Scientists are talking, but mostly to each other: a quantitative analysis of research

[Stavros]

Elsevier = Evil

Elsevier = Evil

Posted on: January 16, 2012 12:45 PM, by PZ Myers

Along with SOPA and PIPA, our government is contemplating another acronym with deplorable consequences for the free dissemination of information: RWA, the Research Works Act. This is a bill to, it says, "ensure the continued publication and integrity of peer-reviewed research works by the private sector", where the important phrase is "private sector" — it's purpose is to guarantee that for-profit corporations retain control over the publication of scientific information. Here are the restrictions it would impose:

No Federal agency may adopt, implement, maintain, continue, or otherwise engage in any policy, program, or other activity that--

(1) causes, permits, or authorizes network dissemination of any private-sector research work without the prior consent of the publisher of such work; or

(2) requires that any actual or prospective author, or the employer of such an actual or prospective author, assent to network dissemination of a private-sector research work.

This is a blatant attempt to invalidate the NIH's requirement that taxpayer-funded research be made publicly available. The internet was initially developed to allow researchers to easily share information…and that's precisely the function this bill is intended to cripple.

Who could possibly support such a bill? Not the scientists, that's for sure; and definitely not the public, unless we keep them as ignorant as possible. The corporations who love this bill are the commercial publishers who profit mightily from scientists' work. And first among these is Elsevier, the gouging publisher scientists love to hate.

If passed, the Research Works Act (RWA) would prohibit the NIH's public access policy and anything similar enacted by other federal agencies, locking publicly funded research behind paywalls. The result would be an ethical disaster: preventable deaths in developing countries, and an incalculable loss for science in the USA and worldwide. The only winners would be publishing corporations such as Elsevier (£724m profits on revenues of £2b in 2010 - an astounding 36% of revenue taken as profit).

Since Elsevier's obscene additional profits would be drained from America to the company's base in the Netherlands if this bill were enacted, what kind of American politician would support it? The RWA is co-sponsored by Darrell Issa (Republican, California) and Carolyn B. Maloney (Democrat, New York). In the 2012 election cycle, Elsevier and its senior executives made 31 donations to representatives: of these, two went to Issa and 12 to Maloney, including the largest individual contribution.

So Elsevier bought a couple of politicians to get their way. It's typical unscrupulous behavior from this company; at least they stopped organizing arms trade fairs a few years ago, so we know their evil can be checked by sufficiently loud public opinion.

Tell your representatives to kill RWA. It's another bill to benefit corporations that will harm science.

 

[Stavros]

Cracking Open the Scientific Process

Cracking Open the Scientific Process

Timothy Fadek for The New York Times
A GLOBAL FORUM Ijad Madisch, 31, a virologist and computer scientist, founded ResearchGate, a Berlin-based social networking platform for scientists that has more than 1.3 million members.

By THOMAS LIN

Published: January 16, 2012

The New England Journal of Medicine marks its 200th anniversary this year with a timeline celebrating the scientific advances first described in its pages: the stethoscope (1816), the use of ether for anesthesia (1846), and disinfecting hands and instruments before surgery (1867), among others.

For centuries, this is how science has operated — through research done in private, then submitted to science and medical journals to be reviewed by peers and published for the benefit of other researchers and the public at large. But to many scientists, the longevity of that process is nothing to celebrate.
The system is hidebound, expensive and elitist, they say. Peer review can take months, journal subscriptions can be prohibitively costly, and a handful of gatekeepers limit the flow of information. It is an ideal system for sharing knowledge, said the quantum physicist Michael Nielsen, only “if you’re stuck with 17th-century technology.”

Dr. Nielsen and other advocates for “open science” say science can accomplish much more, much faster, in an environment of friction-free collaboration over the Internet. And despite a host of obstacles, including the skepticism of many established scientists, their ideas are gaining traction.

Open-access archives and journals like arXiv and the Public Library of Science (PLoS) have sprung up in recent years. GalaxyZoo, a citizen-science site, has classified millions of objects in space, discovering characteristics that have led to a raft of scientific papers.

On the collaborative blog MathOverflow, mathematicians earn reputation points for contributing to solutions; in another math experiment dubbed the Polymath Project, mathematicians commenting on the Fields medalist Timothy Gower’s blog in 2009 found a new proof for a particularly complicated theorem in just six weeks.
And a social networking site called ResearchGate — where scientists can answer one another’s questions, share papers and find collaborators — is rapidly gaining popularity.

Editors of traditional journals say open science sounds good, in theory. In practice, “the scientific community itself is quite conservative,” said Maxine Clarke, executive editor of the commercial journal Nature, who added that the traditional published paper is still viewed as “a unit to award grants or assess jobs and tenure.”

