their similarly sized fish counterparts! That said, not all anemones are created equal, and there are a number of different species that clownfish colonize. So how does a clownfish choose?

In a recent PLOS ONE study, “Searching for a Toxic Key to Unlock the Mystery of Anemonefish and Anemone Symbiosis,” the authors hypothesized that clownfish might choose a home based on the differing levels of toxicity between anemone species. To investigate further, the authors collected nine of the ten anemone species known to host 26 species of clownfish in the genera Amphiprion and Premnas. Next, they retrieved venom samples from the anemones to analyze their levels of toxicity.

pone.0098449 Second Image

By observing the effects of the various venoms on mammalian cells, brine shrimp, and shore crabs, the authors were able to calculate the relative toxicity of each anemone species. They then compared these findings to the already existing knowledge of how many species of clownfish colonize each anemone species.

They found that anemones that produce an intermediately toxic venom were the ones that hosted the most species of clownfish. Moreover, the least and most toxic anemones hosted the fewest clownfish. The below graph (Figure 4 in the published article) shows the toxicity ranking for each species of anemone that the authors investigated, in relation to how many species of clownfish they host.

pone.0098449 Third Image

The authors believe these results can likely be explained by a balancing act for the clownfish, between the benefits of protection and the costs of withstanding the venom themselves. Living in a highly toxic environment provides protection from predators, though scientists aren’t certain how the clownfish defend themselves against these toxins. Some think that it may have something to do with a protective layer of mucus on their skin. Regardless of the mechanism, few defenses are “free”, meaning that the clownfish likely has to spend energy defending themselves from the same toxins that protect them from predators.

The fish aren’t the only ones with something to gain from this relationship. Anemones with clownfish associates also benefit from increased protection against other species of fish, which may be potential predators. Such relationships are known as symbiotic.

pone.0098449 Fourth Image

The authors hope their study will spark an interest in anemone toxicity and potentially lead to further research. Additionally, they note the conservation benefits of studying the toxicity of debilitated anemones to gain a better understanding of how human actions impact anemone health. Some concerns for anemones include over-collection and bleaching, a condition that occurs when an anemone’s symbiotic zooxanthellae leave or die.

In the paper, the authors also discuss how the disappearance of host anemone species may either force clownfish to find new host species, or send them into decline. Further research could help us determine whether clownfish are capable of using different species as hosts. Until then, we might remember that “no matter what obstacles you face in life, just keep swimming.”


Nedosyko AM, Young JE, Edwards JW, Burke da Silva K (2014) Searching for a Toxic Key to Unlock the Mystery of Anemonefish and Anemone Symbiosis. PLoS ONE 9(5): e98449. doi:10.1371/journal.pone.0098449

Mebs D (2009) Chemical biology of the mutualistic relationships of sea anemones with fish and crustaceans. Toxicon 54(8): 1071–1074. doi: 10.1016/j.toxicon.2009.02.027

Images: Images are from Figure 4 of the published article, like NEMO – Daita Saru, Anemonemonemone – Matt Clark, 058 – Anemone, Anemonefish & Divers – Neville Wootton.

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Does Urbanization Always Drive Economic Growth? Not Exactly…


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 health care. Cities create large markets for business, and can attract international investment and tourism from around the world. They are hubs of non-agricultural, high-paying professional jobs like banking, law, and engineering. Diversity and face-to-face interactions can lead to new ideas and cross-cultural collaborations. Conventional wisdom holds that cities are good for the economy.

Indeed, the link between a country’s level of urbanization and the size of its gross domestic product (GDP) is well established. The below graph of 2011 data illustrates the strong positive correlation: developed countries with high GDPs have relatively high proportions of their population living in urban areas, and vice versa.

Correlation graphLooking at this graph, it is small wonder, then, that urbanization has become a widely adopted global development strategy. National governments and international development agencies have embarked upon aggressive programs of accelerated urbanization designed to spur economic growth. Simply attract people into the cities, the thinking goes, and then cash in on the forthcoming economic benefits of a largely urban population. Well, it may be more complex than that, according to new research published in PLOS ONE.

