Nature Geoscience on the pros and cons of online publication


Online publishing has blurred the boundary between accepted and published articles, a topic discussed in an Editorial this month (April) in Nature Geoscience ( 3,219; 2010) . From the Editorial:

With the advent of online publication over the past 10 years, it no longer needs to take months or years for an accepted paper to become available to journal subscribers, and the term ‘monthly journal’ is losing its meaning. Articles are published online weeks to months before publication in print, with benefits all round: authors can make their peer-reviewed results available to the scientific community quickly, readers can keep abreast of the latest developments and publishers can provide a continuous stream of content in an increasingly competitive market.

But the downside of early online publishing is a confusing array of publicly available article types, awaiting print publication in various stages of editorial preparation. Some journals place papers online first for peer review, and then in their final form. As the focus of scientific journals is moving from print to electronic publication, each publisher makes its own decision regarding the balance of speed versus the completeness of published work. But when papers go online before they are in final form, uncertainity arises regarding the canonical publication date.

Publisher’s policies regarding the accessibility of online articles are equally piecemeal. Science Express — where Science papers are posted online up to six weeks ahead of publication in print — is available to site licence subscribers only as a premium add-on. And when journals of the American Geophysical Union publish ‘in press’ papers before their print version, only the titles of these papers are available to non-subscribers. On publication in print, abstracts are also free to access online.

Nature Geoscience papers are published online in their final, definitive form — fully proofread and formatted — and the date of online publication is the date of record. However, we consider papers elsewhere as published as soon as the scientific content is fully available online, with a Digital Object Identifier (DOI). That is, we are happy to highlight ‘in press’ articles, whatever format they are in. We also count them as part of the body of existing literature when assessing the advance of a submitted paper over existing knowledge.

As the demand for print subscriptions wanes, unified payment models for accessing papers online and in print are likely to evolve. What needs to be decided is how much a preliminary paper published online should be allowed to change before it constitutes a new paper.

The human genome ten years on, and introducing the News&Views forum

nature1 April.jpg

The draft human genome sequence, announced with much fanfare in 2000, promised great insights into human biology, medicine and evolution. In a special in this week’s issue, whose content is free to read online, Nature asks whether the sequence has delivered the insights that were anticipated, and what lessons have been learned from the first post-genome decade. Human genetics in 2010 looks infinitely more complex, and questions about how to make sense of the explosion in biological data are only becoming more pressing. Read articles in Editorial, Features, Opinion (including articles by Robert Weinberg, by Craig Venter and by Francis Collins), Books & Arts, and News & Views, listen to our podcast and see past Nature collections.

What did the human genome mean to you? The availability of the human genome sequence shaped scientists’ lives and research in ways they could not have predicted. Help Nature gauge the impact of the sequence by taking part in a brief survey.

I’d like to highlight here Nature ’s Cell biology forum in the News & Views section: Genome-wide view of mitosis, in which Jason R. Swedlow on the one hand, and Cecilia Cotta-Ramusino with Stephen J. Elledge on the other, provide two complementary views on a paper in this issue of Nature describing an exceptionally large-scale project aimed at assigning function to all protein-coding genes in the human genome. This forum, in common with all other articles in this issue and all other issues of Nature, is open for your comments online. We look forward to reading what you think.

Content rules, but commenting can add value


Content rules, writes Nature in an Editorial in the current issue (464, 466; 2010), in which Nature ’s new online commenting facility opens up the entire magazine for discussion. The Editorial is reproduced here:

‘Conversation is king’, according to a mantra frequently repeated by enthusiasts of online social media. But we editors and writers tend to give our first allegiance to content — not least because of our labours to research, commission, select, create and otherwise add value to content, and to do so in a way that informs and stimulates our readers: the people who pay for it.

But, unquestionably, conversation can add value to such efforts. Therefore, this week we introduce an online commenting facility that will allow readers to respond directly to any of our content.

Commenting is not new to Nature. Our online news service has long allowed it, and recent examples show how lively and interesting readers’ observations can be — in their response to our coverage of Google in China, say, or of dismissed researchers in Mexico.

