PLoS ONE News and Media Roundup

Emperor penguin – Credit: British Antarctic Survey

This month in PLoS ONE news: Penguin populations recorded from outer space, super strength bacteria discovered in caves, and much more!

Satellite mapping provides the first comprehensive record of the Emperor Penguin population in Antarctica. Scientists found that the overall population is higher than previously estimated; however, other colonies may have disappeared altogether, most likely due to climate change. Wired Scientific American and BBC covered this article.

Strains of previously undiscovered bacteria found deep in the Lechuguilla Cave of New Mexico, show remarkably strong resistance to modern antibiotics. Scientific American, The Los Angeles Times and National Geographic covered this article.

The commonly used Body Mass Index (BMI) measure may vastly underestimate the ongoing obesity epidemic, according to new research. Read this study and more at The Huffington Post, TIME and The Los Angeles Times.

What makes a good athlete? Traits like problem solving, creativity and quick decision making are commonly referred to as “game intelligence” in sports. According to new research, professional soccer players show increased cognitive abilities, which may be linked to such athletic success. New York Times, Wired and CNN discussed this article.

For more in-depth coverage on news and blog articles about PLoS ONE papers, please visit our Media Tracking Project.

The commonly used Body Mass Index (BMI) measure may vastly underestimate the ongoing obesity epidemic, according to new research.

Save the Date: 2012 Right to Research Coalition General Assembly

The Right to Research Coalition will host its first-ever General Assembly this summer from July 19th through the 21st in Budapest at the European Youth Centre. The meeting will convene leaders of student organizations from around the world to chart the future of student efforts promoting Open Access.

Date and location: July 19th through the 21st at the European Youth Center in Budapest, Hungary.  Participants are encouraged to arrive by 1:00pm on the 19th as the meeting will begin in the early afternoon of that day.  Likewise, participants should try to depart Budapest in the late afternoon of the 21st (after 3:00pm) as there will be morning sessions on the last day.

Who should attend?  All Right to Research Coalition members are encouraged to send one delegate to the General Assembly; however, a number of additional slots will likely be available for organizations interested in sending more than one delegate.

Cost: The participation fee will be approximately €110 and will cover full room and board.  Attendees are asked to cover as much of their own expenses as possible (including travel and the participation fee); however, the Right to Research Coalition will have funding available as a supplement for those who require it. 

To help us get an accurate gauge of how much travel assistance will be needed, please begin the process of securing travel funding as soon as possible, and let us know how much assistance you’re likely to need.  

Program and speakers: The program and speakers will be confirmed over the coming weeks.  Sessions will cover topics such as national and international Open Access advocacy, campus advocacy, best practices on engagement and peer-to-peer education, working with professional societies, Open Access Week 2012, and more.

Registration: Registration for the conference will open in the next two weeks.  In the meantime, please fill out the brief questionnaire below which will help greatly in the planning process.


You will receive an email at the address entered in the form above when registration opens, and we look forward to seeing you in Budapest this summer!  If you have any questions or concerns in the meantime, please email nick [at] arl [dot] org.

Ecology and Evolution – Issue 2.4 is now Live!

Ecology and EvolutionThe April issue of Ecology and Evolution has now been published. This issue includes a number of top quality papers, including the article which was the 100th article published in the journal Projected changes in distributions of Australian tropical savanna birds under climate change using three dispersal scenarios by April E. Reside, Jeremy VanDerWal and Alex S. Kutt.

The paper Egg incubation temperature differently affects female and male hatching dynamics and larval fitness in a leafhopper by  Julien Chuche and Denis Thiéry focusses on  how egg incubation temperature affects development and sex ratio in a leafhopper. It highlights that incubation temperatures experienced by eggs, or more generally the temperature experienced during a narrow window early in development, can have quite large effects on development rate and operational sex ratio in insects. This finding could help understanding the geographical colonization pattern of this grape disease vector.

These are just a small selection of the articles within this issue. Other topics covered include random regression methods based on 31 years of data of owl clutch size, genetic diversity of platypus populations and soil management in semiarid rainfed agriculture. Enjoy reading this issue, and submit your next paper!

Food and Energy Security – Read the Editorial by Martin Parry

Martin ParryFood and Energy Security has published its first editorial by Editor-in-Chief Martin Parry – ‘Food and Energy Security: exploring the challenges of attaining secure and sustainable supplies of food and energy’. Prof. Parry explains the significant research areas which this journal will publish in and why it has been launched. ‘Given the rise in human population and the inevitable consequences of climate change, the challenges of achieving secure and sustainable supplies of both food and energy are Herculean… With the launch of this open access, multidisciplinary journal, our intention is to offer a forum for the discussion of the most important advances in this field and promote an integrative approach of scientific disciplines.’