Researchers in China examined global economic data on urbanization and per capita GDP levels spanning three decades (1980-2011). During this time, the proportion of the world’s population living in cities grew from just 39% in 1980 to 52% in 2011. And while urbanization and per capita GDP may be strongly correlated, the authors found no correlation between the rates of urbanization and economic growth. In other words, fast urban growth doesn’t always translate into fast GDP growth, as witnessed by the graph below. In stark contrast to the first graph, there is no easily discernible pattern connecting the speed of urbanization and the speed of GDP growth.

Graph with no correlation

The authors also point out that over three decades, many countries—for example, Gabon—had rapidly growing urban populations but low and even negative economic growth (top graph in green below). Conversely, many countries, such as Sri Lanka and Uzbekistan, saw negative rates of urbanization— people leaving cities for rural areas—but still had positive overall economic growth (bottom graph in white). These cases do not support the hypothesis that fast urbanization speeds economic growth.


The authors of the study argue that GDP growth may create conditions that organically drive migration from rural to urban areas, but the assumption that urbanization will necessarily drive strong economic growth may be false. Pointing to the numerous examples of accelerated urbanization without strong economic growth (again, the green graph above), they caution that “urbanization is not an automatic panacea” for economic difficulties. Citing other work, the authors suggest that instead of trying to move people into cities, governments and development agencies should focus on creating a mobile workforce, ensuring broad access to goods and markets, implementing government policies that support commerce, and investing in infrastructure. These efforts could make a bigger difference for short- and medium-term economic growth than arbitrary urbanization targets. While economic growth is an incredibly complex process and much work remains, this study serves as a good reminder not to confuse causation and correlation: just because two variables are closely related doesn’t necessarily mean that one directly causes the other.

Related Content:

Does Human Migration Affect International Trade? A Complex-Network Perspective

Welcome to The World’s Largest Ghost City: Ordos, China

Citation: Chen M, Zhang H, Liu W, Zhang W (2014) The Global Pattern of Urbanization and Economic Growth: Evidence from the Last Three Decades. PLoS ONE 9(8): e103799. doi:10.1371/journal.pone.0103799

Images: Images are from Figures 4 and 5 of the published paper, and from Chi King via Flickr.

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Meet PLOS at the Society of Vertebrate Paleontology 2014

SVP Blog ImageWe are excited to announce that PLOS will be exhibiting at the Society of Vertebrate Paleontology 2014 Annual Meeting from 5-8th November in Berlin.

This is only the second time that the meeting takes place outside North America, and the first time it will be held in continental Europe. To celebrate our attendance PLOS ONE Section Editor, Dr Andy Farke, has specially curated some articles recently published by PLOS. Featured articles range from a description of the oldest Caseid Synapsid to the discovery of a new Ankylosaurid dinosaur, plus many more themed selections. We’ll be giving away some PLOS memorabilia and USB drives featuring this specially curated content, so do visit us early before supplies run out!

We’ll be on the Exhibit Floor, at Booth #14 where you can meet Jenni Horsley, PLOS Collections Editorial Project Coordinator and Alejandra Clark, PLOS ONE Associate Editor. We look forward to meeting you in Berlin and hearing your thoughts about PLOS, open access, open data, and open science.

Image: Godoy PL et al., 2014 (CC-BY)

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Going PRO – clinical trials must plan to capture patient-reported outcomes

14425819028_5021bbcb74_zPost authored by David Moher

All participants in research are important. What patients in clinical trials tell us about treatments – patient-reported outcomes (PROs) such as quality of life and symptoms – is being used more and more to improve decisions about patient-centered care and health policy, but poor reporting of these outcomes risks research effort being wasted. Today, PLOS ONE publishes two important papers concerning patient-reported outcomes.[1,2] Professor Melanie Calvert at the University of Birmingham and her colleagues across the UK, Canada and Australia found that not enough attention has been devoted to PROs in clinical trial protocols, the blueprints for how a trial is run and reported.