Dr. Nielsen, 38, who left a successful science career to write “Reinventing Discovery: The New Era of Networked Science,” agreed that scientists have been “very inhibited and slow to adopt a lot of online tools.” But he added that open science was coalescing into “a bit of a movement.”
On Thursday, 450 bloggers, journalists, students, scientists, librarians and programmers will converge on North Carolina State University (and thousands more will join in online) for the sixth annual ScienceOnline conference. Science is moving to a collaborative model, said Bora Zivkovic, a chronobiology blogger who is a founder of the conference, “because it works better in the current ecosystem, in the Web-connected world.”

Indeed, he said, scientists who attend the conference should not be seen as competing with one another. “Lindsay Lohan is our competitor,” he continued. “We have to get her off the screen and get science there instead.”

Facebook for Scientists?
“I want to make science more open. I want to change this,” said Ijad Madisch, 31, the Harvard-trained virologist and computer scientist behind ResearchGate, the social networking site for scientists.
Started in 2008 with few features, it was reshaped with feedback from scientists. Its membership has mushroomed to more than 1.3 million, Dr. Madisch said, and it has attracted several million dollars in venture capital from some of the original investors of Twitter, eBay and Facebook.

A year ago, ResearchGate had 12 employees. Now it has 70 and is hiring. The company, based in Berlin, is modeled after Silicon Valley startups. Lunch, drinks and fruit are free, and every employee owns part of the company.

The Web site is a sort of mash-up of Facebook, Twitter and LinkedIn, with profile pages, comments, groups, job listings, and “like” and “follow” buttons (but without baby photos, cat videos and thinly veiled self-praise). Only scientists are invited to pose and answer questions — a rule that should not be hard to enforce, with discussion threads about topics like polymerase chain reactions that only a scientist could love.

Scientists populate their ResearchGate profiles with their real names, professional details and publications — data that the site uses to suggest connections with other members. Users can create public or private discussion groups, and share papers and lecture materials. ResearchGate is also developing a “reputation score” to reward members for online contributions.
ResearchGate offers a simple yet effective end run around restrictive journal access with its “self-archiving repository.” Since most journals allow scientists to link to their submitted papers on their own Web sites, Dr. Madisch encourages his users to do so on their ResearchGate profiles. In addition to housing 350,000 papers (and counting), the platform provides a way to search 40 million abstracts and papers from other science databases.

In 2011, ResearchGate reports, 1,620,849 connections were made, 12,342 questions answered and 842,179 publications shared. Greg Phelan, chairman of the chemistry department at the State University of New York, Cortland, used it to find new collaborators, get expert advice and read journal articles not available through his small university. Now he spends up to two hours a day, five days a week, on the site.
Dr. Rajiv Gupta, a radiology instructor who supervised Dr. Madisch at Harvard and was one of ResearchGate’s first investors, called it “a great site for serious research and research collaboration,” adding that he hoped it would never be contaminated “with pop culture and chit-chat.”
Dr. Gupta called Dr. Madisch the “quintessential networking guy — if there’s a Bill Clinton of the science world, it would be him.”

The Paper Trade
Dr. Sönke H. Bartling, a researcher at the German Cancer Research Center who is editing a book on “Science 2.0,” wrote that for scientists to move away from what is currently “a highly integrated and controlled process,” a new system for assessing the value of research is needed. If open access is to be achieved through blogs, what good is it, he asked, “if one does not get reputation and money from them?”
Changing the status quo — opening data, papers, research ideas and partial solutions to anyone and everyone — is still far more idea than reality. As the established journals argue, they provide a critical service that does not come cheap.

“I would love for it to be free,” said Alan Leshner, executive publisher of the journal Science, but “we have to cover the costs.” Those costs hover around $40 million a year to produce his nonprofit flagship journal, with its more than 25 editors and writers, sales and production staff, and offices in North America, Europe and Asia, not to mention print and distribution expenses. (Like other media organizations, Science has responded to the decline in advertising revenue by enhancing its Web offerings, and most of its growth comes from online subscriptions.)

Similarly, Nature employs a large editorial staff to manage the peer-review process and to select and polish “startling and new” papers for publication, said Dr. Clarke, its editor. And it costs money to screen for plagiarism and spot-check data “to make sure they haven’t been manipulated.”

Peer-reviewed open-access journals, like Nature Communications and PLoS One, charge their authors publication fees — $5,000 and $1,350, respectively — to defray their more modest expenses.

