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martes, 4 de marzo de 2014

How Academia and Publishing are Destroying Scientific Innovation: A Conversation with Sydney Brenner


The LMB Governing Board, October 1967. Left to right: Hugh Huxley, John Kendrew, Max Perutz, Francis Crick, Fred Sanger, Sydney Brenner. (From the website of the MRC Laboratory of Molecular Biology)


I recently had the privilege of speaking with Professor Sydney Brenner, a professor of Genetic medicine at the University of Cambridge and Nobel Laureate in Physiology or Medicine in 2002. I had originally intended to ask him about Professor Frederick Sanger, the two-time Nobel Prize winner famous for his discovery of the structure of proteins and his development of DNA sequencing methods, who passed away in November. I wanted to do the classic tribute by exploring his scientific contributions and getting a first hand account of what it was like to work with him at Cambridge’s Medical Research Council’s (MRC) Laboratory for Molecular Biology (LMB) and at King’s College where they were both fellows. What transpired instead was a fascinating account of the LMB’s quest to unlock the genetic code and a critical commentary on why our current scientific research environment makes this kind of breakthrough unlikely today.

http://www2.mrc-lmb.cam.ac.uk/wordpress/wp-content/uploads/newlmbslide1.jpg
LMB at Cambridge. Original LMB

It is difficult to exaggerate the significance of Professor Brenner and his colleagues’ contributions to biology. Brenner won the Nobel Prize for establishing Caenorhabditis elegans, a type of roundworm, as the model organism for cellular and developmental biological research, which led to discoveries in organ development and programmed cell death. He made his breakthroughs at the LMB, where beginning in the 1950s, an extraordinary number of successive innovations elucidated our understanding of the genetic code. This code is the process by which cells in our body translate information stored in our DNA into proteins, vital molecules important to the structure and functioning of cells. It was here that James Watson and Francis Crick discovered the double-helical structure of DNA. Brenner was one of the first scientists to see this ground-breaking model, driving from Oxford, where he was working at the time in the Department of Chemistry, to Cambridge to witness this breakthrough. This young group of scientists, considered renegades at the time, made a series of successive revolutionary discoveries that ultimately led to the creation of a new field called molecular biology.

To begin our interview, I asked Professor Brenner to speak about Professor Sanger and what led him to his Nobel Prize winning discoveries.

Sydney Brenner: Fred realized very early on that if we could sequence DNA, we would have direct contact with the genes. The problem was that you couldn’t get hold of genes in any way. You couldn’t purify what was a gene. That is why right from the start in 1954, we decided we would do this by using Fred’s method of sequencing proteins, which he had achieved [proteins are derived from the information held in DNA]. You have to realise it was only on a small scale. I think there were only forty-five amino acids [the building blocks of proteins] that were in insulin. We thought even scaling that up for proteins would be difficult. But finally DNA sequencing was invented. Then it became clear that we could directly approach the gene, and it produced a completely new period in science.

He was interested in the method and interested in getting the methods to work. I was really clear in my own mind that what he did in DNA sequencing, even at the time, would cause a revolution in the subject, which it did. And of course we immediately, as fast as possible, began to use these methods in our own research.

ED: This foundational research ushered in a new era of biological science. It has formed the basis of nearly all subsequent discoveries in the field, from understanding the mechanisms of diseases, to the development of new drugs for diseases such as cancer. Imagining the creative energy that drove these discoveries was truly inspirational. I asked Professor Brenner what it felt like to be part of this scientific adventure.

SB: I think it’s really hard to communicate that because I lived through the entire period from its very beginning, and it took on different forms as matters progressed. So it was, of course, wonderful. That’s what I tell students. The way to succeed is to get born at the right time and in the right place. If you can do that then you are bound to succeed. You have to be receptive and have some talent as well.

ED: Today, the structure of DNA and how genetic information is translated into proteins are established scientific canon. Brenner joked that he “knew that molecular biology was doomed to success when [he] heard two students speaking in a bus once and asking whether they would get the genetic code in the examination. It had become an academic subject.” But in the 1950s, the hypotheses generated at the LMB were dismissed as inconceivable nonsense.

