Nautilus

From Sara Abdulla:
A unique cultural venue opened in London this month. The Wellcome Collection is the first permanent home for the massive, maverick history-of-medicine collection that pharmaceutical entrepreneur Sir Henry Wellcome (1853–1936) gathered throughout his life. Thirty million pounds (US$60 million) and decades in the making, the free venue has three galleries, one of the world's most important history-of-medicine libraries, an original programme of live events, a members' club, a bookshop, a café, a conference centre and Pablo Picasso's Bernal mural.
Wellcome's fortune also created the Wellcome Trust, Britain's main bioscience research funding agency. The trust has now remodelled the compact 1930s building it recently vacated to realize Sir Henry's vision of a 'Museum of Man' and to extend its public engagement activities.
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The second floor brings the trust's vast library into the twenty-first century. Virtual browsing stations and WiFi now complement the graceful galleries long beloved by science-and-society scholars (and TV crews in search of instant gravitas). The top floors house The Wellcome Trust Centre for the History of Medicine at University College London, where much of this thoughtful activity starts.
And what of the members' club? Will it become biology's Algonquin Hotel? Quite possibly: it is inside a thrilling new museum, beside a leading medical school, opposite London's new European rail terminus and encircled by scientific publishers. What better place to raise a glass to humane curiosity, the legacy of Sir Henry Wellcome.

For the rest of this review, see Nature 447, 1056 (2007).

The Wellcome Collection
by the Wellcome Trust, 183 Euston Road, London.

Posted by Maxine Clarke on June 29, 2007
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This week saw the much trailed departure of Tony Blair as UK prime minister. In a Commentary (Nature 447, 1053; 2007) in the current issue of Nature, Sir Robert May, the government's chief science adviser from 1995 to 2000, reflects on the Blair legacy. In many ways, he says, science and engineering prospered. Yet there is general discontent amongst scientists in UK universities, and many current trends are potentially damaging. Blair's successors — Gordon Brown initially — will have much to do if the country is to continue to thrive scientifically.

...why is there discontent among scientists in UK universities? Are we perhaps revealing an inherent, Eeyore-like glumness? I think not. Although student numbers, faculty positions and research funds have all increased, they have not done so in equal proportions. Student-to-staff ratios are almost universally higher than 15 years ago. And research funding — despite its increase in real terms — has not kept pace with the increasing number of active researchers, themselves spurred on by the demands of the Research Assessment Exercise (RAE), which every few years rates individual academic departments. Life seems harder than it used to be. Even more important, in my opinion, than higher teaching loads and the increasingly fierce competition for grants, is the extreme growth of bureaucracy — too often masquerading as accountability. The ballooning of the civil service since 1997 means that there are now more conscientious administrators who hold meetings and send out forms to be filled in. And universities have matched or exceeded the growth in bureaucrats seen in the civil service. This growth is only partly justified by need. One issue that Brown might address is that the current number of central administrative staff is roughly equal to the number of faculty for four major UK universities; this would certainly raise eyebrows at many top US universities.

Posted by Maxine Clarke on June 29, 2007
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Nature Genetics presents a special issue, Structural Variation in the Human Genome, comprised of one commentary and seven perspectives exploring recent discoveries and future prospects in the rapidly growing field of structural genomic variation. As well as comprehensive overviews of this burgeoning area, the articles also propose standards and guidelines for future research. Access this special issue FREE online.
From the Editorial:
From the earliest cytogenetic studies, it was recognized that losses or gains of entire chromosomes or microscopically visible alterations involving very large chromosomal segments were the cause of several common developmental disorders, including Down's syndrome. Beginning in the early 1990s, it also became apparent that submicroscopic gains or losses of specific chromosomal segments were a recurrent cause of many other rare genetic diseases. What was generally unappreciated, up until a few years ago, was the extent to which focal variation in DNA copy number contributed to the range of normal sequence variation among apparently healthy individuals.
In this issue, we present a collection of eight commissioned pieces highlighting recent advances in the field. We hope you enjoy this fresh glimpse into the exciting realm of human genomic structural variation.
Nature Genetics 39, Issue 7s, July 2007.

Posted by Maxine Clarke on June 29, 2007
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The Society for Mucosal Immunology (SMI) and Nature Publishing Group (NPG) are very pleased to announce a new publishing partnership. In January 2008, NPG and SMI will launch a new publication, Mucosal Immunology. Mucosal Immunology is now accepting submissions of papers discussing all aspects of immunity and inflammation involving mucosal tissues. The guide to authors is here and you can submit here.
Mucosal Immunology is the official publication of the SMI. It will provide a forum for both basic and clinical scientists to discuss all aspects of immunity and inflammation involving mucosal tissues. The journal reflects the interests of scientists studying gastrointestinal, pulmonary, nasopharyngeal, oral, ocular and genitourinary immunology through the publication of original research articles, scholarly reviews and timely commentaries, editorials and letters. Publication of basic, translational and clinical studies will all be given equal consideration. 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.
The Editor-in-Chief is Brian Kelsall, MD, of the NIH National Institute of Allergy and Infectious Diseases.
General editorial inquiries and correspondence regarding manuscripts and peer review should be addressed to:
Taylor Bowen, Managing Editor.

