Is Nature’s “free to view” a magnanimous gesture or a cynical ploy?

Macmillan, the publisher of Nature and 48 other Nature Publishing Group (NPG) journals, announced today that all research papers published in these journals would be “made free to read in a proprietary screen-view format that can be annotated but not copied, printed or downloaded”.

If you believe, as I do, that paywalls that restrict the free flow of scientific knowledge are a bad thing, then anything that removes some of these restrictions is a good thing.

This move is fairly typical of Nature as of late. Despite its place as one of the oldest and most august big Kahuna in the subscription publishing world, Nature – and especially its Digital Science division – have been far more attuned to the ways that the Internet has changed publishing than their competitors. And, because of the rise of open access publishing and funder efforts to provide access to their papers, people increasingly expect to be able to access scientific publications, and Nature is responding to that expectation.

There are really two parts of this announcement.

  1. A smallish (~100) media outlets and bloggers will be able to provide a link to Nature papers they are writing about that will allow readers that will allow them to access them for free.
  2. Subscribers to Nature and other NPG journals will be able to generate and share such links by email, on Twitter, etc…

It’s actually kind of brilliant on Nature‘s part. They are giving up absolutely nothing. Readers of news stories about Nature articles were never going to pay to access the actual articles (like other publisher Nature has tried a pay-per-view system that has completely failed). And individuals and institutions that subscribe to Nature aren’t going to give up the convenience of being able to read articles on demand for the challenge of finding a link on Twitter (unless someone were to set up a database of these links…. hmmm….).

And let’s remember that subscribers to Nature were already sharing copies of downloaded PDFs quite abundantly. This was not, as Nature argues happening in an inconvenient way in the dark corners of the Internet. This was happening in email and on Twitter. The problem was that Nature had no control over this sharing. So, really, they’re not changing people’s ability to access Nature very much – what they’re doing is changing where they access it – likely with the hope that they will figure out ways to monetize this attention.

Thus Nature gets lots of goodwill, more people reading their papers, and they lose nothing in the process. At least not immediately. Because the irony of a system like this is that it can’t ever actually do what it purports to do. If it ever actually made it possible to find and get free access to any Nature paper, then people actually would stop subscribing and they’d have to end this kind of access.

At the end of the day, this is a pretty cynical move. I’m sure the people at Nature want as many people as possible to read their articles. But this move is really about defusing pressure from various sources to provide free access. Yet Nature knows that they can’t really provide free access without giving up their lucrative subscription business model, which they are unwilling to do. So they do something that makes it seem like they are promoting free access, while doing nothing to address the real obstacle to free access – subscription publishing.

It is also worth noting how Nature is defining access down. First we had “open access” in which people can download, read, reuse and redistribute content. Then we had “public access” in which people can download and read content. Now we have “free access” in which people can read for free in a proprietary browser, and can’t download or print. This is going in the wrong direction, and it would be a disaster for science if – as Nature clearly hopes – this is the definition of access that sticks.

 

Posted in open access | 14 Responses

Contrary to what you read in Nature, Open Access has not caused the growth in science publishing

I wasn’t planning on spending my Thanksgiving delving into PubMed statistics to refute yet another bogus claim about open access publishing. But being a vegan, I didn’t really have much else to do anyway. So…

The newest Nature has an Op-Ed from Martijn Arns, a brain researcher in the Netherlands with a title I couldn’t ignore: “Open access is tiring out peer reviewers“. He complains about poor quality (not negative) reviews he’s gotten on some recent papers, and asserts that this is due to an increase in the burden on peer reviewers with the rise of digital publishing. I agree with him – there are deep problems with the way we go about peer review – and his solution to the problem – implement post-publication peer review – is spot on.

But as the trolly title of the article (which I suspect was added by Nature and not by Arns) suggests, Arns argues that the increase in publishing volume, and therefore reviewer workload, is due to the rise of open access. It is, of course true, that open access publishing has been growing rapidly, and thus it might seem to some people that the growth in scientific publishing overall is due primarily to open access. But impressions can often be wrong, so I decided to look at some data.

I used PubMed to get data on the total number of papers published annually since 2000 and PubMed Central to determine the fraction of these articles that are open access. (The numbers aren’t perfect, since some journals have made their back content open access, slightly inflating the number of open access articles from early years. But this is a small effect.)

