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Nature's past and future after 140 years

From an Editorial in Nature (462, 12; 5 November 2009):
Nature's first issue appeared on Thursday 4 November 1869. 7,269 issues later, a little bit of satisfaction may be in order given that the journal has survived wars and, so far, the Internet's onslaught on traditional models of publishing. Nature's papers are highly cited for what seem to us to be good reasons. Lots of people (millions online every month) want to read the journal. So where do we need to be self-critical? Readers will no doubt have many answers, but here are a few.

> Others sometimes put more weight on our judgement than it can justifiably bear. Large grants, philanthropic donations and personal chairs have been awarded on the strength of a paper in Nature — in effect, using editors' decisions as a surrogate for independent judgement. This is an abdication of the decision-makers' responsibility, and is a pitfall to be avoided.

> We endorse efforts to create systems that reach beyond the crudeness of the impact factor — systems that make transparent the citations and other effects of papers, and that record impacts of scientists' other work, such as their contributions to databases and the hard slog of peer review.

> We have enhanced our journalism and externally authored opinion in recent years, and readers can anticipate further developments ahead.

> Nature has to reflect the values of its authors and readers. The core values of science — objectivity, independence, self-critical thinking and a relentless urge to observe, experiment and explore — are also important principles of good journalism and editing. As an unusual hybrid of magazine and journal, Nature can only retain readers' respect if it follows those principles while adding substantial value to the lives and work of researchers and others seriously interested in science. Our commitment to fulfil these ambitions is as strong as it has ever been.

More about Nature.
Nature's own history website.

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NPG's annual letter to customers (2009)

Nature Publishing Group's managing director, Stephen Inchcoombe, has just written his annual letter to the company's customers. NPG's customers are varied: as well as authors and peer-reviewers, they include readers, subscribers, librarians, institutions, advertisers, suppliers, partners, sponsors, and more. The annual letter is, necessarily, broad, so I'll highlight here a few points of particular interest to authors:
--A new XML repository for nature.com and other infrastructure improvements are the foundations for NPG to deliver a new wave of applications in the coming year
--In April 2010 we will introduce Nature Communications, an online-only peer-reviewed journal offering rapid publication for high-quality research across the biological, chemical and physical sciences, with a mixed publishing model
--Nature Chemistry, launched in April 2009, showcases the kind of innovative publishing functionality we want to provide. Highlighting chemical compounds in articles, redrawing chemical structures to be machine-readable and enhanced chemical compound reference pages created by journal editors, all further the journal article's role as an integral part of the reader's workflow. These advances will be applied to Nature Chemical Biology, Nature and other NPG journals in the near future
--NPG now publishes 16 of the top 50 (32%) journals by Impact Factor, twice as many as any other scientific publisher
--Expanded content in Nature Medicine from January and significant improvements to Nature later in the year, with no commensurate price increases
--Closer integration of nature.com and Nature Network, our social network for scientists. Comments on online journal articles will become part of the commenter's Nature Network profile, acknowledging that contributions to the scientific record stretch far beyond the journal article itself
--Scientific American became part of NPG in 2009, after many years as a sister Holtzbrinck organization. Expect to see functionality, services and interlinking between Scientific American and NPG journals and resources from next year.

The whole letter is published at NPG's press website; we welcome your feedback and comments.
More information about Nature Publishing Group and its executive committee.

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New NPG journal: Cell Death & Disease

Via press release: Nature Publishing Group (NPG) and the Associazione Differenziamento e Morte Cellulare (ADMC) have announced a new open access journal, Cell Death & Disease. Launching in January 2010, Cell Death & Disease will explore the area of cell death from a translational medicine perspective. The journal is now accepting submissions.
Cell Death & Disease is a sister journal to the well-established and highly respected journal Cell Death & Differentiation. Together, the two journals provide a unified forum for scientists, clinicians and members of the pharmaceutical and biotechnology industry.
Cell Death & Disease is devoted to the biology of cell death in the pathogenesis of human diseases or relevant animal models. The journal aims to publish papers that present novel observations in the field of cell death, with pathophysiological or medical implications. Particular emphasis will be given to clinical, translational and applied research through its five sections: experimental medicine, cancer, immunity, internal medicine and neuroscience.
Cell Death & Disease will be online only and will make all content freely available to all researchers worldwide. There will be an processing charge of £2,000 / $3,000 / €2,400 for each article accepted for publication.
The editorial team is led by Gerry Melino, Guido Kroemer and Pierluigi Nicotera, and will include a highly respected international editorial board.
Cell Death & Disease preliminary website.
Cell Death & Disease: journal scope.
Submit your manuscript to Cell Death & Disease.
The journal's guide to authors.
Summary of author benefits.

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Data sharing discussed at Nature and Nature Network

Sharing data is good. But sharing your own data? That can get complicated. As two research communities who held meetings on this question in Rome and in Toronto in May report their proposals to promote data sharing in biology, a special issue of Nature (10 September 2009) examines the cultural and technical hurdles that can get in the way of good intentions. Some of the authors of these proposals are participating in two online forums (Rome and Toronto) at Nature Network - so please accept our invitation to visit and have your say on these questions.
More details:
The two research communities held meetings with a broad range of stakeholders to discuss ways to promote data sharing in biology. Data producers and users met at a workshop in Toronto to discuss the benefits and best practices of rapid data release prior to publication. Ewan Birney, Tom Hudson and colleagues report the main conclusions of these discussions in a community statement, free to access here.
The Toronto group propose that the principles for early release of genomics data should be extended to other large datasets in biology and medicine. A grace period should be allowed, if requested, to enable data producers to analyse and publish their dataset, but this should be limited to one year. The authors also suggest a set of best practices for funding agencies, scientists and journal editors.
The recommendations are intended to spark community discussion on this subject. Ewan Birney, Tom Hudson and others will be responding to reader comments in our Nature Network forum. Be sure to have your say.
Mouse researchers, along with funding agencies and publishers, met in Rome to address the barriers preventing more effective sharing of data and biomaterials — particularly mouse strains and embryonic stem cells. Their agenda, free to access here, suggests guidelines to enable sharing of materials under the least restrictive terms, avoiding material transfer agreements where possible.
The Rome participants argue that funding organizations, journals and researchers need to work together to encourage better use of public repositories and to promote a ‘research commons’ in mouse biology.
The recommendations are intended to spark community discussion on this subject. Paul Schofield and others will be responding to reader comments in our Nature Network forum. Be sure to have your say.
See also the Editorial (free to access online) in the same issue of Nature (461, 145; 2009): 'Data's shameful neglect', opining that research cannot flourish if data are not preserved and made accessible. All concerned must act accordingly.
Nature's special issue on data sharing.

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Short is sweet, says EMBO reports

Scientific publishing seems to be moving in several contradictory directions. Against these conflicting trends, EMBO reports seeks to re-assert the importance of the short-format article, carrying a single key message of ground-breaking significance. So writes the journal's Editor, Howie Jacobs (EMBO reports 10, 935; 2009). Against a background of screeds of scientific articles, blogs and other commentary available on the internet, and vast mountains of supplementary information and data, the short-format of EMBO reports is increasingly popular. From the Editorial:
"Our philosophy is that science proceeds in steps. Each major conceptual advance towards a complete understanding—whether of a macromolecule, an organelle, the cell or the organism—should be documented properly, judged on its merits and made rapidly available for the community. In a fast-moving field such as molecular biology, erroneous findings inevitably make their way into print; however, any resulting damage is minimized if knowledge is parcelled into manageable chunks. When too many different findings are bundled together, valid results can be 'contaminated' by their association with those that prove to be flawed, and significant errors might be overlooked. More importantly, crucial discoveries should not require sophisticated data-mining tools to be accessible."
The Editorial goes on to define the key features the editors look for in a "short report" - encapsulation of the key message in a single sentence, novelty, significance for the field, and broad interest to the molecular biology community. Those who think their work fits these criteria and are considering submitting to EMBO reports will find the Editorial a helpful guide.

EMBO reports guide to authors.

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End of the line for print journals?

Are the days of print journals numbered — and if they are, what will that mean for how we interact with the scientific literature? These questions are asked in Nature Chemistry's September Editorial (1, 421; 2009). The Editorial is sparked by The American Chemical Society's announcement that, with the exception of the Journal of the American Chemical Society and two review journals, "ACS titles publishing primary research will be printed in a landscape fashion that puts two article pages side-by-side on a single physical page. These changes are accompanied by new pricing schemes that will eliminate discounts for hardcopy journals, while offering subscribers incentives to upgrade from print to digital formats." This is inevitably seen by several observers as a precursor to eliminating the print editions of these journals.
Although, as the Nature Chemistry Editorial notes, there are many advantages to the online journal format, both in terms of the content itself and in terms of the financial and environmental cost of the printed medium. The Editorial concludes: "in all likelihood, it will probably come to pass that as this century grows older, printed journals will be consigned to history. And in some ways, that would be a shame. Printed materials have their own charm and practicality — no batteries required! — and will always have a loyal following. Whereas some individuals may be happy to replace their dusty bookshelves and their contents with a plastic electronic reader of some description, many would shudder at the thought.
Moreover, should chemistry publishing become an online-only endeavour, the concept of 'issues' also comes into question. With the ability to dynamically group articles on a website using criteria such as dates or keywords, does journal content need to be collated into bite-sized chunks if print is no longer a consideration? And without issues, what becomes of cover images? These serve to advertise both the journal and people's work — many conference talks are proudly emblazoned with journal covers, as doubtless are many people's offices.
Assuming sustainable models, the continued co-existence of print and digital editions of journals (especially for those that publish more than just review and research articles) would satisfy the needs of all readers — but whether this is a realistic goal in the long term remains to be seen."