Posted by Maxine Clarke on June 28, 2007
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Dr Monica Zoppè writes: The Nature News story 'Applicants challenge male order at Howard Hughes' (Nature 447, 242-243; 17 May 2007) highlights only some aspects of the gender imbalance that dominates the science system everywhere. All scientific funding agencies distribute money on the basis of competition, which is an attitude typical of males. Women are more inclined to collaboration than competition, and if forced to compete do so reluctantly. Some refuse even to take part, hence relegating themselves to the lower steps of the career ladder.
Women often feel that competition can easily degenerate into rivalry and open hostility, which is damaging to everyone, but is an issue often overlooked by men. If Howard Hughes, or any other funding agency, really believes that scientific excellence is equally distributed among men and women, then the best way to grant women their share of funding (50%) would be to have separate distribution avenues: one for men, in which male scientists set the rules and judge applications; and one for women, managed by and dedicated to female scientists.
This would be a very bold and unusual move for any funding agency, and it would need to run for several years before women could define a 'female road of science' independent of the typical 'competition road' to which we have had to adapt until now. Yet it may eventually allow women to demonstrate that a different attitude is possible, scientifically as good, or even better. Of course, it is necessary to define terms like 'success' or 'good science' according to a more (gender)-balanced value system: I am sure that many women are ready to participate in such a discussion, if it is started.
Monica Zoppè
Institute of Clinical Physiology
Pisa, Italy

Posted by Maxine Clarke on June 28, 2007
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Nature China has just been updated. Every week, the editors write research highlights to summarize the best research published in mainland China and in Hong Kong. This week's selection:
Axon differentiation: Dishevelled neurons
The signalling protein Dishevelled helps to regulate axon growth
Microemulsions: A dry mix
Scientists create a microemulsion of two ionic liquids
Nanotubes: Slowly but surely
Single-walled nanotube arrays have been synthesized using ultralow gas-flow deposition
Zinc oxide: Crystal under pressure
A model explains how the crystal structure of zinc oxide is transformed at high pressures
Super-excited states: Change the channel
The super-excited states of fluorine molecules are studied using quantum-defect theory
Fluid dynamics: Understanding Hurricane Katrina
Solutions to the Euler equations provide a means to study a wide range of physical phenomena, including natural disasters such as Hurricane Katrina.
Please visit Nature China to read these highlights, which are all free, and sign up to receive weekly updates, as well as to rank the selections and recommend your own favourites.

Posted by Maxine Clarke on June 27, 2007
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Frank Gibson, a Research Associate at Newcastle University, UK currently working on the e-neuroscience project CARMEN, has written an essay Do scientists really believe in open science? , in which he collects current opinions of “Open Science”. He was stimulated to write the essay because of his role in the CARMEN project which, he writes, has exposed him to a domain of the life-sciences to which "data sharing and publicly exposing methodologies has not been readily adopted, largely it is claimed due to the size of the data in question and sensitive privacy issues."

The essay is available here. It addresses definitions of "open science" and summarizes the standards used in disciplines other than neuroscience. You can see the Nature journals' policies on data availability here, which apply to all the original research articles our journals publish. Via this web page, you can provide us with your comments and views on recent journal editorials about emerging policies on data availability in a range of disciplines and circumstances.

Among other aspects of "open science", Dr Gibson discusses the "open notebook" approach pioneered by J-C Bradley. He also notes that Postgenomic produces an "up-to-the minute list of the open science discourse". (Postgenomic is a website that tracks hundreds of science blogs and "does interesting things with that data".) "Although early days", continues Dr Gibson, "maybe even the "open science group" on Scintilla (still undecided on Scintilla) will be the place in future for fostering the open science community".
Scintilla is one of Nature Publishing Group's very latest products. It collects data from hundreds of news outlets, scientific blogs, journals and databases and then makes it easy for you to organize, share and discover exactly the type of information that you're interested in. For example, you can keep track of life science podcasts, or the latest papers on schizophrenia, DNA methylation, physics or immunology. It is free to join, so take a look at what it has to offer and, if you wish, contribute to the open science group, or join one of the many other interest groups there.

Posted by Maxine Clarke on June 27, 2007
Categories: Data availability, Disciplines | Permalink | Comments (0)

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

Posted by Maxine Clarke on June 26, 2007
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There is a forum for Nature Precedings on Nature Network, where you can ask questions, receive answers and join the debate about this new way to post your results. (It is all free, but you need to sign up to Nature Network first.) One such question asked of Nature Precedings by a science blogger is: Why post on Precedings when one can just post on one’s blog? Hilary Spencer, product development manager for Nature Precedings, provides a reply at the Nature Network forum:

To me, there seem to be very good reasons to post on Precedings, the first of which involves stability. Blogs, and personal webpages, can be ephemeral. If the author changes affiliations, domain names, or even blog publishing software, blog postings may disappear. One of the goals of Precedings is to create a stable permanent archive for researchers. We anticipate that the content will be mirrored by one or more of our partner organizations, thus ensuring that the researcher’s work will always be available.
The second related reason involves ”citability”. Blogs citations currently fall in a gray area—there is no definitive way to cite a blog posting, although this is changing. One of the benefits of Precedings is that every document posted is citable, thus ensuring that the author can be properly credited with the idea. We assign a DOI or a handle to every submission, which provides a permanent identifier for the document and can be used in citations.
A final reason is exposure. For many researchers, posting to a central archive provides more exposure for their ideas than they would receive by posting it on their website. For example, I think authors tend to get more exposure when their documents are also listed in PubMed rather than only on their personal website. (Precedings allows researchers to link submissions to postings on their blogs for redundancy.) To that end, we hope Precedings will help researchers reach a wider audience for their ideas.
Nature has always been very supportive of the blogging community, but we feel that Precedings fills a gap between (informal) blogs and (formal) peer-reviewed publications. What are your thoughts?