YearPubMedOpen AccessFraction OA
200052987134380.006
200154477840980.008
200256212245530.008
200359243554890.009
200463747475320.012
2005697839118560.017
2006744503150650.020
2007782502204680.026
2008831834325760.039
2009872229590480.068
2010935583818540.087
201110109901119100.111
201210731581465610.137
201311305541798710.159

You can see several things in these data. First, the number of papers in PubMed has increased dramatically with more than 2.1 times as many papers published in 2013 as in 2000. At the same time the fraction of articles in PubMed that are open access has increased even more dramatically, from basically nothing in 2000 to 15.9% of articles in PubMed in 2013.

Interestingly, in the last few years, the annual grown in open access papers has exceeded the annual growth in non-open access papers. The graph below plots, for each year, the annual growth in open access (the number of open access papers published in that year minus the number of open access papers published in the previous year) as a fraction of the annual growth in papers published (the total number of papers published in that year minus the total number of papers published in the previous year).

 

OA as fraction of total new papers

(Not sure what’s going on with 2009 – something is weird with that datapoint).

But does this mean that open access is driving the increase in scientific publishing output? Of course not. Just because open access is capturing market share doesn’t mean that it is driving an overall increase in the size of the market. If it were, than you would expect the annual increase in the number of papers published to be increasing as open access has risen. But this is not the case. The number of papers published has been increasing at roughly 6% since for the last 10 years, with no relationship to the number of open access papers published, which has been increasing steadily every year.

OA_Output

Thus we are really looking at two essentially independent phenomena. There is clearly a rise in the total number of papers published. And open access has been capturing an increasing fraction of this growing market. But it is simply false to assert that open access has been driving this increase in scientific output.

That said, I agree completely with Arms that there is a big problem here. It IS a huge burden to try and find reviewers for all of these paper. And more importantly, this process has gotten slower and slower. The real failure of digital publishing is not that the number of papers has increased – it’s that the time it takes to publish papers has not improved at all. It’s ridiculous that we live in a world where it is possible to share information across the globe instantaneously, but that science as an enterprise has chosen to delay the sharing of new scientific knowledge for an average of 9 months as we go through a byzantine process of pre-publication peer review.

We need to – as Arms suggests (and I have written about previously) move to post-publication peer review. But in doing so we need to focus on the problem – peer-review. And in order to do this, we have to shift away from paywalled, subscription journals which depend entirely on pre-publication peer review to justify their existence. Thus, rather than mistakenly blaming open access for creating problems with peer review, we have to recognize that it is an important part of the solution.

 

Posted in open access | 13 Responses

NIH Director Francis Collins’ ridiculous “We would have had an Ebola vaccine if the NIH were fully funded” meme

Almost as soon as the African Ebola epidemic hit the headlines, NIH Director Francis Collins was making the rounds arguing that we would have had an Ebola vaccine by now, if only Congress hadn’t slashed the NIH budget.

Lest you think I’m taking his words out of context, here is what he said to a House Energy and Commerce Subcommittee on Health Roundtable Discussion on Health and Medicine Issues on September 10, 2014:

The NIH began working on a vaccine for Ebola in 2001. We have steadily pursued that effort over these last 13 years, hoping that by the time a big outbreak occurred we would be ready for it. That vaccine has now been in animal trials, shown to be highly effective. But as of this summer, when the outbreak really began to catch fire, had not yet quite reached the point of a phase 1 clinical trial.

We worked in record time with enormous assistance from our colleagues at FDA to speed up the process. And last week, the first volunteers at the NIH clinical center were injected with this vaccine in a phase 1 trial to determine whether in fact it is going to be safe. And in another two or three months we will know that, and then hopefully be in a position to begin a phase 2 trial in the places where it’s most needed in Africa.

But I have to tell you, if we had not gone through this 10-year decline in the support of biomedical research, we would be a year or two ahead of where we are now. And think about the difference that would make, had we in 2014 been in the position to distribute rapidly tens of thousands of doses, in collaboration with our colleagues at GSK, of this vaccine, how much different would this be and how many lives would have been saved.

I read this testimony at the time, and was taken aback by this statement, but I was a bit reluctant to undermine efforts to increase NIH funding, no matter how cynical they might be. It was, after all, Congressional testimony, and one can forgive a bit of exaggeration in pursuit of remedying the horrible financial situation the NIH (and, thus its grantees and would be grantees).