Food and Energy Security is a fully open access journal which is published in association with the Association of Applied Biologists (AAB). You can find out more about the journal by visiting the journal homepage. To submit your article please visit our online submission site.

My virtual talk in Poland


I am presenting a talk in Poland today – although I am in Rome.

Open science & education conference, Poland

13 Apr 2012 – 14 Apr 2012 Nicolaus Copernicus University (NCU) invites you to the Third International Conference on Open Access, that will take place on 13-14 April in Bydgoszcz, Poland, at Collegium Medicum NCU. This year’s theme is Open science and Open education. More information.

I hope to be on skype from Rome airport – it may be rather hairy.

I tried to create a set of slides and run an audio over them. I used Powerpoint, because it allowed narration easily. It was quite easy to create and I made a 6 minute introduction. But trying to upload it was a disaster – the upload is so asymmetric that it was taking hours and crashing. So I have changed the strategy.

We’ll play the first 6 minutes.

Then if we can’t skype it is worth playing the OKF/JennyMolloy/PMR video

If we can skype then Cameron Neylon has agreed to click through the points and links below while I speak.

Start with the “Academic Spring” The Guardian’s remarkable and remarkably apposite

General points

  • Most science research/data is never properly published or used => Bad science, duplication
  • This costs/loses 100 Billion+ per year; so HUGE opportunities for new business/products. Europe or Silicon Valley??
  • The long-tail of science; scholarship OUTSIDE academia?
  • Conventional publication does not work for data
  • Diversity. No single solution. Communities of scholarship. HEP, Astronomy, Chemistry
  • Domain repositories essential; Inst Repos don’t work for science
  • OPEN. Must be BOAI-compliant: use CC-BY/CC0
  • Are universities the solution or the problem?
  • Sustainability. Funders and National Laboratories
  • Mandates are poor instruments; Culture must change. Rewards?
  • Create an author-centric culture/technology. Semantic documents. “ScienceForge”
  • Sustainability. Alliance with wealth-generation industries?
  • Text-mining VERY topical
  • Theses. Must become centralised semantic, Europe?? NL++, UK–
  • Demos: text-mining, repositories
  • Growing points:
    • Open (Web) Technology continues to advance
    • Linked Open Data / Semantic Web
    • Graduate students
    • Scholarly poor
    • Wikip(m)edia
    • Open Knowledge Foundation

“Slide links” – bold is priority

And a big thank you to everyone in Poland for their patience and to Cameron for helping

Why PMC & UKPMC Should Harvest From Institutional Repositories

PubMed & PubMed Central are wonderful resources, but not nearly as resourceful or wonderful as they easily could be.

(1) PMC & UKPMC should of course be harvesting or linking institutional repository (IR) versions of papers, not just PMC/UKPMC-deposited and publisher-hosted papers.

(2) Funders should be mandating IR deposit and PMC harvesting rather than direct PMC/UKPMC deposit. By thus making funder mandates and institutional mandates convergent and collaborative instead of divergent and competitive, this will motivate and facilitate adoption and compliance with institutional mandates: institutions are the universal providers of all research output, funded and unfunded.

(3) IRs should mandate immediate deposit irrespective of publisher OA policy: If authors wish to honor publisher OA embargoes, they can set access to the deposit as Closed Access during the embargo and rely on providing almost-OA via the IR’s email eprint request button

(4) Funder mandates should require deposit by the fundee — the one bound by the mandate — rather than by the publisher, who is not bound by the mandate, and indeed in conflict of interest with it.

(5) Publishers (partly to protect from rival publisher free-loading, partly to discourage funder mandates, and partly out of simple misunderstanding of network capability) are much more likely to endorse immediate institutional self-archiving than institution-external deposit. This is yet another reason funders should mandate institutional deposit and metadata harvesting instead of direct institution-external deposit.

A Big Paper for a Tiny Dinosaur

In paleontology, the fossil is the basic data point for any research, regardless of the amount of technology used. Consequently, descriptions of a fossil’s anatomy are critical for scientists answering a variety of questions. What species is this animal? Look to the fossil. What did it eat? Look at the teeth. Where does the animal fit on the evolutionary tree? Compare its fossil with other fossils. Detailed documentation and description of a specimen isn’t particularly glamorous, but absolutely necessary.