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Dangers of scientific publicity machines

A hyped-up fossil find highlights the potential dangers of publicity machines, according to one of the Editorials in today's Nature (459, 484; 2009 - free to access online). The Editorial describes last week's publication of paper describing a 47-million-year-old fossil primate with a remarkable degree of preservation, which quickly led to enormous media and internet coverage, including claims that the fossil is a "missing link" in human evolution. The Editorial describes how, "in the paper the authors explicitly state that Darwinius masillae "could represent a stem group from which later anthropoid primates evolved, but we are not advocating this here, nor do we consider either Darwinius or adapoids to be anthropoids". The authors also refrain from claiming that the fossil changes our understanding of primate evolution."
But the circumstances surrounding the paper's publication were anything but normal. Before the paper had even been submitted, a television documentary and an accompanying book about the find had been commissioned; a week publication of the paper, the book is out and the documentary has been aired on TV in several countries. The Editorial continues:
"Both book and documentary include the the suggestive words 'The Link' in their titles. A press release associated with the New York press conference at which the fossil was first officially described claimed that the fossil represents revolutionary changes in understanding. The History Channel website calls the find a "human ancestor", and the BBC website describes it as "our earliest ancestor".
To be fair, the authors' claims at the press conference were appropriately measured. Nonetheless, the researchers were fully involved in the documentaries and the media campaign, which associate them with a drastic misrepresentation of their research.
Another damaging aspect of the events was the unavailability of the paper ahead of the press conference and initial media coverage. This prevented scientists other than those in the team from assessing the work and thereby ensuring that journalists could give a balanced account of the research.
There is no reason to think that PLoS ONE's editors and reviewers did less than their duty to the paper. Nonetheless, the clock was ticking at the time of submission. Nature has over the years received occasional offers of papers associated with television documentaries, and the offers usually come with broadcast dates attached. Where the refereeing process might have been compromised, we have always said no to these papers. When time is tight, there is a risk that the broadcast will go out even if any problems uncovered by peer review cause the paper to be delayed or rejected.
In principle, there is no reason why science should not be accompanied by highly proactive publicity machines. But in practice, such arrangements introduce conflicting incentives that can all too easily undermine the process of the assessment and communication of science."
Amid all the vast quantity of media and internet coverage of this research, I highly recommend this excellent post, 'Why Darwinius is not our ancestor', by Karen James at her Data Not Shown blog. I also recommend this Nature Network blog post by senior Nature editor Henry Gee.
Nature journals' embargo policy.
Nature journals' policy on confidentiality and pre-publicity.


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Using the law to stifle scientific debate

A court case between one of Britain's leading science writers and an organization representing alternative medicine practitioners is causing renewed concern about the potential for libel laws to stifle debate on scientific issues (Nature News, 13 May 2009).
Simon Singh, author of Fermat's Last Theorem and other books, is being sued for libel by the British Chiropractic Association over an article he wrote for the Guardian newspaper last year. In an unusual move, the BCA is suing Singh personally, and not the newspaper.
The case has international implications for science reporting and journalism more generally, warns Singh. It comes against a background of increasing concern in many quarters that litigants opt for British courts as they are seen as easier places to get a favourable result; a problem labeled 'libel tourism'.
Neil White, a partner at legal firm Taylor Wessing (which undertakes some legal work for Nature), says the case should serve as a warning not just for science writers, but more generally for scientists and all who write about similar topics. "I think there is a degree of ignorance on the part of scientists about libel law, particularly UK libel law," he says. "I do think there are some scientists who are rather arrogant about it, and think because they're scientists with a view to express on a matter of potentially considerable importance they can say what they please. That is just not the case. The lesson I think they need to learn is you can usually say what you want to say in a way that doesn't expose you to litigation, by taking a bit of care and taking a bit of advice."
Edzard Ernst, professor of complementary medicine at Peninsula Medical School in Plymouth, UK, says, "Recent history shows quite clearly there is a danger people can be silenced by the financial and legal might of their opponents."
What are your views? Please let us know, either by commenting at the Nature Network Opinion forum or at the Nature News website (where there is a comment in favour of the BCA, as well as others taking the opposite view). How confident are you about expressing a scientific opinion publicly? How well-informed are you about the legal consequences of what you might write on your blog or for a publication?
See also this Nature Network blog post by Stephen Curry and this alert at Nature Network by Brian Clegg .
Readers' comments at Nature Network or here will be considered for publication in Nature as Correspondence.

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Effect of recession on publishing models

In a Correspondence in the current issue of Nature (458; 967, 2009), Raf Aerts of the Katholieke Universiteit Leuven writes:

Your Commentaries on 'How to survive the recession' devote much discussion to the effects of the global recession on science (Nature 457, 957–963; 2009). However, the financial squeeze may also be affecting the publication output of research institutions in a more subtle way. It could be boosting the traditional reader-pays publication model for scientific journals at the expense of the author-pays, or open-access, model.
Open-access journals ask authors to pay for processing their manuscripts (which involves organizing a form of quality control, formatting and distribution) so that the final product becomes freely available, and free to use if properly attributed. This model is widely believed to increase the visibility, dissemination and, eventually, the citation and impact of research findings.
However, few peer-reviewed open-access journals have so far had a high impact factor in their field, except for a small number such as those published by the Public Library of Science and BioMed Central. They are therefore struggling to emerge and to attract the most prestigious research findings.
This situation could deteriorate further if open-access journals are forced to move to (partial) site licensing in order to cover their production costs — a shift recently undertaken by the Journal of Visualized Experiments, for example as authors become increasingly reluctant or unable to pay in the current financial climate.

(This is an slightly shortened version of the Correspondence. The full version is available online at Nature's website.)

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Frank Gannon says farewell to EMBO reports

Frank Gannon says goodbye as senior editor at EMBO reports in the journal's April issue (10, 293; 2009). I shall certainly miss his monthly editorials, which I always looked forward to reading and often mentioned on this blog. On the occasion of his goodbye, he looks back at his contribution:

"EMBO reports has not only garnered a reputation for reporting good science, but also paved the way with a novel Science & Society section. It has been a joy to help mould this section into something that our readers appreciate. A related major task—and a great pleasure—has been writing monthly editorials. When I had finished the first editorial, I experienced a moment of panic as I was faced with the challenge of finding a topic for the next month and beyond. More than one hundred editorials later, that concern has long gone. There are so many topics to write about that are relevant to scientists and that are not often addressed in other journals. Some of my favourites include language barriers for non-English speaking scientists (March, 2008), The downsides of mobility (March, 2007), the fate of scientists who reach retirement age (March, 2004), bullying (October, 2008), Family matters (November, 2005), and role models and mentors (December, 2006). Then there are all of the societal topics that address how science is catering to, and is directed by, politics and business, such as the 'Faustian' bargain of private interests and university research (March, 2003), or the role of government in directing science (December, 2003). My editorial, An NIH/NSF for Europe ( June, 2002), was one of the first serious calls for a European Research Council, which has now become a reality. And, of course, it is always fun to take a sidelong look at the scientific community and comment on how we behave. My favourites on this theme are Conformists (October, 2007) and Meeting standards ( January, 2006). It was similarly amusing to write a tongue-in-cheek rejection letter to Charles Darwin ( January, 2009) while a crowded world of communication was eulogizing him for his two-hundreth birthday."
And there is news of the new order:
"Howy Jacobs has agreed to become the new Senior Editor of EMBO reports. I have known Howy for many years, both as a great scientist and communicator, and I have had many thought-provoking and enjoyable discussions with him. I have no doubt that the journal is in good hands for the years to come. I am certain that with Howy's guidance, EMBO reports will increase even further in value and stature as an important source of information for the scientific community—and our broader readership—communicating both insightful scientific research, and commenting on and reporting the ongoing debates about how science and society shape one other in the twenty-first century."