Online discussions about our research papers are likely to be considerably more subdued, according to the experience of other publishers who already allow commenting. This is understandable. Commenting on a paper in the rather formal context of a journal’s website may seem daunting to some scientists, and to others may pose a needless risk of offending colleagues, or of making an unguarded statement that may come back to haunt them. Perhaps more importantly, a commenter acquires no formal academic credit for his or her efforts, making the time spent commenting seem like time wasted. For that reason, we will continue to publish formal responses to papers in our online Brief Communications Arising section, in which contributions are peer reviewed and have a high threshold for acceptance.

As for the acceptance thresholds for readers using the new commenting facility, we are adopting a twin-track approach. For News & Views, Reviews and primary research, we will vet submitted items before they are allowed to appear on our site. Our intention is to remove only those submissions that are clearly subject to legal concern, obscenity or unjustified assertions. We will not seek to prohibit trivia, for example — although we’d be glad if our commenting readers could help keep the signal-to-noise ratio as high as our critically minded audience expects and deserves.

All other sections will be run on the same basis as online news is now: submitted comments will appear online immediately, without any monitoring or vetting beforehand. But they will be promptly removed on receipt of a substantive objection from a reader, on similar grounds to those above. People wishing to comment should be alert to the currently unavoidable weight of English libel law, which places a heavy burden of proof on those making allegations, rather than on the subjects of the allegations who choose to sue, as generally applies in the United States. We will review our approach after a few months.

Meanwhile, we welcome all our readers’ contributions to the conversation.

Some comments from readers to this Editorial:

Todd Gibson said: In light Nature attaching a commenting feature to research papers, I once again encourage researchers hosting journal clubs to task their charges with writing up a consensus review of each article discussed, and posting it to the commenting facility. The article’s authors will almost invariably respond enthusiastically. The activity would both enliven underutilized paper comments, and further develop skills valuable to nascent researchers.

Nick ONeill said: Congrats! I think this is a really great step for Nature, and a step beyond what was “required” in opening your news to everyone online. Very commendable!

William Gunn said: Todd – that’s a great idea. To extend it further, one could imagine the comments section to be a “rolling attendance” journal club.

While I understand the motivation to require registration and to moderate comments and it’s not at all unexpected given the policies in force at Nature Network, I just don’t think silly comments are really the biggest problem.

Timothy Roberts said: Well done!

Frank Norman said: Nice title! I hope the rules for commenters will not put off genuine commenters. It will be interesting to review the level of commenting in a year’s time, and to compare with other sites.

Tyler Kokjohn said: Will conversation add value to content? Let’s examine the evidence. Todd Gibson’s idea is a true gem that was immediately seized on by commentors who have begun to augment it along productive lines. Initially skeptical, I recognize a great start when I see one. Let’s hope the journal club idea is emulated by many others who recognize that although they may yield no formal academic credit, such discussions can be of enormous value.

Nitin Gandhi said: Science is one of the profession where one cannot progress just by doing good PR job and get away. It is now very easy to know where the scientist stands just by click of mouse. With the web-based data like Pub-med, Scopus, etc.

“Nature” has taken one step further by starting this “risky” venture of on-line comments on published paper, this will benefit both he commenter’s and comment upon.

I thank “Nature” to give this opportunity to comment and get commented upon if the commentator is giving time without the apparent benefit – the pleasure will be to realize that science in general getting benefited.

I also feel that all the other journals take the cue from “Nature” and start this system -the global discussion!

I am sure that one day even tgrants evaluation will become transparent and one can see the comments and markings the grant evaluator has made and reader can also make the comments this will certainly revolutionize the science, this will help greatly separate out wheat and chaff.

“Nature” has taken the first step -Congratulations.

You are welcome to add your own views to the dicussion, either here or at Nature’s website.

