Best Bone Structure

2009 was a big year for paleontology research in PLoS ONE and our Paleontology Collection now contains over 40 papers. Scott Hocknull’s discovery of three new dinosaurs in Australia appeared in ABC Science’s review of 2009 and National Geographic’s top 10 (most viewed) dinosaur and fossil finds; this National Geographic list also included PLoS ONE research published by Jack Horner and Mark Goodwin that suggests three dinosaurs thought to be separate species may actually be from the same species. The report of two 47.5-million-year old whale fossils discovered in Pakistan, one of which was a pregnant female, was featured in the “Life” category of Science News’s top stories of the year and was one of four PLoS ONE studies to make Not Exactly Rocket Science’s review of 2009. Unsurprisingly, the fossil that appeared in most lists was Darwinius masillae, aka Ida. As well as some of the stories mentioned above, Ida was discussed in the annual round-ups of New Scientist, LiveScience, the BBC News, among others.

The W.C. Fields Award for Best Study Involving Animals

W.C. Fields is credited with the line, “never work with children or animals.” Well, he should be glad he wasn’t a scientist! A number of interesting and intriguing animal studies appeared in the 2009 round-ups, covering categories from “cleverest” and “biggest” to “best candidate for a 2010 Ignoble.”

Sakamoto and colleagues studied black-browed albatrosses by affixing a small camera to them and watched the birds interacting with a killer whale; this study was highlighted in the BBC’s list of “clever nature” in 2009. Another clever creature was the crow in Alex Kacelnik’s study, which found the birds could use up to three tools sequentially – a study which appeared in the Science News “life” round-up.

If asked the question, “does my web look big in this?” by a spider from the new species Nephila komaci, the answer is definitely yes.  Kuntner and Coddington reported that the new spider is one of the largest known orb-weaving spiders and the study made National Geographic’s top 10 new species of 2009. The chimpanzees that exchanged sex for food on a long-term basis were included in ABC Science’s list of the year, and perhaps unsurprisingly, the study reporting fellatio in bats was named as one of the weirdest science stories of the year by Cosmic Log, Conservation Maven and New Scientist.

The Human Condition: Best Study about People

Of course, we don’t just like to read about animals in the news; we want to know more about ourselves—people. A study published last January reporting the potential use of the video game Tetris to prevent post-traumatic stress disorder, made Not Exactly Rocket Science’s Review of 2009, as well as the New York Times’s Year in Ideas and the top 10 psychology studies at True/Slant. What may have been one of the scariest studies of the year (Indicution of Empathy by the Smell of Anxiety by Prehn-Kristensen and colleagues) appeared in Discover Magazine’s top 100 science stories of 2009, a list that they are continuing to expand through the end of the month. People also turned out to be one of the most surprising creatures to glow, according to this review in Scientific American. In the “best use of science to solve a historical mystery” category, one of the candidates must surely be the paper that revealed that inbreeding may have been responsible for the decline of the Habsburg dynasty in Spain; this was another study included in the Not Exactly Rocket Science round-up.

Most Innovative

As many of you will know, PLoS ONE won the ALPSP’s award for Publishing Innovation of 2009 and we were very proud to be recognised for our constant efforts to innovate and to change the face of scientific publishing. In 2009, we launched our new programme of article-level metrics, which was nominated as one of the open science breakthroughs of 2009 on the World Association of Young Scientists blog. According to The Scientist, meanwhile, Mark Welch’s study, reporting a new recipe for protein expression, is one of the top 10 innovations of 2009.

It goes without saying, that 2009 was a great and superlative-filled year for PLoS ONE and we wish all of our readers, authors, editors and reviewers a very happy New Year!

You can read more about PLoS ONE papers in the news via the Media category of this blog and our Media Archive also lists much of the news coverage for many of the papers published in PLoS ONE since our launch in 2006.

As over 200 of our papers were covered by the international press and bloggers in 2009, it hasn’t been easy to choose, but here are some of the highlights from PLoS ONE’s year of headlines (in roughly chronological order). As with all PLoS articles, you can see how many times each one has been downloaded (and blogged about, bookmarked, rated etc) by clicking on the ‘Metrics’ tab at the top of the article.