Can you post on both Precedings and your blog? Go to the forum to give us your views and see our responses to questions like this, or add your comments here. Other topics being disussed at the Precedings Network forum are whether PowerPoint presentations are acceptable for Nature Precedings, the site's rating system, and what drives people to post preprints in a public website.

Posted by Maxine Clarke on June 26, 2007
Categories: Author Services Feedback, Policies Feedback, Publications | Permalink | Comments (0)

From this week's (21 June issue) Nature Correspondence (Nature 447, 908; 2007):

The US Educational Commission for Foreign Medical Graduates (ECFMG) processes the applications of foreign students for the US Medical Licensing Examination, which evaluates candidates' basic and clinical knowledge in medicine. The examination has two steps, both of which must be passed for the ECFMG to recognize the individual as a medical doctor in the United States.
As a medical student, I applied for step 1 in January 2007, entering my country (Iran) in the contact address section. A message in red letters appeared on the registration page: "It has come to our attention that ECFMG may be subject to specific United States federal regulations that prohibit entities from doing business with or providing a service to any individuals who have an address of residence in specific restricted countries. The country of Iran is included on this list of restricted countries. In light of this, ECFMG is not able to allow you to request this service."
The political status of Iran or any other nation is not relevant to education. The result of the restriction is that all medical students and graduates who live in Iran are prevented from taking the US licensing examination. This surely is academic discrimination against a whole country.
Sina Zarrintan
Tabriz University of Medical Sciences, Iran

Posted by Maxine Clarke on June 25, 2007
Categories: Careers, Ethics | Permalink | Comments (0)

In which I contemplate the unsung scientific record - Mind the Gap - Jennifer Rohn's blog on Nature Network

There is a very chatty conversaton happening at the above post on MInd the Gap, Jennifer Rohn's Nature Network blog. Jennifer's post is about the plea In Nature by Sydney Brenner and Richard Roberts to scientists to save their notebooks and correspondence and donate them to historians.

Jennifer writes: "Of course I agree that such materials should be preserved, which is probably why I can’t bring myself to throw away the two boxes of gently moulding lab notebooks, spanning thirteen years of research, stashed up in the loft. I’m sure these are not the papers that Brenner and Roberts had in mind, though – they want to preserve the detritus of the Watsons and Cricks of this world, not of ordinary research folk like me.
But then I got to wondering. Why not? My lab notebooks might make pretty compelling reading to some future historian starved for scraps of how 99.9% of (non-celebrity) researchers spent their days and nights in the lab. Why not document the parade of meaningless or ambiguous data that make up most researchers’ records? The ‘non-Eureka moments’, if you will? "

Join in the conversation here or at the Mind the Gap post's comments section, which has taken some fascinating tracks along avenues of clear communication and the virtue of electronic notebooks as well as the importance of a good cup of coffee.

Posted by Maxine Clarke on June 25, 2007
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"I'm a strong believer in allowing commenting on online papers", says Euan Adie on his blog Flags and Lollipops in a post titled Publishers, trackbacks and shared data. "This is something under serious discussion at Nature (the question is how to do it properly). The vast majority of researchers read, organize and discover papers online; we should give them the tools and opportunity to discuss papers online, too."
The Flags and Lollipops posting contains a discussion of technical ways to alert authors when there are new comments on their published paper, and ways to create systems to track "informal" comments and writing, so it can be part of a scientist's accredited boldy of work, and hence a more attractive proposition. We are interested in knowing your views -- Nature authors past, present and future, among the scientific community. Comments are open.

Posted by Maxine Clarke on June 22, 2007
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From this week's issue of Nature, Correspondence page (Nature 447, 908; 2007).

Your News story 'Anger at "unfit" museum design' (Nature 447, 239; 2007) reports some people's belief that the design of the Natural History Museum's Darwin Centre Phase Two is unfit for purpose, as the building will not have room to house the entire insect and plant collection.
The crux of the issue is that the public is being given access to our science, and this takes space. Building new facilities for the entirety of our collections, research and public access in one go is not feasible, with current funding. Instead we are taking it by stages. With the completion of Darwin Centre Phase Two, we will have more than half of our 70 million specimens in high-quality storage.
Balancing the needs of collections, research and public access will help us to advance knowledge of the natural world and to communicate this to the public. It will mean some changes in how we work and it will take time to adjust. However, we think that the new building will lead to a long-term improvement in the way we carry out and communicate the museum's work in taxonomy and systematics.
We have received a high level of support for this project, and are confident that it will be a real benefit to the museum, the scientific community and the wider public.
Richard Lane
Natural History Museum, London.

See here for the News story on which Dr Lane's letter comments, which reports criticisms of the directors of the Natural History Museum over their plans to split parts of its world-renowned collection of biological specimens on a permanent basis. Some of the museum's curators are angry that plans for a new building to store the bulk of the museum's entomology and botany collections remain unaltered three years after being branded unfit for the purpose by museum staff, according to the News story.

Posted by Maxine Clarke on June 22, 2007
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Nature Chemical Biology is pleased to present a special focus on natural products (and terpenes in particular) in the July 2007 issue of the journal. Investigations into natural products have recently regained prominence with the increasing understanding of their biological significance and increasing recognition of the origin and function of their structural diversity. This issue highlights some of the major questions and advances in natural products research, from recent synthetic approaches to access complicated natural products to a new educational program which utilizes natural products as a basis for discovery-based research. The entire contents of the July issue of Nature Chemical Biology are free for one month, including the focus on natural products, which is available here.