Nature Chemistry celebrates its first birthday


April 2010 marks the first anniversary of the launch of Nature Chemistry. To celebrate, the editors have put together a compilation of their favourite articles from the first 12 issues. The selection, from ‘Chemistry goes global in the virtual world’ by Jeffrey S. Moore and Philip A. Janowicz last April, to ‘Single-molecule spectroscopy: Caught in a trap’, a News and Views article by Peter Dedecker and Johan Hofkens in the March 2010 issue, reflects the breadth of topics covered by Nature Chemistry. The collection is free to read online until the end of June 2010.

Nature Chemistry first year highlights.

Nature Chemistry journal home page.

The journal’s guide to authors.

The Sceptical Chymist, the Nature Chemistry blog.

Tomorrow’s Giants conference in July


The Royal Society and Nature present: Tomorrow’s Giants, a conference on 1 July 2010 at the Queen Elizabeth Hall, Southbank Centre, London, UK

Tomorrow’s Giants will bring together scientists and policy makers to gather scientists vision of the next 50 years, to address questions such as: What is required to enable academic achievement of the highest quality? What will science be like in 10 and in 50 years time? What will be the main goals and challenges?

Attendance at the conference is by application. Applications are encouraged by The Royal Society and Nature from early and mid-career scientists with an interest in the key topics of the conference and who wish to make a positive contribution to the parallel sessions and the panel discussion.


Thursday, July 1, 2010

9:00 a.m.

-Welcome and Introduction

-Lord Martin Rees, President, The Royal Society – Philip Campbell, Editor in Chief, Nature

9:30 a.m.

-Parallel Sessions

-Leaders in the field will be raising questions and looking at the challenges across three major themes identified for Tomorrow’s giants.


Moderator: Dame Sally C Davies, Director General of Research and Development and Chief Scientific Adviser for the Department of Health and NHS -Careers

Moderator: Robin Williams, Director of the Research Centre for Social Sciences at the University of Edinburgh -Measuring and assessing

Moderator: David Sweeney, Director (Research, Innovation and Skills) at the Higher Education Funding Council for England

11:00 a.m.

-Feedback session

1:45 p.m.

Keynote Speaker: Dame Wendy Hall, Professor of Computer Science, University of Southampton

2:45 p.m.

-Panel Discussion

-Our Panel of leading policy and decision makers along with representatives for the three themes will answer questions raised in the parallel sessions and discuss selected topics from the event’s Nature Network Forum


John Beringer, University of Bristol

Lord Paul Drayson, Minister for Science and Innovation Tony Hey, Corporate Vice President of External Research, Microsoft Terence Kealey, Vice-Chancellor, University of Buckingham Adrian Smith, Director General, Science and Research, BIS

3:45 p.m.

-Concluding remarks

Tomorrow’s Giants conference website and online application form.

Nature’s collection on biodiversity


Nature presents a supplement on biodiversity, in this International Year of Biodiversity. As nations come together to reduce the alarming loss of species taking place worldwide, we hope that these features, opinion pieces, News & Views articles and original research papers will provide a useful snapshot of the problems faced and solutions proposed. All the articles in this supplement are free to read online for six months from the publication date, and a free print copy can be requested.

From the supplement’s Editorial: "The rich variety of the natural world that Charles Darwin memorably imagined as an “entangled bank”, and that E. O. Wilson labelled “biodiversity”, is in crisis. The International Union for Conservation of Nature (IUCN) calculates that one-fifth of mammals and nearly one-third of amphibians are threatened with extinction. Some estimate that only half of the species alive today will survive to 2100. Others describe the pace of biodiversity loss as 100 times the rate of natural extinctions. Less-diverse ecosystems are less productive, less stable and less robust. So loss of biodiversity may weaken ecosystems and make them more fragile, especially in the face of climate change, with grave consequences for food security, among other things.

This year, therefore, has been designated the International Year of Biodiversity (IYB) by the United Nations General Assembly. Throughout the year, evolutionary biologists, ecologists, conservationists, policy makers and communicators will be negotiating how best to reduce the rate of loss of biodiversity.

