Nautilus

Nature and Nature journal authors, and indeed editors of the journals, have been in hot water with eagle-eyed readers in the past for publishing papers without proper definition of error bars. As a result, we produced a statistical checklist (including advice) for authors, as it became clear that there is widespread uncertainty about this statistical measure. Now, Cognitive Daily blog features an "error bar challenge". Accept if you dare.

For the faint-hearted, here is a link to the Cognitive Daily post containing the answers. If you are not sure of your confidence intervals and standard deviations, or would like a brush-up, the two Cognitive Daily posts are very useful.

Posted by Maxine Clarke on March 29, 2007
Categories: Writing | Permalink | Comments (0)

This month's molecule is... | nodalpoint.org

If you like to keep up to date with interesting protein molecules, the blog Nodalpoint recommends a couple of good minireview sites that feature a different structure each month, "worth a quick read because they can help bio-literate users to increase and reinforce their knowledge relatively quickly."

Posted by Maxine Clarke on March 29, 2007
Categories: Disciplines | Permalink | Comments (0)

The United Kingdom Serials Group (UKSG), in association with the online usage metrics organisation COUNTER, is funding a study to explore how online journal usage statistics might form the basis of a new metric of journal quality, the "Usage Factor". The first stage of this project involved a series of interviews with various stakeholders, and the second, current stage involves a web-based survey designed to obtain the views of many more librarians and authors than was possible for the interview stage.

If you are an author of a publication in any of the Nature or Nature Publishing Group journals, we hope you can spare a few minutes to complete this important survey, which you can do by clicking on this link. The survey aims to:

* Discover what you think about the measures that are currently used to assess the value of scholarly journals (notably impact factors);
* Gauge the potential for usage-based measures;
* Provide an opportunity for you to suggest possible different, additional measures.

See here for the author survey. It will take less than 5 minutes to do; because it is due to close by 30 March (though it may be extended for a few days), please do visit the survey site now if you are interested in contributing your views and experience.

Posted by Maxine Clarke on March 28, 2007
Categories: Access, Citation analysis, Quality measures | Permalink | Comments (0)

Business writing clinic: Technical Writing in Ten Easy Steps

Kathy Lawrence, who runs the "Business Writing Clinic" blog, was clearing out old files when she came across a chapter she wrote for a book "Professional Communication and Information Design" (see link above for more details of the book). Her chapter, written with Ronald A. Brown, describes the technical editing process. Here's a short excerpt from the introduction:

We’ve all had work edited. Sometimes we almost dread the process, imagining that the editor is a fierce critic who is just itching to condemn you for sloppy work and inconsistencies. But this is far from true. In reality, the editor is your friend, who wants to work with you to improve your document, whether it’s paper or electronic. We look first at how you need to consider the document you are editing as a whole, and then focus on the nuts and bolts of the editing process.

The link at the top of this post will take you to the list of the "ten easy steps", which I think seems pretty useful, especially if you are writing your first commissioned article, such as a review.

Posted by Maxine Clarke on March 28, 2007
Categories: Writing | Permalink | Comments (1)

Cognitive Daily: CogDaily's blogroll; Encephalon
Dave Munger of Cognitive Daily has collected together a list of the cognitive/neuroscience blogs that he reads regularly. See the link above for the collection.

Posted by Maxine Clarke on March 27, 2007
Categories: Communication | Permalink | Comments (0)

Interested in bioinformatics and computational biology? Need to know the basics to apply to your own research? Euan Adie, in his Nature Network blog FnL, highlights Bio::Blogs, "a freely available compilation of the best bioinformatics blogging from the past month, in easy to print PDF format". Euan writes:

It’s a good read and a gentle introduction to scientific blogging in general. The PDF is a relatively recent development but a welcome one – it means that you can print out all of the posts at once to read at your leisure. After downloading B::B you should check out Nodalpoint, the ‘by the people for the people’ bioinformatics group blog founded by Greg Tyrelle which has recently seen a resurgence of activity. Some of that activity has been focused on updating a list of blogs about computational biology which is worth going through to find good reads.

Bath optional.

Posted by Maxine Clarke on March 27, 2007
Categories: Communication | Permalink | Comments (0)

From a distinguished correspondent, via e-mail:
While one could have long discussions about the exact meanings of words like bird, fish, insect, plant, tree, alga, cell, bacterium, prokaryote, flagellum, etc., I wonder whether they could not be better dealt with in a separate journal, leaving Nature to deal more with science.