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Nature Clinical Practice journals evolve into Reviews journals

In 2000, Nature Publishing Group launched the first three of the Nature Reviews series. By 2002, the series had grown to seven monthly review journals and quickly became the highest impact-factor journals in their fields — gaining a reputation for publishing superbly illustrated reviews written by leading international researchers. The Nature Reviews journals will double in size next month (April), when all eight Nature Clinical Practice journals will be relaunched as "Nature Reviews". These clinical Nature Reviews journals will be printed in colour and will have the same high production values that have helped make the life-science Nature Reviews journals so successful, and each issue will contain more content, including Editorials, Research Highlights, News & Views, Reviews, Case Studies and Perspectives articles. The clinical journals will not alter their editorial scopes or commissioning strategies and will retain their distinguished external Editors-in-Chief and international Advisory Boards.
The clinical Nature Reviews journals (as of April 2009):
Nature Reviews Cardiology
Nature Reviews Clinical Oncology
Nature Reviews Endocrinology
Nature Reviews Gastroenterology & Hepatology
Nature Reviews Nephrology
Nature Reviews Neurology
Nature Reviews Rheumatology
Nature Reviews Urology
Some authors' questions answered:
I had a paper published in a Nature Clinical Practice journal. Will the citation to that paper change?
No, the citation will remain the same and the article will continue to be indexed in MEDLINE in perpetuity.
What will happen to the impact factor of the Nature Clinical Practice journals?
The clinical Nature Reviews journals will receive their first impact factors in June 2011. The Nature Clinical Practice journals will receive their last impact factor in June 2012. Thomson-Reuters, the company that calculates impact factors, will allow the two impact factors to be averaged in 2011 and 2012 to give the "unified" impact factor of the two journals.
I would like to write an article for one of the new Nature Reviews journals. What should I do?
The instructions to authors for each of the journals can be found on their homepages. Please contact the Editor with your proposal before writing the article.
Will the aims and scope of the journals change?
No, the journals will continue to publish a mix of news, opinion, and review articles to keep clinicians up to date with the latest advances in medical research.
Will the journals publish original research?
No. When Nature Clinical Practice Cardiovascular Medicine becomes Nature Reviews Cardiology in April, it will no longer publish original research. There are no plans to introduce original research in any of the clinical Nature Reviews journals.
Will readers be able to download PowerPoint presentations of the figures from the Review articles?
Yes.
Will the search function cover all content from the old Nature Clinical Practice issues and the new issues?
Yes, searches will include both journals, so readers only have to perform one search for each journal's archive.
Will URLs change? If there is to be a redirect, for how long?
The articles published in the Nature Clinical Practice journals before April 2009 will be moved to the new Nature Reviews site in April. However, the old Nature Clinical Practice URLs will be redirected indefinitely to the new Nature Reviews URLs and all old dois will resolve to the articles in their new location. The new URLs and ISSNs are listed on the main Nature Clinical Practice page and are always available from the publications site index or the Nature family of journals page.


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Journal removes article after legal threat

According to an online News story at the Nature website (doi 10.1038/news.2009.99; 16 February), The Swedish Research Council is becoming involved in a row over academic freedom after a peer-reviewed journal removed a published paper — by two Swedish academics — from its website following a threat of legal action from the company whose technology the research criticized. The News story describes how the paper 'Charlatanry in forensic speech science: a problem to be taken seriously', was first published in the International Journal of Speech, Language and the Law in December 2007. In it, the authors examine voice-analysis technologies, stating there is no scientific basis for one of them. Lawyers for the manufacturers complained and the paper was removed from the journal website (the abstract and an explanatory note from the editors remain). Several members of the Swedish Research Council have signed an expression of concern about the removal, which according to the journal was for reasons of possible defamation rather than for any problem with the accuracy of the scientific content.
We welcome your comments, here or at the Nature News website.


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Nature Genetics on teamwork and consortia

For the genetics field as well as others, an increasing number of research papers are the products of research consortia. In its January Editorial, Nature Genetics (41, 1; 2009) reports on how the journal is coping with the effects of team knowledge production on publication, and advises authors of what they can do to expedite the publication of their work.
One of several points made in the Editorial is that "Scientific productivity is rapidly increasing thanks to collaboration, and this has created a greater need for communication and coordination. In response, publishers have now begun to offer researchers customized unique contributor identification services such as ResearcherID. However, we recognize that it would be unrealistic to expect something as central as individual identity and reputation to be definitively provided or controlled by any organization. What is really needed is a database or convention of online contributor identity, controlled by knowledge producers themselves, a service that records consortium membership with dates of joining and leaving, roles within consortia and authoring groups, and funding sources."
Nature Genetics guide to authors.
The Nature journals' policies on authorship.

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Audible science journals needed

Science journals have been slow to make themselves audible, according to a Correspondence by Wouter M. J. Achten of the Katholieke Universiteit Leuven in Nature 455, 590 (2008). The Correspondence is reproduced here:

Podcasting has become very popular, mainly as a medium for entertainment. But it also holds huge potential for the visually impaired and others, such as dyslexics, who have reading difficulties. Simultaneously reading and listening to read-aloud news articles and scientific papers, for example, could increase readers' concentration and absorption of information. Such audio files would open a new world for the blind or partially sighted.
Software is available that translates text from digital files or directly from the Internet into a listener-friendly audio file, but it is expensive. Some freeware has built-in 'read out-loud' functions, but the quality is generally inferior.
Several newspapers and magazines already offer subscribers podcasts containing complete and navigable issues in read-aloud format. But the scientific press seems to be lagging behind. The Nature podcasts are a good start, but when shall we be able to listen to sections such as Research Highlights, News and Correspondence as downloadable audio?

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European Commission survey on Internet resources for research

Via e-mail from Arnaud Berghmans of Deloitte Belgium on behalf of Augusto Burgueño of the Research Directorate-General of the European Commission:
Deloitte is conducting, on behalf of the European Commission, a survey on Internet-based services in support of the research process. So far, responses have been received from more than 3,500 EU researchers. As a benchmark, Deloitte would like to get the opinion of researchers already using the Internet for research and is asking readers of this website for their help by taking the survey.
About the survey
With this survey, the European Commission would like to find out which Internet-based resources (such as websites, wikis, social networks, mailing lists, bulleting boards, chat rooms, etc) the research community at large currently uses when carrying out research, and which ones it would be willing to use in the future.
The survey has six sections corresponding to the following phases of a research project: (1) Generate, elaborate and refine ideas; (2) Find partners; (3) Set up the research project; (4) Seek funding; (5) Run the research project; and (6) Exploit results. Each section has 3 questions.
The results of this survey will help the European Commission better understand what Internet-based services could in the future facilitate the participation of the research community in the European research and innovation programmes.
The questionnaire is anonymous and responses are aggregated for analysis. It takes ten minutes to complete.
Upon request, the survey results can be shared.
Link to the survey is here

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A new Resource for Nature Structural and Molecular Biology

Nature Structural & Molecular Biology (15, 767; 2008) announces a new section of the journal for articles that serve primarily as resources and also lead to novel molecular insights. Nature Structural & Molecular Biology focuses on the underpinnings of biological processes at the molecular level. However, in this era of large-scale, high-throughput experimentation, an increasing number of submissions to the journal describe mammoth data sets and the tools that facilitate their analysis. The new Resource section is for analyses of new data sets that lead to novel and arresting conclusions, as described in the journal's Guide to Authors. Resources are broad in scope and, in an era of burgeoning and ever-expanding technological advances, the approaches and findings that characterize this section will undoubtedly change over time. There are two examples of Resource articles in the journal's August issue:

Fission yeast SWI/SNF and RSC complexes show compositional and functional differences from budding yeast pp873 - 880
Brendon J Monahan, Judit Villén, Samuel Marguerat, Jurg Bahler, Steven P Gygi and Fred Winston
The Schizosaccharomyces pombe SWI/SNF family of ATP-dependent chromatin-remodeling complexes is now comprehensively analyzed, through composition, phenotypic and microarray analyses, thus broadly setting the stage for S. pombe as a new model organism for examining the SWI/SNF family remodelers. The S. pombe complexes are more akin to the metazoan SWI/SNF remodelers and have specific roles in repression of iron-transport genes.

A comprehensive library of histone mutants identifies nucleosomal residues required for H3K4 methylation pp881 - 888 Shima Nakanishi, Brian W Sanderson, Kym M Delventhal, William D Bradford, Karen Staehling-Hampton and Ali Shilatifard
A comprehensive library encompassing alanine scanning mutations across yeast histones is presented as a Resource that will facilitate screening of chromatin processes. The utility of the library is indicated by screening in cis and in trans for residues that affect histone H3K4 trimethylation, a modification that is associated with actively transcribed genes and known to be mediated by the Set1-COMPASS complex.

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Preservation of content in electronic journals

Via Knowledgespeak press release:
Two years after a meeting calling for urgent action to preserve scholarly e-journals, the results of a survey of 1,371 library directors of four-year colleges and universities in the United States have been released.
Most library directors who responded believe their own institution has a responsibility to take action to prevent intolerable loss of scholarly records. But although larger libraries support one or more e-journal preservation initiatives, most respondents from smaller libraries are yet to support any preservation effort and secure permanent access to e-journals for their institutions.
The survey, conducted by Portico and Ithaca, raises questions about how the responsibility for preservation of critical electronic resources should be supported by the community, even as electronic resources expenditures expand substantially at libraries across the spectrum. The organizers hope that the report will be a catalyst for leaders of libraries, consortia, and other organizations to provide a mechanism for digital preservation. The full report is available for download as a PDF. (A summary is available here.) Readers are also invited to share comments and reactions in the provided online discussion space.

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Nature's Managing Director on future trends in publishing

Steven Inchcoombe, who became Managing Director of Nature Publishing Group (NPG) last October, is interviewed in the June/July issue of Research Information. He answers questions about the main information needs of researchers, the role of peer-review, NPG's position on open access, and provides some predictions for the future.