SB: To have seen the development of a subject, which was looked upon with disdain by the establishment from the very start, actually become the basis of our whole approach to biology today. That is something that was worth living for.

I remember Francis Crick gave a lecture in 1958, in which he discussed the adapter hypothesis at the time. He proposed that there were twenty enzymes, which linked amino acids to twenty different molecules of RNA, which we call adapters. It was these adapters that lined up the amino acids. The adapter hypothesis was conceived I think as early as 1954 and of course it was to explain these two languages: 
DNA, the language of information, and 
proteins, the language of work.

Of course that was a paradox, because how did you get one without the other? That was solved by discovering that a molecule from RNA could actually have function. So this information on RNA, which happened much later really, solved that problem as far as origins were concerned.

ED: (Professor Brenner was far too modest here, as it was he who discovered RNA’s critical role in this translation from gene to protein.)

SB: So he [Crick] gave the lecture and biochemists stood up in the audience and said this is completely ridiculous, because if there were twenty enzymes, we biochemists would have already discovered them. To them, the fact that they still hadn’t went to show that this was nonsense. Little did the man know that at that very moment scientists were in the process of finding the very first of these enzymes, which today we know are the enzymes that combined amino acids with transfer RNA. And so you really had to say that the message kept its purity all the way through.

What people don’t realise is that at the beginning, it was just a handful of people who saw the light, if I can put it that way. So it was like belonging to an evangelical sect, because there were so few of us, and all the others sort of thought that there was something wrong with us.

They weren’t willing to believe. Of course they just said, well, what you’re trying to do is impossible. That’s what they said about crystallography of large molecules. They just said it’s hopeless. It’s a hopeless task. And so what we were trying to do with the chemistry of proteins and nucleic acids looked hopeless for a long time. Partly because they didn’t understand how they were built, which I think we molecular biologists had the first insight into, and partly because they just thought they were amorphous blobs and would never be able to be analysed.

I remember when going to London to talk at meetings, people used to ask me what am I going to do in London, and I used to tell them I’m going to preach to the heathens. We viewed most of everybody else as not doing the right science. Like one says, the young Turks will become old Greeks. That’s the trouble with life. I think molecular biology was marvellous because every time you thought it was over and it was just going to be boring, something new happened. It was happening every day.

So I don’t know if you can ride on the crest of a wave; you can ride on it, I believe, forever. I think that being in science is the most incredible experience to have, and I now spend quite a lot of my time trying to help the younger people in science to enjoy it and not to feel that they are part of some gigantic machine, which a lot of people feel today.

ED: I asked him what inspired them to maintain their faith and pursue these revolutionary ideas in the face of such doubt and opposition.

SB: Once you saw the light you were just certain that you had to be right, that it was the right way to do it and the right answer. And of course our faith, if you like, has been borne out.

I think it would have been difficult to keep going without the strong support we had from the Medical Research Council. I think they took a big gamble when they founded that little unit in the Cavendish. I think all the early people they had were amazing. There were amazing personalities amongst them.

This was not your usual university department, but a rather flamboyant and very exceptional group that was meant to get together. An important thing for us was that with the changes in America then, from the late fifties almost to the present day, there was an enormous stream of talent and American postdoctoral fellows that came to our lab to work with us. But the important thing was that they went back. Many of them are now leaders of American molecular biology, who are alumni of the old MRC.

ED: The 1950s to 1960s at the LMB was a renaissance of biological discovery, when a group of young, intrepid scientists made fundamental advances that overturned conventional thinking. The atmosphere and camaraderie reminded me of another esteemed group of friends at King’s College – the Bloomsbury Group, whose members included Virginia Woolf, John Maynard Keynes, E.M. Forester, and many others. Coming from diverse intellectual backgrounds, these friends shared ideas and attitudes, which inspired their writing and research. Perhaps there was something about the nature of the Cambridge college systems that allowed for such revolutionary creativity?