The largest journal publisher, Elsevier, whose products include The Lancet, Cell and the subscription-based online archive ScienceDirect, has drawn considerable criticism from open-access advocates and librarians, who are especially incensed by its support for the Research Works Act, introduced in Congress last month, which seeks to protect publishers’ rights by effectively restricting access to research papers and data.
In an Op-Ed article in The New York Times last week, Michael B. Eisen, a molecular biologist at the University of California, Berkeley, and a founder of the Public Library of Science, wrote that if the bill passes, “taxpayers who already paid for the research would have to pay again to read the results.”
In an e-mail interview, Alicia Wise, director of universal access at Elsevier, wrote that “professional curation and preservation of data is, like professional publishing, neither easy nor inexpensive.” And Tom Reller, a spokesman for Elsevier, commented on Dr. Eisen’s blog, “Government mandates that require private-sector information products to be made freely available undermine the industry’s ability to recoup these investments.”

Mr. Zivkovic, the ScienceOnline co-founder and a blog editor for Scientific American, which is owned by Nature, was somewhat sympathetic to the big journals’ plight. “They have shareholders,” he said. “They have to move the ship slowly.”

Still, he added: “Nature is not digging in. They know it’s happening. They’re preparing for it.”

Science 2.0
Scott Aaronson, a quantum computing theorist at the Massachusetts Institute of Technology, has refused to conduct peer review for or submit papers to commercial journals. “I got tired of giving free labor,” he said, to “these very rich for-profit companies.”

Dr. Aaronson is also an active member of online science communities like MathOverflow, where he has earned enough reputation points to edit others’ posts. “We’re not talking about new technologies that have to be invented,” he said. “Things are moving in that direction. Journals seem noticeably less important than 10 years ago.”

Dr. Leshner, the publisher of Science, agrees that things are moving. “Will the model of science magazines be the same 10 years from now? I highly doubt it,” he said. “I believe in evolution.

“When a better system comes into being that has quality and trustability, it will happen. That’s how science progresses, by doing scientific experiments. We should be doing that with scientific publishing as well.”
Matt Cohler, the former vice president of product management at Facebook who now represents Benchmark Capital on ResearchGate’s board, sees a vast untapped market in online science.

“It’s one of the last areas on the Internet where there really isn’t anything yet that addresses core needs for this group of people,” he said, adding that “trillions” are spent each year on global scientific research. Investors are betting that a successful site catering to scientists could shave at least a sliver off that enormous pie.

Dr. Madisch, of ResearchGate, acknowledged that he might never reach many of the established scientists for whom social networking can seem like a foreign language or a waste of time. But wait, he said, until younger scientists weaned on social media and open-source collaboration start running their own labs.
“If you said years ago, ‘One day you will be on Facebook sharing all your photos and personal information with people,’ they wouldn’t believe you,” he said. “We’re just at the beginning. The change is coming.”

A version of this article appeared in print on January 17, 2012, on page D1 of the New York edition with the headline: Cracking Open the Scientific Process.

 

[DWhatley]

Open source in action

This was from an Octobot post entitled Science copies how squid change color (colour since is a BBC video ) but the scientists are primarily promoting the speed the internet and tools have added and the open source that will allow ease of access to their new findings. Very cool!

 

[DWhatley]

... and still not open enough to each other

Another octobot post from Science 2.0 blog's Squid A Day, this one entitled Neurotoxins In Stranded Squid (With Bonus Rant About Academic Publishing) calling for more "to each other" communication

This is why we in the life sciences (and all the rest of science) really need to get on board with arXiv or something like it. If we were posting pre-prints of our work, we would be connected. We each would have been able to cite the other group's article, and write more comprehensive dicussions. We could even have improved each other's work--Group #1 might have been inspired to look at PST, and Group #2 to look at plankton blooms in the water.

I hope in a few years we'll look back on this as the Time for opening science . . .

 

[Architeuthoceras]

Through venues such as the "Present and Past Symposium" held every four years, fossil cephalopod workers, for the most part, all know what the others are working on. I know my work has been enhanced because I attended the last one. TONMO could also be a good venue for collaboration if we could only get more scientists to join up, and share their work...

 

[Stavros]

Another octobot post from Science 2.0 blog's Squid A Day, this one entitled Neurotoxins In Stranded Squid (With Bonus Rant About Academic Publishing) calling for more "to each other" communication

Through venues such as the "Present and Past Symposium" held every four years, fossil cephalopod workers, for the most part, all know what the others are working on. I know my work has been enhanced because I attended the last one. TONMO could also be a good venue for collaboration if we could only get more scientists to join up, and share their work...

