Public Library of Science

Open access anxiety in the publish or perish world

Jocalyn Clark — Wed, 3 Sep 2008 11:31:39 -0700

I gave research rounds at a university hospital yesterday on a topic that seems to simultaneously inspire and provoke: open access publishing.

My sense—having socialized as a medical academic before defecting to the editorial world—is that one thing alone matters: Publish or Perish. (Or as my former colleague Joel Ray says, “PubMed-ish or perish.”). This will come as no surprise to anyone in the academic health sciences. Publishing is the chief currency in this universe, the main source of validation of one’s research, and often the key indicator of academic success. Promotion and tenure committees (and colleagues, chairs, deans) value peer-reviewed publications above all;...that is, regrettably, even above clinical performance or community service.

That “publish or perish” (PorP) generates perverse incentives and sometimes bad publication behaviour is a topic for another day.

But as the broader scientific landscape is shifting toward the importance of open access to the literature, the traditions of medical publishing—which prop up PorP—persist: the “top five” hierarchy, the importance of the impact factor, the codified order of authorship etcetera. To succeed in medical academia means to play by these rules, but these rules work to eclipse an interest in disseminating one’s work widely, the central benefit of open access (OA).

They do so partly because traditional medical publishers (except for the BMJ) do not as of yet provide OA. But these rules also create anxiety among medical academics because of some common misconceptions about open access publishing: OA publications don’t use peer review, OA journals are of lesser quality and reputation, authors “buy” their OA publications, and anyone can publish in an OA journal.

Debunking these misconceptions surely is one of the key challenges to the open access movement in medicine.

So after a lively discussion with colleagues during research rounds I was grateful this morning to receive this week’s edition of Peter Suber’s outstanding newsletter. In it he takes on this idea that OA cannot equate with prestige.

Peter’s treatise is long but well worth reading. I was particularly interested in the following arguments that have relevance to publishing in medicine:

On incentives:
- As OA proponents we have to “start working with the existing system of incentives”.... and that “researchers are not so preoccupied by their research that they can’t be induced to pay attention to relevant differences among journals, or at least the differences which universities make relevant. This gives hope to a strategy to get faculty to pay attention to access issues.” [my emphasis]

On prestige:
- “If most OA journals are lower in prestige than [traditional] journals, it’s not because they are OA. A large [part] of the explanation is that they are newer and younger” ... “There is already a growing number of high-prestige OA journals.”

(OA journals like PLoS Medicine, whose impact factors have consistently put it among the top 5 of general medical journals and whose influence means its articles are regularly cited in media and policy discussions).

On promotion and tenure reviews:
- “Universities tend to use journal prestige and impact as surrogates for quality. The excuses for doing so are getting thin” ... “If you've ever had to consider a candidate for hiring, promotion, or tenure, you know that it's much easier to tell whether she has published in high-impact or high-prestige journals than to tell whether her articles are actually good.” ... “When we want to assess the quality of articles or people, and not the citation impact of journals, then we need measurements that are more nuanced, more focused on the salient variables, more fair to the variety of scholarly resources, more comprehensive, more timely, and with luck more automated and fully OA.”

What I take from this is that we need in medical academia to care more about quality than prestige: the quality of our research, of our publication and dissemination goals, of the impact of our work, and of our hiring and promotion decisions. So instead of “Publish or Perish,” perhaps our mantra ought to be “Quality or Quit.”

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Computational Neuroscience, Developing Countries and more

Evie Browne — Fri, 29 Aug 2008 03:57:01 -0700

Today marks the publication of a special neuroscience Review in PLoS Computational Biology that we expect will become a key reference work. Gustavo Deco, Viktor K. Jirsa, Peter A. Robinson, Michael Breakspear, and Karl Friston present the results of several years of collaboration in response to a challenge posed at a Brain Connectivity Workshop to define and clarify the true meanings and usage of models in constant, but approximate use. Terms such as mean-field approximations, mass-action, neural-mass models, neural-field models, density-dynamics, etc. were in regular use but in undefined ways. This article tries to address how different models, used to simulate and predict observed brain dynamics, can be traced back to their common fundaments. In an accompanying Editorial also published today, Karl Friston, PLoS Computational Biology’s neuroscience editor, explains the origin and purpose of the article, which should standardise many concepts for some time.