Patient-reported outcomes are now getting the focused attention they deserve. In the United States the Patient-Centered Outcome Research Institute was set up in 2010 to conduct “research that answers patients’ questions”, spending nearly $700 million USD on 360 projects. The Canadian Institutes of Health Research recently established the Strategy for Patient-Oriented Research. However, PROs must be collected rigorously from the beginning to minimise loss of research information. CONSORT, the Consolidated Standards of Reporting Trials, has long been the gold standard for trial reporting. In 2013 the CONSORT-PRO Extension was introduced, promoting the transparent reporting of PRO data from trials. However, this guidance is aimed at the end of the research process and may be too late to make researchers think more about patients earlier on – at the protocol stage. Guidance on preparing trial protocols themselves has been developed – the Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) checklist was also published in 2013. However, this does not offer PRO-specific guidance.

In the first paper, Calvert and colleagues review the existing guidance for protocol writers on PROs.[1] They found that guidance was hard to access, lacked consistency and may be challenging to put into practice.  In total they uncovered a confusing mix of 162 recommendations across 54 publications.

In the second paper, Kyte and colleagues studied 75 protocols funded by the UK National Institutes of Health Research’s Health Technology Assessment program in 2012-3.[2] About two-thirds of the protocols complied with reporting SPIRIT items. Most troubling was that two of items about randomization – the unique characteristic of randomized trials – were missing in about a fifth of the protocols. Anything less than 100% is avoidable waste and the funder is not getting value for money. More than a third of the sample selected was from 2012, prior to the introduction of SPIRIT, however the NIHR website’s guidance for prospective protocol developers still only suggests using SPIRIT (in section 4.4). This is in contrast to a stronger endorsement of PROSPERO, a registry for systematic review protocols. Clearly there is an opportunity to more strongly recommend using SPIRIT, incorporating PRO issues at the same time.

These papers point to a clear need for more attention to PROs when developing trial protocols, and Prof. Calvert and colleagues used rigorous evidence-based methods that were explicitly reported in sufficient detail to allow interested readers to replicate them.

One suggestion to improve reporting is the development of a SPIRIT PRO extension. The EQUATOR Network already has a library of more than 200 reporting guidelines, with lots more in development. Reporting guideline developers have worked hard to help authors more completely report their research, but the marketplace is getting full. The SPIRIT-PRO extension would need to be both accessible and acceptable to researchers who wish to incorporate PROs in their trials and we need to ensure we don’t make using guidelines, such as a SPIRIT PRO extension, so complicated that it becomes a barrier to using them. We need to consider how to best ease using reporting guidelines: technology might be helpful here.

Another way to increase the use of SPIRIT and PRO guidance would be to build them into teaching about trials in university graduate programs, such as epidemiology and biostatistics. However this is done, researchers need to improve the reporting of patient-reported outcomes for the sake of both the trial participants and the patients who rely on this evidence to improve their health.

Citations: [1] Calvert M et al. (2014) Patient-Reported Outcome (PRO) Assessment in Clinical Trials: A Systematic Review of Guidance for Trial Protocol Writers. PLOS ONE  9(10): e110216 doi:10.1371/journal.pone.0110216

[2] Kyte D et al. (2014) Systematic evaluation of the patient-reported outcome (PRO) content of clinical trial protocols. PLOS ONE  9(10): e110299. doi:10.1371/journal.pone.0110229

Image: Hands_II – Oleg Afonin

david_moherDavid Moher is a senior scientist in the Clinical Epidemiology Program, Ottawa Hospital Research Institute, and Associate Professor, Department of Epidemiology and Community Medicine, University of Ottawa, where he holds a University Research Chair. He has a special interest in journalology (publication science), including ways to improve the quality of reporting health research. He spearheaded the development of the CONSORT Statement for reporting randomized trials, the PRISMA Statement for reporting systematic reviews and meta-analyses, and has been involved in many other reporting guideline initiatives, including SPIRIT and CONSORT PRO. Dr. Moher is associated with many journals: an editor-in-chief of Systematic Reviews; an editorial board member of several journals, including PLOS Medicine, a member of PLOS ONE’s Human Research Advisory Group, the advisory board for the International Congress on Peer Review and Biomedical Publication, and a member of the EQUATOR Network’s steering group.

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