Nautilus

The journal Cell Death & Differentiation presents its first special issue of its 2007 series with 'Caspases', cysteine proteases that are essential for executing apoptosis (programmed cell death). This research and teaching resource includes comprehensive articles on the basic biology of caspases, their mechanisms of activation, cellular substrates, natural and synthetic inhibitors, apoptopic and non-apoptopic functions and their role in inflammation and immunity. The "capsase" special issue of Cell Death & Differentiation is available free online.

Posted by Maxine Clarke on February 28, 2007
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Q. Dear Editorial Office,

I would like to get your advice on the following: my project was accepted for presentation at a scientific meeting. Part of the requirements for attending this meeting and presenting there is to submit a 4-page paper. Since in a few weeks I will submit my data to your journal, I do not want to jeopardize my chances of publishing in a Nature journal. Enclosed is the Copyright Transfer that the the meeting organizers have requested me to sign. I would appreciate if you can check it out and let me know if there is any potential conflict which may prohibit my project from any future publication in your journal. The data I will present is only part of the entire data I plan of submitting to your journal.

A. We have looked at the document you sent. To speak at the meeting you do not need to sign it: the document only relates to publication of the paper that the conference organisers may wish to publish themselves after the meeting. You can present the data at the conference, but not publish them in the form of a paper, if you wish to submit them to a Nature journal afterwards. This particular agreement requires that the conference organization be acknowledged as having published the work first, in any subsequent publication. This is not appropriate for publication of the data in a Nature journal.
As a general point, Nature journals encourage scientists to present their research at meetings, and it is perfectly acceptable for them to publish the abstract(s) of their talk(s) in conference proceedings, and subsequently submit a paper containing this work to a Nature journal. Details of our policy are available on the Author and Referees' website.

Posted by Maxine Clarke on February 27, 2007
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Nature Network is now live. Please log on and experiment, spread the word to your own scientific network, and contact us with any questions or suggestions. You can use the site to create personal profile pages to describe yourself and your research. You can form topic-based groups, contribute to forums, view and announce seminars and conferences, read news and browse local job listings.

We hope that the network will help scientists everywhere to identify like-minded researchers, hold online discussions, showcase their work via personal homepages, share information with groups (open or private), comment on content and tag it. Participation is free to all, requiring little more than www.nature.com registration. Like all Web 2.0 products, launch is the beginning, not the end, of the road, so user-driven upgrades will be added regularly from now on.

Nature Network will, we hope, stimulate and facilitate scientific communication and collaboration in innovative, flexible and forward-thinking ways. It should be especially appealing to postdocs and junior faculty.

Nature Network also features local hubs, offering all the global tools plus area news, features, blogs, jobs and events. The first local site is Nature Network Boston, which has been in beta version over the past eight months, and now containing new features. Nature Network Boston supports, celebrates and connects scientists in the city, with rich daily editorial coverage of Boston-area research and researchers, Boston bloggers, a calendar of Boston-area lectures, seminars and conferences and listings of Boston-area jobs for scientists. Coming in March: Nature Network London.

An early indicator of the potential of the Nature networks is shown by Michael Durney, a postdoc at Harvard Medical School, who has grown his Biomolecular NMR Spectroscopy group on Nature Network Boston from less than 10 members to 40. Groups like Durney’s will continue to grow, and will become more international, at which point online data-sharing tools that NPG will provide, would start to become useful. The value of the networks lies in information about local organizations, research and events, ensuring relevancy for the user as well as allowing scientists attending conferences or visiting those areas for other reasons, to find local events and connect with like-minded researchers. We hope you'll use the network, and give us your opinion of it.

Posted by Maxine Clarke on February 26, 2007
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This month's Editorial in Nature Chemical Biology, A mechanistic meeting point, addresses the divergent ideas among different communities of scientists of what constitutes mechanistic insight into a biological system. From the Editorial:

"Obviously, it is ideal for scientists from many disciplines to agree that a scientific result is insightful and exciting, because it means that the conclusion crosses scientific borders. Accordingly, chemical biologists should plan their projects and publications to consider each of these fundamentally distinct approaches from the outset. Interaction with colleagues and collaborators with different backgrounds can facilitate these excursions into foreign intellectual territory. In addition, authors should use referee reports as an important guide for developing improved papers that more effectively balance the requirements of research at the interface of chemistry and biology. The integration of expectations concerning mechanistic insight into a new, cohesive, community mind-set will serve as the foundation for chemical biology moving forward."