Open access means that authors or their funders may have to pay to publish papers and I think this will make them demand a higher level of service from publishers. They will want more visibility about what is happening in the publishing process. And once papers are published, authors will want to know who has accessed them as they might want to approach them about possible collaborations. In addition, self-archiving mandates require authors to do more work. If publishers are clever they will offer authors more help to do this. Also, as more authors are not native English speakers, publishers may have to help them more in how they express themselves in their papers. There are more and more versions of content available to readers. To justify their versions, publishers must offer serious value such as in forward and backwards citation linking. Another big challenge will be bringing in rich media such as audio and video.

See the Research Information website for the full article.

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A 3D revolution in communicating science

Jérôme Murienne, Alexander Ziegler & Bernhard Ruthensteiner write in a Correspondence to Nature (453, 450; 2008):
Since the release of Adobe Systems' Portable Document Format (PDF) version 1.6 in 2004, it has become possible to view interactively three-dimensional models that are embedded into PDF files. This attribute will dramatically increase information content as well as data transparency in scientific papers. Additionally, replacing multiple two-dimensional figures of a three-dimensional structure with one integrated interactive three-dimensional model will reduce the need for supplementary material.
The potential of this technological advance for all science is obvious. Because of the foreseeable rise in demand by the scientific community, publishers and scientific institutions need to work hand in hand to support the implementation of this highly desirable technique.

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Nature Chemical Biology on the role of Correspondence

The Editorial in the June issue of Nature Chemical Biology (4, 323; 2008) discusses Correspondence, an essential mechanism for mediating scientific debates, and the ways to foster scientific communication offered by the Internet. The primary aim of the journal's Correspondence section is to provide a forum for readers to engage in scholarly debate about original research papers that have appeared in Nature Chemical Biology. From the Editorial:

We believe that correspondence serves an essential purpose in the advancement of science, and so the question becomes how new web technologies can further enhance scientific interaction and debate. We are interested in what Nature Chemical Biology readers think. What types of correspondence warrant publication in print? Would you value the ability to comment on or 'rate' papers online? Should we create a chemical biology blog? What is the best use of online social networking to foster scientific discussion? We invite you to join us at the Nature Publishing Group chemistry blog The Sceptical Chymist to discuss these and other questions related to correspondence and the future of online scientific communication.
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Nature Network posts, events and good reading

A few useful links and some weekend light reading suggestions via Nature Network:

Who's got an opinion on public engagement with science? asks Nature Network London editor Matt Brown.

An overview of science-related "stuff" at Second Life, by T. Troy McGonaghy of Science in the Metaverse. Via the link, you can see the slides and a video of Troy's presentation at the recent Virtual Worlds: Libraries, Education and Museums conference.

On the Visualization and Science forum, Hilary Spencer posts what she calls a "rant" about powerpoint, public speaking and blog posts. I'd define it as a strongly opinionated article: it contains her reactions to presentations at a recent conference she attended, and provides some useful advice about how to make and how not to make helpful slides. In a post with a related theme, Nuruddeen Lewis at his blog Lab Daze provides a very useful primer about how to give a talk: 'Tips for nailing your next presentation'.

Martin Fenner on his excellent blog Gobbledygook writes on the "complicated" aspects of paper writing: all those policy and format requirements, ethical bodies' requirements, and international nomenclature committees' pronouncements. And Richard Grant, at The Scientist blog, hosts a discussion on writing style: 'On the care and training of students, especially the training.'

Stew at Flags and Lollipops picks up on various recent posts and articles about the lack of take-up among scientists of the online commenting facilities often offered by journals on the papers they publish. Stew takes previous suggestions with a pinch of salt, homing in on the two main reasons he believes inhibit people from writing comments on published papers.

LabLit publishes the first installment of Private Investigations, a four-part story about the adventures of a very special scientist-for-hire. The author? He or she is not unknown to Nature Network, as a small amount of detective work will reveal.

What is the best way forward for Eastern Europe's science? asks Mico Tatalovic at Cambridge Student blog, in an article featuring the new life-sciences institutue MedILS at Split, Croatia.

If you are in reach of London, there are some unusual science-related events coming up, listed by Li-Kim Lee (see links for further details): Elizabethan Sea Charts and Maps (behind the scenes); Francis Crick - DNA and beyond; Leonardo's philosophical anatomies; and my favourite, Prince Rupert, Cavalier and Scientist.

Today (14 March, which in the US style is 3.14) is Pi day; see Gobbledygook for links to the Pi day website, but also to some music, including the American Pi song -- as Martin points out, best listened to at 1:59 today.

And finally, again from Matt Brown, Nature Network's ten most prolific bloggers over the past six months, with links to the blogs concerned. They'll give you a good taste of the lively discussion on the network - do join us there.

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Language of scientific publishing

Frank Gannon in his EMBO Reports editorial this month (9, 207; 2008), Language barriers, writes about the stark contrast between his own ability to write in English and "the difficulties faced by scientists for whom English is a second language, and who have to cope with the much more restricted style of a scientific report." Dr Gannon goes on to discuss the differences between standard English language and the arcane, depersonalised style favoured by (or taught to) many when writing scientific reports, quoting the view that "the public would not bother to read scientific papers even if the journals were lying around for free, simply because scientific prose is largely unreadable for the non-expert—and often only barely readable for the expert."
Although English seems set to be the main language of science for the foreseeable future, it is worth noting that the Nature journals do encourage authors to use direct, plain prose. Our subeditors and copyeditors help authors of accepted manuscripts who are not native English speakers, and we provide advice on our website which we hope will be useful to scientists preparing a paper before submission to one of our journals. Advice is also available at Nature Network, for example at Linda Cooper's excellent advice blog Time for a change, and Ai Lin Chun's forum Nature Nanotechnology -- Asia Pacific and beyond.

See related article in the same issue of EMBO Reports as the Editorial discussed here:
Six senses in the literature: the bleak sensory landscape of biomedical texts by Raul Rodriguez-Esteban and Andrey Rzhetsky (EMBO R. 9, 212–215; 2008).


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Non-traditional publishing choices for biologists

Zeba Wunderlich and Kishore Kuchibhotla of Harvard University write in Nature's Correspondence page (451, 887; 2008):
The paramount importance of publishing in biology dissuades many young scientists from making non-traditional choices with regard to where and how we publish our work. My colleagues and I believe it is in our own interests to identify the shortcomings of traditional publishing and to explore other publishing possibilities that are free of those problems.
What can we do? First, learn about our options. There are several innovative developments poised to change the publishing landscape dramatically. Video publications, preprint archives and high-throughput online journals are but a few that have recently surfaced (for a discussion, see Nature Network's Publishing in the New Millennium forum).The onus is on all of us to investigate these resources and to consider how they might enrich our science.
To make a difference, we also need to contribute. Frustrated by technical difficulties in reproducing published experiments? Then publish a video protocol in the Journal of Visualized Experiments. Have you benefited from a colleague's comments at a conference? Then extend the experience, and comment on articles published by PLoS One and posted on Nature Precedings. These initiatives will take hold and achieve their full potential only with strong support from the scientific community.
If we collectively embrace these ideas, publishing will become more effective. Although the psychological and social barriers to submitting a contribution initially are surprisingly high, becoming involved has proved to be rewarding. Ultimately, scientific progress and the published record have a symbiotic relationship — improved communication will enhance the pace, progress and efficiency of research.
[Note added by Maxine: In addition to the resources mentioned above, Nature Protocols is an online resource which welcomes the upload of protocols, in video or written form, and provides users with an interactive network for comments and additions.]

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Social network for nephrologists

The International Society for Nephrology (ISN) Nephrology Gateway is being completely redesigned this month (March 2008), with many new interactive features. Since its initial launch in 2005, the gateway has become an important online resource for nephrologists worldwide, including many educational projects, and providing links to news and literature, ISN contact information and membership highlights, a conference centre with announcements, and career resource links. The ISN is one of Nature Publishing Group’s valued society partners, with more than 8,000 members worldwide. The gateway also supports the ISN's membership service activities, connecting nephrologists with information and each other to improve patient care.
The latest addition to the site is the ISN Network, where nephrologists can log in, create a profile, set up discussion groups and participate in online forums. There is already a special discussion group on the ISN Network for all those involved in editing and publishing the journal Kidney International.
More enhanced search features within the gateway will soon follow these initial features.

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Due credit for Asian authors

Chinese authors are publishing more and more papers, but are they receiving due credit and recognition for their work? Not if their names get confused along the way. Jane Qiu investigates these, and other questions, in a Nature news feature in the current issue of the journal (Nature 451, 766-767; 2008). The article covers the huge problem of how to distinguish between Asian researchers, given the vast numbers of people sharing relatively few surnames. The problem is particularly challenging in the publishing sphere, not only in identifying an author correctly in citation databases and other indeces, but for editors in choosing appropriate peer-reviewers. Asian researchers suffer in being hampered from full participation in the international scientific community, for example they are less likely to be invited to contribute to conferences, to be successful in grant applications or to win awards.
The news feature provides a clear overview of these issues, and more, from a range of perspectives. Some journals have begun to provide author names in original (not Latin) characters, and there are various initiatives to provide unique author identifiers. At this stage, however, there is no consensus as to the best way to proceed: there are problems of technical compatibility between publishing, database and indexing systems, of agreement on universal standards, and other challenges, such as the high mobility of scientists, making it difficult to track the author of several publications.
Nature Network has a forum "What's in an Asian name?", in which several Asian and other researchers provide their perspective of this challenging issue for publishers and database curators. A Nautilus post last year highlighted the efforts of the Human Frontiers Program to help Japanese and other Asian scientists to improve their international visibility.