This point of 'doing' science definitely deserves a thread of its own. Unfortunately, most grad programs do not teach us on how to form collaborations and more often than not, a student strives to become a 'one-man-show' rather than a collaborator outside his/her lab. Different folks may have different reasons for deciding to go solo- pride and inability to trust others have a lot to do with it, as well as the false romantic belief of a lone, silent researcher succeeding against all odds and with no help from the gods.

However, the main reason for this is the fact that science is highly competitive and it feels, therefore, more natural for one not to share results, or for early-career researchers to wait until they are able to publish results before coming in the open to establish their presence. At the end of the day though, science is social and depends on clear communication and community collaboration. Collaboration slices down the time it takes for a project to get done (resources, equipment, skill set and so on), and that means more projects at the end of the day. And it's more fun this way. The learning that takes place in settings like this, working with new people and sometimes from different fields, is unparalleled and definitely not matched by a lone worker. Lastly, the other extreme is when there are a lot of roosters and only one dawn, meaning that for the sake of doing team-work, people are put on a project that requires one person only and that can be costly as well.

 

[Stavros]

Comfort is the death knell of academia: why I’m standing down as a journal referee

Been busy the last 3 weeks, here are some of the articles written since.

Comfort is the death knell of academia: why I’m standing down as a journal referee

Concerned that his field is completely beholden to closed access publishers, Matthew Todd calls an end to his time as a referee and author for Elsevier journals and joins over 2,500 academics who have signed an online petition in an effort to push for open access publishing and the transformative benefits that they see lying behind the ability to tinker, re-mix and play with open data.

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Academics to boycott Elsevier journals

Thousands to refuse work related to publisher over profit-making tactics

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Elsevier — my part in its downfall

Timothy Gowers, professor of mathematics at Cambridge, has suggested that mathematicians should boycott leading journals published by Elsevier.

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The Cost of Knowledge

The key to all these issues is the right of authors to achieve easily-accessible distribution of their work. If you would like to declare publicly that you will not support any Elsevier journal unless they radically change how they operate, then you can do so by filling in your details in the box below.

 

[Stavros]

Academic publisher Elsevier hit with growing boycott

Not sure how much change this will bring to the status quo, but it surely is an exciting time in academia...



Critics say campaign unfairly singles out firm over widespread practices
Australian Broadcasting Corporation
Posted: Feb 17, 2012 9:54 AM ET
Last Updated: Feb 17, 2012 11:23 AM ET

Dutch-based Elsevier publishes 250,000 articles a year and its archives contain seven million publications.

To publish or not to publish? That is the question medical and science academics are asking after 6,000 of their colleagues boycotted one of the world's largest publishers.

The "Cost of Knowledge" campaign was started by an international group of researchers in January after a blog post by Cambridge University math professor Timothy Gowers. He criticized the Dutch-based publisher Elsevier for charging "very high prices" for access to its articles, using a "ruthless" approach to negotiations with academic libraries and supporting legislation that could hamper the move to more open access to published research.

Since then, thousands of researchers around the world, including several university and government researchers in Canada, have publicly committed to the protest by declaring they will not publish in Elsevier journals, peer review papers for those journals, or do editing work for them.

But others say they don't know what all the fuss is about.

Elsevier publishes 250,000 articles a year and its archives contain seven million publications.

This week a number of Australian academics joined a global protest against the scholarly publishing powerhouse.

"The boycott is saying we are no longer going to provide our services to you for free. We are no longer going to write articles and submit them to your journals, and we are no longer going to review for your journals," says Danny Kingsley an expert in scholarly communication at the Australian National University's Centre for the Public Awareness of Science.

The petition's signatories have two complaints: the publisher is charging excessively for its journals, and is pushing to stop free access to taxpayer funded research.

"Well for a start it's just a moral issue that money that [the scienstists are] spending in taxes is having to be double-dipped to prop up a publishing industry which is making extraordinary profits in times where other industries are falling down completely," says Kingsley.

"The feeling has been for some time that the research itself has been paid for by the public purse and the peer-review process and often the editorial process is also being paid for by the public purse in the form of academic salaries; and then the public purse has to again pay to get subscriptions to the work."

In 2010, Elsevier made $1.6 billion for an operating profit margin of 36 per cent.

Andrew Wells from the Council of University Librarians believes Elsevier is being unfairly singled out.

"The practices that Elsevier has both in dealing with authors and in selling scholarly content to libraries are very similar to those used by many other scholarly publishers such as Wiley-Blackwell and Taylor & Francis and Springer," he says.

"The real issue here is how the whole scholarly publishing system works and certainly that's a good topic for authors."
Blocking pre-publication

Academics often submit an original research paper to their university before it goes to peer review and is published. University websites typically make these available to the public for free.

