Rediscover your Nature

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A message from Dr Philip Campbell, Editor in Chief of Nature:

From today, Nature has a new look, a clearer structure, and contains new types of content. Above all, our underlying goal is greater clarity in the reading experience, and this blog post describes a few of the changes we’ve made to this end. More details are given in the official press release.

For authors of original research and commissioned articles we provide an improved online template for the full-text version of articles (an example is here, free to access online). We’ve also updated and clarified Nature‘s guide to authors, including downloadable summary sheets to help in submission and preparation of manuscripts.

The print magazine component of Nature is now structured in a clearer way. The introductory material has been reduced to a simple table of contents. A new section called This Week contains Nature’s Editorials and summaries of recent developments in and around science. It also includes a new page, World View, in which external authors give prompt personal perspectives on live issues. More analytical and reflective content, presenting developments in the world of science in greater depth, appears as journalism in News in Focus and News Features, or as Comment, a forum for essays, debates, reviews, and readers’ correspondence. Online, these are presented as a unified News and Comment section for easy access to these features as well as to the journal’s specials.

The Research section includes accessible summaries of the latest research articles available now online, News and Views, review articles, and primary research content of Nature – its Articles and Letters. To provide additional and useful navigation for readers and authors, these contributions are presented online by subject as well as in the more conventional temporal (by issue) method.

Within these sections we have tried, in the redesign of our print layouts and key elements, to ensure that the reader gains as quickly as possible a clear idea of just why he or she should be reading an article. We’ve created space for more descriptive headlines and other display elements that allow a reader to get an immediate sense of what an article has to say and who its authors are. The new design also emphasizes the use of charts and graphics that offer a quick summary of the key data underlying an opinion piece or news story. It allows for more inventive, attractive pages as well.

Both in print and online, these changes have been developed over more than a year in consultation with members of the scientific community in their guises of readers, authors and peer-reviewers, with much positive feedback in the process. We have listened and we have changed. We hope that Nature’s subscribers will look forward to their weekly magazine all the more, and enjoy the improved online experience by a similarly enhanced degree.

As well as in print and online media, Nature is also available from today in a new, much improved digital edition. By visiting this link you can sign up for a free, three-month trial of the digital edition, and watch a video demonstrating the many new features in the journal.

As well as print, online or digital, you can read, follow and access the journal via our iPhone app, our weekly podcasts, or by video, Twitter, Facebook and Nature Network. Whether for readers or for authors, Nature is everywhere that matters. And, of course, we want to know what you think of it all, ideally by undertaking our brief survey.

Further reading:

Announcement: Nature‘s new look ( Nature 467, 368; 2010).

Grrl Scientist’s blog at Nature Network.

Press release.

Comment articles on genetics and genomics research

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From the Editors of Nature Reviews Genetics ( 11, 309; 2010):

Since the launch of Nature Reviews Genetics almost a decade ago, we have used a variety of ways to communicate the most important advances in genetics and genomics. As well as the classic Review format, our Perspective, Analysis and Progress articles have enabled authors to tackle topics in a range of useful and interesting ways. This month’s issue (May) sees our first Comment article, a new format that we hope you will find engaging and informative.

As the name suggests, Comment articles allow authors to provide a commentary on issues that are having an impact on how genetic, genomic and related research is carried out and applied. Such issues might range from the ethical to the technical, and will have broad relevance to the journal’s readership.

On p. 310, Sharon Terry uses the Comment format to argue that the traditional way of allocating funding for disease research is stunting the translational impact of genetics and genomics. She sees the earmarking of funds for research on specific diseases as outdated in an era in which genomics approaches are providing unprecedented means to identify connections between diseases.

Terry’s Comment calls on striking examples of how Mendelian diseases can inform about diseases with a multifactorial basis, and vice versa.

NSMB’s tips for revising your paper in response to reviewers

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From: Nature Structural & Molecular Biology 17, 389 (2010)

Your paper went out to review, and after anxious waiting, you receive the letter asking for a revised paper. However, those ever-demanding editors and reviewers want more. One of the most important elements of a revision is the point-by-point response. Here are some tips for making it more effective.

Keep to the point. We [the NSMB editors] internally call this a point-by-point rather than a rebuttal, implying that it makes a series of points in response to each point raised by the reviewers. We will, and indeed have, read through 17-page point-by-points. But the longer the document gets, the more likely it is that the essence of your arguments will be lost in the mix.

Keep it objective. We have received comments from bewildered reviewers who do not understand why the tone of the point-by-point is so aggressive. Therefore, we will sometimes ask you to rewrite your response if it is overly pugnacious and we feel that this could affect the outcome of the review.