Posted by Maxine Clarke on June 22, 2007
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Nature Protocols June issue is now out. Any scientist can upload his or her own protocol and comment on the protocols already uploaded into the website for free on the interactive Protocols Network.
Make suggestions as to how to improve current protocols, or share what worked and what didn't for you as well as uploading your own protocols for further feedback and refinement. You can also discuss protocols in our free forum on Nature Network, where Katharine Barnes, Editor of Nature Protocols, and her colleagues invite you to post questions relating to techniques and to answer the queries of other scientists in your field.

Posted by Maxine Clarke on June 22, 2007
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News from the Neuroscience Gateway: The Allen Institute for Brain Science has released an upgrade to the Allen Brain Atlas, offering improved browsing and navigation and enhanced data mining. Updates to the Atlas application include:
NeuroBlast, a blast search tool that allows users to easily retrieve a list of genes with expression patterns similar to a gene of interest.
Easy Browsing and Quick View options that allow users to quickly access and browse raw data and data summaries by gene or brain structure.
Improved navigation allows users to synchronize raw data images with corresponding anatomic reference plates from the Allen Reference Atlas.
The Neuroscience Gateway, a comprehensive source for the latest research, news and events in neuroscience and genomics research, is a collaboration between the Allen Institute for Brain Science and Nature Publishing Group. The Allen Brain Atlas is a freely available scientific resource developed by the Allen Institute, which provides maps of the expression of approximately 20,000 genes in the mouse brain. Together, the Neuroscience Gateway and the Allen Brain Atlas are new tools to help researchers navigate neuroscience and genomics research. See more details about the Allen Brain Atlas here.

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

Small changes that work for writer and reader - Time for a change - Linda Cooper's blog on Nature Network

In her Nature Network blog Time for a Change (click on the underlined sentence above), Linda Cooper provides suggestions to help researchers marshal their data into a coherent story; such suggestions also help readers because a logically structured account of the significant finding is so much easier for them to understand than a random or semi-structured compilation of data. In the post linked to above, Linda provides tips that relate to the structure and content of a manuscript, beginning with the paper Abstract.

Linda provides specific advice if you comment at her blog. For example, Kathryn Holt asks: "I would be interested to read your posts on any of the topics you suggest, but in particular I’d like to hear your thoughts on “how to transform convoluted sentences into sentences where ideas shine through”. This can seem a very difficult task, especially when the writer has in their own mind a great many details behind every statement they make, and indeed is expected to provide evidence for all their claims." And Linda replies:" I’ve deconstructed the Abstract to your paper on “Multidrug-resistant Salmonella enterica serovar Paratyphi A” and would be happy to give you some editing suggestions.."

Time for a Change provides several very useful posts on how to write a clear scientific manuscript, so please do check it out. A clearly written paper is better understood by editors and readers, and is likely to have more impact after it is published.

Posted by Maxine Clarke on June 21, 2007
Categories: Writing | Permalink | Comments (0)

This letter is reproduced in entirety from Nature's Correspondence in today's (21 June) issue (Nature 447, 908; 2007).
Scientists should promote co-operation, not boycott

Since 1931, the International Council for Science (ICSU) has upheld the principle of the universality of science, based on the right of scientists to work without discrimination on the grounds of citizenship, religion, creed, political stance, ethnic origin, race, colour, age or gender.
The entire ICSU membership, representing the scientific community in 112 countries and all disciplines, has consistently expressed its unequivocal support for this principle. This stance has stood the test of time throughout the Cold War, apartheid in South Africa and the new challenges posed by international terrorism. It is a strong expression of solidarity across the international science community: a critical reference point for individual scholars confronted with threats to their freedom.
The decision by the congress of the UK University and College Union to recommend that its members bar academic exchanges with Israeli researchers is a flagrant breach of this principle. It has rightly drawn substantial adverse comment from scientists, newspaper columnists and human-rights activists in the United Kingdom and internationally.
It is easy to understand the strong feelings generated by conflicts and people's desire to demonstrate their opposition to the actions of governments. But to do so through the medium of individual scholars is to sacrifice a profoundly important principle of freedom and solidarity. In situations of strife and conflict, it is surely the duty of scientists to promote international understanding and co-operation — not to penalize each other for the shortcomings of their governments.

Bengt Gustafsson
ICSU Committee on Freedom and Responsibility in the Conduct of Science

Posted by Maxine Clarke on June 21, 2007
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In a post entitled Nascent: Word 2007 and the STM Publisher Ecosystem, Howard Ratner, Chief Technical Officer of Nature Publishing Group, writes about how he has become involved in "a very lively conversation with Microsoft staff about why Word 2007 is not being actively endorsed by STM publishers. It has recently come to Microsoft's attention that Nature , Science and many other scholarly publishers do not accept files from authors in Word 2007. Both Science and Nature Publishing Group have been in correspondence with Microsoft staff on this important issue. The staff there have been very willing to engage in this conversation."

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

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

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

Posted by Maxine Clarke on June 21, 2007
Categories: Policies, Publishing, Writing | Permalink | Comments (1)

Since their introduction to medicine, Magnetic Resonance Imaging (MRI) and Positron Emission Tomography (PET) have greatly contributed to medical research and clinical practice. In particular, brain imaging with MRI and PET scans has led to important insights into both the normal and diseased brain. With increasingly advanced technology, scanning techniques, and clinical applications, brain imaging is a continuously evolving field. A web focus, presented by the Journal of Cerebral Blood Flow & Metabolism, compiles many of the most important research papers on the techniques and applications of cerebral MRI and PET imaging from Nature Neuroscience, Nature Medicine, NCP Neurology and Journal of Cerebral Blood Flow & Metabolism. There is free access to MRI & PET Imaging research for a limited time.