Posted by Maxine Clarke on March 27, 2007
Categories: Writing | Permalink | Comments (0)

The online edition of the Nature Publishing Group catalogue has been given a thorough overhaul in its design, navigation and behind-the-scenes authoring tools. The site holds all the information from the printed catalogue, including journals' aims and scopes; impact factors and rankings; launch dates; editors; and society owners. The site can be searched by keyword and subject-related journals, plus a full A-Z list. Visitors can also order a printed catalogue or view as a (rather large) PDF.

Posted by Maxine Clarke on March 26, 2007
Categories: Publications | Permalink | Comments (0)

There is a post on Cosmic Blog about journals' embargo policies, specifically those of the journals Nature and Science. Donald Kennedy, Editor-in-Chief of Science, is quoted from a talk he gave at a conference "Best practices: covering science in cyberspace" earlier this month. Dr Kennedy suggested that print versions of papers in future might be much shorter and "user-friendly", with the full account, complete with multimedia, appearing online only.

"It's going to create a problem for the people who try to manage science news," Kennedy said. "My guess is that the embargo system will either be abandoned, in which case it'll be a free-for-all ... [or] it's certainly likely that embargoes will be shortened, and the distribution of news to mainstream news media - which used to happen in clumps so that embargoes for an entire clump could be organized - is going to happen in driblets. So there will have to be a more confusing embargo environment."

Nature's embargo policy can be found here, and an article about how its press office operates is here.

Posted by Maxine Clarke on March 26, 2007
Categories: Access, Author benefits | Permalink | Comments (0)

This month, Nature Reviews presents a collection on fluorescence imaging which includes Research Highlights, Reviews and Perspectives articles from Nature Reviews Cancer, Nature Reviews Neuroscience and Nature Reviews Molecular Cell Biology. The articles highlight the versatility of fluorescence imaging and its applications in studying basic cell-biological processes and in understanding disease aetiology and therapeutics. They are freely available online until 30 September 2007.

While on the topic of the Nature Reviews journals, Nature Reviews Cancer is the no. 1 monthly review journal in oncology with an impact factor of 31.694 (Thomson ISI). This month, the journal is offering free online access to the entire April issue, so what better opportunity to take a look?

Posted by Maxine Clarke on March 23, 2007
Categories: Publications | Permalink | Comments (0)

Nature Network London, the second city hub on the Nature Network, launched a couple of days ago. Here's a link to its "getting started" page. Nature Network works on two levels. On the global pages, you can interact with scientists all over the world, browse and join groups and forums, and read about international science in the blogs. Within Nature Network, we also have a number of local hubs - beginning with Boston and London - where you can meet local scientists, find events listings, seek jobs and read lively articles related to science in those places. You can also filter the groups/forums and blogs by locality.
Your Network is your collection of friends, contacts or just people you find interesting on Nature Network. Think of your network as the people you want to read and talk to. You can add anyone to your network, and then Your Network Snapshot will track their activity on the site. Likewise, anyone who lists you in their network can easily keep up-to-date with your contributions. Members of your network can be named as 'contacts' or 'friends (attributions only you will be able to see), allowing you to filter communications to the right people within your network.
Enjoy Nature Network, the social scene for scientists.

Posted by Maxine Clarke on March 23, 2007
Categories: Publications | Permalink | Comments (0)

The 300th anniversary of the birth of Linnaeus is on 23 May this year. LInnaeus, the scientist who laid the foundations for the modern scheme of nomenclature, is regarded by many as the founder of taxonomy and ecology. The 15 March issue of Nature celebrated the event by a special collection of articles, including News stories looking at the current state of phylogenomics, the politics of the Endangered Species Act and an assessment of the role of amateur taxonomists; and Commentaries on the problem of keeping the Linnaean taxonomic legacy on track despite rapid developments in the life sciences, and on challenges to the way new species names are communicated. An Essay intriguingly suggests that the risqué concepts laid out in Linnaeus’s great work Systema Naturalae may have contributed to the popularity of taxonomy as a hobby. Two scientific research papers complete the collection, which can be purchased as a limited edition reprint.