Another special notice for this month is the new Developing Computational Biology Collection, available for free at: http://collections.plos.org/ploscompbiol/developing.php. These articles, published over the last year, are a series of personal Perspectives from computational biologists in a variety of developing, and often under-represented, countries. Featuring viewpoints from Goran Neshich in Brazil, Sebastian Bassi in Argentina, Liping Wei in China, and more, the series has brought a different voice to science around the world.

And finally, PLoS Computational Biology also sheds light on the difficulties for some of these same scientists to travel internationally, either to conferences or for more permanent work. In an Editorial published in collaboration with the International Society for Computational Biology following a survey conducted by the Society, Barb Bryant considers the travel restrictions imposed on many scientists, especially with regard to US visas. If you have anything you would like to add to this topic, please use our commentary features to add your thoughts.

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When do we stop stating the obvious?

Jocalyn Clark — Thu, 28 Aug 2008 13:23:53 -0700

Inequality is an area I’m very interested in but I’m always frustrated by headlines like this: “Social injustice is killing people on a grand scale”

To me this seems to state the obvious.

In this case, the headline belongs to a news article about a report released yesterday by the World Health Organization’s Commission on Social Determinants of Health called “Closing the gap in a generation: Health equity through action on the social determinants of health.”

According to the press release, the report “shows how the conditions in which people live and work directly affects the quality of their health.”

Sound familiar?

The report runs over 250 pages long and essentially reminds us that social determinants (housing, nutrition, physical activity, the environment) are more important to health than biomedical ones (medical care, drugs, hospitals, technological interventions). The Commission's three recommendations to reduce health equity are to 1) improve daily living conditions; 2) tackle the inequitable distribution of power, money and resources, especially between the genders; and 3) measure, understand, and evaluate the problem of health inequity.

I have no doubt a lot of time and effort was involved in the Commission’s work, and I do hope it succeeds in raising awareness about social injustice. But I feel like this message about the social determinants of health has been out there a long time with little action or progress.

I dusted off my copy of the Lalonde Report, a Canadian governmental report that is considered by many to be the first acknowledgment by a major industrialised nation that health is determined by more than just biological factors. It was produced in 1974.

The Lalonde report was seminal, and led to other important international documents like the WHO’s Declaration of Alma-Ata. This for the first time internationally asserted the importance of primary health care, but is also credited with advancing the notion of health as a human right.

Alma-Ata also declared the inequity between the developed and the developing world to be unacceptable, stated that economic and social development was necessary for health, and that in turn health contributes to economic and social development and world peace. Alma-Ata was released in 1978.

Given the conclusions of yesterday’s report, it’s fascinating to look back over these declarations and see how prescient they were. The Lalonde report, for example, begins with these words: “Good health is the bedrock on which social progress is built. A nation of healthy people can do those things that make life worthwhile, and as the level of health increases so does the potential for happiness.”

It goes on to state “The health care system, however, is only one of many ways of maintaining and improving health....For these environmental and behavioural threats to health [environmental pollution, city living, habits of indolence, the abuse of alcohol, tobacco and drugs, and eating patterns which put the pleasing of the senses above the needs of the human body], the organized health care system can do little more than serve as a catchment net for the victims.”

Thirty four years later we have a new report, with seemingly no new messages. Regrettably I think we can assume no new progress on social justice.

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Participate in Open Access Day and help celebrate our 5th birthday

Liz Allen — Wed, 27 Aug 2008 15:02:55 -0700

We’re pleased to announce the creation of a new blog site to help us promote and organize the first ever Open Access Day which will be held on October 14, 2008. This is the day after our birthday (the fifth publishing anniversary of our first ever journal PLoS Biology is October 13, 2008, a public holiday in the USA).

When we were thinking about ways to celebrate our birthday, we did two things. We talked to some of our fans and asked them what they would like to see us do and we discussed it amongst ourselves.