But now Collins has gone public with this claim, in an article in the Huffington Post, and so it’s time to call this for what it is: complete bullshit.

First, let’s deal with the most immediate assertion – that if there had been more funds there would be an Ebola vaccine today. Collins argues we’d be a few years ahead of where they are today, and that, instead of preparing to enter phase 1 trials today, they’d have done this two years ago. But last time I checked, there was a reason we do clinical trials, which is to determine if therapies are safe and effective. And, crucially, many of these fail (how many times have we heard about HIV vaccines that were effective in animals). Thus, even if you believe the only thing holding up development of the Ebola vaccine was funds, it’s still false to argue that with more money we’d have an Ebola vaccine. Vaccine and drug development just simply doesn’t work this way. There are long lists of projects, in both the public and private sector that have been very well-funded, and still failed.

It is a gross overtrivialization of even the directed scientific process involved in developing vaccines to suggest that simply by spending more money on something you are guaranteed a product. And, if I were in Congress, frankly I’d be sick of hearing this kind of baloney, and would respond with a long list of things I’d been promised by previous NIH Directors if only we’d spend more money on them.

Second, let’s assume Collins is right. That the only reason we don’t have an Ebola vaccine today was that the project wasn’t properly funded. If this is true, than one should rightly ask why this wasn’t given a higher priority. The potential for a serious Ebola outbreak has been there for a long time. And while money is tight at the NIH, they still manage to find funds to do a lot of stuff I would not have prioritized over an Ebola research program it it was really on the crux of delivering a vaccine. So there is an element of choice here too that Collins is downplaying.

But what really bothers me the most about this is that, rather than trying to exploit the current hysteria about Ebola by offering a quid-pro-quo “Give me more money and I’ll deliver and Ebola vaccine”, Collins should be out there pointing out that the reason we’re even in a position to develop an Ebola vaccine is because of our long-standing investment in basic research, and that the real threat we face is not Ebola, but the fact that, by having slashed the NIH budget and made it increasingly difficult to have a stable career in science, we’re making it less and less likely that we’ll be equipped to handle all of the future challenges to public health that we’re going to be face in the future.

Don’t get me wrong. I get what Collins is trying to do. I just think it’s a huge mistake. Every time I see testimony from NIH officials to Congress, they are engaged in this kind of pandering – talking about how concerned they are about [insert pet disease of person asking question] or that and how, if only they could get more money, we’d be able to take make amazing progress. But guess what? It hasn’t worked. The NIH budget is still being slashed. It’s time for the people who run the biomedical research enterprise in this country to make basic research the center of their pitch for funding. Collins had a huge opportunity to do that here, but he blew it.

 

 

 

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Meet Kent Anderson, anti-#openaccess campaigner, publisher of Science

The news that the American Association for the Advancement of Science named Kent Anderson as its new Publisher was met with shock and widespread derision by myself and other supporters of open access publishing. In the often mocking banter about this hire, a number of people wondered what we were getting all worked up about. So, for benefit of those unfamiliar with Mr. Anderson, here is a brief introduction of his oeuvre, and an explanation of what we find so troubling about the idea of him running Science.

Anderson has a long career in medical publishing, having worked for the New England Journal of Medicine for a decade before becoming publisher of The Journal of Bone and Joint Surgery. But he is most well-known for his role as the primary author and moderator of The Scholarly Kitchen, a blog launched by Anderson under the auspices of the Society for Scholarly Publishing to provide “timely updates and interpretation on research that publishers, librarians, authors, and other individuals involved in scholarship might want to know about”.

Anderson was fairly prolific at TSK, publishing over 1,000 posts over his 5 years at the helm, but I hadn’t heard of him or read his work before an April 2010 missive, “PLoS’ Squandered Opportunity — Their Problems with the Path of Least Resistance“, which begins thusly:

[An earlier post] reminded me of what I think is a sad story, one that hasn’t been told outside of private discussions, at least as far as I know. It’s the story of an opportunity sacrificed at the altar of open access, of a radicalism blunted into tradition, of audacity channeled down the path of least resistance.

It’s the story of the Public Library of Science.