As a contribution to IYB, this collection of reported features, expert opinion pieces, News and Views articles and original research papers published recently in Nature provides a useful snapshot of the complexity of the biodiversity problem, and the solutions proposed and tried."

Other Nature collections.

Levels of editing at Nature


Q: Is editing support given to manuscripts published in Nature? What level of editing is done? Is this editing done in house or outsourced? Are you and the authors pleased with the level of editing?

A: When a manuscript is submitted to Nature it goes through several rounds of peer review – the manuscript as accepted is very different from the version submitted. The peer-reviewers (typically 2 or 3) and the editors provide substantial structural (developmental) editing suggestions. All manuscripts accepted in principle for publication go through a detailed checklist procedure to guide the author both in matters of clarity and in important points such as financial interest declarations, supplementary information, and so on.

After acceptance, we use a combination of automatic editing tools for routine structuring (eg ordering and styling reference lists) but have a dedicated team of sub (copy) editors who edit the manuscript in Word, sending the author an edited version of the ms with changes tracked. The subeditor also manages the artwork process (all figures are relettered and sized by a dedicated art department), and the proofing-out process in which the author is sent a PDF to sign off. We officially don’t accept “new” changes on proof but in practice we do if they are reasonable. The subeditors also manage any post-publication correction process, in consultation with the manuscript editors.

The only part of this editorial process that is done externally is the typesetting. The rest of it is done in-house, with an increasing number of technical tools such as tracking systems.

Nature also has review, opinion and comment sections as well as a comprehensive weekly and daily news service. These are all produced in-house: editing, graphics, art, layout. All of our web production and processes are done in-house, some parts of the process are managed by our team in Bangalore but all of our standard web production and development is done in-house.

Nature authors are pleased at the level of editing help they receive – we regularly conduct author experience surveys, and are currently doing market research among groups of readers. As a senior editor at Nature I am very happy with the subediting process we run here – having the team in-house is extremely flexible for adding in web functionality, metadata and developing new templates and other projects, as well as the more traditional editing tasks.

The editorial process at Nature.

Getting published in a Nature journal.

Advice on writing a paper for a Nature journal.

Nature Physics calls for support of the arXiv preprint server


Funding of the arXiv preprint server must now be shared by more of its users, says Nature Physics in its March Editorial (6, 147; 2010) From the Editorial:

The arXiv preprint server has become central to the working lives of most physicists: ‘checking the arXiv’ is the starting point of many a daily routine. Founded by Paul Ginsparg, the arXiv has expanded to include not only physics — astrophysics, condensed matter, and high-energy physics being heavily represented — but also mathematics, computer science, quantitative biology and even quantitative finance. The arXiv now hosts nearly 600,000 preprints from 101,000 registered submitters in 200 countries, and serves more than 2.5 million article downloads every month to 400,000 users.

The statistics are remarkable. And it is also remarkable that, having initially been hosted at the Los Alamos National Laboratory, the server has in recent years been funded and managed by a single institute, Cornell University. Now the operating costs of the ever-growing arXiv match the entire Cornell library budget for physics and astronomy, and the university has made a plea for help in funding it.

As a short-term solution, Cornell is approaching the top 200 user-institutions of the arXiv — who account for 75% of institutional downloads — for a financial contribution to the maintenance of the arXiv. It is heartening that help has already been promised from several large universities and laboratories, but wider support is still being sought. For the longer term, Cornell will assess, with those who come forward to support the arXiv, what the options are in developing a sustainable model for the future.

Secure, ongoing funding of the preprint server is vital, and surely deserves at least national endorsement from US funding bodies, if not some international arrangement. The fast communication of results — data or theory — between experts that the arXiv facilitates is a boon to physics, and one well recognized by Nature Publishing Group: any submission to Nature Physics or its sister journals may be posted, in that original submitted form, on the preprint server (although we do ask that the final, revised and accepted version is not posted until six months after publication in the journal; the published version, in the Nature Physics layout, may not be posted).