Our community of supporters very much wanted us to focus on the achievements of the Open Access (OA) movement and find fun, cool and interactive ways to get the broadest possible audience to understand what OA is all about and we agreed with that. The end result of this informal dialogue is the first ever Open Access Day.

This educational and fun series of events, competitions, and give-aways is brought to you by SPARC (the Scholarly Publishing and Academic Resources Coalition), Students for Free Culture, and the Public Library of Science.

Open Access Day will help to broaden awareness and understanding of Open Access, including recent mandates and emerging policies, within the international higher education community and the general public.

The Day will include:

- Two live Webcasts from the Nobelist Sir Richard Roberts and PLoS Computational Biology Editor-In-Chief Dr Philip E Bourne. They will discuss how Open Access impacts research and will answer questions on this topic from participating university campuses.

- Voices of Open Access Video Series. Key members of the research community, including a teacher, a librarian, a researcher, a patient advocate, and a funder, will speak on why Open Access matters to them.

- Blog competition about why Open Access matters to you, goodie bag and blog publicity to the winner.

- Free PLoS branded goodies. Your choice of T-shirt design, 25 to give away and 50 runners up get OA buttons.

Here's what, Peter Jerram, PLoS CEO, said today about the announcement of the Day (you can read more in the full press release). "The momentum behind Open Access to research has been accelerating for some time now, even before the mandates at the U.S. National Institutes of Health and Harvard University. Events beyond the US especially underscore the higher education community's commitment to having the access they need. Open Access Day will provide a perfect way for folks to come together, consider and celebrate the ramifications of the global shift that we are experiencing".

To all you fans of PLoS out there - whether you are reading our journals, publishing with us, blogging about us, running libraries that support us, developing our websites and applications, working for us or just like what we stand for generally – please join in by getting behind this day and help us to celebrate being five in style.

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Max Planck Society covers publication fees for PLoS journals

Mark Patterson — Thu, 21 Aug 2008 07:44:04 -0700

PLoS and the Max Planck Society (MPS) have recently established an agreement whereby open access publication fees in PLoS journals will be paid directly by the MPS for articles from researchers at Max Planck Institutes.

The MPS is one of the world’s leading research organizations whose researchers have an international reputation for scientific excellence. We are delighted to be collaborating with the MPS in this way so that more MPS researchers will be encouraged to publish their work in PLoS journals, and to promote open access to research literature more broadly. For papers accepted in PLoS journals after July 1st, 2008, MPS will pay the publication fee directly to PLoS for all articles where the corresponding author is affiliated with a Max Planck Institute.

In 2003 MPS was the co-initiator of the Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities and ever since then, MPS has demonstrated consistent and strong leadership in the promotion of open access to research results.

With the ever-expanding range of open access options available to authors, we encourage other research funders to set up funds to cover publication fees in open access journals or to include such expenses within their grants and research awards.

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Max Planck Society covers publication fees for PLoS journal

from Coffee and Sci(ence) on Fri, 2008-08-22 05:43

That’s a quite clever move. I wonder how other research organizations will do in the near future.One can always dream to get a cherry at the top of his grant to decorate the publish milestone.

Max Planck Society covers publication fees for PLoS...

The Neuroscience of Things That Make You Go "Ew!"

Rebecca Walton — Mon, 18 Aug 2008 12:04:22 -0700

Paul Sereno’s paper wasn’t – by any means – the only PLoS ONE paper published last week to have been covered by the press and by bloggers.

Reporting in PLoS ONE on August 13, Matt Finer, of Save America's Forests, and colleagues at Duke University and Land Is Life tracked hydrocarbon exploration projects across the western Amazon and generated a detailed map of oil and gas activities across the region, which, the researchers found, overlaps considerably with the latest biodiversity maps for amphibians, birds and mammals. Unlike the eastern Brazilian Amazon, the western region is still largely intact but large reserves of oil and gas lie below the landscape of the latter and growing global demand is leading to increased exploration and development in the region. There were news stories on the study in The Guardian, New Scientist and The Associated Press and it was blogged by Daily Kos, The Intersection and DigitalJournal.com.