As a founder of the Public Library of Science, I took some umbrage at what turned out to be an ill-informed attack on open access publishing. Worse, it impugned our motives, suggesting (without having ever spoken to any of us) that the launch of PLOS ONE was motivated not by a desire to reform scholarly publishing, but by a simple desire to make money. This post began what can only be described as a four year long campaign to discredit open access publishing in general, and PLOS in particular. I can not begin to fully summarize his writings on the topic, so instead I’ve compiled a list so you can see yourself and decide what you think.

Kent Anderson on Open Access

Kent clearly does not like open access. He thinks it is bad for scholarly publishing – that it undercuts publisher’s ability to make money, and, more importantly to him, it erodes the quality of the products they produce (which is why we all find it so ironic that his first job at AAAS is to launch a new open access journal).

He at times raises important issues. If he were just an open access skeptic, that would be one thing. But his writing on the subject is marked by several other deeply troubling features:

  • An utter disdain for the supporters of open access and a tendency to impugn our motives.
  • The belief that science exists to serve science publishing and not the other way around.
  • The dismissal of government efforts to promote open access (especially public access mandates and PubMed Central) as needless subsidies, but the view that the product of tens of billions of dollars of public investment in research, as well as nearly ten billion dollars in subscription fees, is not a subsidy, but some kind of publisher birthright.

It is one thing when a blogger – even a prominent and institutionally sanctioned one – has these points of view. It is another when they are held by someone who is the chief publishing executive of the largest and most powerful scientific society in the world. In his new role, Anderson will not only set publishing policies at influential journals, he will be seen – and I’m sure present himself – as the publishing representative of the scientific community to Congress and other policy makers.

I fear the affect this hire will have. I am disturbed that the AAAS board chose to ignore his views of science and science publishing – or worse chose him because of these views. However, I think we should give him a chance. He knows the industry well, and is undoubtedly qualified for the position. And for all of his bluster about open access, he doesn’t seem to be stuck entirely in the past. I hope that he views his new position not as a bigger and better platform from which to promote his previously expressed views, but as an opportunity to actually represent the scientists of America, and build a publishing system that truly serves their interests, and not those of the AAAS or any other publisher.

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Yoshiki Sasai and the deadly consequences of science misconduct witchhunts

People who know me or read my blog will know that, in 1987, my father, a scientist at the NIH, killed himself after a member of his lab committed scientific fraud and he got caught up in the investigation. So I found the news this morning that Yoshiki Sasai, a Japanese stem cell scientist, committed suicide in the wake of the STAP controversy disturbing.

I don’t know all of the details, but the parallels between the two cases are haunting. As was the case with my father, it does not seem like anyone thinks Sasai was involved in the fraud. But as the senior scientists involved, both Sasai and my father bore the brunt of the institutional criticism, and both seem to have been far more disturbed by it than the people who actually committed the fraud.

It is impossible to know why they both responded to situations where they apparently did nothing wrong by killing themselves. But it is hard for me not to place at least part of the blame on the way the scientific community responds to scientific misconduct.

Obviously, fraud is a terrible thing. Nothing provides as deep an existential threat to the scientific enterprise than making up data. But as bad as it is, there is something deeply ugly about the way the scientific community responds to misconduct. We need to deal swiftly with fraud when it is identified. But time after time I have watched the way not only the accused, but everyone around them, is treated with such sanctimonious disdain it is frankly not surprising that some of them respond in tragic ways.

Imagine what it must be like to have devoted your life to science, and then to discover that someone in your midst – someone you have some role in supervising – has committed the ultimate scientific sin. That in and of itself must be disturbing enough. Indeed I remember how upset my father was as he was trying to prove that fraud had taken place. But then imagine what it must feel like to all of a sudden become the focal point for scrutiny – to experience your colleagues and your field casting you aside. It must feel like your whole world is collapsing around you, and not everybody has the mental strength to deal with that.

Of course everyone will point out that Sasai was overreacting – just as they did with my father. Neither was accused of anything. But that is bullshit. We DO act like everyone involved in cases of fraud is responsible. We do this because when fraud happens, we want it to be a singularity. We are all so confident this could never happen to us, that it must be that somebody in a position of power was lax – the environment was flawed. It is there in the institutional response. And it is there in the whispers – I still remember how the faculty in my graduate department talked about David Baltimore during the Imanishi-Kari incident.