Posted by Maxine Clarke on February 22, 2007
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Announcing Nature Geoscience – first issue January 2008. Nature Geoscience will be a monthly, multidisciplinary journal aimed at bringing together the most significant research across the entire spectrum of the Earth Sciences.

Published in print and online, the journal's content will reflect the core subject disciplines of the Earth Sciences and related subject areas, extending from atmospheric science, climate science, geochemistry, geology, oceanography, planetary science, seismology and tectonics to space physics and volcanology. Edited by Heike Langenberg, PhD, the journal will contain primary research, review articles, news and views, reports highlighting important papers published in other journals, commentary and analysis.

More about Nature Geoscience , including the aims and scope, e-alerts, information on call for papers (coming in the Spring) and news of further editorial appointments.

Posted by Maxine Clarke on February 22, 2007
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Despite the inroads into publishing made by the open-access journals highlighted by the News articles in Nature (445, pp 347 and 351; 2007), there is one domain where traditional for-profit publishers still reign supreme: the academic edited book containing a set of chapters written by individual authors. Such books continue to be valuable to the scientific community. Many provide a collection of works on a single topic by authors with different perspectives, all guided by an editor who is one of the leading experts in the field. Today, publishers still churn them out, but increasingly books suffer in comparison to electronic journals. By the time all the authors send in their chapters and the book is typeset, printed, and purchased by libraries and individuals, the content is likely to be out of date. Unfortunately, the academic edited book is also usually expensive and not as widely available as most journals.

To save the academic edited book, it could be reinvented as an online open-access web resource. Speedy publication would result, publication costs would be low, and the "chapters" would be free to all. The only critical losses might be that of the promotion provided by the traditional publisher and the publisher's imprint, which certifies quality. But these roles could easily be taken on by open-access publishers or professional societies. By promoting the book in their publications and website, and lending their imprimatur to the website of the book, the society or publisher would signal that they were satisfied that the editor and authors met the standard of an academic book. Furthermore, online reader annotation tools could allow the book's value to grow with time rather than dwindle.

A possible objection to this scheme is that some open-access journals publish special issues, which already provide a collection of related articles, like the chapters of an edited book. But a special issue is a somewhat different animal, because for that the journal's editors expect the same peer review process and criteria as for the normal issues of the journal. The online edited "book" - a collection of invited manuscripts - would allow the book's editor and authors to better realize their vision, with a far greater audience than with a traditional book.
Alex O. Holcombe, PhD
School of Psychology
University of Sydney
Brennan MacCallum Building (A18)
Sydney NSW 2006
Australia

Posted by Maxine Clarke on February 20, 2007
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Nature Publishing Group is offering free online access to the entire March issue of Nature Reviews Microbiology. The journal has the highest impact factor, 13.989, of any monthly microbiology review journal, so do check it out. Reviews in the March issue include: "The antibiotic resistome: the nexus of chemical and genetic diversity" by Gerard D. Wright; "The road to chromatin - nuclear entry of retroviruses" by Youichi Suzuki and Robert Craigie; "Virus trafficking - learning from single-virus tracking" by Boerries Brandenburg and Xiaowei Zhuang; "Microfabrication meets microbiology" by Douglas B. Weibel, Willow R. DiLuzio and George M. Whitesides; and "Cannibalism and fratricide: mechanisms and raisons d'etre" by Jean-Pierre Claverys and Leiv S. Havarstein.