Posted by Maxine Clarke on March 23, 2007
Categories: Publications | Permalink | Comments (0)

Each week, Nature's author page features "making the paper", a behind-the-scenes look at one of the research papers in the current issue. This week's (446, xi; 22 March 2007) featured author is Jeffrey Moore, a coauthor of the Letter "Biasing reaction pathways with mechanical force" (page 423), which describes a molecule that undergoes chemical reaction in response to stress.

From the "making the paper" article: " 'Self-healing' materials that can automatically repair their daily wear and tear could produce lenses that never scratch or cars that always look new. In 2001, Jeffrey Moore and his colleagues Scott White and Nancy Sottos at the University of Illinois at Urbana-Champaign, described one such self-healing polymer. Into the basic polymer material were embedded tiny capsules filled with liquid monomer. When the material was broken, the capsules ruptured, releasing monomers into the crack, where a catalyst induced their formation into new polymer to repair the break.
Moore and his colleagues wanted to find ways of promoting this repair without having to add a catalyst. They thought they could create molecules that would undergo the desired reaction in response to the physical stress itself. The idea that mechanical force can induce a chemical reaction has been around for years, but so far scientists had only used such force to break bonds. "If you can use mechanical force to break bonds, why not do something more interesting, like creating a reactive intermediate that might alter the material in useful ways," says Moore. "We did not see any fundamental limitations."
Read more about making the paper, in print or online, in the 22 March issue of Nature.
See here for a freely available video stream of the mechanically morphing molecules.

Posted by Maxine Clarke on March 22, 2007
Categories: Author benefits | Permalink | Comments (0)

From the current (April 2007) issue, Nature Chemical Biology is introducing functionality that allows readers to view and manipulate chemical compounds in three dimensions on the journal web site. As well as being an author service we are delighted to introduce, this functionality will allow readers to view chemical compounds in 3D using a jmol window within the ‘compound data index page’ for a paper. Selected articles are free to view online, allowing you to explore this new functionality including: "Discovery of a natural thiamine adenine nucleotide" (Nature Chemical Biology 3, 211-212; 2007); and "Structure-guided development of affinity probes for tyrosine kinases using chemical genetics" (Nature Chemical Biology 3, 229-238; 2007).
The Nature Chemical Biology editorial team welcomes contributions from academic, industrial and government sectors across all areas of chemical biology. To submit your next paper to Nature Chemical Biology, visit the journal's electronic submission website.

Posted by Maxine Clarke on March 21, 2007
Categories: Author services, Publications | Permalink | Comments (0)

The sensation of pain results from the interplay of sensory and cognitive mechanisms. Research during the past decade has led to a remarkable increase of our understanding of the basis of pain. A new Nature Reviews Neuroscience poster by Stephen McMahon and David Bennett provides an overview of the neuronal circuitry, molecules and signalling pathways involved in normal pain perception and chronic pain. The poster is available free online.

The April issue of Nature Reviews Neuroscience is now out. This month's featured article is "The Machinery of Colour Vision" by Samuel G. Solomon and Peter Lennie.

Posted by Maxine Clarke on March 21, 2007
Categories: Publications | Permalink | Comments (1)

This month’s Nature Reviews Genetics Focus issue reflects the broad impact of epigenetic research, from insights into basic mechanisms of gene regulation to potential biomedical applications. The topics covered range from chromosome biology and gene regulation, to stem cell research, environmental epigenetics and cancer epigenomics, areas in which exploring the role of epigenetics has the potential to lead to clinical advances.There is an accompanying library of the most relevant recent publications from across Nature Publishing Group.

Posted by Maxine Clarke on March 20, 2007
Categories: Publications | Permalink | Comments (0)

March is Age-related Macular Degeneration (AMD) awareness month, in recognition of which, the journal Eye has brought together its most recent content in the area and made it freely available online. Eye is the official journal of the Royal College of Ophthalmologists, and is published by Nature Publishing Group. It aims to provide the practising ophthalmologist with information on the latest clinical and laboratory-based research.
A selection of the free online articles:
Editorial
Intravitreal injection: balancing the risks
Clinical Studies
Lack of benefit of early awareness to age-related macular degeneration
Characteristics of progression of early Age-related macular degeneration: the Cardiovascular Health and Age-related maculopathy study
Relationship between foveal birefringence and visual acuity in neovascular age-related macular degeneration
Follow-up after intravitreal triamcinolone acetonide for exudative age-related macular degeneration .