Given the horrible incentive structure we have in science today – Haruko Obokata knew that a splashy result would get a Nature paper and make her famous and secure her career if only she got that one result showing that you could create stem cells by dipping normal cells in acid – it is somewhat of a miracle that more people don’t make up results on a routine basis. It is important that we identify, and come down hard, on people who cheat (although I wish this would include the far greater number of people who overhype their results – something that is ultimately more damaging than the small number of people who out and out commit fraud).

But the next time something like this happens, I am begging you to please be careful about how you respond. Recognize that, while invariably fraud involves a failure not just of honesty but of oversight, most of the people involved are honest, decent scientists, and that witch hunts meant to pretend that this kind of thing could not happen to all of us are not just gross and unseemly – they can, and sadly do, often kill.

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The DOE’s public access policy sells out the public

Yesterday the Department of Energy became one of the first federal agencies to announce its plan to comply with a 2013 White Houses directive ordering federal agencies to provide the public with access to the results of research that they fund.

Here are the main features:

  • DOE will host a centralized database of metadata (title, authors)
  • The full-text of the articles will be made available on publisher websites, primarily through their CHORUS system
  • Articles will be made available within 12 months of publication

Although it may not seem like it at first glance, this is a terrible turn for public access. Yes, this policy will make a good number of publications freely available, and that is a step forward. But the choice to go with the “link to publisher website” model being pushed by publishers, instead of the centralized database model already successfully used by the NIH, is a disaster.

Most importantly, the DOE has bought into the ridiculous notion that publishers should own the results of federally funded research, and that the interest of the publishers in maintaining control of the content they publish trumps the public interest in making this content freely available and free to use.

PAGES does not include, as far as I can tell, the ability to do full-text searches. Because access will be provided by publishers and not the DOE itself, the process of getting and reading articles will likely be cumbersome. But the clearest evidence that the DOE cares more about publishers than the public is found in their attitude towards bulk-downloading of the freely-available content (see page 6 of the formal policy announcement):

The distributed nature of PAGES’ full-text content inherently makes unauthorized mass downloading and redistribution more difficult. For the limited full-text content it hosts publicly, OSTI will enforce a download limit and post appropriate fair use policies.

Note that not only does this policy prevent the perfectly reasonable action of downloading and reusing content produced by US taxpayer dollars, the DOE is celebrating the fact that they have made this impossible. This is completely unacceptable.

By any reasonable standard the product of government-funded research should belong to the public. And indeed, it DOES belong to the public, until the moment that authors assign their copyright over to journals. All the DOE has to do is forbid their authors from assigning copyright to publishers and instead place them in the public domain. This would not only ensure public access, but would also enable researchers and companies access to the full contents to develop new and interesting ways to use the results of publicly-funded research.

That the DOE eschewed this path in favor of reifying publisher ownership and control of government-funded literature is unforgivable.

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On Nicholas Wade and the blurring of boundaries between science and fantasy

I just finished reading Nicholas Wade’s “A Troublesome Inheritance”, his latest effort to explain all of his personal racial prejudices in the light of recent human evolution. In this book he sets out to convince readers that many aspects of modern society – the English capacity for industrialization, Jewish intelligence, the inability to establish democratic institutions in the Middle East and Africa – have a strong genetic basis, the result of natural selection acting quickly to enshrine various aspects of culture in a people’s genetic makeup.

As many others have pointed out, the book is riddled with scientific and logical flaws, and the overall impression you get from Wade is not of a science journalist, but an unhinged racist who thinks his views are ok because he’s “telling it like it is”. And it is tempting to simply ignore him. But, unfortunately, I think this book needs to be dealt with seriously, because while this particular work may be dismissible, the line of reasoning it represents is both very dangerous, and here to stay.

The reason that this is issue is bigger than Wade’s book is that, while Wade’s representation of modern genetics is simplistic and selective, and he veers sharply into racist claptrap, the points that he is trying to emphasize about human evolution are, in broad strokes, right. Human genetic diversity does mirror geography, as does much phenotypic diversity. While random drift likely accounts for most of both genetic and phenotypic variation, natural selection clearly has shaped recent human evolution, and there is the potential for cultural forces to impact genetic variation over relatively short timeframes.