Posted by Maxine Clarke on February 19, 2007
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Nature Publishing Group has launched a new web-based publication, Nature China. Nature China seeks to highlight the best scientific research published in Mainland China and Hong Kong in one convenient portal. AstraZeneca, as sponsor, will support the website for the next two years. In the past decade, the output of research papers from China in the Thompson ISI database has soared from 10,000 papers a year to more than 80,000, which is the same numerical level as the United Kingdom and Japan. The number of very high impact papers (citations in excess of 20) from China has increased ten-fold to several hundred. Nature China is dedicated to highlighting the best research from mainland China and Hong Kong, to provide scientists from around the world with a convenient portal into research drawn from across the scientific and medical literature in all disciplines.
The website is currently in beta form as an archive is built extending back over the past six years to provide short summaries of some of the best research articles published from China in Nature journals and other leading scientific publications since 2000. In the case of Nature journals, access to the original full text articles is also provided. Once the archive is complete in April, each week thereafter, Nature China editors will select the best recently published research and provide a summary of the results. Readers can also recommend papers to be included in Nature China and vote/comment on those suggestions. The best of these, chosen by the site's users, will be included within the Nature China archive.
Futher explanation about Nature China can be found on the site's "frequently asked questions" page.

This month's featured papers on Nature China.

Posted by Maxine Clarke on February 16, 2007
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Nature Reviews Immunology has published a poster on phosphoinositide 3-kinase (PI3K) signalling in the immune system. The poster provides an overview of p110-delta and p110-gamma signalling in T cells, B cells, mast cells and neutrophils, and characterizes the biological consequences. The poster is available free online, and there is an accompanying review article in the journal.

The Journal of Investigative Dermatology is making selected immunology papers available free online. If cutaneous biology is your research area, enjoy reading these articles from this well-cited journal, which is the official journal of the Society for Investigative Dermatology and the European Society for Dermatological Research.

Posted by Maxine Clarke on February 16, 2007
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There has been some discussion in Nature's Correspondence section about the difficulty experienced by colour blind readers in interpreting colour figures.
Chris Miall of the University of Birmingham, UK, started the topic in his letter pointing out that a significant number of readers cannot distinguish red from green. He cited issue 7120 of Nature, which, he says, contains six figures whose only two colours are red and green.
John Runions, of Oxford Brookes University, UK, then pointed out that magenta and yellow, a combination apparently encouraged by some journals, are not a good combination either. From his letter: "Magenta and yellow in overlay produce 'almost white' — virtually indistinguishable from the yellow in tiny images. Red and green, the standard colour pair, produce yellow when overlaid, and this is very easy to interpret. I suggest that journals continue to publish these images in red/green, but that they make alternatively coloured images available online as supplementary information for readers who have impaired colour vision."
Last week, Joseph Ross of the Fred Hutchinson Cancer Research Center in Seattle drew attention to an excellent website. From his letter:
"As a red-green colour–blind (deuteranope) scientist and graphic designer, I have long campaigned for figures to be accessible to an entire audience. I do so, in part, by leading seminars training my colleagues to create accessible figures.
One of the key resources I employ in this crusade is a website by Masataka Okabe and Kei Ito: 'How to make figures and presentations that are friendly to color-blind people'.
I strongly urge all authors to visit this site, which both describes the need for creating accessible images (including simulations of colour-blindness for those who are curious) and, more importantly, provides instructions for making figures comprehensible to everyone. This includes instructions on how to pseudo-colour images containing red and green fluorescent signals — one of the most hated types of graphic among people with colour-blindness. Authors will find it is surprisingly easy to accommodate the colour-blind when creating figures.
Anyone who needs to be convinced that making scientific images more accessible is a worthwhile task should consider that colour-blindness is common, affecting 5–10% of males. If your next grant or manuscript submission contains colour figures, what if some of your reviewers are colour-blind? Will they be able to appreciate your figures? Considering the competition for funding and for publication, can you afford the possibility of frustrating your audience? The solution is at hand."

Posted by Maxine Clarke on February 16, 2007
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Jim Giles reports in Nature's news pages this week about a collaborative wiki approach for sharing biological information. From the article: "Barend Mons's first objective would be ambitious enough for most people: to meld some of the most important biomedical databases into a single information resource. But that's just the beginning. Mons, a bioinformatician at the Erasmus Medical Centre in Rotterdam, the Netherlands, also wants to apply the Wikipedia philosophy. He's inviting the whole research community to help update a vast store of interlinked data. If he and his colleagues can pull it off — and even the project's advocates are not sure they can — they could transform the databases that are central to the work of many life scientists.
A test version of the project, provisionally dubbed Wiki for Professionals , is due to launch in the next month."
The rest of the story is at the news @ nature.com site, where readers can add their comments online.