PLoS ONE paleontology articles proved to be of frequent interest to the media this year, right from the start, with some of the most widely covered papers including: Andy Farke’s paper on combat in Triceratops, Philip Gingerich’s report of two 47.5 million year-old whale fossils, including a pregnant female, and Leon Claessens’s article on respiration and flight mechanics in Pterosaurs. Other articles that made the headlines in January and February included Julian Finn’s study on dolphins’ culinary (or, at least, cuttlefish handling) skills and a study by Oxford University researchers on the potential use of the game Tetris to reduce post-traumatic flashbacks.

Clickstream Map of Science (Fig. 5 from PLoS ONE e4803)

In March, Johan Bollen’s article, Clickstream Data Yields High-Resolution Maps of Science, was published; as well as featuring prominently in the news, Figure 5 from the paper now appears on the t-shirts available to buy from the new PLoS store. In other news that month, Michael Singer and colleagues reported a case of self-medication in the woolly bear caterpillar and Michael Coble’s study confirmed, via forensic DNA testing, that skeletal remains of two individuals discovered in Russia in 2007 belong to the two missing children of the last Tsar of Russia (the Crown Prince, Alexei Romanov and one of his sisters).

Another historical mystery was solved in April with the publication of a paper about the Habsburg kings of Spain. The researchers used genetic evidence to show that the high frequency of inbreeding (mating between closely related individuals) was a major cause for the decline of the dynasty with the death of King Charles II in 1700. In the same month, Cristina Gomes reported the long-term exchange of meat for sex among chimpanzees—male chimps that share the meat gained from their hunting expeditions were found to mate twice as often as other males.

Darwinius masillae (from Fig 2. of PLoS ONE e5723)

One of the biggest news stories of the year followed the publication of a paper describing an extremely well-preserved, 47-million-year-old primate fossil, formally named Darwinius masillae and nicknamed “Ida.” We rounded up some of the news and blog coverage of the paper in earlier blog posts and with over 70,000 views of the full scientific article, Ida is still being discussed more than six months later. The Darwinius paper wasn’t the only PLoS ONE paper to make the news in May, however; a study reporting a 4,000-year-old case of leprosy and a paper on the commonness of data fabrication and falsification among scientists also generated major news coverage.

Scientometrics also featured in PLoS ONE’s June media coverage in a study that reported that the reliability of research findings published in the scientific literature decreases with the popularity of the field. June also saw the publication of one of the year’s many psychology and behavioural neuroscience papers to attract media interest: a paper by Bettina Pause and colleagues, which investigated empathy induced by the “smell of fear” (the lucky study participants got to smell sweat samples produced by students about to take an exam and those about to exercise—only the former appeared to activate the part of the brain associated with empathy).

Diamantinasaurus matildae (Artwork by Travis R. Tischler)

PLoS ONE showed no signs of disappearing from the press or the blogosphere over the summer months. In July, Scott Hocknull and colleagues reported the discovery of not one but three new species of dinosaur in Queensland, Australia; the dinosaurs, nicknamed Matilda, Banjo and Clancy, brought an end to Australia’s dinosaur dearth. In Evan Wolff’s paper, meanwhile, he and his colleagues reported that Tyrannosaurus rex might have died out because of an infectious disease similar to trichomonosis. Other popular studies from the summer included: a cell-phone based microscope application with implications for the diagnosis of infectious diseases in the developing world, research on the impacts of climate policy on natural habitats in the US, and the rise in hospital deaths during August—when trainee doctors start work.

October could have been Albatross Month for PLoS ONE with widespread news coverage about both Kentaro Sakamoto’s article on the interactions between black-browed albatrosses and a killer whale, captured on video by a small camera attached to the birds, and Lindsay Young’s on plastic ingestion by Laysan albatrosses in the Pacific. October’s other popular studies included: the discovery of a new species of giant, orb-weaving spider, a report of fellatio in bats and the revised understandings of both Archaeopteryx (now thought to be less avian and more dinosaurian) and of the dinosaurs Stygimoloch and Dracorex (now thought to be juveniles of Pachycephalosaurus). Four of these articles were highlighted by the New York Times.

One of the last dinosaur papers published in 2009 was by Herman Pontzer and colleagues, who studied 14 species and reported that many dinosaurs were probably warm-blooded like present-day birds and mammals rather than cold-blooded like present-day lizards. Later in November and just in time for Thanksgiving came Kevin Hall’s article on the environmental problems posed by America’s growing food waste production.