Posted by Maxine Clarke on March 19, 2007
Categories: Publications | Permalink | Comments (0)

Readers who enjoy listening to the regular Nature podcasts might be interested to read Open Culture: Podcasts Primer. As its title suggests, the article explains what a podcast is, how to download one via iTunes, rss or to your own media player; how to play, listen and even to make your own podcasts.

Nature provides a free podcast each week. The current edition highlights Kuiper belt collisions, the roots of flowering plants, Linnaeus’ legacy, the birth and death of photons and swarms of mini-quakes. The podcast is featured on the journal's home page, but if you go to NPG's podcast index, you'll also find subject-focused podcasts on stem cells, systems biology, neuroscience, chemistry, genetics and more.

Posted by Maxine Clarke on March 19, 2007
Categories: Communication | Permalink | Comments (0)

The Pathway Interaction Database is a free, high quality resource of signalling pathways in human cells for biologists and bioinformaticians to explore, visualize and mine signalling events.
This month's update features:
LPA receptor-mediated events and Role of calcineurin-dependent NFAT signaling in lymphocytes.

Sign up to receive the monthly update alert for the NCI-Nature Pathway Interaction Database.

The UCSD-Nature Signaling Gateway is updated every week; you can sign up for regular alerts to that, also. This week, we are delighted to announce the creation of a four-person advisory board to appoint the most appropriate mix of experts for the Editorial Board, and to identify and invite new members. The new advisory board consists of Michael Berridge, Pat Casey, Tony Hunter and Robin Irvine. Read more about the future of the Signaling Gateway Molecule Pages database.

Posted by Maxine Clarke on March 16, 2007
Categories: Publications | Permalink | Comments (0)

"Are blogs the new way to get a job? With 55 million blogs on the Internet and 100,000 more being created daily, some bloggers are wondering whether personal weblogs will replace traditional CVs and résumés when job-hunting." Paul Smaglick's Prospect column in this week's Nature discusses some of the advantages and disadvantages of blogs as career tools.
Full article at: Nature 446, 343 (2007) | doi:10.1038/nj7133-343a.

Posted by Maxine Clarke on March 15, 2007
Categories: Careers | Permalink | Comments (1)

In this week's Nature, Hanno Wuerbel of the Justus Liebig University of Giessen, points out that although a large majority of the public is supportive of the principles of animal experimentation to improve biological knowledge, human and veterinary health, nature conservation and animal welfare, the public also expects strict adherence to the 3R-principle (replace, reduce, refine) to minimize animal numbers, pain, suffering and lasting harm.
A set of News Features in Nature (444; 807-816; 14 December 2006) identified considerable scope for advancing the 3Rs. Dr Wuerbel proposes that journals could play a much more effective role by including a 3R section in the methods section of published papers: first, to allow authors of controversial papers to detail their measures to minimize pain, suffering and lasting harm in the animals; and second, to allow authors to describe novel tools or techniques applied in the published work that serve the 3Rs.
More details about the proposal are described in the Nature Correspondence. We welcome views from authors and other scientists about the proposed policy.

Posted by Maxine Clarke on March 14, 2007
Categories: Animal experiments, Public and media | Permalink | Comments (17)

How do you go about publishing your research in a Nature journal? What happens after you submit your paper? What is the editorial process? We have recently updated our advice to authors, which is available in newly translated French, German, Italian and Spanish versions. As ever, we welcome questions and comments about the editorial process and about getting published in our journals. Read all about it in:
English
French
German
Italian
Spanish
You can also visit our Asia-Pacific gateway for versions in Chinese, Japanese and Korean.

Posted by Maxine Clarke on March 14, 2007
Categories: Author services, Writing | Permalink | Comments (1)

Nature Publishing Group is one of several publishers whose policy on picture copyright is examined on the blog Public Rambling. The verdict on us?

"In their page on rights and permission they write:

"Permission can be obtained for re-use of portions of material - ranging from a single figure to a whole paper - in books, journals/magazines, newsletters, theses/dissertations, classroom materials/academic course packs, academic conference materials, training materials (including continuing medical education), promotional materials, and web sites. Some permission requests can be granted free of charge, others carry a fee."