SB: In most places in the world, you live your social life and your ordinary life in the lab. You don’t know anybody else. Sometimes you don’t even know other people in the same building, these things become so large.

The wonderful thing about the college system is that it’s broken up again into a whole different unit. And in these, you can meet and talk to, and be influenced by and influence people, not only from other scientific disciplines, but from other disciplines. So for me, and I think for many others as well, that was a really important part of intellectual life. That’s why I think people in the college have to work to keep that going.

Cambridge is still unique in that you can get a PhD in a field in which you have no undergraduate training. So I think that structure in Cambridge really needs to be retained, although I see so often that rules are being invented all the time. In America you’ve got to have credits from a large number of courses before you can do a PhD. That’s very good for training a very good average scientific work professional. But that training doesn’t allow people the kind of room to expand their own creativity. But expanding your own creativity doesn’t suit everybody. For the exceptional students, the ones who can and probably will make a mark, they will still need institutions free from regulation.

ED: I was excited to hear that we had a mutual appreciation of the college system, and its ability to inspire interdisciplinary work and research. Brenner himself was a biochemist also trained in medicine, and Sanger was a chemist who was more interested in chemistry than biology.

SB: I’m not sure whether Fred was really interested in the biological problems, but I think the methods he developed, he was interested in achieving the possibility of finding out the chemistry of all these important molecules from the very earliest.

ED: Professor Brenner noted that these scientific discoveries required a new way of approaching old problems, which resist traditional disciplinary thinking.

SB: The thing is to have no discipline at all. Biology got its main success by the importation of physicists that came into the field not knowing any biology and I think today that’s very important.

I strongly believe that the only way to encourage innovation is to give it to the young. The young have a great advantage in that they are ignorant. Because I think ignorance in science is very important. If you’re like me and you know too much you can’t try new things. I always work in fields of which I’m totally ignorant.

ED: But he felt that young people today face immense challenges as well, which hinder their ability to creatively innovate.

SB: Today the Americans have developed a new culture in science based on the slavery of graduate students. Now graduate students of American institutions are afraid. He just performs. He’s got to perform. The post-doc is an indentured labourer. We now have labs that don’t work in the same way as the early labs where people were independent, where they could have their own ideas and could pursue them.

The most important thing today is for young people to take responsibility, to actually know how to formulate an idea and how to work on it. Not to buy into the so-called apprenticeship. I think you can only foster that by having sort of deviant studies. That is, you go on and do something really different. Then I think you will be able to foster it.

But today there is no way to do this without money. That’s the difficulty. In order to do science you have to have it supported. The supporters now, the bureaucrats of science, do not wish to take any risks. So in order to get it supported, they want to know from the start that it will work. This means you have to have preliminary information, which means that you are bound to follow the straight and narrow.

There’s no exploration any more except in a very few places. You know like someone going off to study Neanderthal bones. Can you see this happening anywhere else? No, you see, because he would need to do something that’s important to advance the aims of the people who fund science.

I think I’ve often divided people into two classes: Catholics and Methodists. Catholics are people who sit on committees and devise huge schemes in order to try to change things, but nothing’s happened. Nothing happens because the committee is a regression to the mean, and the mean is mediocre. Now what you’ve got to do is good works in your own parish. That’s a Methodist.

ED: His faith in young, naïve (in the most positive sense) scientists is so strong that he has dedicated his later career to fostering their talent against these negative forces.

SB: I am fortunate enough to be able to do this because in Singapore I actually have started two labs and am about to start a third, which are only for young people. These are young Singaporeans who have all been sent abroad to get their PhDs at places like Cambridge, Stanford, and Berkeley. They return back and rather than work five years as a post-doc for some other person, I’ve got a lab where they can work for themselves. They’re not working for me and I’ve told them that.

But what is interesting is that very few accept that challenge, providing what I think is a good standard deviation from the mean. Exceptional people, the ones who have the initiative, have gone out and got their own funding. I think these are clearly going to be the winners. The eldest is thirty-two.