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What's in a Jane?

Martijn J. Schuemie and Jan A. Kors (Bioinformatics doi:10.1093/bioinformatics/btn006 ) have created a freely available web-based application that, on the basis of a sample text, can suggest "journals and experts who have published similar articles". Their aim is to help scientists to determine which journal is most appropriate for publishing their results, and which other scientists can be called upon to review their work. The application is called Jane (for journal/author name estimator).
I inputted some sample text to Jane, and was told that the Saudi Medical Journal was my top choice. No disrespect to that journal, but I know (because I am a person and not a computer) that this journal would be inappropriate for my test sample in at least two ways.
I would not primarily recommend an automatic selector to authors trying to decide where to submit their articles. When someone is ready to submit a paper, she or he will have given talks about the work and circulated drafts for comments from others in the field. That is a good time to ask for suggestions and advice about journals in which to publish. The scientist is then well-advised to read the author guidance on a few journals' websites, to find out about editorial scope, impact factor and so on.
I think it is possibly counter-productive to use this kind of text-based comparison system on its own for making decisions about journal submission. At Nature, for example, we are looking for novel results, not something similar to what we have just published. Other journals are the same – most of them are looking for distinctive articles, not incremental repeats.
Rather than relying on computer searches to choose where to submit, I highly recommend looking at our free Author and Reviewers’ website for writing and submission advice. From there one can go straight to a great set of articles written by professional journal editors about how, where and why to submit and publish at the free science-information website SciDev.Net.
In addition, scientists can upload a draft manuscript into a community preprint server, where others in the field can comment and suggest. (Nature Precedings is one such, which provides meta-features such as alerting people in the field when new preprints have been uploaded, but many others. ArXiv is another, for the physical sciences.)
I think it will be a sad day when science journals publish “articles selected for us by computer”.
(I first read about Jane at Nature Network in a post by Graham Steel.)


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Ask the Nature editor about all kinds of subjects

One of the longest, and longest-lasting, Nature Network discussions in which I have participated is called "High Impact made by famous ones", started in October 2007 by a graduate student known as "Universal research" as part of the "Ask the Nature editor" forum.
The forum, incidentally, is hosted by the editors of Nature Network, and is for scientists who want to learn more about getting their work published in Nature and the Nature journals, and about careers in scientific editing, straight from the editors of these journals. You are welcome to join the group and post your questions.
Returning to the discussion thread about those "famous ones". The Nature and Nature journal editors who regularly handle manuscript submissions provide their answers to a wide range of questions, including whether being well-known or having a stellar track-record is more likely to get your mansucript sent for peer-review or published (answer: no); blinding of the peer-review process (double-blinding gets an airing, but Nature journal editors explain why they feel the system of single-blinding is best for scientists); duplicate publication (or "salami slicing" as it is often known); and independence of editors from those whose work is being considered.
This thread may not be the longest or the oldest that I have ever seen, but it is certainly among the most focused and useful for authors, and I highly recommend you read it for a unique insight into the editors' thought-processes. If you are at the start of your publishing career as a scientist, you are likely to find this forum very helpful. We welcome you there.

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Repaying the rewards of research

Fundamental research can yield unforeseen benefits of great value for society, but often this happens only many years after the initial breakthroughs have been made. Can society find a way to pay back this debt?
In a Commentary in this month's issue of Nature Physics (3, 824-825; 2007), Leon N. Cooper of Brown University, writes that "Money is required to do science and as systems become more complex, more people, equipment, and therefore more money is required for each new result. Naturally, people hark back with sentimentality to the good old days when results could be obtained on a tabletop. In fact, some results are still obtained on tabletops, but the tables are getting larger and the tops more expensive. More and more results come from huge collaborations demanding enormous resources. And this brings us inevitably to the questions of who pays, how and why."
After outlining some of the problems in supporting the fundamental research necessary for science to progress, Professor Cooper suggests three measures to improve the current system, involving investment, distribution, and a clear distinction between fundamental and applied research. Referring to the breakthroughs in superconductivity research, he writes: "No single method can solve all of our problems, but the measures outlined above would substantially improve our present system. I would hope that they would make it easier for some current gifted program officer to reach as wise a decision as was made in the Army Ordnance Office fifty years ago."
Read the full article, entitled "The unpaid debt", in the December issue of Nature Physics.

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Tim O'Reilly visits Nature Publishing Group

Tim O’Reilly, head of the company bearing his name that, since 1978, has been a “chronicler and catalyst of leading-edge development, homing in on the technology trends that really matter and spurring their adoption by amplifying "faint signals" from the alpha geeks who are creating the future”, recently visited Nature Publishing Group’s London offices. Rosamund Daw, a senior editor in Nature’s physical sciences team, attended his talk, and here reports her impressions.

Tim O'Reilly's talk was a fascinating insight into the mind of someone who thinks about new ways of getting people together in real life and on the internet to generate new stuff (ideas, information, products). His presentation was a Q+A forum, which he kicked off by introducing the concept of “Web 2.0” as the phoenix rising from the ashes of the dot-com bust of the early 2000s. The concept of Web 2.0 seems to be based around harnessing the interactive networking power of the internet to provide new functionality and information.
Topics discussed in the forum included concerns with privacy on networking websites. O'Reilly believes that attitudes to privacy more generally are changing: that privacy is something that people are prepared to compromise if they can clearly see the benefits – one of his examples was surveillance cameras, and another is the relaxed attitude that can be seen at the social networking site Facebook.
Another topic was open access. When asked whether making content free led to mediocrity in publication quality online, O'Reilly responded he didn't believe that this had to be the case, giving Wikipedia as an example.
Anther question concerned what's at the "edge" of Web 2.0 ? O'Reilly discussed the idea of sensing: generating, for example, new information content through combining imagery posted on the internet. Imagine wandering through the streets of Paris on a virtual site generated from thousands of images of Paris posted on the internet from different people!
O'Reilly was exceptionally kind about NPG's efforts at the frontline of web developments. He and his colleagues blog at O’Reilly Radar , and you can find out more about his company’s activities here .
You can read another account of Tim O’Reilly’s talk, including a picture, over at Nascent, NPG’s web publishing blog.

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Molecular Systems Biology's new author licence

Via Seven Stones blog:
Molecular Systems Biology (published by a partnership of the European Molecular Biology Organisation and Nature Publishing Group) has changed its publishing licence for all articles accepted after 1 October 2007 (see updated instruction to authors). The new procedure allows the journal's authors to choose between two Creative Commons licences: one that allows the work to be adapted by users ("attribution-noncommerical-share": by-nc-sa), the other that does not allow the work to be modified ("attribution-noncommercial-no derivative": by-nc-nd). The first articles to be published under the new licence are appearing online at the beginning of this month. The journal's content is therefore not only freely available to all, but also authors can decide to make their research fully open for reuse and adaptation.

Thomas Lemberger, EMBO editor of Molecular Systems Biology, who runs the Seven Stones blog, notes that he initially wanted to make this announcement only after the first paper published under the new licence (accepted after 1 October) had appeared online, but in light of a recent Editorial in PLoS Biology (“When Is Open Access Not Open Access?”), reviewing in detail the subtleties of publishing licenses and the concept of “open access”, he bought forward the announcement of Molecular Systems Biology's new policy. "Unfortunately, this Editorial, at the time of its publication (16 October), included erroneous information on Molecular Systems Biology, given that we had updated our policy on 1 October.", Thomas writes. "In any case, it is somewhat ironic that MacCallum chose to stigmatize Molecular Systems Biology as an example of a journal that “promulgates” confusion about open access. As it turns out, Molecular Systems Biology is dedicated to the concept of making research freely available and to engage authors themselves in decisions that would achieve this goal with their own research. It is in this spirit of openness and respect for authors that we have recently adapted our license to publish."


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Ask the Nature editor: scientific publishing careers

The Ask the Nature Editor forum on Nature Network is now taking questions on careers in science publishing. Moderator Corie Lok (also Editor of Nature Network) writes: "Have you ever wondered about careers in scientific publishing? What is it like being a manuscript editor, a science writer, or a copy editor? You can find out by posting your careers question here. Editors at Nature, including ones who hire editors here, will answer your queries."
If you have questions about publishing in the Nature journals, peer review, writing your paper, and so on, you can still post them in the Ask the Nature Editor forum, and they will be answered by Nature editors, including me (Maxine), Karl Ziemelis (Chief Physical Sciences Editor), Ritu Dhand (Chief Biology Editor), Natalie De Witt (senior biology editor), Chris Gunter (senior biology editor) and Linda Miller (US Executive Editor), and Nature journal editors, including Laurie Dempsey (senior editor, Nature Immunology). We are receiving some interesting questions, and are enoying answering them and interacting with you.

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Choose your favourite article from Nature

Have you ever seen something in Nature — be it a research paper, news story or an editorial — that you thought deserved far more attention that it received? We value your opinion, so we've launched a website, 'Best of Nature ', that allows readers to nominate, vote for and discuss content from Nature's past. Please vist, and tell us what we may have missed while compiling the 'History of the Journal Nature ', a newly launched website which explores Nature's history back to the first issue in 1869, and of which more later.