Posted by Maxine Clarke on June 20, 2007
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The Functional Glycomics gateway is updated today (20 June) -- a one-stop online resource designed to keep readers in touch with the latest and hottest research in glycobiology, in collaboration with the Consortium for Functional Glycomics. Each month we showcase two exciting new glycobiology articles from the current literature. Nature Publishing Group papers are available free for 3 months and the Editor's Reviews are free indefinitely. This month's two featured articles are: Glycosylation effects: core contributions, which describes how distant carbohydrate substitutions at the N-glycan core alter glycan lectin affinity, glycoprotein-mediated cell binding and serum clearance; and Tumor Growth: at the end of a snake bite in which it is described how the C-type lectins lebectin and lebecetin isolated from the venom of the blunt-nosed viper (Macrovipera lebetina) inhibit tumor angiogenesis through a direct interaction with epithelial cell integrins.
Also in the Functional Glycomics gateway are Research Highlights (short summaries of research papers); the Research Library; and the Consortium Quaterly, the latest news and findings from the Consortium for Functional Glycomics.

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

For readers who are interested in knowing more about the virtual world Second Life, there is a nice article on the Booksquare blog called Publishers Explore the Metaverse in which the writer has trawled Second Life to see what (book) publishers are up to there. Perhaps more directly relevant to readers of Nautilus is a post called A sampler of science in Second Life on Troy McConaghy's Nature Network blog, Science in the Metaverse.
After seeing all the online activity there, Nature journal authors might want to consider giving a virtual talk in Second Life. Drop a line in the comments, if so, or contact Joanna Scott of our web publishing department (Joanna Wombat in Second Life).

Posted by Maxine Clarke on June 20, 2007
Categories: Communication, Public and media | Permalink | Comments (0)

Timo Hannay, head of NPG's web publishing department, provides some more information about Nature Precedings on the Nascent blog . From his post:

"all the content is released under the Creative Commons Attribution License and the service is free to authors and readers. We're working with some of our partners to mirror the content to ensure its [Nature Precedings'] long-term free availability (whatever might happen to Nature Publishing Group). And what a great list of partners they are: the British Library, the European Bioinformatics Institute, Science Commons and the Wellcome Trust. See our press release for their statements about the project.
We expect to add one or two more partners in the not-too-distant future, and convene a group of forward-thinking senior scientists to advise us on future development of the service. Right from the beginning, Precedings was conceived not as an NPG-only project but as a collaborative endeavour to open up scientific communication. To that end, we'll also be reaching out to other publishers in the weeks to come to ensure that this initiative works effectively alongside the existing journal publishing channel, which Precedings seeks to complement.
If you've got comment, please post it below, go to the Nature Precedings Group on Nature Network, or write to precedings-at-nature-dot.com."

Posted by Maxine Clarke on June 19, 2007
Categories: Publications | Permalink | Comments (3)

Vaccines are among the most useful and cost-effective tools for reducing the morbidity and mortality associated with infectious diseases. This month, a special Focus issue of Nature Reviews Microbiology highlights some of the latest progress in vaccine development and the pitfalls that have been encountered along the way.The topics covered range from advances in our understanding of the immune response that will help in the development of new adjuvants and anti-bacterial vaccines, to the latest work on the development of a dengue virus vaccine. The accompanying library collects the most relevant recent publications from Nature Publishing Group.

Here is the table of contents for the vaccine focus collection.

Posted by Maxine Clarke on June 19, 2007
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The Omics Gateway is the portal for all information relevant to large-scale genomics and biology from Nature Publishing Group. Regularly updated, this comprehensive collection enables you to view relevant archived and recent content drawn from the complete range of our publications. Most of the content is free for you to view online. The latest article higlight is GeoChip, a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. from the ISME Journal. This article describes the first use of GeoChip, a comprehensive functional gene microarray suitable for studying the geochemical, ecological and environmental processes of diverse microbial communities. This new methodology allows for the screening of environmental samples across more than 10,000 genes belonging to over 150 of the most important functional gene families.
The Omics Gateway provides life scientists a convenient portal into publications relevant to large-scale biology from journals throughout NPG. By organizing our papers and web focus projects on large-scale biology into this comprehensive, topical, one-stop web portal, we hope to help you quickly reach the resources you need to study the "ome" of your choice and to keep you up-to-date with the most significant research in that area.