So it is possible to get permission to use their content but it has to be obtained on a case by case basis and it might cost money. I tried getting permissions to use pictures from a Nature Biotech paper for a educational website and it cost nothing for 1 to 3 pictures. Above that it starts costing 150 dollars. It also costs nothing to get permission to include less than 400 words but above that we have to pay. The procedure is very straightforward and can be done in a minute."

Posted by Maxine Clarke on March 13, 2007
Categories: Access | Permalink | Comments (0)

The Library Journal has just selected its best science books of 2006. Science's Big Picture—Best Sci-Tech Books 2006 - 3/1/2007 - Library Journal

"Of the 34 books selected as the best of 2006, three—Amir Aczel's The Artist and the Mathematician, Steven Johnson's The Ghost Map, and Chet Raymo's Walking Zero—draw both sobering and inspiring lessons for today from science's long history. And what's in store for the future of science? As Elizabeth Kolbert's Field Notes from a Catastrophe and Tim Flannery's The Weather Makers compellingly detail, global warming remains one of our most pressing concerns. At the same time, new theories in the physical and natural sciences, explored respectively by Charles Seife's Decoding the Universe and John Whitfield's In the Beat of a Heart, have great potential."

Congratulations to John Whitfield, who was a subeditor and then a news reporter for Nature before writing his book on the search for an underlying order in the biological world. David Robinson, reviewing the book in Nature, wrote:

"Whitfield does a fine job of describing the logic behind the theory and its antecedents. He unpacks its key assumptions and describes what the fractal plumbing system responsible for quarter-power scaling would look like. No armchair pundit, Whitfield interviewed the theory's authors and their colleagues, censused trees in Costa Rican forests with Enquist's team of students and postdocs, and spent a few less arduous hours having his own metabolism measured in London. His first-hand experiences at the subject's coalface are vividly readable. Whitfield's later chapters consider how metabolism relates to biodiversity and biogeography, and how it might dovetail with genetics. They also dwell on how these grand ideas might apply, or not, to the largest part of the tree of life: microbes. Overall, Whitfield's book provides the best available introduction to West, Brown and Enquist's big idea."

Posted by Maxine Clarke on March 13, 2007
Categories: Writing | Permalink | Comments (0)

The first bumper issue of The ISME (International Society for Microbial Ecology) Journal is now in press, and will be published by Nature Publishing Group on 1 May. A description of the full scope of the new journal, sample copy request form, and subscription information are available at the journal's website.
The editors and publishers will be showcasing the new journal at the forthcoming 107th general Americal Microbiology Society meeting in Toronto from 21 to 25 May, so if you are attending, please look out for ISME editors Mark Bailey (Centre for Ecology and Hydrology, Oxford), John Heidelberg (University of Southern California) and George Kowalchuk (Netherlands Institute of Ecology), as well as the journal team from Nature Publishing Group.
ISME's web site provides further information on the society's activities.

Posted by Maxine Clarke on March 12, 2007
Categories: Publications | Permalink | Comments (0)

"An inherent principle of publication is that others should be able to replicate and build upon the authors' published claims. Therefore, a condition of publication in a Nature journal is that authors are required to make materials, data and associated protocols available to readers promptly on request." This excerpt from our guide to authors may seem obvious, but judging from the number of discussions we have had with authors and referees, we would like to clarify one specific point: at Nature Methods, the definition of "materials, data and associated protocols" includes custom-designed software necessary for the method's implementation. Yet there are several ways of making software available, with various degrees of disclosure and in a choice of formats.
The details are provided in this month's Editorial in Nature Methods.

The Nature Methods editors welcome comments on this policy at Methagora, the Nature Methods blog. We also welcome your views on the application of this policy to other Nature journals.

Posted by Maxine Clarke on March 09, 2007
Categories: Data availability | Permalink | Comments (0)

Abderhalden's fraud still wins him some supporters : Article : Nature

In this week's Correspondence pages of Nature (see above link for full text), U. Kutschera of the Univeristy of Kassel reminds readers that an old case of fraud is still being ignored in some quarters. From the Correspondence:

"Your Misconduct Special (Nature 445, 240–245; 2007) calls South Korean stem-cell biologist Woo Suk Hwang "arguably the highest-profile fraudster ever". A look into the history of fraud in the biomedical sciences reveals at least one other strong candidate for this title.