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Science publishing forum organized by students

What’s the impact of the “impact factor”? Are you satisfied with the current scientific publishing process? Will the internet revolutionize publishing? What are your thoughts on open access publishing and how it will affect the future of scientific publishing? If you are interested in these questions, join the Nature Network forum "Publishing in the New Millennium" , which is linked to a conference on Friday 9 November 2007, 1:00 – 6:00 p.m., at Harvard Medical School.
The conference is organized by students, and will convene experts from across the world to discuss the state of publishing in the biological sciences. The keynote address will be by Nobel laureate Harold Varmus, former director of the NIH, now head of the Memorial-Sloan Kettering Cancer Center.
The State of Publishing will critically assess the impact that scientific publishing has on scientific research, with panellists including Robert Kiley, head of e-Strategy of the Wellcome Library; Isaac Kohane, director of the Countway Library at Harvard University; Emilie Marcus, Editor-in-Chief of Cell Press and Editor of Cell; and professor Stuart Shieber of Harvard University. Publishing 2.0 will examine the future of publishing in an increasingly digital world. Panelists include Moshe Pritsker, Editor-in-Chief of the Journal of Visualized Experiments; Hilary Spencer of Nature Precedings; John Wilbanks, executive director of Science Commons; and Bora Zivkovic of PLoS ONE.
By joining the Nature Network forum, you can discuss topics before the meeting, receive updates, suggest topics, and see who else is going.

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Twenty pearls of wisdom in your life

"What would you do if you could publish only 20 papers throughout your career?" asks Juan-Carlos Lopez on Spoonful of Medicine blog, referring to this month's Nature Medicine editorial (free access at Nat. Med. 13, 1121; 2007). If scientists would agree to limit their output to 20 papers over a career, would this clean up the scientific literature and improve on the peer-review process? Juan-Carlos writes: "many articles reporting incremental advances would no longer be written, and many specialized journals would disappear. And with far fewer papers to read, each one reporting a much more complete piece of research, search committees or funding bodies could directly evaluate the work of a given scientist, instead of leaning on surrogate indicators such as a journal's impact factor or number of citations, "evil" numbers that many researchers love to hate."
See the Nature Medicine editorial for further details of this radical proposal.


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Biotechnology publishing trends

For those interested in following biotechnology publishing trends, there is a useful resource in the September issue of Nature Biotechnology: Trends in biotech literature 2006. Andrew Marshall and Gaspar Taroncher-Oldenburg write: "unsurprisingly, microRNAs dominate the list of highest cited papers, and the area is witnessing rapid growth. The number of papers in other fields, such as proteomics, nanotech and RNA interference, also continues to expand; 80% of the publications specifically reporting cancer stem cells were published in the past two years. China and India continue to increase their output of biotech papers; France fell behind Spain and Italy; Switzerland entered the top 15 for the first time." For futher details, see:
Number of biotechnology articles per region.
Historical trends in biotechnology fields.
Biotechnology journal impact.
Most cited institutions in pharmacology and toxicology.
Top cited papers by field.
(Gaspar Taroncher-Oldenburg is Editor of the Nature journals' special pharmacology projects; Andrew Marshall is Chief Editor of Nature Biotechnology.)


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A rough guide to publication

Nature Methods' September Editorial, A 'rough guide' to publication (Nature Methods 4, 675; 2007) describes the process of submitting or resubmitting a manuscript—some important steps and decisions along the way.

The path to publication is a well-beaten one for some scientists but seems more like a dark, unmarked road to others. It helps to know what to expect from peer review (see our May 2006 editorial), but a number of other procedural steps often cause disorientation as well. Here are some trail blazes and travel advice.

You can comment on the Editorial at Methagora, Nature Methods' blog.

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Papers should not need supplementary information

Larry Benson of the Chief Arid Regions Climate Project in Boulder, Colorado, writes in this week's Correspondence in Nature 449, 24 (6 September 2007):
Until the past few years, both Nature and Science confined their articles and letters to a rather small number of words. This was both good and bad; good in that the articles were short and to the point; bad in that it eliminated studies that were complex. I first thought that the Supplementary Information sections were a great idea. Here was a way to place at the readers' disposal important data (tables or figures) that were necessary background to the work, but not necessary to the reading and understanding of the paper.
However, some recent articles refute my thinking. One or two have contained tens of pages of this supplementary material, essential to the reading and understanding of the article. Ten pages of Supplementary Information are not unusual, and the average for Nature is about five pages.
I suggest either that you either publish hard-copy papers whole and integrated in a long form, or publish them whole and integrated on the web, as you now do with Methods sections.

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Update on writing manuscripts in MS Word 2007

Nature Publishing Group (NPG)'s Chief Technology Officer, Howard Ratner, has posted an update on Nascent (NPG's web publishing blog) about Microsoft Word 2007 (DOC X) for authors writing for science, technology and medicine (STM) publications.
Howard hosted a meeting on 25 July 2007 at the NPG office in New York for staff from Microsoft, the American Institute of Physics, the American Geophysical Union, Science, Inera (producers of the eXtyles automatic editing tool), Aries (in this context, producers of manuscript tracking systems) and NPG. The publishing participants provided a high-level overview of the various stages involved in a typical journal's publication process, from the author writing the manuscript, through submission to publication, including a quick overview of the types of software systems and standards used to aid in these workflows. This was then followed up by presentations from Inera and Aries detailing the problems Word 2007 is causing for editing tools and manuscript tracking systems.
In his Nascent post, Howard details some of the outcomes of this fruitful meeting:
--Microsoft will establish a page on one of its websites with more advanced details on how to best use Word 2007 in a publishing environment. (For example, an image of an equation created when saving a Word 2007 file to Word 2003 carries semantic information that can be reused when reopening in Word 2007 file.)
--Microsoft will consider adding text to its help file with Word 2007 especially about its Math Markup Language Support.
--Microsoft will educate publishers by more frequent presentations at publisher events.
Howard also provides links to more information of use to authors, including this summary by Bruce Rosenblum of Inera, and this set of Connotea bookmarks on DOC X , to which you can add.
Nature is currently testing Word 2007 manuscripts in its editorial production system. If you are using Word 2007 and have a sample manuscript (created from scratch in Word 2007) that you can send us, please do so, as an attachment, to the authors' email address. We are particularly interested in equation-heavy manuscripts, as our experience is that equations and symbols (Greek letters and so on) provide the most stringent test.

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Nature seeks a Books&Arts editor

Nature, the leading international journal of science in print and online, seeks a full-time Books & Arts Editor to play a key role in the development of its growing Opinion section.
The Books & Arts Editor will be responsible for producing timely, authoritative, urbane, informative, useful, competitive, entertaining, opinionated and engaging culture coverage in print and online, from commissioning to publication. Their section must review, preview and reflect upon the most important developments and trends in books, media, film, theatre, dance, music and visual art of interest to a broad, literate, global audience of working scientists and science-interested opinion leaders.
The ideal candidate will be passionate about science, books, the arts and the internet, educated to Masters level or beyond, with exemplary scientific and cultural contacts and at least 3 years editing experience, preferably in running a similar magazine section. S/he will thrive on ideas, deadlines, collaboration and innovation. The post is London based, but may involve some travel to Nature's overseas offices.
All candidates must demonstrate the right to live and work in the UK to be considered for the vacancy.
Contact Details:
Applicants should email a covering letter, 3 clips of their writing and editing, a CV of no more than 2 pages, and an outline of no more than 400 words of how they would cover Autumn 2007's biggest books and arts stories, quoting reference number NPG/LON/694, to Geetika Juneja at londonpersonnel@macmillan.co.uk by 29 August 2007.

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Getting stem-cell research published in Nature

For advice about how to get your stem cell paper in Nature, senior editor Natalie DeWitt, will answer your questions about how the editorial process works, common misconceptions and other topics in the stem-cell field. Please send Natalie an email containing your question.

Highlights from this month's Nature Reports Stem Cells include:

California stem-cell research: assessing return on investment
Read our commentary by Stanford researcher Michael T. Longaker that explores how Californians can figure out whether its landmark, debt-funded investment in stem-cell research will pay off.
Why are recipients of California stem-cell grants using lines that are eligible for federal funding?
A Nature Reports Stem Cell survey of researchers examines the grants designed to bring new researchers into the stem-cell field.
Bureaucracy blocks work on embryonic stem cells in Japan
Kyoto University's Norio Nakatsuji argues that irrational regulations stifle research in his country.
What experiments should be legal on animal-human chimaeras?
With new legislation covering the use of animal-human chimeras in the works in the United Kingdom, Nature Reports Stem Cells summarizes the report from the UK Academy of Medical Sciences.
Embryonic stem cells for drug discovery
In Nature Reviews Drug Discovery, experts from Monash University describe the advances needed to make assays feasible.
Also read about a survey finding that most fertility patients would donate left-over embryos for stem-cell research and the latest news and views on engineered pluripotent stem cells from Nature.

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August editorials on sharing, naming and credit

The Nature journals this month (August) feature several editorials on the publishing process. A short round up (with links) follows:

Nature Genetics (39, 931; 2007), in 'Compete, collaborate, compel', calls for procedures for microattribution to be established by journals and databases so that data producers have an overwhelming incentive to deposit their results in public databases and thereby to receive quantitative credit for the use of every published data accession.