Posted by Maxine Clarke on June 18, 2007
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Last week, Nature held mini-conferences in Beijing and Shanghai to celebrate the launch of Nature China. There were over 200 attendees in Beijing, and Liu Depei, president of the Chinese Academy of Medical Sciences and vice president of the Chinese Academy of Engineering, gave the opening remarks, together with Daoxiang Sun of Tsinghua University Council. Also speaking were Huang Laiqiang of Tsinghua University, who last year was a coauthor of a paper in Nature on self pollination in orchids (Nature 441, 945-946; 2006), and Xiaolin Zhang, head of the Innovation Center China of AstraZeneca and sponsor of Nature China, who outlined the company's activities in the region.
A similar event was held at the Shanghai Institutes for Biological Sciences (SIBS), organized by Dangsheng Li, deputy editor in chief of Cell Research, a journal based at SIBS and part of Nature Publishing Group's Asia-Pacific academic journal programme. The meeting was attended by about 120 people, with talks by Jarui Wu, vice president of SIBS, and Hong-Wei Xue, deputy director of the Institute of Plant Physiology and Ecology of the Chinese Academy of Sciences, who provided tips on publishing in international journals.
According to results presented at the conferences, in 2006, scientists from mainland China and Hong Kong published more than 80,000 scientific papers that were indexed by the Institute of Scientific Information (ISI), bringing the output of scientific research at the same level (in numbers) as the United Kingdom and Japan.
Additional data from ISI indicate that the number of high impact papers from China with large numbers of citations is also increasing rapidly in number year on year.
Every week, Nature China’s editors select some of the best recently published research from across the scientific and medical literature, and provide short easy-to-understand summaries of the results. The website also allows users to recommend research articles for inclusion, and to vote on those recommendations. Furthermore, the website has an archive of highlights of 154 research articles published in top scientific journals since 2000, and in the case of research articles highlighted from Nature journals, the original full text scientific articles are made freely available to registered users of Nature China.

Posted by Maxine Clarke on June 18, 2007
Categories: Author services, Publications | Permalink | Comments (0)

Nature Precedings, as its title implies, enables researchers to share, discuss and cite their early findings on the web -- all free access. It provides a lightly moderated and relatively informal channel for scientists to disseminate information, especially recent experimental results and emerging conclusions. In this sense, it is designed to complement traditional peer-reviewed journals, allowing researchers to make informal communications such as conference papers or presentations more widely available and enabling them to be formally cited. This, in turn, allows them to solicit community feedback and establish priority over their results or ideas.
Covering biology, medicine, chemistry and the Earth sciences, the site will host a wide range of research documents, including preprints, unpublished manuscripts, white papers, technical reports, supplementary findings, posters and presentations. All submissions are reviewed by staff curators and accepted only if they are considered to be legitimate scientific contributions. No judgement is to be made about the quality or uniqueness of the work, and submissions are not subjected to peer review before they are released. Because of this, accepted submissions will usually be published within one working day, and no charge is made to either authors or readers.
Nature Precedings makes use of social features such as tagging, voting and commenting to facilitate the discovery of especially interesting and relevant content. As well as an RSS feed for recent submissions, there are separate RSS feeds available for 13 broad subject categories, so scientists can keep an eye on newly uploaded content in their own fields.
We anticipate that the content will be mirrored by academic partner organizations, several of whom have been involved with Nature Publishing Group in developing this service. As well as allowing it to become incorporated into the substantial information hubs already provided by these organizations, this federated approach will also help to ensure the long-term availability of the content — and act as a practical guarantee of the Nature Publishing Group's pledge not to charge readers for access.
Find out more about Nature Precedings here.

Posted by Maxine Clarke on June 18, 2007
Categories: Communication, Partners, Publications | Permalink | Comments (0)

If you’ve wondered about starting your own blog, have a look at Nature Network, where scientists of all kinds are blogging. It is free, quick and simple to set up the blog, and you’ll find yourself connected with researchers and others with overlapping interests.
You can see who is blogging at Nature Network by going to the blog index and reading whichever blogs catch your interest. Recent posts from all the blogs are featured on the blog index page, so that's another way to see what's truly current. Here are a few posts that I’ve enjoyed reading this week:
In her blog Mind the Gap, Jennifer Rohn records what it’s like to return to the bench after a spell in the science literary scene running the LabLit website. The post In which I rejoice in muscle memory is a vivacious description of planning her first experiment since her long break. "With due consideration of my long hiatus, I showed what I thought was a ridiculously stripped-down plan to the lab’s two leading experts on Drosophila cell culture RNAi: a pilot tissue culture experiment with a mere eight samples. I waited expectantly as the Ph.D. student studied my scribbles. But then he slowly started shaking his head. “Your first experiment in four years?” he said dubiously. “Only four wells, maximum. Get rid of half of this.” "
Attila Csordas, whose Network blog is called Science Hacker, looks at the role of comic books in science popularization. Cartoons are terrific education tools, writes Attila, as well as howtoons, cartoons showing kids of all ages “How To” build things. "What about cartoons for scientists? After all, experimental results, short communications and complete articles could be presented in a cartoon way, let us just juxtapose the figures of an article with good graphics and build a story upon them." Nature 's synthetic biology cover and online comic in its issue of 24 November 2005 being a good example.
In her Network blog Time for a Change, Linda Cooper suggests that "there's a better way to write a scientific article. Currently, published articles are unnecessarily difficult to read and researchers need to be trained in how to write about their research." Here she explains why the active voice, useful transitions and clear subjects help readers. The post at the link takes a paragraph from the Allen Brain Atlas part by part, providing an original, a descontstruction and a revised version of each section. Head on over and tell her which you think is best.
These are just three of the many lively blogs on the Nature Network. Check it out, and have a go yourself.

Posted by Maxine Clarke on June 15, 2007
Categories: Author benefits, Communication, Publications | Permalink | Comments (2)

The ENCODE (Encyclopedia of DNA Elements) project has set out to identify all the functional elements in the human genome. Detailed in a Nature web focus, a pilot project on 1% of the genome reveals new insights about how the information coded in the DNA blueprint is turned into functioning systems in the living cell. You can download a free poster at the Nature web focus, read the free-access article by the ENCODE project team (Nature 447, 799-816; 2007), and read related news stories, articles and information about the project.