In the area of human reproductive biology, the Korean scandal is overshadowed by the case of the influential German physiologist Emil Abderhalden (1877–1950) and the non-existent Abwehrfermente or 'defence enzymes' he claimed to have discovered. The shocking story of his fraudulent work, over a long period, has been told by Ute Deichmann and Benno Müller-Hill (Nature 393, 109–111; 1998).

Briefly, Abderhalden — a powerful and influential scientist — published a first paper on his "most important discovery" in 1909, and a widely read and translated book on the subject followed in 1912 (E. Abderhalden Abwehrfermente: Die Abderhaldensche Reaktion Theodor Steinkopff, 7th edn, 1944). The 'Abderhalden reaction' was used as a pregnancy test, and to treat various diseases. From 1914 on, biochemists tried to repeat Abderhalden's experiments, but failed to achieve this. A number of experts published their negative findings, but Abderhalden continued to publish fabricated data until his death."

Prof. Kutschera concludes: "Worst of all, Abderhalden's myth is still alive. For instance, on the German site of the Internet encyclopaedia Wikipedia, Emil Abderhalden was until this year listed as an "important physiologist and discoverer of the specific Abderhaldensche Abwehrfermente — he developed the first pregnancy test". Similar admiring descriptions can still be found in the latest editions of German lexica such as Die Zeit: Das Lexikon 2005 . The authors refer to Abderhalden's book, which remains available in libraries and second-hand, and is still taken seriously in the popular literature on biomedicine."

Posted by Maxine Clarke on March 09, 2007
Categories: Ethics | Permalink | Comments (2)

Pedro Beltrao, on his bioinformatics blog Public Rambling, has updated his blogroll into four categories, one of which is "publishing and general science". Nautilus and Peer to Peer feature in this category, with the comment "Nautilus and Peer-to-peer provide mostly useful information and a way to interact with Nature services". If you know of other useful science publishing-related blogs you can recommend, please let Pedro know at the link. Indeed, let us know here, too.

Posted by Maxine Clarke on March 08, 2007
Categories: Publications, Writing | Permalink | Comments (0)

Beginning this month (March 2007), Nature Biotechnology is recommending that authors deposit raw data from proteomics and molecular-interaction experiments in a public database before manuscript submission to the journal. The reason for this recommendation? "The lack of raw data sets associated with proteomics and molecular-interaction papers is a long-standing and pernicious problem. It not only stymies the exchange, comparison and reanalysis of experimental results, but also inhibits the development of new algorithms and statistics that could improve the confidence in data and conclusions. In addition, it undermines the ability of referees to fully evaluate the quality of data supporting a manuscript's conclusions, sometimes forcing them to assess results simply on 'good faith'. Contrast this with the situation in genome research and structural biology, where there is an abundance of public data sets from DNA microarrays, genome sequencing and X-ray crystallography studies, and it is not difficult to understand why progress in proteomics has lagged."

For further information and links to the public databases, see the full text of this editorial: Nature Biotechnology 25, 262 (2007); doi:10.1038/nbt0307-262b

See the authors' and peer-reviewers' website for a description of the Nature journals' policies on data and materials availability, with links to relevant editorials.

As ever, we welcome your feedback and comments.

Posted by Maxine Clarke on March 08, 2007
Categories: Data availability | Permalink | Comments (0)

As previously announced on Nautilus, Nature Publishing Group is launching a web portal to keep abreast of the best research emerging from China.

Cell biology research in China is a relatively young plant that has been growing apace with the country's rapid global development. Indeed, the plant is also increasingly bearing fruit — not just in the shape of new and well-equipped research facilities such as the SIBS's Institute of Biochemistry and Cell Biology, which would not be out of place in Shanghai's famous architectural show room along the Huangpu River, but also in terms of high profile papers. China's publication rate in peer reviewed journals has risen eightfold in the past decade to rival that of the UK and Japan. Importantly, the number of papers with in excess of 20 citations has also risen tenfold, although in terms of absolute levels they remain in the hundreds, and biomedical science represent less than 20% of mainland China's high-impact papers. We have also noticed a similar tenfold rise in submissions from China to this journal over the past seven years, which we hope will be reflected in a proportional representation in print. However, to put things into pers