Posted by Maxine Clarke on February 16, 2007
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Nature Publishing Group and the Society for Mucosal Immunology (SMI) are embarking on a new publishing partnership this autumn, with the launch of a new publication, Mucosal Immunology.

The Editor-in Chief of Mucosal Immunology will be Dr Brian Kelsall of the National Institutes of Health's National Institute of Allergy and Infectious Diseases. The journal will aim to provide a forum for both basic and clinical scientists to discuss all aspects of immunity and inflammation that involve mucosal tissues. "Mucosal Immunology will be the first journal dedicated to this field of science. I am greatly looking forward to collaborating with NPG on this important project," said DrKelsall.

Mucosal immunology research has the aim of understanding diseases such as AIDS, asthma and inflammatory bowel disease. The journal will be devoted to publishing high-quality original research, reviews, commentaries, editorials and letters that reflect the interests of scientists studying gastrointestinal, pulmonary, nasopharyngeal, oral, ocular and genitourinary immunology. In addition, Mucosal Immunology aims to provide a primary method of communication for the SMI governing board and its members through the publication of society news, announcements of planned meetings and conferences, discussions of policy concerns and advertisements for job and training opportunities.

Journal website, including call for papers.
Society for Mucosal Immunology website.

Posted by Maxine Clarke on February 14, 2007
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In a blog post entitled: Booksellers Association: Open Access - Who Pays?, Martyn Daniels of the Booksellers' Association discusses a Guardian article on "open access" publishing. Mr Daniels summarizes the scientific publishing process succinctly:
"Today researchers give their research papers to publishers who get them peer reviewed, edited, marketed, published and distributed through their branded journals. The practice seems very laudable in that the publisher acts as the arbitrator of quality, ensuring their value and the appropriate indexing, referencing, citations etc are correct and that the paper is brought to the attention of the academic community."
He goes on to discuss the European Research Council's recent report, looking at journal price and editorial workflows. He concludes: "There is no easy answer to the digital relationships that need to exist between publishers, creators and channels. This problem is not unique to journals but also has implications across the total social publishing environment. Perhaps there is logic in looking back to a time before publishers became the dominant players? What is clear is that the answer will not be found in the recent printed journal model and there is a need for all parties to recognize and respect the value each brings to the table in the digital world."

Posted by Maxine Clarke on February 13, 2007
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Nature Publishing Group hosts several blogs, all of which can be directly reached from the left-hand sidebar here. These blogs all have their different goals, identities and readerships, but one of them, Methagora, is the most different -- so far. The journal Nature Methods has created an online space inviting readers' contributions, in particular comments on published papers. The site's name comes from the ancient Greek agora, and the journal plans for the site to become a public place where 'citizen readers' assemble and discuss important (methodological) matters. But is there much debate, in fact? From this month's Nature Methods Editorial, "Happy to take questions":

"But the uptake is slow. Of course, these are still early days, and many people may not even be aware of this forum—hence this editorial and upcoming promotion. Other similar initiatives, however, such as those ongoing at Cell and Nature Biotechnology, experience an equally scarce response. Particularly worrisome is the fact that the Nature Biotechnology initiative and one of the Methagora postings are seeking community feedback on papers that outline proposed reporting standards. Despite the potential impact that such standards, if adopted, would have on individual researchers, only a handful of the interested have taken the time to comment. This lackluster reaction makes us pause and speculate about scientists' motivations for the commenting activity."

Posted by Maxine Clarke on February 13, 2007
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"Climate change, medicine, the food we eat, the way we give birth, the way we die. Science governs every aspect of our lives. But can we trust politicians to make the right decisions for us about those vital issues?" Former UK government chief scientist and president of the Royal Society, and many times Nature author Lord May, examines the "crucial but uneasy relationship between politics and science" on Radio 4, Thursday 15 Feb, 2100-2130 GMT in a programme entitled "Scientists advise ministers decide. "

Past, current and indeed future science programmes can be heard via the BBC radio 4 science website.