Posted by Maxine Clarke on June 14, 2007
Categories: Disciplines, Partners, Publications | Permalink | Comments (0)

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

Posted by Maxine Clarke on June 14, 2007
Categories: Awards, Public and media, Publishing, Writing | Permalink | Comments (0)

From this week's Correspondence page (Nature 447, 775; 2007): Ours is a world in crisis. We are despoiling our habitat, outstripping our resources and failing to provide an acceptable living standard for much of the world's population. Although academic institutions are equipped to help remedy these problems by informing the leaders of tomorrow, they often fail to do so. Increasing pressure for specialization has led universities to trade breadth for depth in curricula, thereby depriving students of an understanding of complex, interconnected global issues. For example, solutions to our energy crisis span economics, engineering and politics, yet the typical student is exposed to only a portion of this spectrum.
Here, we propose a first step in addressing such shortcomings. We, the undersigned graduate students, have created a campus-wide 'State of the Planet' course at Cornell University under the mentorship of faculty members Tom Eisner and Mary Lou Zeeman.
Our goal is threefold: to improve understanding of complex issues; to add global context to disciplinary education; and to motivate action and involvement. To this end, we recruited experts, mostly resident faculty members and community leaders, to address the challenges we agreed were paramount.
Administrative support was quick to materialize, as was a pool of enthusiastic participants. We launched the course in January 2007, after campus-wide publicity highlighting its multidisciplinary nature. Our 250 current students come from 45 different majors ranging broadly across the humanities and basic and applied sciences. In lectures, experts familiar with our most pressing global problems emphasize how solutions span disciplines. Students participate in discussion groups led by graduate assistants, where they not only build on ideas presented in lectures, but also set up projects aimed at solving problems.
Mid-semester student evaluations have been overwhelmingly positive, with 93% saying that the course has changed their views on education, career plans and lifestyle, and 95% believing that their peers should also take this course.
Comments include: "This course has influenced my perspectives on almost everything, from the food I eat to how long I leave my computer on" and "The course demonstrates how many different skills and backgrounds can help shape policy that is instrumental for the planet."
We are continuing to expand our course in the hope that it will become a campus-wide requirement. Our vision is that other universities will adopt similar courses as a curriculum component for all students. We extend an open invitation to like-minded people at other institutions to join us, and others launching parallel efforts, in what we believe will be a modest but fundamental change to university education.
We maintain the optimistic belief that, given the right information, people will change their habits and their world. But the burden is on us, as educators, to motivate this change.
Krystal L. Rypien, Jill Anderson, Jason Andras, Rulon W. Clark, Gretchen A. Gerrish, James T. Mandel, Marie L. Nydam & Daniel K. Riskin
Department of Ecology and Evolutionary Biology, Cornell University.

Posted by Maxine Clarke on June 14, 2007
Categories: Careers, Disciplines, Public and media | Permalink | Comments (0)

The authors of a controversial paper on stem cells publish a correction of their work in this week's issue of Nature (447, 880-881; 2007) but state in it that the errors do not affect the conclusions of the article. A News story also in this week's issue (Nature 447, 763; 2007) describes how the paper in question, published in 2002, claimed to find evidence for so-called 'multipotent adult progenitor cells', or MAPCs, in mouse bone marrow (Y. Jiang et al. Nature 418, 41–49; 2002). The work was led by Catherine Verfaillie, now director of the Stem Cell Institute at the Catholic University of Leuven.
From the News story: The paper challenged the prevailing idea that only stem cells derived from embryos were highly flexible. Some of its results have been reproduced by other labs, but no one has been able to replicate the work independently in its entirety. "I believe that despite the hype over the mistake, we and Nature made the conclusion that the final findings of the paper still stand," says Verfaillie.
This February, an investigation convened by the University of Minnesota — Verfaillie's former institution — found that her group had used incorrect procedures in the Nature paper, and that some of the data contained in it might be flawed. The investigation was a response to questions from a reporter from the magazine New Scientist, who pointed out that the figure from the Nature paper that has now been corrected was partly reproduced with different labels in another paper in another journal, Experimental Hematology (Y. Jiang et al. Exp. Hematol. 30, 896–904; 2002).
In response to the investigation, Nature convened a peer-review panel to analyse the data from the 2002 paper. According to Nature, the experts concluded that although the figure data were flawed, the paper's conclusions are still valid. No allegations of fraud or misconduct have been levelled at Verfaillie or anyone from her group. Verfaillie says her group cannot explain how the errors in the Nature paper occurred: "Why this happened, we have not been able to determine," she says.

Posted by Maxine Clarke on June 14, 2007
Categories: Data availability, Disciplines, Ethics, Policies | Permalink | Comments (0)

US universities must act to recruit and retain minority faculty members.

From an Editorial in Nature 447, 753-754 (2007): The diversity of the typical American research university is widely admired, but is fashioned mainly on the basis of students and staff recruited from abroad. The universities have done less well at harnessing the talents of the racial minorities within the US population.
So-called under-represented minorities — African Americans, Latinos and Native Americans — formed more than a quarter of the American population in 2000, and are projected to account for more than 40% of it by 2050. Yet according to a 2005 study of 50 élite universities, undertaken by Donna Nelson, a chemist at the University of Oklahoma, they account for only 3% of tenured or untenured faculty in mathematics, physics, chemistry, biology and astronomy. Numbers are only slightly higher in engineering (4.6%).