Elsevier wants to change that arrangement and has thrown its support behind three bills currently before the US Congress. They could, among other things, prevent universities from holding pre-publication versions of research papers.

It means Australian academics will have to pay to access research that's already been paid for.

Gavin Moodie, the principal policy advisor at RMIT University in Melbourne added his name to the boycott.

"But it has been stronger in its opposition to digital publishing rights and its attempt to close down websites which it claims infringes copyright. I think that's the main distinction from the other big publishers and that's mainly why I signed the petition," says Moodie.
Research at stake

Kingsley says researchers depends on funding from two sources; through block funding to university and grants funding.

"A large portion of what your grant relies on is your track record of publication," she says. "So publication is central, not just to actually having research continue, in that you can read what other people have done and continue with that, but also it's central to your career in terms of being able to have some money so that you can do your research."

Some Australian research bodies such as the National Health and Medical Research Council will change their funding model later this year. They'll mandate that any work they contribute to must be available to the public for free.

With files from CBC News
© Australian Broadcasting Corporation, 2012

 

[OB]

Every single scientist looking for open access publication of their paper is free to submit to PLoS One, if they wish. The reason why they often don't, is that open access publishing requires authors to pay for publication, rather than their institutional libraries for access (subscription). That, combined with the outdated notion of using the Impact Factors of journals published in (to see how well Academic groups are performing), will mean we have quite a bit of road, still ahead.

You can not have a free system, where both the author as well as the reader get to publish and access for free, respectively. The taxmoney spent on research is gone, and unless we wish to cannibalize some of that to pay for the publication and dissemination of the acquired knowledge, someone will always have to pick up the tab.

The much more fundamental discussion is why we as societies spend trillions of Euros and US dollars annually on pointless ads, sales and marketing activities, unnessesary consumer goods, company restructurings, bloody wars in far away places and then some, when we could be spending a tiny fraction of that on science and technology and VASTLY improve our outlook within 4 to 5 generations.... Why aren't we on Mars, yet? Why does the majority of people think the latter to be a nonsensical question? Think about it.

 

[Stavros]

Thanks for clarifying OB. I'm sure it's going to take time for things to shift, especially to get public's interest on it.

What part of the process of publishing a journal is more costly? Paying the staff or paying the printer? I guess a solution would be to only have PDFs to save the printer costs, but I'm sure there are multiple reasons why it has not been applied yet.

I'm just glad that some are willing to fight this fight for the rest of us in academia- it's not worth going against the system all the time.

 

[Stavros]

Tim Gowers' reply to Elsevier's open letter.

From Tim Gowers' blog

Elsevier’s open letter point by point, and some further arguments
February 26, 2012

I’ve had this post sitting around half written for a long time, so I’ve decided to post it without saying everything I wanted to say and have done with it. Even the things I do say are not as organized as I’d normally like.

In response to the recent boycott and the discussion it has generated, Elsevier has put out an open letter entitled A message to the research community: journal prices, discounts and access. It was more or less guaranteed that I would not be satisfied by what they had to say, since my view is that the entire system of commercial publishing of academic papers needs to be replaced, whereas Elsevier was almost certain to be arguing from within the current system. When a paradigm shift takes place, one does not expect the main players to remain the same.

Nevertheless, it seems only fair to make some attempt to respond to the points Elsevier has to make, rather than simply saying that there is nothing they can do, or at least nothing they can do that they would be likely to be prepared to do. So let me explain why I find their open letter unsatisfactory even on their own terms (that is, even if we make the assumption that what is needed is more like an adjustment to the current system than a replacement of it). The letter starts with some statements of the kind one might expect, about how their mission is to serve the research community and so on. The substantive part of their letter is then divided into bullet points, where they claim to correct the distortions that have been advanced. I’ll look at each of those in turn.

Read the rest of this entry »

 

[OB]

I would say the most costly aspect of it all is keeping a system alive which allows for access ad infinitum. In the old universe of print, you'd archive in a library/depository, in pdf or hypertext you'll need to keep verything intact and available for continuous access, linking and future reference... And then, back in my days a s science publisher, there was my expense account

 

[Architeuthoceras]

Between a rock and a hard place

 

[Architeuthoceras]

What is the world coming to?

Solid Earth; An Interactive Open Access Journal of the European Geosciences Union

Open Access – Public Peer-Review & Interactive Public Discussion

 

[DWhatley]

It looks like someone put a lot of effort into a best of class attempt (why only solid earth though?) format. If qualified people participate, it could be a great template for additional topics.