They can have some money, and of course they’ve got to accept the responsibility of execution. I help them in the sense that I oblige them and help them find things, and I can also guide them and so on. We discuss things a lot because I’ve never believed in these group meetings, which seems to be the bane of American life; the head of the lab trying to find out what’s going on in his lab. Instead, I work with people one on one, like the Cambridge tutorial. Now we just have seminars and group meetings and so on.

So I think you’ve got to try to do something like that for the young people and if you can then I think you will create. That’s the way to change the future. Because if these people are successful then they will be running science in twenty years’ time.

ED: Our discussion made me think about what we consider markers of success today. It reminded me of a paragraph in Professor Brenner’s tribute to Professor Sanger in Science:

“A Fred Sanger would not survive today’s world of science. With continuous reporting and appraisals, some committee would note that he published little of import between insulin in 1952 and his first paper on RNA sequencing in 1967 with another long gap until DNA sequencing in 1977. He would be labelled as unproductive, and his modest personal support would be denied. We no longer have a culture that allows individuals to embark on long-term—and what would be considered today extremely risky—projects.”

I found this particularly striking given that another recent Nobel prize winner, Peter Higgs, who identified the particle that bears his name, the Higgs boson, similarly remarked in an interview with the Guardian that, “he doubts a similar breakthrough could be achieved in today’s academic culture, because of the expectations on academics to collaborate and keep churning out papers. He said that: ‘it’s difficult to imagine how I would ever have enough peace and quiet in the present sort of climate to do what I did in 1964.’”

martes, 10 de diciembre de 2013

in PLOS - parody of Lady Gaga's "Applause"

"We're touched and can't stop laughing after watching this video made by grad students at UCB D-lab. Highly recommended!" (PLOS)



ORIGINAL: DLab Follies

lunes, 2 de septiembre de 2013

eLife digital publication

ORIGINAL: http://elife.elifesciences.org/about-the-journal

eLife is a researcher-led, open access digital publication for outstanding research in life science and biomedicine.

The eLife journal is a platform to maximise the reach and influence of new findings and a showcase for new approaches to the presentation, evaluation and use of research.

eLife is a collaboration between the Howard Hughes Medical Institute, the Max Planck Society, the Wellcome Trust, and over 200 of the world’s most talented biomedical scientists.

We aim to make eLife the first choice journal for all researchers, in particular for early-career researchers. It’s important that early experiences of publishing are constructive and fair. eLife is a publishing venue to advance careers in science; the editors act decisively and provide a swift, fair and supportive author experience; and we maximise the potential exposure for all published works.

At eLife, our goal is to accelerate scientific advancement by making new research available quickly, openly, and in a way that helps others to build upon it. We make data more accessible and more useable. We aim to create a broader audience for important discoveries, and to track and report the impact of published articles – on research, and on society as a whole.

Review Process



eLife returns decisions on important papers quickly. Our peer-review process is rigorous, but decisive, constructive, and fast.

At eLife, we’ve taken a fresh approach to peer review to save you time, and to provide clear direction and constructive input.
  • Decisions are quick and efficient
  • Revision requests are designed to be clear and manageable
  • Multiple rounds of revision are usually avoided

Here's how it works

Submissions are evaluated by a team of academic editors who are active and respected researchers, who have expertise across disciplines, and who are committed to assessing submissions efficiently and fairly. Our approach focuses on delivering the highest level of service to authors and saving time along the way.

Initial decisions are delivered quickly

Our Senior Editors decide whether initial submissions are appropriate for in-depth peer review, usually in consultation with members of the Board of Reviewing Editors. We ask for the research article in a single PDF along with a cover letter. Only once editors commit to full review are authors asked to provide additional information and files to support the peer-review process. We aim to return initial decisions within three to five days. 

Active scientists make all decisions
A Senior editor assigns a member of the Board of Reviewing Editors to oversee the peer-review process. The Reviewing editor usually reviews the article him or herself, calling on one or two additional reviewers as needed.