The problem is that – for the moment at least – that’s about all we can say. It turns out to be far easier to demonstrate that there has been a fair amount of recent natural selection acting on the human population, than it is to pinpoint specific examples, or to rigorously evaluate specific hypotheses. The reason is that different types of evolution (drift, positive selection, purifying selection) leave different fingerprints in the genome, and we can use these to estimate how prevalent each of these forces has been in human history, and, to a lesser extent, identify regions of the genome that have been subject to certain types of selection.

But the effect of specific examples of selection are almost always weak – especially the kinds of transient selection affecting relatively small groups of people on which Wade hangs his speculation. Furthermore, while natural selection leaves a signal behind in the genome, the signal is primarily that it happened – it’s much more difficult to precisely identify what was being selected, let alone why or how.

Knowing that natural selection has occurred, in some cases recently, but being unable to be more specific leaves a huge void – and it is into this void that Wade has inserted himself. He spends the first half of his book summarizing (albeit it inaccurately and incompletely) a decade of huge advances in human genomics, but then shifts abruptly from science to speculation.

In making the leap from the broad to the specific – from signature of natural selection in the human genome to explanations of the industrial revolution, Jewish Nobel Prizes and political turmoil in Africa and the Middle East – Wade tries to paint himself as a courageous scholar, going places with modern evolutionary biology that scientists WILL not go. But the truth is that scientists don’t go there, not because we are afraid to, but because we CAN’T. The data we have before us simply do not allow us to reconstruct human evolutionary history in this way.

In spending the first half of the book rooted firmly in modern evolutionary genetics, Wade is doing more than just trying to educate his readers. He is trying to give the ideas that he presents in the second half of the book the authority of science. This is crucial to his entire mission. What separates Wade’s theories – in his own mind – from those of a garden variety racist is that they are undergirded by genetics.

Wade weaves a bunch of yarns about how natural selection could have affected some phenotype using the language of modern genetics. But genetics is a science, not a series of fairy tales. Wade ignores the the fact that geneticists have developed a sophisticated set of approaches and tools designed specifically to answer the kind of questions he is raising – approaches and tools that have failed to uncover evidence for the kind of things Wade is trying to convince us must have been true. He can not have it both ways – he can not wear the mantle of a geneticist, but reject its precepts when they are inconvenient.

My concern about this runs deeper than annoyance at someone for failing to use the tools of my trade, or for cleaving to our authority. The scientific method arose as a way to understand the world because the kind of just-so storytelling that Wade is engaging in is useless. Is it a surprise that Wade just happens to find evolutionary explanations for the most pervasive racist attitudes of the day? Of course not. Because unmoored from data and logical rigor, one can make up an evolutionary explanation for anything.

I am an evolutionary biologist. I spend my days studying natural phenomenon and conceiving of possible explanations for why things are the way they are. But, unlike Wade, I know that, without evidence, these stories are bullshit. I could tell you stories all day about how microorganisms have evolved to manipulate the behavior of animals (one of the things my lab studies), but I don’t expect you to take them seriously until I demonstrate that they are true. Wade fails to recognize this. He seems to think that the science described in the first part of his book lends support to his theories. But in fact, it is categorically opposed to it.

This, to me, is the real danger of this work. By using the language of genetics to tell his stories, Wade is trying to obscure the distinction between science and storytelling. He is trying not just to make it ok to voice racist theories about the origins of human phenotypic variation, he is yearning to give them the validity of science. And he has to, because without the imprimatur of genetics, Wade’s stories really are nothing more than rewarmed racist rants.

But I fear that this distinction will be lost on many people. Genetics has a powerful hold on the public – they are fascinated by stories about how there’s a gene for this or that phenotype. And it terrifies me that more people will follow Wade’s lead and use the reality of genetic variation and natural selection in humans to justify to themselves and others whatever it is they want to believe about humanity (see an excellent warning about just this in a 2007 article by Amy Harmon).

This is why it is so important that scientists speak out about not just this book, but all of the related efforts now and in the future to distort science in this way. We are all used to fights with people who overtly reject science – creationists, climate change denialists, anti-vaccine wackaloons and GMO fearmongers. But here we are dealing with someone who is, on the surface at least, CELEBRATING science. But just as we speak out forcefully to explain what science does say (evolution and climate change are real, vaccines and GMOs are safe), we have to be equally forceful in communicating what science can not, or at least does not yet, say.