Another study raising environmental issues – this one by Alex Pyron and colleagues at The City University of New York – outlined the potential effects of climate change on Burmese python populations in the United States. The PLoS ONE study found that, contrary to previous research, the pythons were unlikely to spread beyond the Floridian everglades in which they make their homes. The researchers used records on the distribution of pythons in their native range along with high resolution global climate databases to predict the potential extent of the python’s distribution in the U.S. and model the possible effects of global warming on the snakes. The results suggest that the pythons are restricted to the vicinity of the Everglades in extreme south Florida. The study was featured on Live Science and was also picked up on some of the wires.

As an ophidiophobic, reading Pyron’s article and some of the news stories (especially those with accompanying images) made me feel a little uneasy. In their article published in PLoS ONE last week, Mbemba Jabbi at the National Institutes of Mental Health, along with colleagues at the University Medical Center Groningen, shed some light on how reading a book or watching a film can invoke in us the same emotions as if we were experiencing the events ourselves. Focusing on the emotion of disgust, the researchers used an fMRI scanner to measure the participants’ brain activity while they: had drops of an unpleasant, bitter liquid placed on their tongue; watched a video of “disgusting” behaviour; and read a passage of disgusting text. They found that the same areas of the brain – the anterior insula and adjacent frontal operculum – were activated both when the participants tasted the liquid and when they watched the video and read the passage. The article was covered by New Scientist (although, note the disclaimer – “Warning: this story contains a paragraph of disgusting text” at the top of the story), Wired, PsychCentral and Discount Thoughts.

Finally, researchers led by Daniel Perez at the University of Maryland studied the H9N2 strain of the influenza virus, publishing their findings in a paper entitled, Replication and Transmission of H9N2 Influenza Viruses in Ferrets: Evaluation of Pandemic Potential. The scientists used ferrets (whose biology is very close to humans when it comes to flu) to characterise the mechanism of replication and transmission of recent avian H9N2 viruses and, according to the paper, the results suggest that, “the establishment and prevalence of H9N2 viruses in poultry pose a significant threat for humans.” There were news stories about the study in Reuters, AFP, Science News and Discover Magazine.

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Digging into the "Green Desert" of Niger's Holocene Past

Rebecca Walton — Mon, 18 Aug 2008 11:47:14 -0700

After the massive media buzz surrounding the last paper published in PLoS ONE by Paul Sereno, in which he and colleagues described the anatomy and behaviour of Nigersaurus taqueti (dubbed “the Mesozoic cow” by the press), you can imagine that we were quite excited to receive another paper from the University of Chicago Palaeontologist and National Geographic Explorer-in-Residence.

Sereno and his team had originally been on a dinosaur-hunting expedition in the Ténéré Desert in Niger (which is where the Nigersaurus fossil was discovered) when they happened on a large, Stone Age graveyard. In the new PLoS ONE article, Lakeside Cemeteries in the Sahara: 5000 Years of Holocene Population and Environmental Change, the researchers outline the findings from a series of new archaeological sites at Gobero, dating from the Holocene and preserving the earliest Saharan cemetery from around 9500 years ago, as well as burials from two separate periods of occupation spanning more than 5000 years. Arid conditions forced the initial occupants to abandon the area a little over 8000 years ago but with the return of more humid conditions, around 6600 years ago, the region was repopulated by a more gracile people who left behind elaborate grave goods, including animal bone and ivory ornaments, many of which are pictured in the paper.

One of the graves contained the skeleton of a small Tenerian woman facing the skeletons of two small children (a photograph of this by Mike Hettwer, captioned Stone Age Embrace, has been widely used alongside many of the news stories on the article). Samples from the grave contained pollen clusters, suggesting the individuals had been laid to rest on a bed of flowers.

Some of the accompanying images are part of the published paper (and so can be reused in line with the terms of the Creative Commons Attribution License); other images, along with more information about the expedition can be found on the Project Exploration website (Project Exploration being a nonprofit science education organization that makes science accessible to the public—especially minority youth and girls—through personalized experiences with scientists and science). Any users registered on the PLoS ONE site can, of course, post notes and comments and rate the paper online.