Keep things under control. There are definitely times for making a logical argument rather than adding new data and experimentation. That said, when fundamental technical concerns are raised or missing controls are being requested, the point-by-point is not the place for trying to dazzle your reviewers with argument and debate skills. Know when to go to the bench and when to argue.

The scope of things. Some requests might genuinely be beyond the scope of the manuscript or might simply be unfeasible. Make your response here as objective as possible. Say clearly and succinctly if something is unfeasible or if you think the results of such an experiment would be uninterpretable, and in both cases explain clearly why (pointing to the literature if needed) and how long the experiment will take to help make the case.

Some final points. There are some don’ts that should be obvious; but just in case, here are a few, in no particular order:

Telling us about your reputation, your pedigree, number of citations of your previous papers, your h-index, other Nature journals you have recently published in, etc. All interesting information but not pertinent to deciding the fate of the paper at hand.

Celebrity endorsements. Letting us know that a Nobel laureate enjoyed your talk at a recent meeting. Good to know but relatively meaningless. In fact, you never know—they could be moonlighting as your most critical anonymous reviewer.

Trying to guess who the reviewers are and then launching into a diatribe about their qualifications (or lack thereof).

And finally: “You recently published an even worse paper.”

All of these can be amusing to varying degrees but will do little to further your case.

Overall, it can be helpful to put yourself in the reviewer’s shoes and compose a response s/he would find appropriate, where the concerns raised are considered and fully addressed. In its ideal state, the review process is a positive and constructive back and forth, an intellectual discussion in which the manuscript is the ultimate beneficiary. Although it can be frustrating to be told at this stage that further revisions and experiments are a condition for publication of work that you felt was complete enough to submit, a common refrain after publication is for authors to express that, with the benefit of hindsight, the review process strengthened the paper. And a strengthened paper submitted at revision is the strongest rebuttal of all.

Nature Communications, a new multidisciplinary journal

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From Nature 464, 958 ( 2010):

This month sees the launch of the seventeenth Nature journal, Nature Communications. All the previous Nature research journals have focused on a particular discipline or community of research interests. Their aim is to publish the most original and scientifically impact-making research appropriate to those particular audiences. Their high ranking in the citation league tables would suggest that this goal is generally being fulfilled.

Nature Communications differs in being multidisciplinary. It aims not to compete with the established Nature journals, but to publish rigorous and comprehensive papers that represent advances of significance to specialists within each field. In addition, it welcomes submissions in fields that are not represented by a dedicated Nature research journal — for example, developmental biology, plant science, microbiology, ecology and evolution, palaeontology, astronomy and high-energy physics. Readers will find in the launch issue papers on topics including classical and quantum correlations under decoherence; a candidate gene for mechanoreception in Drosophila sensory cilia; a strategy to obtain sequence-regulated vinyl copolymers using metal-catalysed step-growth radical polymerization; how a ritualized vibratory signal evolved from locomotion in territorial caterpillars; and more besides.

Like all Nature journals, Nature Communications is editorially independent. It is also the first Nature research journal to be funded in hybrid fashion: by both subscriptions and optional authors’ fees that allow instant free access to their published papers. Furthermore, it is the first Nature journal to be launched entirely without a print edition: its content is available only online.

Nature welcomes this distinctive new sibling publication — this time, serving the whole research community.

See the inaugural editorial in Nature Communications, providing more details of the journal’s scope and pubilshing model.

Nature Communications guidelines for authors and peer-reviewers.

More about the journal.

Latest articles in Nature Communications.

Submit your research to Nature Communications.

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

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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

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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

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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.

Nature’s collection on biodiversity

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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

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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.

Special focus on genome instability

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The March issue of Nature Reviews Molecular Cell Biology presents a web focus on genome instability. The integrity of the genome is crucial for tumour suppression and for the propagation of genomic information to subsequent generations. DNA damage can result from cellular metabolism, exogenous genotoxic agents or routine errors in DNA replication and recombination. To combat these attacks and maintain genome integrity, cells have evolved a response system that induces cell cycle arrest, allowing sufficient time for DNA repair by specialized proteins. The DNA damage response system activates the appropriate DNA repair pathway or, in the case of irreparable damage, induces apoptosis. The special focus contains research highlights, review articles, a journal club and a NPG library of related articles. There is also a brief editors’ summary of the contents.

Accompanying the same issue of Nature Reviews Molecular Cell Biology is a Poster, by Eric J. Bennett, Mathew E. Sowa and J. Wade Harper, which illustrates the different deubiquitinating enzyme (DUB) families and highlights the cellular pathways in which some DUB-associated complexes act. Download a copy here.

Nature Reviews Molecular Cell Biology journal home page.

About the journal.

All Nature Reviews journals in the life and clinical sciences.