The tiny plant-eating dinosaur Fruitadens scurried through the underbrush of Colorado around 150 million years ago, long before the rise of the Rocky Mountains. First named in a brief article in 2010, Fruitadens made a splash for its diminutive length of less than 1 meter and estimated body mass of under 1 kilogram. Unfortunately, the original publication did not have space for more than a general anatomical description as well as confirmation that Fruitadens’ small size wasn’t because it was “just” a baby of a larger species. Thus, a new paper in PLoS ONE by Richard Butler, Laura Porro, Peter Galton, and Luis Chiappe fills in many of the essential details.

Artist’s reconstruction of Fruitadens. By Smokeybjb, licensed under Creative Commons Attribution-Share Alike 3.0 Unported license.

Fruitadens belonged to an unusual, widespread, and rare group of dinosaurs called heterodontosaurids. They first appeared around 200 million years ago in South Africa, and persisted until around 140 million years ago in England. Heterodontosaurids were small (no more than 2 meters in maximum body length) and characterized by unusual fangs at the front of their jaws. Fruitadens was no exception—although its lower jaw is incomplete, the preserved portion of the teeth shows that it too probaby had fangs. The rest of the teeth are more conventional, similar to those seen in other small plant-eating dinosaurs.

So, how did Fruitadens and other heterodontosaurids use their tiny, fanged jaws? The researchers developed simple two-dimensional models of the jaws in heterodontosaurids, reconstructing the movements associated with the bones and muscles. A basic difference between early and late-surviving heterodontosaurids (including Fruitadens) was identified. Specifically, Fruitadens and its close relatives had simpler jaw anatomy than their ancestors, suggestive of a switch to simpler, weaker, and more rapid jaw movements. Although much more work remains, Butler and colleagues suggest that Fruitadens may have been an ecological generalist subsisting on a variety of plants, insects, and other small organisms. This contrasts with the diet of its ancestors, subsisting primarily on plants.

A reconstruction of the skull of Fruitadens, from Butler et al. 2012.

Because they are so small, heterodontosaurid fossil are pretty scarce, and details of their evolutionary relationships are sketchy. Butler and colleagues carefully documented all of the relevant anatomical details in Fruitadens through photographs, CT scans, and text. In the process, the researchers identify some previously unrecognized features that characterize heterodontosaurids as a whole, and other formerly recognized features that do not. Although much work remains—particularly through the collection and description of new fossils—this new paper is an important step towards better understanding Fruitadens and its enigmatic kin.


Butler RJ, Galton PM, Porro LB, Chiappe LM, Henderson DM, Erickson GM (2010) Lower limits of ornithischian dinosaur body size inferred from a diminutive new Upper Jurassic heterodontosaurid from North America. Proc Roy Soc B 277: 375–381.

Butler RJ, Porro LB, Galton PM, Chiappe LM (2012) Anatomy and cranial functional morphology of the small-bodied dinosaur Fruitadens haagarorum from the Upper Jurassic of the USA. PLoS ONE 7(4): e31556. doi:10.1371/journal.pone.0031556


Top image from, licensed under Creative Commons Attribution-Share Alike 3.0 Unported license.

Bottom image from Butler et al. 2012, Figure 1.

About the Author: Dr. Andrew Farke is a vertebrate paleontologist and an academic editor at PLoS ONE. He handled the manuscript described in this post. Andy also has a blog, The Open Source Paleontologist and can be followed via Twitter @andyfarke.

Horizon2020 what I said in Rome (and what Neelie said)

I always try to blog what I said in meetings as I don’t (can’t) use traditional slides. Today I scraped slides off the web and my talk was significantly different from what I had prepared. This was in considerable part because of what had been said in the morning by, among others, Neelie Kroes (Deputy European commissioner) and Geoffrey Boulton (Royal Society). They anticipated many of my concerns (previous blog post) and I could simply praise them for it. Neelie Kroes was veyer impressive. She knew the field very well and was clearly fundamentally committed to making it happen. Europe can feel proud of her.

I was able to aks her a question – shouldn’t we be supporting young people and how can we get them to contribute to European wealth creation. Why no Euro Google/facebook, etc.? She was very excited and recounted how she’d been to a young person’s hacker camp (? In Spain) with ?thousands camping in tents. And how when she asked a 14-year old “aren’t you afraid of giving away information” – he said “you don’t get it, it’s about sharing”. We exchanged cards and I’m hoping that I can get some of the young people in the OKF involved.