Posted by Maxine Clarke on February 13, 2007
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Pipes is a new application from Yahoo that lets the user "remix feeds and create new data mashups in a visual programming environment". Although this is rather technically expressed, Pipes is a graphical environment for a specific type of programming that takes the form of a kind of flowchart. It is a browser-based application that lets the user input RSS feeds, then filter them for text, images or other data -- which the user can then process and merge with other feeds, making the output (another RSS feed) reusable for anybody. There are lots of good examples on the Pipes site.
A more detailed commentary on Pipes, calling the application "a milestone in the history of the Internet" can be found on O'Reilly Radar, but there are plenty of other analyses on many Internet sites and blogs.
Alf Eaton at Nature Publishing Group has already created a pipe of all the NPG blogs, by combining their RSS feeds and filtering by user-defined keywords. Have a try, at the link provided.
http://pipes.yahoo.com/pipes/pCo8Tmy32xG5lPXzXqIxGw/

Posted by Maxine Clarke on February 12, 2007
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The lastest in Nature Publishing Group's Milestones programme is Milestones in Cutaneous Biology, an online resource that brings together key discoveries that have shaped the field of cutaneous biology over the past 100 years. Published in quarterly installments, each milestone will highlight a classic finding. More than 30 international leaders in epidermal and dermal structural proteins, cell differentiation, vascular and tumour biology, autoimmunity, photobiology, and genetic disease were enlisted to edit the series, which will provide a powerful instructive tool for students and investigators, as well as an information resource for anyone interested in the topic. A subject area index page is provided, featuring an interactive graphic diagram of the skin.

Posted by Maxine Clarke on February 08, 2007
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Q. Dear Nature editors

I am a graduate student pursuing masters in biotechnology at a university. I am taking "Ethics and Professionalism Course" which is dealing with ethics, record keeping, laboratory notebook and paper publishing. I have been assigned a course work to inquire from one of the NATURE editors "What would be the reasonable time limit for keeping the data of a published paper ?".

Could you please spare some time to reply me and give me your opinion of what would be a reasonable time limit for keeping the data (record keeping) of a published paper in your journal.

I really appreciate your help in doing my course work.

A. Dear graduate student

Permanently.

Yours sincerely
Nature

Posted by Maxine Clarke on February 08, 2007
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Special report : science career issues and alternative jobs for scientists : Naturejobs

"The nervous Japanese postdoc spent two weeks creating slides, 30 hours drafting a script and 44 hours rehearsing. Altogether, she spent one month away from the bench so that she would not disappoint her supervisors and colleagues during a short informal presentation, in English, before co-workers. Yet they remembered only the mistakes, she says.

Seasoned scientists also feel under pressure when speaking in English. Masahiko Takada at the Tokyo Metropolitan Institute for Neuroscience admits that, even after years of working in English, "I sometimes feel frustrated when I have to discuss research data with foreign scientists."

Language mastery, be it of one's native or adopted tongue, provides the communicative ease that says: "I am capable." In science, weak English hinders a successful career. Improve your English proficiency, and confidence will follow — or so the people of many non-English-speaking nations believe.

Concerns about the dominance of the English language in science are being raised around the world. Researchers in Germany and France, for example, are grumbling about the frustration of working and publishing in English — and, perhaps more surprisingly, so are those in nations that have typically been viewed as consumers of basic science, rather than contributors."

So writes Bonnie Lee La Madeleine of the RIKEN Brain Research Institute. Read the rest of this special report on the Nature website (subscription or site licence required).

Please let us know your own experiences and views, via the comments to this post.

Posted by Maxine Clarke on February 07, 2007
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This month's editorial in Nature Structural and Molecular Biology discusses Joshua Lederberg, whose latest honour is the Presidential Freedom Award. The editorial discusses the career and achievements of this remarkable scientist, concluding:

"A detailed account of Lederberg's contributions to science and the public interest can be found at the US National Library of Medicine Profiles in Science. The formal citation accompanying the Medal of Freedom says, "The US honors Joshua Lederberg for his achievements in scientific discovery and his commitment to improving the lives of others." Not a bad example to try to follow."

Posted by Maxine Clarke on February 06, 2007
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The British Journal of Pharmacology has just published a free guide to receptors and channels by S. P. H. Alexander, A. Mathie and J.A. Peters. From the introduction: "The great proliferation of drug targets in recent years has driven the need to organise and condense the information in a logical way. This is the underlying reason for this Guide to Receptors and Channels, distributed with the British Journal of Pharmacology. Our intent is to produce an authoritative but user-friendly publication, which allows a rapid overview of the key properties of a wide range of established or potential pharmacological targets. The aim is to provide information succinctly so that a newcomer to a particular target group can identify the main elements "at a glance"."