 

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Seeking a postdoctoral fellow hellbent on understanding how transcriptional enhancers work

Michael Eisen’s lab in the Department of Molecular and Cell Biology at The University of California Berkeley and the Howard Hughes Medical Institute is seeking a talented, ambitious and hard-driving postdoctoral fellow to work on one of the major unsolved problems in molecular biology: how the transcriptional enhancers that control pattern gene expression during animal development work. The postdoc will pursue this question using the early Drosophila embryo as a model, and will utilize cutting edge genomics, imaging and genome editing techniques along with advanced computation. The ideal candidate will have a PhD in molecular biology or similar field and have expertise in methods immediately related to the question at hand. Only scientists willing to publish all of their work in open access journals should apply. Please send CV and letters of recommendation to mbeisen+postdoc@gmail.com.

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Why I, a founder of PLOS, am forsaking open access

PLEASE NOTE BEFORE YOU READ THIS THAT IT WAS WRITTEN FOR APRIL FOOLS DAY!!!


I co-founded the Public Library of Science (PLOS) in 2002 because I believed deeply that the open access publishing model PLOS espoused and has come to dominate was good for science, scientists and the public.  Over the past decade open access has become a personal crusade – my own religion – one I have fervently promoted here on this blog, on social media, and to thousands of colleagues at meetings and social engagements. To back up my commitment to open access, since 2000, I have exclusively published papers from my lab in open access journals, and have urged – some might say hectored and harassed – my colleagues to do the same.

But in the last few weeks I have had a major change of heart. Yesterday at group meeting I told the members of my lab that they are free to send their papers to any journal they want to – including (and especially) the previously reviled especially Nature, Cell and Science. I am announcing this here today because I have been so publicly associated with open access, and I felt I owe my readers and the community an explanation for why I have made this dramatic change.

The most immediate reason is that, to be honest, I’m jealous. I just got back from the annual fly meeting in San Diego. Throughout the meeting – after talks, in the poster sessions and at the bar – people kept coming up to me and telling me how much they love our work, how they’re using our data, our methods or our ideas. But these words of praise rang hollow, lacking as they did that glint in the eye people get when they say “I really loved your Nature paper”.

It used to be cool to publish in PLOS. The small band of early open access adherents  – identifiable by our gaudily colored, slightly risqué  t-shirts (“Where would Jesus publish?”) – were everyone’s favorite rebels with a cause. Maybe people didn’t share our willingness to stand up to The Man. But they wished they did. And we had their respect.

But now those t-shirts are ratty, and PLOS has become The Man. Its reviews are slow. Its editorial decisions are capricious. And, frankly, nobody ever really cared about whether the public could read their papers anyway.

What people do care about is the cachet that comes from having an overworked editor at one of the big three journals decide that their paper is “The One”. I could see it in my students’ and postdocs’ eyes every time we passed by an adoring horde gathered round the latest winner of the great “Science, Nature and Cell” game, listening to them tell tales of how they worked the latest buzzwords into their abstract and buried all their confusing data in supplemental materials. Who am I to deny this joy to the young scientists who have entrusted their careers to me, just because I don’t think it’s “right”?

And who’s to say what’s right anyway. I’ve been going back over the last several years of posts from The Scholarly Kitchen. And when I listen to what they – especially Kent Anderson – say free of the haze of an open access zealot they start to make a lot of sense.

First of all, the whole idea that the public is clamoring for free access to the scientific literature is a pipe dream. Sure PubMed Central – the free database of papers produced with funding from the National Institutes of Health – gets over 1,000,000 hits a day. But do you really believe numbers from the government? After all, these are the same people who are saying that 7,000,000 people have signed up for Obamacare. The open access lobby can always dig up some people – cancer patients or something like that – who have benefited from open access. But we never hear about the people who’ve been hurt – like all the students at places like Harvard and Stanford who no longer have better access to the scientific literature than hoi poloi at lesser institutions.

And now that I’ve had a chance to think about it, it makes no sense to wrest the system of forging new scientists, making promotions and assigning tenure at institutions of higher learning away from the for-profit corporations that control it today. Who’s going to do it instead? Scientists???? Have you been to a faculty meeting? Or served on a study section? These kind of decisions are best left to people who are far removed from the messy details of the science and who care primarily about making money – only they can be truly objective.