In 'Got data?', Nature Neuroscience (10, 931; 2007 ) points out that data sharing is not only good citizenship for researchers, but is also required by funding agencies and many journals. The scientific community needs to develop better incentives to encourage compliance and reward those who share.

And in 'Name that gene!', Nature Structural & Molecular Biology (14, 681; 2007) warns that scientists coin new terms, or neologisms, at a tremendous pace, but name choice can have unforeseen results.

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Molecule search in Second Life

Chemist Jean-Claude Bradley, a friend of Nautilus's comments section, writes a post on Useful Chemistry blog about indexing molecules in Second Life

He writes: "As I've recently commented, there has been media interest in the use of the virtual online world Second Life for chemistry. We also recently demonstrated on Drexel Island that it was possible to visualize molecular docking using the molecular rezzer developed by Andrew Lang.
Nature Island [Second Nature is Nature's island in Second Life] also hosts several common molecules, including buckyballs. As more people start to experiment with representing chemicals and chemistry research in Second Life it would be nice if such examples were discovered by a simple Google search."

Check out the rest of the post, contribute to Prof Bradley's collaborative wiki "molecule indexing" project if you can (which seems to be working, from the comments to the Useful Chemistry post) --- and maybe even take a trip to Second Life.

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Timo Hannay and the Daily Transcript on "the web opportunity"

In this post on Nascent, NPG's web publishing and science blog, Timo Hannay provides a draft of his recent article in STM news : Nascent: Foo and beyond. The whole section is worth reading (and there is a good graphic of the opportunities provided by the "scientific web"), but here is an excerpt:

"The idea that everyone can now do their own publishing, making publishers superfluous, is misguided. But publishers do need to adapt. Online communities don't just happen, they require initiators, motivators, organisers, moderators, summarisers and guides. They also need trust systems based on user identification and reputation. In many ways, these, too, are traditional publishing roles, but they require new skills. Writers and editors now need to double as moderators and hosts. Publishers need to become adept at mitigating gaming and spamming of their systems, and at monetizing web traffic rather than selling subscriptions. On top of that, they need to become better at cooperating — with each other and with other organisations outside the industry. This particularly applies to online interoperability (even horror of horrors, with competitors), which is a positive-sum game that can benefit all participants. CrossRef has blazed a trail in this area, and we should build in its success.
Above all, publishers need to be leading the online charge, not following the scientists we serve. We are the information dissemination experts, so if we aren't pushing the boundaries and testing what's possible in this new world then we're not merely missing out, we're also not doing our jobs. Cynics will point out that most apparent 'opportunities' are a long way from turning a profit, and many probably never will. They're right. Do any of the STM projects I've mentioned above make a lot of money? No. But are they representative of the future of scientific communication, and do they provide a platform on which to build information businesses of the future? You'd better believe it."

In a similar vein, Alex Palazzo of The Daily Transcript blog wrote about Nature Publishing Group's "game plan" as he calls it, regarding science publishing and web "2.0" (the social, interactive web). The post arose from Alex's attendance at Nature Network Boston's pub night. This post, and the lively set of comments accompanying it, range over the the topic of the value of publishing in a journal, "open access" publication, and whether the unit of publication will become the paper itself rather than the journal in which it is published.


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History timeline for Nature

Nature Publishing Group has published an expanding, illustrated online timeline of the history of the company and its journals. Click on the arrow to expand each year's entry. The first segment, The first 100 years (1869 - 1969), celebrates the journal Nature : "What a glorious title, Nature, a veritable stroke of genius to have hit upon. It is more than a cosmos, more than a universe. It includes the seen as well as the unseen, the possible as well as the actual, Nature and Nature's God, mind and matter. I am lost in admiration of the effulgent blaze of ideas it calls forth." J.J. SYLVESTER, MATHEMATICIAN .
The second two segments are called Branching out (1970 - 1999) and NPG in the new millennium (2000 - 2007). All three timelines detail the fascinating progression of Nature, Macmillans and Nature Publishing Group: new editors, the origin of peer review, new journal launches, office openings, and more recently NPG's entry into realm of Web 2.0. All against a diverse selection of the science we have published since Nature's first issue in 1869.


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Starting an online conversation about your paper

"I'm a strong believer in allowing commenting on online papers", says Euan Adie on his blog Flags and Lollipops in a post titled Publishers, trackbacks and shared data. "This is something under serious discussion at Nature (the question is how to do it properly). The vast majority of researchers read, organize and discover papers online; we should give them the tools and opportunity to discuss papers online, too."
The Flags and Lollipops posting contains a discussion of technical ways to alert authors when there are new comments on their published paper, and ways to create systems to track "informal" comments and writing, so it can be part of a scientist's accredited boldy of work, and hence a more attractive proposition. We are interested in knowing your views -- Nature authors past, present and future, among the scientific community. Comments are open.

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Word 2007 and science publishing

In a post entitled Nascent: Word 2007 and the STM Publisher Ecosystem, Howard Ratner, Chief Technical Officer of Nature Publishing Group, writes about how he has become involved in "a very lively conversation with Microsoft staff about why Word 2007 is not being actively endorsed by STM publishers. It has recently come to Microsoft's attention that Nature , Science and many other scholarly publishers do not accept files from authors in Word 2007. Both Science and Nature Publishing Group have been in correspondence with Microsoft staff on this important issue. The staff there have been very willing to engage in this conversation."

The rest of Howard's Nascent post is the text of a letter to Microsoft by Bruce Rosebaum of Inera, which well explains the issues for science and technical publishers attempting to integrate this format with their typesetting and web coding systems. The letter concludes: "Those of us in the scientific community look forward to a dialog to articulate scholarly publishing requirements to Microsoft so that Microsoft can provide products that serve the needs of the entire scholarly community."

James McQuat, London Nature journals' Editorial Production Director, draws attention to an article by Margaret Heffernan at The Huffington Post, one of the world's most popular blogs, on this issue. It is a much more upfront analysis of the situation, but encapsulates it well.

In a comment to the Nascent post, Bruce D'Arcus writes: "There's another issue with backwards compatibility for scholarly workflows. Word 2007 supports new citation and bibliography fields. But if you open such files in previous versions of Word, the fields are converted to plain text. This means scholarly collaboration becomes impossible unless all parties are using Word 2007. I'm sure MS thought this a smart business decision, but I beg to differ. I think it'll mean many scholar won't bother with Word 2007, or its citation features."

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The Best Writing on Science Blogs 2006

Excerpted from Nature 447, 779 (2007).
Paul Stevenson reviews the book The Open Laboratory: The Best Writing on Science Blogs 2006,
edited by Bora Zivkovic. Lulu: 2007. 336 pp. $19.85, £10.99
The Open Laboratory is a collection of writing from science blogs, selected and published by the energetic biologist-blogger Bora Zivkovic with the help of the blogging community. In the run-up to the first conference of science bloggers earlier this year in North Carolina, Zivkovic took it upon himself to collate the fifty best posts put up by the end of 2006. Topics include micro black holes, bird migration, human sleep patterns, evolution, quantum mechanics and psychology. The writing ranges from PhD students enthusing about concepts from their research areas, to opinion pieces on themes such as the rights and wrongs of particle-physics funding, intelligent design and political interference in science policy.
This wide-ranging book provides something — hopefully many things — for everyone. Particularly enjoyable is browsing entries about areas of science away from one's own research interests. As a physicist, I learned a lot about the origin of mitochondria from the representative entry of Carl Zimmer's award-winning blog The Loom. I was pleased, too, to see entries from some of the highly trafficked blogs that I habitually read and enjoy, such as The Panda's Thumb and Cocktail Party Physics.
By their nature, blogs are dynamic. A post typically bristles with links out to elsewhere on the web and accretes an ever-changing exchange of comments between readers and the author. To capture this energy and texture in a static book is a challenge that the editor fully acknowledges in his introduction. The solution Zivkovic fixes on for The Open Laboratory is to pick posts that he feels work in isolation, to list links as footnotes and to omit the comment strings.
The entries highlight the great variety of styles that can thrive in the blogosphere. Most of the pieces are a little chattier than the usual book or magazine article, but those chosen are formal enough not to grate on the printed page. Occasionally, the prose is loftier than a typical popular science book. Some even veer too much towards the tone of a research article — leaving terms like suprachiasmatic nucleus or a zygomaticomaxillary suture unexplained.
The book works well enough as a standalone anthology of science writing, but I share the editor's hope that it will prompt eager print readers hitherto unfamiliar with the vibrant young medium that is science blogging to have a look, and maybe even have a go. Nominations for next year's anthology are already being sought.

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Tim Berners Lee on video

Web inventor Tim Berners-Lee Unplugged: Semantic Web better than APIs for data access

Via Berlind's Testbed blog, Sir Tim Berners-Lee, inventor of the world-wide web, received the 2007 lifetime achievement award of the Massachusetts Innovation and Technology Exchange in Boston on 5 June. After the reception to honour his achievement, "Sir Tim" (as David Berlind calls him) answered questions about the semantic web, data access and standards. The session is captured on video at the link above.