Revision requests are consolidated
Reviewers get together online to discuss their recommendations, communicating openly with one another before a decision is reached, refining their feedback, and striving to provide clear and concise guidance. If the work needs essential revisions before it can be published, the Reviewing editor incorporates those requirements into a single set of instructions. We aim to deliver decisions after peer review within a month of receiving the full submission.

Limited rounds of revision
Further rounds of revision are largely eliminated, as the Reviewing editor is able to assess most revised submissions without further outside review.

Decisions and responses are available for all to read
We include the most substantive parts of the decision letter after review and the associated author responses alongside published articles, subject to author agreement, so that readers can assess and comment on the review process too.

viernes, 21 de junio de 2013

Nature Publishing Index 2012 Global

ORIGINAL: Nature

We are delighted to present the first global overview of high quality research output from the world’s many countries and institutions based on the Nature Publishing Index (NPI), which tracks the number and affiliations of primary research articles published in 18 Nature-branded journals. 
Download PDF [10.6mb]
Created in 2009 to focus on the Asia-Pacific region, the NPI now covers the entire world. Using the Index, we are able to track output by institution and country. The NPI is a unique resource that spans all types of research institutions — not only universities but government research institutes and private sector companies.

What are the most noteworthy messages from this supplement? Unsurprisingly, the United States dominates the rankings, being home to five of the top ten research institutions in the NPI. What is more striking is the rapid rise of China, which has nine institutions in The Top 200 — up from just three a year earlier. China is now clipping the heels of France in the country rankings. The Chinese Academy of Sciences has, as of January 2013, surpassed the University of Tokyo as the top institution in the Asia-Pacific. Despite its dire economic circumstances, Ireland is emerging as a rising star — jumping from 30th to 20th in the NPI between 2008 and 2012. Similarly, Brazil has moved up seven places to 27th. Saudi Arabia and Kenya also stand out as newly emerging players in the Index.

Our interpretations and presentations of the NPI data are not definitive. Users are free to access the NPI online, read the abstracts of the papers on which it is based, and derive their own interpretations of the data (provided they acknowledge the NPI as the source). To that end, we strive to make the Index and the methodology behind it as transparent as possible: the underlying data for the past year can be viewed on the NPI website at nature.asia/publishing-index-global. We hope the analysis presented here will stimulate further use of the NPI by institutions and individuals, and we welcome your feedback.

David Swinbanks
Managing Director, Regional Markets and Science & Medical Communications,
Nature Publishing Group
Managing Director, Australia and New Zealand,
Macmillan Science and Education

Contents
1 Opening. By David Swinbanks
2 The world of science. An overview of a growing world of scientific achievement
4 United States. A player without peer, the undisputed leader continues to dominate
8 United Kingdom- As budget cuts hit blue-sky research, scientists must do more with less
10 Germany. Integration strategies aim to bring more institutions to an elite level
14 Japan. Newly elected president sets science as a top priority
20 France. Education and employment law reforms create divisions in science
24 Five countries to watch. A look at fast risers in the NPI: China, Ireland, Brazil, Kenya and Saudi Arabia
30 A guide to the NPI. How to navigate the index to get the best out of it
32 Global top 200. The great and the good of the world’s research institutions
38 Top 10 countries by journal. Countries show their strength in different disciplines
40 Top 5 institutions by journal. The breakdown reinforces the existence of an elite set of organizations
42 Top 100 countries. The world’s most scientifically productive nations

Interactive graphic
How countries compare
The Nature Publishing Index (NPI) Global ranks countries and institutions according to their output of primary research articles in the 18 Nature research journals. This graphic allows comparison of countries by corrected count or article count in each of the four main subject areas, and in each of the past 5 years. The graphic only includes the top 30 countries overall. The NPI Global supplement lists the Global Top 100.