PLoS ONE papers continued to feature prominently in the news throughout December, with studies reporting: the results of an ancient DNA analysis of the Tomb of the Shroud in Jerusalem, the better than expected performance of orphanages in terms of the healthcare and emotional wellbeing of the children who occupy them, and the discovery in California of a 13,000-year-old tree that may have survived climate changes by cloning itself.

It is also worth mentioning that throughout the year we ran a “blog post of the month” competition to recognise some of the high quality blog posts that are being written about our articles. The list of winners can be found in these posts.

These papers barely scratch the surface (in variety and scope) of the 4,400 articles that were published in PLoS ONE this year and we look forward to publishing many more papers in 2010—regardless of whether they make the headlines.

The start of the year saw us developing new functionality, with the launch of Collections on PLoS ONE. This began with the publication of the ‘Stress-Induced Depression and Comorbidities’ Collection in January, followed by our second in February – the  PLoS ONE Paleontology Collection. We subsequently launched the Prokaryotic Genome Collection in June and the Structural Genomics Consortium Collection in October (a collection which provides ‘enhanced versions’ of papers, incorporating advanced 3D interactive simulation software – an excellent example of the creative re-use of Open Access content).

In March, we launched everyONE, our community blog site; we announced our ability to accept LaTeX submissions; and we upgraded our site with a redesigned ‘tabbed’ user interface to accommodate our newly launched Article-Level Metrics functionality (of which more later).

In April, we announced our ‘Blog Post of the Month Competition’ (in collaboration with researchblogging.org) which has since gone on to award a winner every month.

In May, we redesigned our email Table of Contents alerts so that recipients now receive an email categorized by subject area, and this was also the month in which we publicly thanked the 9,000 peer reviewers who gave us their expert opinions during 2008.

Our 2009 media coverage will be reviewed by Bex in a different post, but in May we published a paper that sparked our largest media story of the year – the Darwinius masillae (or ‘Ida’) paper – “Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology”. The coverage of this paper was overviewed in three separate blog posts.  

May also saw a major event in the development of PLoS’s technology platform – with the migration of PLoS Biology and PLoS Medicine, we were finally able to have all seven of our titles on Topaz, which is now our shared online platform.

In July, we began a partnership with DeepDyve to improve our search capabilities and we also launched the “Worth a Thousand Words” blog series (featuring a selected image from each week’s publications). July also saw PLoS publicly express our opinion that there is more value in measuring impact at the article level than at the journal level – something which coincided with the announcement that we would no longer be promoting Impact Factors on our sites.

In August, PLoS ONE was featured in the popular internet comic, “PhD Comics” as part of their “Nature vs Science” series, and in the same month PLoS launched an important experiment in rapid publication – PLoS Currents: Influenza, a collaboration between PLoS, Google Knol and the NCBI

In September, PLoS ONE was immensely proud to win the ALPSP Award for Publishing Innovation, 2009 – this is a major industry award and a testament to the rapid pace of innovation that the journal has pioneered in the 3 years since launch.

September was also the month that saw our Article-Level Metrics program expand in a significant way, by displaying usage data on every article in the PLoS corpus. In December, we also added data from ResearchBlogging.org to the program.  We regard Article-Level Metrics as a significant new development in academic publishing and we  expect to significantly expand it in 2010. Several presentations were made through the year on the topic of Article-level Metrics, for example to NISO, to the ElPub Conference, and to UCSF/Berkeley and these are all archived with audio if you wanted to delve into the details.

In October, OASPA, the new association for Open Access Scholarly Publishers was launched and PLoS was proud to be a founding member. This coincided with Open Access Week, 2009. And in November, in response to many requests over the years, we launched our new PLoS store.

And finally, after a year of incredible developments, 2009 has culminated with what may yet turn out to be the most significant development of all – the request by the White House Office of Science and Technology Policy (OSTP) for public comments on the issue of broadening public access to publicly funded research. You still have time to provide your feedback and there would be no better New Year resolution than to make your voice heard in this forum.

Thank you to everyone who has supported us in 2009, and over the last three years – in particular thank you to our (almost) 1,000 Academic Editors, all of our peer reviewers and of course, all of our authors. We look forward to publishing more great science in 2010!