It’s up to physicists now to sustain their arXiv, encouraging their institutions’ libraries in particular to engage in its development. More information is available; and comments and suggestions may be sent by e-mail.

Nature journal policies on posting material before and after publication.

Nature Climate Change


Nature Climate Change will launch later in 2010. It will be a monthly journal providing in-depth coverage of scientific and impact-based research relating to the Earth’s changing climate. A multidisciplinary journal, Nature Climate Change will publish high-quality papers across both the natural and social sciences, as well as place the latest research into a wider economic, social and political context. The journal’s scope will cover research in the climate sciences but will cast a wider net to cover the implications of climate change for the economy, policy and society. As well as reflecting the traditional core subjects relating to climate change and its impacts, such as atmospheric science, biogeochemistry, geography, geomorphology, ecology, environmental economics, geoengineering, modelling and prediction, oceanography, palaeoclimatology and paleaoecology, the journal will also cover related subjects including climate and society interactions, political impacts and environmental assessment and management. More information about the journal is available here.

Contact the journal.

A limited number of personal subscriptions to Nature Climate Change will be made freely available to researchers working on the scientific understanding and impact of the Earth’s changing climate as well as policy makers, economists, sociologists and other researchers on the periphery of climate related research. Further information about qualifying for a free subscription will be available shortly via the journal’s website.

General subscription information for Nature Climate Change.

See also: Climate Feedback, the blog that facilitates discussion on climate change, covering the latest research, news, opinion and analysis. It is an informal forum for debate and commentary among the science community and the wider interested public on climate science in our journals and others, in the news, and in the world at large.

Nature’s Middle East portal


The Arab world has a rich history of scientific enquiry. During the Golden Age of Science, the Arab world was influenced by texts from neighbouring regions of Greece, Persia and India, and built on them with great discoveries and inventions such as algebra, optics, medicine and many others. For more than 500 years Arabic was the language of science. Following translation into Latin, Arabic scholarship fed back to these neighbouring regions and helped lay the foundation for the European enlightenment and current Western science.

Nature Middle East has been created with an understanding of the potential of the Arab world to once again be an important centre of science. It covers a diverse group of 18 nations: Algeria, Bahrain, Egypt, Iraq, Jordan, Kuwait, Lebanon, Libya, Morocco, Oman, the Palestinian territories, Qatar, Saudi Arabia, Sudan, Syria, Tunisia, United Arab Emirates and Yemen. Nature Middle East is about recognizing the contribution of many different peoples working together, united by a common language.

Nature Middle East is a comprehensive portal site for information on scientific and medical research in the Arabic-speaking Middle East, the research community and its activities. It is a site with a broad scope that caters for scientific and medical researchers at all levels, from students to post-doctoral fellows to principal investigators. Most importantly, Nature Middle East will be a unique online platform for the scientific and medical research community to connect, network and exchange information or ideas, to promote good science and stimulate research and debate.

In its March Editorial, Nature Cell Biology ( 12, 201;2010) welcomes this newest NPG regional gateway: “Nature Publishing Group has initiatives that aim to stitch together scientific communities within specific regions. As this issue of Nature Cell Biology goes to press, ”">Nature Middle East, a website dedicated to serving the science community in Arabic-speaking countries of the Middle East, is being launched. The site aims to become a comprehensive source of information on scientific and medical research, with a target audience of students, postdoctoral trainees and principal investigators from Arabic-speaking countries across the Middle East, and for researchers outside the region who may have an interest in the emerging science of the Arab world. Following the success of two equivalent gateways — Nature China and Nature India — Nature Middle East will have content mainly in English, with some content being translated into Arabic. The content will include highlights of select research published in Nature journals and elsewhere, news items and commentaries. By providing links to jobs and events in the region and creating a platform for discussion via blogs and other online social networking tools, the website will also serve as a networking forum to engage the science community in this region, and facilitate further integration with the global scientific community.

A global scientific society that values open communication, collaboration and sharing of resources could become a powerful medium for change if these attributes take root in other spheres of human activity."