Article count 2012 All fields

USUKDEJPFRCNCHCANLAUITESSEBEKRDKATILSGFINOIERUBRTWGRISINNZHUArticle count 2012 All fields02004006008001,0001,2001,4001,6001,8002,0002,200
* Mouse over a bar to reveal exact count



lunes, 29 de abril de 2013

Announcement: Reducing our irreproducibility

ORIGINAL: Nature
24 April 2013

Over the past year, Nature has published a string of articles that highlight failures in the reliability and reproducibility of published research (collected and freely available at go.nature.com/huhbyr). The problems arise in laboratories, but journals such as this one compound them when they fail to exert sufficient scrutiny over the results that they publish, and when they do not publish enough information for other researchers to assess results properly.

From next month, Nature and the Nature research journals will introduce editorial measures to address the problem by improving the consistency and quality of reporting in life-sciences articles. To ease the interpretation and improve the reliability of published results we will more systematically ensure that key methodological details are reported, and we will give more space to methods sections. We will examine statistics more closely and encourage authors to be transparent, for example by including their raw data.

Central to this initiative is a checklist intended to prompt authors to disclose technical and statistical information in their submissions, and to encourage referees to consider aspects important for research reproducibility (go.nature.com/oloeip). It was developed after discussions with researchers on the problems that lead to irreproducibility, including workshops organized last year by US National Institutes of Health (NIH) institutes. It also draws on published concerns about reporting standards (or the lack of them) and the collective experience of editors at Nature journals.

The checklist is not exhaustive. It focuses on a few experimental and analytical design elements that are crucial for the interpretation of research results but are often reported incompletely. For example, authors will need to describe methodological parameters that can introduce bias or influence robustness, and provide precise characterization of key reagents that may be subject to biological variability, such as cell lines and antibodies. The checklist also consolidates existing policies about data deposition and presentation.

We will also demand more precise descriptions of statistics, and we will commission statisticians as consultants on certain papers, at the editor’s discretion and at the referees’ suggestion.

We recognize that there is no single way to conduct an experimental study. Exploratory investigations cannot be done with the same level of statistical rigour as hypothesis-testing studies. Few academic laboratories have the means to perform the level of validation required, for example, to translate a finding from the laboratory to the clinic. However, that should not stand in the way of a full report of how a study was designed, conducted and analysed that will allow reviewers and readers to adequately interpret and build on the results.

To allow authors to describe their experimental design and methods in as much detail as necessary, the participating journals, including Nature, will abolish space restrictions on the methods section.

To further increase transparency, we will encourage authors to provide tables of the data behind graphs and figures. This builds on our established data-deposition policy for specific experiments and large data sets. The source data will be made available directly from the figure legend, for easy access. We continue to encourage authors to share detailed methods and reagent descriptions by depositing protocols in Protocol Exchange (www.nature.com/protocolexchange), an open resource linked from the primary paper.

Renewed attention to reporting and transparency is a small step. Much bigger underlying issues contribute to the problem, and are beyond the reach of journals alone. Too few biologists receive adequate training in statistics and other quantitative aspects of their subject. Mentoring of young scientists on matters of rigour and transparency is inconsistent at best. In academia, the ever increasing pressures to publish and chase funds provide little incentive to pursue studies and publish results that contradict or confirm previous papers. Those who document the validity or irreproducibility of a published piece of work seldom get a welcome from journals and funders, even as money and effort are wasted on false assumptions.

Tackling these issues is a long-term endeavour that will require the commitment of funders, institutions, researchers and publishers. It is encouraging that NIH institutes have led community discussions on this topic and are considering their own recommendations. We urge others to take note of these and of our initiatives, and do whatever they can to improve research reproducibility.

Nature 496, 398 (25 April 2013) doi:10.1038/496398a

domingo, 13 de enero de 2013

Our tribute to Aaron Swartz – #pdftribute

January 13, 2013

Swartz at 2009 Boston Wikipedia Meetup
Aaron was an activist, a champion, and an incredibly smart guy who worked on things he really cared about. So much has been said about his life, his death, and his fight for research open access — and I’m glad to be part of this conversation.