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Posted by Maxine Clarke on February 06, 2007
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'Futures', Nature's award-winning science-fiction series, has moved to Nature Physics. Read the new, specially commissioned physics series of essays from January 2007, at Nature Physics. The Futures essay in the current issue is "Giving up Meat", by Jess A. Brewer.

Nature published 156 Futures between 1999 and 2006, ranging from the serious to the whimsical. An anthology is planned. As H. G. Wells, in Nature 65, 326–331; 1902, wrote: "the question what is to come after man is the most persistently fascinating and the most insoluble question in the whole world".

Posted by Maxine Clarke on February 05, 2007
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The solution to the November 2006 Nurture crossword is shown on the "continue readng" page of this post. The prize, a copy of The Science of the Hitchhiker's Guide to the Galaxy, published by Macmillan Science books, was won by Marc Swisdak of the US Naval Research Laboratory. Congratulations, Marc.
Readers who have not seen the crossword and wish to attempt it can download the digital edition of Nurture free of charge.
The crossword was set by Sian Lewis.

The solution follows:

Continue reading "Nurture crossword solution" »

Posted by Maxine Clarke on February 05, 2007
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The Research Library of the Signaling Gateway brings together all recent cell-signalling-related research published in the Nature Publishing Group journals. Divided up into subject categories or by date, you can be guaranteed to find what you are looking for. Here is a selection of the latest research published this week:
Transcription factor control of asymmetric cell divisions that establish the stomatal lineage.
Nature 445, 537-540 (1 February 2007).
Notch signal organizes the Drosophila olfactory circuitry by diversifying the sensory neuronal lineages.
Nature Neuroscience 10, 153-160 (2007).
The energy sensing LKB1-AMPK pathway regulates p27kip1 phosphorylation mediating the decision to enter autophagy or apoptosis.
Nature Cell Biology 9, 218 - 224 (2007).
The research library is one of the many ways in which Nature Publishing Group extends the reach of articles published in its journals. Discipline-specific areas on the nature.com site, varoius web focuses on the journals' websites, and many other collaborations between journals collect articles together in different combinations, which draws them to the attention not just to readers of the journal in which they were published, but to researchers using nature.com to find out what's hot in their field more generally.

Posted by Maxine Clarke on February 02, 2007
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Tickets are now on sale for the Royal Institution evening public lecture series on polymathy and science, chaired by Oliver Morton, Chief News and Features Editor of Nature. The programme is run by Sara Abdulla, Editor of Nature Networks and publisher of Macmillan Science books. All are welcome.
Two lectures on great polymaths in March and April will be followed by a debate in May about whether interdisciplinarity is alive, dead, possible, desirable, vice or virtue.

March 21: Andrew Robinson on Thomas Young: ‘The last man who knew everything’
April 18: John Whitfield on D’ Arcy Wentworth Thompson: ‘The last man who read everything’
May 16: Panel debate: What happened to the polymaths

Venue: The Royal College of Surgeons of England, 35–43 Lincoln’s Inn Fields, London WC2A 3PE, UK.
Tickets: www.rigb.org ; (+44) 0 20 7409 2992
Details: 7-8.30 p.m. Price £8 (£5 for Ri Members, RCS Fellows/Members and concessions). You can book for all three of the Polymaths Series events at the special price of £20 (£12 Ri Members, RCS Fellows/Members and concessions).

Posted by Maxine Clarke on February 02, 2007
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The Nature Podcast is a free weekly audio show that you can play through your computer. Every show features highlighted content from the week's edition of Nature, including interviews with the authors, and in-depth commentary and analysis from journalists covering science around the world. This week, hear about conserving the Amazon with a scientific SWAT team, redrawing the hydrological cycle from space, micro-organisms forming new relationships, and virtual quantum computing on chips. To subscribe to the Nature Podcast, copy and paste this URL into your RSS reader, iTunes or your preferred media player:

http://www.nature.com/nature/podcast/rss/nature.xml

An archive of Nature podcasts is available on the Nature Newsblog.

Posted by Maxine Clarke on February 01, 2007
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