Understandably, the article received huge amounts of coverage in the media and in the blogosphere (despite “Bigfoot”’s efforts to steal the spotlight). As well as making the front page of Slashdot, the story was the top Associated Press science story on Thursday (it was also one of the overall top stories), it was in Yahoo science news’s most viewed list on Friday, and in the New York Times most-emailed list. There were several hundred news stories on Google News, so here are a few highlights of the coverage (see also Knight Science Journalism Tracker and A Blog Around the Clock):

News:

New York Times – Graves Found From Sahara’s Green Period
Washington Post – Excavations Show a Lush Life in the Sahara
Los Angeles Times – Archaeologists get a glimpse of life in a Sahara Eden
Reuters – Stone Age graveyard shows Sahara was once green
National Geographic – Ancient Cemetery Found; Brings "Green Sahara" to Life
Scientific American – Paleontology's Indiana Jones
New Scientist – Stone Age mass graves reveal green Sahara
Nature News – Back when the desert was green

Blogs:

Wired – Saharan Snapshot of Stone Age Life
Pharyngula – I Wish I Was a Paleontologist
Greg Laden’s Blog – Stone Age Graveyard Reveals Lifestyles of a Green Sahara
Stones, Bones ‘n’ Things – Paleontology Meets Archaeology
Anthropology.net – The Kiffian & Tenerean Occupation Of Gobero, Niger: Perhaps The Largest Collection Of Early-Mid Holocene People In Africa
Metafilter – Lost Tribes of the Green Sahara

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To screen or not to screen?

Gavin Yamey — Tue, 5 Aug 2008 16:08:55 -0700

To screen or not to screen? One of the more “interesting” experiences of my journalistic career was co-authoring an Op-Ed for the San Francisco Chronicle in 2002 on the lack of evidence for prostate cancer screening using the PSA test.

The piece caused quite a reaction, which we later discussed in the BMJ:

“Within hours of our piece being published, prostate cancer charities, support groups, and urologists around the country had circulated a "Special Alert" by e-mail. This community has huge faith in PSA tests, and it did not care for our opinion. The e-mail, under the header "ATTENTION MEN!!" urged the community to take action. By the end of the day, accusations, abuse, and personal threats jammed our e-mail inboxes. We were compared to Josef Mengele, and accused of having the future deaths of hundreds of thousands of men on our hands.”

I suspect that this same community will now be up in arms about the latest guidance from the US Preventive Services Task Force (USPSTF), one of the best respected independent health agencies in the country.

As the New York Times reports in a huge cover story today, headlined Panel Urges End to Prostate Screening at Age 75, the task force has systematically reviewed the best evidence on the value of such screening and concludes:

“The USPSTF recommends against screening for prostate cancer in men age 75 years or older.”

It also concludes that “the current evidence is insufficient to assess the balance of benefits and harms of prostate cancer screening in men younger than age 75 years.”

The New York Times notes that the new guidance, which now clearly advises against screening men aged 75 and older, represents "an abrupt policy change by an influential panel," a panel that had previously withheld giving specific advice regarding screening for prostate cancer.

In a terrific NPR commentary today on the new guidance, Doug Kamerow says:

“There just aren't any good studies to show that men who get screened and treated for prostate cancer live longer than those who don't. So the benefits are unknown. But the harms of screening and treatment are real and well documented. They include not just the costs and pain of treatment, but also the incontinence and impotence that some men get after surgery. The problem is that some prostate cancer grows quickly and is lethal. Some, especially in older men, is slow-growing and never causes a problem. That is why people say that more older men die with prostate cancer than of prostate cancer.”

I suspect that despite the new USPSTF guidance, the “great prostate debate” is far from over. It is merely, says NBC news’ chief science correspondent Robert Bazell, “the latest shot in an ongoing war among many factions who hold various positions on this disease.”

Hopefully the war will be settled when we have the results of two ongoing clinical trials of prostate cancer screening, one in the U.S. and one in Europe.

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ONE journal, two birthdays

Liz Allen — Fri, 1 Aug 2008 10:32:43 -0700

The English Monarch has two birthdays – their real date of birth is celebrated in private with family and friends and the official date (which could historically be moved should their real birthday fall at a time of year when the weather was inclement) which is celebrated in public through the Trooping of the Colour Ceremony and a fly-past over Buckingham Palace in London.