Late last night, I noticed that @evavivalt was opening access to her papers online in tribute to the memory of Aaron Swartz. I tweeted to some people I know in Silicon Valley, and to some friends of Aaron’s, and then Anonymous picked it up — and it just caught on. We’ve now had over 3.5 million impressions and over 500 tweets per hour.

This is something we can do for the memory of Aaron Swartz, and to lead the way toward more access to the scientific process for everyone.

Now is the time to participate.

If you’re in the UK, write to @ukhouseoflords using this link as they are accepting comment on these issues over the next couple of weeks. If you’re in the United States, perhaps you can help launch a similar inquiry at the US House of Representatives Committee on Science, Space, and Technology by tweeting to @SciSpaceTechCmt.

For hackers, perhaps you can take all of the #pdftribute files and put them on a central web page. Maybe other journals will follow (or exceed!) JSTOR’s lead and give more open access. Whatever happens, let’s all be a part of it.

Please tweet your papers using #pdftribute!

Aaron H. Swartz (November 8, 1986 – January 11, 2013) was an American computer programmer, writer, archivist, political organizer, and Internet activist. Swartz co-authored the "RSS 1.0" specification of RSS[2], and built the Web site framework web.py and the architecture for the Open Library. He also built Infogami, a company that merged with Reddit in its early days, through which he became an equal owner of the merged company.[i]

Swartz also focused on sociology, civic awareness and activism. In 2010 he was a member of the Harvard University Center for Ethics. He cofounded the online group Demand Progress (best known recently for its campaign for Richard O'Dwyer) and later worked with US and international activist groups Rootstrikers and Avaaz.

On January 6, 2011, Swartz was arrested in connection with systematic downloading of academic journal articles from JSTOR, which became the subject of a federal investigation.[3][4] JSTOR offended Swartz mainly for two reasons: 

  • it charged large fees for access to these articles but did not compensate the authors and 
  • it ensured that huge numbers of people are denied access to the scholarship produced by America's colleges and universities.[5][6] 
On January 11, 2013, Swartz was found dead in his Crown Heights, Brooklyn, apartment, where he had hanged himself.[7][8][9]

UPDATE: #pdftribute hashtagged tweets http://t.co/7PjIZp5y by @patricksocha and @devopstom

martes, 2 de octubre de 2012

A major step forward for open-access publishing (at CERN)

ORIGINAL: CERN

Photo: CERN
Representatives from the science-funding agencies and library communities of 29 countries are meeting at CERN today to launch the Sponsoring Consortium for Open Access Publishing in Particle Physics (SCOAP3) initiative.

At a meeting last week the CERN Finance Committee officially approved the award of contracts for the provision of peer-review, open access and other publication services for the benefit of SCOAP3. The consortium aims to provide unrestricted access to high-energy-physics (HEP) research literature in its final, peer-reviewed form, by sharing the cost of the peer-review service between funding agencies, research institutions, libraries and library consortia, while publishers make electronic versions of their journals open access.

"The Finance Committee's approval is a watershed, with a large exclamation mark!" says CERN librarian Jens Vigen. "After years of design and consensus building, we can now move on to the implementation phase of the project. This is the first time ever that an entire field is concretely moving towards open-access publishing."

The goal of open access is to grant anyone free access to the results of scientific research. But the current model of scientific publishing – where journal access is restricted to paying customers and reuse of material is hindered by copyright restrictions – is at odds with this idea. Traditionally libraries have paid, on behalf of their readers, for access to content. However, the service needed by the community is the peer-review and quality-assurance service, as in the field of high-energy physics community preprints of articles are generally made available online long before they appear in journals. SCOAP3 is putting this service at the centre, remunerating the publishing industry for it, while content will be open access.

"The issue is that people in our field don't tend to read the journals, they read the arXiv," says Vigen. "This said, peer-reviewed journals add an indispensable quality stamp. The new system enshrines the role of the journals in providing the peer-review service rather than repositories of content."