I’d love to blog other aspects of the meeting – don’t even know whether it’s being tweeted

Open Infrastructure for Open Science/Data; and Academic Spring


I am presenting this afternoon in Rome to an important group of science-oriented people/organizations – about 70 people will be there. As always I try to talk to people before the presentation. I’ve got 20 minutes, and I want to get across both ideas and examples. So I can’t do it all. This is my “checklist” for things I think are important. (Almost all my “slides” are scraped from the web and I will publish the links shortly in a separate blog).

  • Most science research/data is never properly published or used => Bad science, duplication
  • This costs/loses 100 Billion+ per year; so HUGE opportunities for new business/products. Europe or Silicon Valley??
  • The long-tail of science; scholarship OUTSIDE academia?
  • Conventional publication does not work for data
  • Diversity. No single solution. Communities of scholarship. HEP, Astronomy, Chemistry
  • Domain repositories essential; Inst Repos don’t work for science
  • OPEN. Must be BOAI-compliant: use CC-BY/CC0
  • Are universities the solution or the problem?
  • Sustainability. Funders and National Laboratories
  • Mandates are poor instruments; Culture must change. Rewards?
  • Create an author-centric culture/technology. Semantic documents. “ScienceForge”
  • Sustainability. Alliance with wealth-generation industries?
  • Text-mining
  • Theses. Must become centralised semantic, Europe?? NL++, UK–
  • Demos: text-mining, repositories
  • Growing points:
    • Open (Web) Technology continues to advance
    • Linked Open Data / Semantic Web
    • Graduate students
    • Scholarly poor
    • Wikip(m)edia
    • Open Knowledge Foundation

Ask everyONE: Why does my corrected article show up twice in PubMed?

After my paper was published, I discovered an error and contacted PLoS ONE to have it fixed. Now my paper shows up twice in PubMed. Is this a mistake?

If your paper had a formal correction, then this is not a mistake: your paper will be listed on PubMed twice.


In short: it’s because the formal correction counts as a different publication. On the PLoS ONE journal site, the correction of the error will be integrated into the original article and this correction will be announced via text in a red box at the top of the article page; however, in PubMed, the original article and the corrected are listed separately.

In more detail: if a published paper contains a major error, we issue a formal correction to fix that error, and the formal correction has its own DOI, or Date of Original Issue, from PLoS ONE.  The formal correction then receives its own, separate entry in PubMed in order to link to the original document. The corrected entry will contain the word “correction” in its title, while the original will not. PubMed mandates that the original and the correction must both be entered in its database, as you can see here.

Please note that your corrected paper will show up only once in PMC (PubMed central), because the correction will be embedded in the PMC entry.

If you discover an error after publication and you feel that it’s important that your paper be listed only once in PubMed, you have two options. First, you can request that PLoS issue a minor correction, which will appear only on the manuscript page and not on PubMed; alternatively, you can request a republication, although this option is only available to you if you catch the error 48 hours or less after the date of publication in PLoS ONE. An important proviso: it’s ultimately up to the PLoS Publication department to decide what type of correction to issue, so please understand that while we will do our best to accommodate your requests, we’ll also need to keep journal policies and procedures in mind.

As you can see, the corrections process is a little on the complex side, even if you have a PhD like many members of the PLoS community do! Since PLoS ONE doesn’t have an author proofing step, let me put in a plug here to remind you to double-, triple-, and quadruple-check your paper before you approve it for publication.

e-Infrastructures for Open Science – my talk in Rome

I have been invited to Rome to help start the Horizon 2020 Consultation for future European funding:

It’s an important meeting and follows a morning presentation by Neelie Kroes (European Digital Agenda) and responses by National scientific societies.

This blog helps me to coordinate my ideas and also acts as a record of them. My remit is to introduce this theme: “Open e-Infrastructures for Open Science” which then devolves into 3 parallel sessions:

  • Open global data infrastructure
  • Open scientific content
  • Open research culture

I’m interested in all of these and shall try to address all of them – of course there is a lot of overlap. I apologize for any UK-centricity but I hope the issues are genera. I bring the following experience:

  • A practising scientist in “long-tail science”, mainly on the informatics side. Heavily involved in the UK eScience programme.
  • Spent time in industry and academia.
  • Active in the Open Knowledge movement (especially science data and open source code/informatics).

I’ll divide this into these areas and probably be slightly controversial:

What have we learned in the last 10 years of eScience?