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Podcast on science publishing and the web

south by southwest festivals conferences

At the link above is a podcast of a session from the SXSW (South by South-West) Interactive Festival in Austin, Texas, held in March. From the conference website: "New publishing technologies challenge the traditional structure of peer-reviewed scientific journals. For hundreds of years the "article" has been the primary vehicle for conveying scientific information - but semantic markup, tagging and wiki are reconstructing scientific publications into a flexible and evolving concept." The panel looked at the social and legal implications of "Web 2.0" and the "Semantic Web" as they impact science and scientific knowledge. The moderator was John Wilbanks, Executive Director of Science Commons, Creative Commons, and one of the invited speakers was Timo Hannay, Director of Web Publishing of the Nature Publishing Group. The podcast has just been uploaded to the SXSW site, and is freely available by going to the link at the top of this post.


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Key narrative

From Nature's Authors page (Nature 447, xi; 2007):
It's one thing to review a book about events in your scientific field; it's quite another to find yourself a character in the story. Per Ahlberg, a palaeontologist at Uppsala University in Sweden, says he experienced "a dislocating feeling" while reviewing Swimming in Stone: The Amazing Gogo Fossils of the Kimberley by John Long. Ahlberg found that he had a "walk-on part" in the story about the finding, excavation and analysis of a treasure trove of fish fossils in an Australian barrier reef that is now above ground. Ahlberg's feeling of displacement increased when he came across "a rather unflattering photo of me with Mike Coates in the field".
Perhaps because of his proximity to the story, Ahlberg enjoyed the review process. "The pleasure of reviewing a book like this one is that not only is the subject familiar to me, but I've been to the locality and I know many of the people who featured in it." Despite some minor quibbles about details, Ahlberg was able to give the book his seal of approval. "I didn't have to throw the thing at the wall in frustration," he smiles.

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Right to cite, or citing not right?

Euan Adie, on his Nature Network blog FnL, posts about Shelley Batts' Retrospectacle review of a paper about treating fruit with natural volatile compounds to make it last longer, in which she included a figure and chart from the paper (the source was cited). An editorial assistant at the Journal of the Science of Food and Agriculture – where the paper was published – threatened her with legal action unless she removed the images immediately. The blogosphere reacted with predictable speed and free-expresssion, documented in Euan's FnL post.
Euan goes on to ask whether the reaction is, in the cold light of a couple of days later, reasonable, looking at the incident both from the point of view of the publisher concerned as well as the blogger. As he puts it: "Storm in a teacup or dark conspiracy?" There is a good debate in the comments to the FnL post, so if you are interested in weighing up these pros and cons, and would like to add your take, please take a look.

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When an editor discovered the Hobbit

Henry Gee, in his review of the book The Discovery of the Hobbit by M. Morwood and P. Van Oosterzee (Nature 446, 979-980;26 April 2007), describes what it was like to read what seemed to be the equivalent of a description of the discovery of a unicorn:

"Many manuscripts received by Nature are full of the confidence of scientists who know precisely what they have found and why it is important. But a paper that landed unannounced on my desk on 3 March 2004 was surprising, not only for the extraordinary discovery that it reported, but for the matter-of-fact, almost muted, tones in which it was described. Reading between the lines, it seemed as if the discoverers of Sundanthropus floresianus weren't entirely clear in their own minds about what manner of unicorn they had unearthed."

He goes on to recount: "The referees responded with one accord. To be sure, the creature was strange, but the strangeness might be a consequence of its size. The skull, though, was clearly that of a member of our own genus, Homo. In addition, one referee commented specifically on the specific name, floresianus, noting that generations of students would dub it 'flowery anus'. The authors duly changed the generic and specific name to Homo floresiensis and, after several iterations, that was the name attached to the fossil when the discovery was published in Nature on 28 October 2004."
See the complete book review here.

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Journals need to unify their style requirements

Biji T. Kurien, Yaser Dorri and R. Hal Scofield write:
While it is a fact that editors of scientific journals feel the pinch when authors use redundant prose (see the Correspondence by Cheryl Strauss in Nature 446, 725; 2007), it is also true that authors feel intense pain as a consequence of the differences in the style and format of reference required by many journals, as well as from the lack of general standardization criteria for units.
Many high-impact journals have a low acceptance rate, so most authors have to resend their manuscripts to other journals. At this juncture they are forced to spend long hours to reformat their manuscript to accommodate different submission requirements.
The two main methods of referencing articles in journal and book publications are the Harvard (author-date) and Vancouver (author-number) reference systems, although many journals have their own variants. There are also other reference styles, for example British Standards 1629 and 5605.
The Harvard style uses the author's name and publication date in the body of the text, with the bibliography arranged alphabetically by author. Several universities use variants of this style in their own institutions.
Vancouver style differs from Harvard by using a number series to indicate references. Bibliographies list these in numerical order as they appear in the text. The US National Library of Medicine provides sample references for about 40 different circumstances. Even though several top-tier medical journals use the Vancouver style, it is essential to consult 'Instructions for Authors' for any publication before submitting a paper. The Mulford Library at the Medical College of Ohio, for example, keeps a list of journal instructions to authors for more than 3,000 health sciences journals.
In several journals, in-text numbers cite references in superscript. Some journals require capitalization of titles, even for names, whereas others require author names in bold and yet others require the initials of the first author to be on the right side with initials of subsequent authors on the left. Some require author’s first and last name spelt out, whereas others prefer initials. Some require only the first page number, whereas others require abbreviated ranges (501-7) and yet others full page ranges (501-507). Punctuation conventions vary so widely as to drive one crazy. One journal even requires that 75% of the references in an article need to be indexed by ISI and published after 1998. Some need the volume in bold or just italics, some require the year of publication following author names, and yet others want it later on. It goes on and on.
Having a uniform submission and data expression system not only saves time for authors and readers , but can also help to eliminate citation mistakes, unnecessary headaches and speed up the submission and publication process.
Biji T. Kurien, Yaser Dorri and R. Hal Scofield
Oklahoma Medical Research Foundation, 825 NE 13th Street,
Oklahoma City, Oklahoma 73104, USA

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E-book developments for researchers

Via Outsell/Insights, I read that the International Association of Scientific, Technical and Medical (STM) Publishers last week held its Book 2.01 Seminar in London as part of the London Book Fair. The event set out to examine where STM publishers are heading with their e-book strategies, and to look at where future developments might lead.
One of the speakers, Professor Martin Hofmann-Apitius, of the Fraunhofer Institut for Algorithms and Scientific Computing, talked about scientists´ use of book content and about the innovative applications his institution has produced to interpret chemical resonance structure diagrams in scanned text in a way that can then be used for experimentation.
There was discussion about making books available through routes that have traditionally been used by researchers to find journal articles. This year many more e-book chapters may start to be indexed by Pubmed, Scopus and other abstracting and indexing services, bringing together book and journal content where researchers can find and use it. "Good news for researchers", according to Outsell/Insights.
The Book 2.01 presentations are available from the association's website.

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Length of time to write, and publish, a manuscript

Professor Stephen Seligman writes:
Nature's News article on Darwin and the 20-year publication gap (Nature 446, 478-479; 2007) discusses some of the controversies surrounding the reasons for the 20-year delay between the time that Darwin began to think about evolution and the publication of Origin of Species.
Whatever the cause of the delay, there is little disagreement about the chief factor that forced Darwin eventually to publish (The Encyclopaedia Britannica, 11th edn VII, 840-843; Cambridge University Press,1910). On 18 June 1858 he received a letter from A. R. Wallace, then at Ternate in the Maluku Islands, describing a theory of natural selection strikingly similar to his own. Darwin, taken aback by the realization that he could be scooped, consulted colleagues, who sent Wallace's essay, together with an abstract of Darwin's work, as a joint article that was read in a meeting of the Linnaean Society on 1 July of the same year.
Thus a procrastination of two decades was ended in 13 days. Both men had been stimulated by reading Malthus on population. While lying ill with fever in Maluku, Wallace developed the theory of natural selection in two hours and completed his essay in three days. By modern standards, both men would have been eligible to share a Nobel.

Stephen J. Seligman, MD
Research Professor
New York Medical College
Valhalla, New York 10595, USA

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Agreement on the scholarly communication process

Goals for Public Policy - Scholarly Communications Statement of Principles | RIN

The UK's Research Information Network (RIN) has brought together research institutions, publishers, funders and libraries, who have reached agreement on a statement of "the principles and goals at the heart of the scholarly communications process". The signatories so far include:
Association of Learned and Professional Society Publishers (ALPSP)
The British Library
The Consortium of Research Libraries in the British Isles (CURL)
The International Association of Scientific, Technical and Medical Publishers
The Joint Information Systems Committee (JISC)
The Publishers Association
Research Councils UK (RCUK)
The Research Information Network (RIN)
The Society of College, National and University Libraries (SCONUL)
The Wellcome Trust.

The statement can be downloaded as a PDF (8 pages). The organizations have signed up to seven principles, including the aims and quality of research; recognition and reward; dissemination, publication and access; and preservation of printed and digital output.

According to an article in Research Information, "Michael Jubb, director of RIN, admitted that ‘at one level, the statement states the blindingly obvious’, but he was keen to point out that this is the first time that all the major players have agreed on what the goals of scholarly publishing are. ‘The next step is for us all to discuss how best to achieve these goals,’ said Jubb."