In the SCOAP3 model, HEP funding agencies, research institutions, libraries and library consortia, which today buy journal subscriptions to implicitly support the peer-review service, instead pool their resources explicitly to cover the cost of this service, while publishers make the electronic versions of their journals open access. SCOAP3 partners recover their contributions by redirecting the funds they currently use for journal subscriptions. 

With a projected SCOAP3 budget of 36 million Swiss francs over three years, 12 journals from 7 publishers are now on the list for a possible contract for the provision of peer-review, open access and other publication services. Over 6600 articles relevant to the field were published in these journals in 2011; this represents the vast majority of the literature.

"It has taken an amazing team effort to get here, with volunteers from the library community, research institutions and funding agencies working hard together to steer the initiative, alongside constructive discussions with the publishers of the field," says Salvatore Mele, head of Open Access at CERN, who convened the SCOAP3 Steering Committee over a year and a half. "This bodes well for the next crucial steps as SCOAP3 moves forward."

"I think neighbouring fields like nuclear physics and astrophysics might be inspired by this model in some way," says Vigen. "When we initiated the process six years ago, open access publishing was in its infancy – today it has become mainstream. We have entered into an era that will accelerate science."
FIND OUT MORE:

martes, 25 de septiembre de 2012

Open-access deal for particle physics

ORIGINAL: Nature
24 September 2012

Consortium brokers agreement with 12 journals.


Freeview: experimental results from high-energy physics, such as this fireball of quarks and gluons, should soon be published in open-access papers. CERN


The entire field of particle physics is set to switch to open-access publishing, a milestone in the push to make research results freely available to readers.

Particle physics is already a paragon of openness, with most papers posted on the preprint server arXiv. But peer-reviewed versions are still published in subscription journals, and publishers and research consortia at facilities such as the Large Hadron Collider (LHC) have previously had to strike piecemeal deals to free up a few hundred articles.

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After six years of negotiation, the Sponsoring Consortium for Open Access Publishing in Particle Physics (SCOAP3) is now close to ensuring that nearly all particle-physics articles — about 7,000 publications last year — are made immediately free on journal websites. Upfront payments from libraries will fund the access.

So that individual research groups do not need to arrange open publication of their work, the consortium has negotiated contracts with 12 journals (see ‘Particles on tap’) that would make 90% of high-energy-physics papers published from 2014 onwards free to read, says Salvatore Mele, who leads the project from CERN, Europe’s high-energy physics laboratory near Geneva, Switzerland, and home of the LHC. According to details announced on 21 September, six of the journals will switch their business models entirely from subscription to open access. It is “the most systematic attempt to convert all the journals in a given field to open access”, says Peter Suber, a philosopher at Earlham College in Richmond, Indiana, and a proponent of open access.




Publisher
JournalNo. of high-energy-physics articles in 2011Charge per article
American Physical SocietyPhysical Review C107US$1,900
American Physical SocietyPhysical Review D2,989US$1,900
ElsevierPhysics Letters B1,010US$1,800
ElsevierNuclear Physics B284US$2,000
HindawiAdvances in High Energy Physics28US$1,000
Institute of Physics/Chinese Academy of SciencesChinese Physics C16£1,000 (US$1,600)
Institute of Physics/DPGNew Journal of Physics20£1,200 (US$1,950)
Institute of Physics/SISSAJournal of Cosmology and Astroparticle Physics138£1,400 (US$2,270)
Jagiellonian UniversityActa Physica Polonica B23€500 (US$650)
Oxford University Press/Physical Society of JapanProgress of Theoretical Physics46£1,000 (US$1,600)
Springer/Società Italiana di FisicaEuropean Physical Journal C326€1,500 (US$1,940)
Springer/SISSAJournal of High Energy Physics1,652€1,200 (US$1,550)
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Acta Biológica Colombiana. Vol 17, No 2 (2012)


Inicio > Vol 17, No 2 (2012)
Cárdenas Toquica Martha , Restrepo Restrepo Silvia
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