PLoS ONE also celebrates twice (but far less grandly) – first there’s the date we opened our doors for submissions, 4 August 2006 (the date of our conception) and then there’s the date we launched (our birth), 20th December 2006.

Within less than 3 weeks of opening our doors we had received 70 manuscripts which represented far more papers flowing far faster than we’d ever experienced before. Now, two years later, we receive approximately 350 submissions per month. Not surprisingly, the PLoS team has grown since then to cope with the increased workload.

Two folks who deserve special mention for being there at the start and still being on board now - they are Bex Walton and Lindsay King.

Two years on, the person who still sums up our publishing philosophy well is the author of the first paper accepted for PLoS ONE, Andrej Romanovsky of St. Joseph's Hospital, Phoenix, Arizona, USA. He said "A traditional publisher uses complex rules to determine who, when, how, and at what price will be allowed to see your results. You can continue supporting this system ... or you can submit your next paper to PLoS”.

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Happy, er, conception-day?

from A Blog Around The Clock on Mon, 2008-08-04 04:55

Two years ago on this day, PLoS ONE opened for submissions (and surprisingly many manuscripts - 70 - got submitted immediatelly)....

Tyrannosaurus Re-examined

Rebecca Walton — Fri, 1 Aug 2008 08:38:54 -0700

This week saw the publication of another dinosaur study in PLoS ONE. In the article, entitled, Dinosaurian Soft Tissues Interpreted as Bacterial Biofilms, Thomas Kaye, at the Burke Museum of Natural History, and colleagues reported that material recovered from dissolved dinosaur bones by palaeontologists in 2005 (and believed to be dinosaurian soft tissue) may actually have been slimy biofilm created by bacteria that coated the voids once occupied by blood vessels and cells.

This study has already generated a large number of news articles and blog posts, including the following: New Scientist (T. rex 'tissue' may just be bacterial scum), Scientific American (Presumed dinosaur flesh may just be bacterial sludge), National Geographic (Dinosaur Slime Sparks Debate Over Soft-Tissue Finds), USA Today (New study has a bone to pick about dinosaur soft tissue), Aetiology (Dinosaur soft tissue--just bacterial biofilm?) and Pharyngula (Tyrannosaur morsels).

Several comments have already been posted on the published article and you can join in the discussion once you have created an account on the PLoS ONE publication website.

On the topic of biofilm, Carsten Matz’s paper, Marine Biofilm Bacteria Evade Eukaryotic Predation by Targeted Chemical Defense, published last week also picked up some coverage in the Washington Post (Social Lives of Bacteria May Yield Benefits for Humans) and Chemistry World (Biofilms deploy chemical weapons).

Also on a watery theme was Natalia Ospina-Álvarez and Francesc Piferrer’s paper on the potential effects of climate change on sex determination in fish. In vertebrates with separate sexes, sex determination can be genotypic (GSD) or temperature-dependent (TSD). The Spanish researchers used field and laboratory data to critically analyze the presence of TSD in the 59 species of fish where this type of sex determining mechanism had been postulated and found that increasing temperatures invariably resulted in highly male-biased sex ratios and that even small changes of just 1-2°C can significantly alter the sex ratio from 1:1 (males:females) up to 3:1 in both freshwater and marine species. Time Magazine covered the article (Global Warming's Fish-Sex Effect) and the story has also been Dugg several times.

Danish palaeontologist Per Christiansen compared the evolution of skull and mandible shape both in modern cats and in (the now extinct) sabercats; Greg Laden has posted a nice write-up of the study on his blog and there also posts on The Dragon’s Tales and on Counter Minds.

Finally, here is a quick round-up of some of coverage of several papers published in PLoS ONE on July 23^rd: Does Pathogen Spillover from Commercially Reared Bumble Bees Threaten Wild Pollinators? (New Scientist, Reuters, Greg Laden’s blog); Sample Size and Precision in NIH Peer Review (The Scientist, Mike the Mad Biologist); and Changes in Gray Matter Induced by Learning—Revisited (Mind Hacks).

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