The UK eScience programme broke much new ground. Its greatest success was bringing groups of scientists and computationalists together and that continues (e.g. in the Oxford eResearch Centre) and that has made it eminently worthwhile. But I’ll also comment on things that didn’t work:

  • Top-down design. Technology progresses so rapidly in the Internet world that trying to design the future doesn’t work.
  • Academic-industry infrastructure. The problems of shared vision and a secure collaborative infrastructure are too difficult and expensive for either partner. Instead we should concentrate on areas where industry can share the results of academic work through an Open Infrastructure
  • Universities are generally not the best place for managing collaborative research infrastructure on an ongoing basis. Institutional repositories do not effectively serve science. In contrast inter/national research organisations have the infrastructure and the mission to make this happen.
  • There was and is very little investment in infrastructure for “long-tail science” – I exclude bioscience supported by EBI/NCBI, etc. There are no useful repositories for many of the disciplines, few ontologies, and little interest in the dissemination of science
  • Academia and many scientists are conservative and increasingly driven by self-interests. Open practice will not happen rapidly.

What are the current problems?

The eScience program has had little impact on the current practice of science. Informatics is carried out using whatever commodity tools are available and the culture is dominated by commercial scientific publication. This has not changed in 10 years and is now seriously holding back innovation in several ways.

  • The result of research is a “PDF”, not scientific information
  • The rewards are almost solely based on “citations” – a flawed measure of value
  • Almost everyone outside academia (and many within) is denied effective access to scientific output “the scholarlyPoor”.
  • Young researchers are stifled by the system and institutionalised.

There is little incentive to change the system or to build a better infrastructure.

And alongside this we have the battle between commercial closed “walled gardens” and Open knowledge (CC-BY, CC0 – anything other is almost valueless). Academia is NOT committed to Openness – it points inwards and builds systems for itself, not the world. And there is a dysfunctional academic-publisher complex which reinforces stagnation.

What are we losing?

We can consider this both in world terms and European terms. There is now huge potential in new information industries downstream of scientific publication “Google for Science”. I have estimated to the UK Hargreaves enquiry that in chemistry alone this could be “low billions” worldwide. Are we going to let Silicon Valley capture yet another new market?

  • We lose the value of the research we fund.
  • We lose the opportunity of creating new information industries
  • We make seriously bad decisions
  • Our science is worse – often unchallenged or duplicated
  • Or culture does not reward change.

What are the growing points?

We must not ignore the rest of the world. Our greatest human capital is OUTSIDE academia. Examples of worldwide growth are:

  • Wikipedia etc. (probably the greatest communal effort to build quality public science in many disciplines)
  • Open Streetmap. An unfunded project that shows what one person can make happen and within a few years become a word resource and standard
  • Open Source software.
  • Open Knowledge
  • Open science (Open Source Drug Discovery). Open Science moves faster than conventional because it grows communities rapidly, shares knowledge and avoids mistakes.
  • Internet-aware interest and practice groups (e.g. Malaria World)
  • Young people. One graduate year can create a high-quality growing point: Figshare, Altmetrics, and PMR group (OSCAR/OPSIN chemical NLP, Crystaleye – all now being taken up). Give undergraduates and graduates encouragement to explore and innovate
  • Open publishers (PLoS, Wellcome, BMC(Springer))

What should we do?

We have to change the culture. I don’t know how to do that in detail, but here are some things I’d like to see happen.

  • A scientist-oriented system for scientific research. “ScienceForge”. It’s been solved for computer programming (“SourceForge”) without any central investment. It can’t be top-down; it has to grow organically. It has to support scientists in their daily work so naturally that they don’t notice it. A scientist should then be able to share their work anywhere. It should support embargoed publication, on scientists’ terms not publishers.
  • 3rd year graduate students designing the informatics structure and training
  • Use multiple metrics for science output not just “citations”
  • Actively involve the “scholarlypoor” outside academia. Reward successful extra-academic enterprise
  • Put national laboratories at the centre of the infrastructure for long-tail scientific information.
  • Develop sustainable profitable business models based on Open practice.

I’ll think of some more on the plane. And I shall, as always, react to what is said before me. I am very impressed with Nellie Kroes and hope I get a chance to meet

Alma Swan: UNESCO Open Access Policy Guidelines


United Nations Educational, Scientific and Cultural Organization (UNESCO) Communication and Information Sector

EXCERPTS: …Policies can require ?green? Open Access by self-archiving but to preserve authors? freedom to publish where they choose policies should only encourage ?gold? Open Access through publication in Open Access journals… Evidence has unequivocally demonstrated that to have real effect policies must be mandatory, whether institutional or funder policies…. Evidence shows that researchers are quite happy to be mandated to act in this way… The optimum arrangement, one that accommodates the needs of all stakeholders, and has the potential to collect the greatest amount of Open Access content, is for a network of institutional repositories to be the primary locus for deposit and for centralised, subject-specific collections to be created by harvesting the required content from that network of distributed repositories…