I have come to appreciate the important role that prestigious journals like Science, Nature and Cell play in filtering out bad science, and protecting both the public and other researchers from wasting their time reading about – or following up on – results that are not believable. You have all, undoubtedly heard about recent studies examining the reproducibility of scientific results. For example, a recent Nature paper [paywalled, so you can believe it] described how scientists at drug company Amgen were able to successfully replicate six of 53 landmark studies in cancer research.

As these were landmark studies, most were published in the highest profile subscription journals. And these results prove that – contrary to what I would have expected – the top subscription journals doing a great job of picking papers. First, Amgen, who doesn’t like to waste their money, found 53 of these studies important enough to try to replicate. I don’t think they’ve bothered to try even a dozen PLOS ONE papers. But more amazingly these scientists at Amgen were able to get the same results as important academic scientists OVER ten percent of the time. This means that the papers must have described the methods extremely clearly – a hallmark of high profile journals.

Finally, there’s the issue of money. Funding agencies and universities across the world spend over $10,000,000,000 a year subscribing to research journals in science, technology and medicine that publish, collectively, about 1,500,000 articles (or around $6,500 per article). We all know that the point of economies is to expand, and journal  publishing has been doing its part, with costs increases exceeding inflation (meaning it is growing fast!) every year for the past few decades. But imagine what will happen if we switch to universal open access as I have been advocating. Everyone agrees that open access journals charge scientists a lot less than $6,500 to publish their papers. So, if we start publishing more open access papers, we’ll be spending less money (a LOT less if publishers like PeerJ get their way) for every article, and therefore LESS money on publishing. This is called contraction, and it’s what caused the Great Depression.

This is why I now strongly support CHORUS – the publisher’s answer to calls from Congress and The President to provide better public access to government funded research. CHORUS will provide people with access to papers after a delay – timed to ensure that no subscription revenues will be lost. Thus for the entire period of time when articles are actually useful to people they will be behind a paywall where they can generate money for the economy. This makes sense, whereas using “open access” publishing to make these articles immediately freely available to everyone at a lower cost clearly does not.

I have a lot to answer for. I want to apologize to all the people who have followed me into the abyss of open access. All I can say is that I meant well, and that I hope you will forgive me for the joy I have taken out of your lives and for the broken dreams of the career you could have had if you’d only published your postdoc paper in Cell.

Posted in My lab, open access, PLoS, public access | Comments closed

FIRST of all, THIS is why you should never trust publishers

When President Obama announced last year that he was requiring federal agencies that fund science to develop policies to make papers arising from the work they publish freely available to the public, major subscription-based publishers responded in a generally favorable manner – reflecting the extent to which they had drawn the White House back from more aggressive proposals on the table. They even put forth a proposal – called CHORUS (Clearinghouse for the Open Research of the United States) through which they offered to implement  these public access policies for federal agencies – providing free access to articles on their own websites.

wrote at the time about why CHORUS was a ruse, that would never work. In particular, I warned that, despite their public veneer of support, publishers would continue to work to reverse these public access policies, and, because with CHORUS they would never have to give up control of published papers, they could just turn off public access if they ever succeeded.

Well, they’re trying to do just this. Last week a bill was introduced – The Frontiers in Innovation, Research, Science and Technology (FIRST) Act of 2014 – a section of which (Section 303) is designed to undermine this already fairly weak policy. The language is a bit dense and confusing, but here is what it would do.

  • The surest way to kill a policy initiative in DC is to call for more study. FIRST calls for 18 additional months of study of public access policies, specifically calling for “data-driven” justification for embargo periods. This is language publishers have used before and is code for “set embargo periods so that they do not harm the bottom line of publishers”.
  • It calls for the use of existing infrastructure, including the NLM, but also in the private sector, and minimizing the burden of providing access – things that the publishers use to promote CHORUS
  • It weakens the embargo period to 24 months from its already unacceptably long 12 months, and allows for agencies to EXTEND this period for up to an additional year

I don’t have direct evidence that publishers are behind this, but it echoes all the main talking points they’ve been using to complain about public access. It’s not clear how far this will go, since this is just the House version of the bill, and the Senate version has not emerged. But it’s worth using the tools available through SPARC to voice your opposition to this bill.

Posted in open access, politics, public access | Comments closed