Continue reading "Academic diversity in universities" »

Posted by Maxine Clarke on June 14, 2007
Categories: Careers, Ethics | Permalink | Comments (0)

The first e-newsletter of Nature Reports Stem Cells, out now and free (sign up at the home page), provides the latest news and information about research, policy, ethics, business and medicine of stem cell science. The editors' welcome letter is here, and the associated blog, The Niche, is here.
A selection of this week's stories:
Skin Cells to Stem Cells
Recent research promises embryonic stem cells, minus eggs and embryos. Three labs transformed mouse skin cells (fibroblasts) into cells that seem to pass muster as embryonic stem cells. If it works for humans, a simple biopsy could yield patient-specific sources of neurons, cardiomyocytes, or any other useful cell type. Read an interview with Shinya Yamanaka, a scientist who found the transforming recipe.
Man or Beast? Man and Beast!
Ian Wilmut is Nature Reports Stem Cells’ first Featured Editor. This week, he writes about how part-human part-animal cells could produce some of the most powerful tools yet for unraveling human disease, he talks about current research that excites him most, and he remembers Dolly.
Eggless cloning
Unfertilized eggs have long been the limiting resource for attempts to make genetically tailored human embryonic stem cells. If a new technique for cloning mice from fertilized eggs works in humans, they might not be necessary. This week Monya Baker writes about whether the new procedure for cloning using zygotes instead of oocytes changes the ethical terrain, and also tries to define just what eggs have that makes reprogramming work. Read an interview with Davor Solter, a scientist who, decades ago, convinced researchers that eggs were essential.
And now for something completely different
For a really fresh perspective on the technique for cloning from zygotes, read this fortnight’s Inside the Paper. Pioneered by Nature Reports Stem Cells, this new form of science reporting posts edited discussions between authors and reviewers from the peer review process. Learn what the foremost experts in the field had to say about a paper’s context, strengths, and shortcomings. See what the authors saw, and read their responses. (And you can add your own comments on The Niche.)
See all this, and more, at Nature Reports Stem Cells -- and it is all free.

Posted by Maxine Clarke on June 13, 2007
Categories: Communication, Publications | Permalink | Comments (0)

Nascent: Scintilla

The latest new website in a week of new launches hectic even by the standards of Nature Publishing Group is a social site called Scintilla. Alf Eaton, who with Euan Adie in NPG's web publishing division created the site, explains all at the above-linked post at Nascent. Briefly, Scintilla is an aggregator of publication databases, news stories and blogs about science which users can read, rate and recommend to each other. It has its own discussion group here, for people to provide comments and feedback.

Scintilla has been welcomed by several scientist bloggers, including Neil Saunders. Attilla Csordas, who blogs at Partial Immortalization and at The Niche (the Nature Reports Stem Cells blog), having earlier in the week called Nature Publishing Group the Google of science publishing, is now moved to refer to us as "Natureplex". (Read his initial reactions to Scintilla here.) What next?

Posted by Maxine Clarke on June 12, 2007
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The Wellcome collection's Medicine Life + Art opens on 21 June in London. The venue is open every day, with galleries open from Tuesdays to Sundays. Exhibitions and events are free. There is also a library, conference centre and club, as well as a cafe and the inevitable shop.
The exhibitions present a rich picture of the cultural and social implications of medicine past and present, through three galleries including exhibits and artworks from Henry Wellcome's original collection, as well as current medical topics such as obesity, genetics and malaria through the eyes of scientists, artists and patients. The opening programme includes exhibitions about the heart as well as sleeping and dreaming, examining each subject from a scientific, cultural and social perspective.
For more information and details of how to get there, see the Wellcome collection website.

Posted by Maxine Clarke on June 12, 2007
Categories: Communication, Public and media | Permalink | Comments (0)

Nature Nanotechnology is now in volume 2. The latest issue of this second volume covers topics as diverse as: processing nanowire devices; imaging defects in nanotubes; DNA nanochannels; transparent and flexible nanoelectronics; polymer nanofibres; and the separation of left- and right-handed nanotubes. These original research articles are complemented by the News & Views section, a Commentary article about the challenges and opportunities that ‘post-academic’ science presents for the nanoscience and technology community, an Editorial about the role of nanoscience in combating climate change, and a Thesis article about the regulation of new nano-enabled products and devices in nanomedicine.
June's Progress article, FREE to access online, is Biomimetics of photonic nanostructures, by Andrew R. Parker and Helen E. Townley. It reviews the use of diatoms, viruses and other living objects to fabricate photonic nanostructures.

Posted by Maxine Clarke on June 11, 2007
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Consiglio Nazionale delle Ricerche and Nature Medicine present Translational Approaches to Cardiovascular Research, from 14 to 16 October 2007, in Capri, Italy. This conference will focus on new genetic and molecular mechanisms that underlie cardiovascular disease, as well as on new diagnostic tools and innovative therapies. The goal of the meeting is to stimulate interdisciplinary discussion and collaboration between academic and clinical researchers in the area.
See the conference website for more details of the programme, accommodation details and to download a free poster.

Posted by Maxine Clarke on June 11, 2007
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The Washington, DC, office of Nature will be closed the week of 18 June for renovations. We expect to re-open on Monday 25 June and be back to full operations on Tuesday 26 June.
All staff will be working at home for the week, except for the office manager Katie McGoldrick, who will be answering the main phone line and email. Staff will provide contact details by voicemail or forward calls to their home or cell numbers. They will be responding to email. But please bear in mind things will be running a bit more slowly than usual.

Posted by Maxine Clarke on June 11, 2007
Categories: General | Permalink | Comments (0)

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

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

Posted by Maxine Clarke on June 08, 2007
Categories: Access, Communication, Publishing | Permalink | Comments (0)

Free Association: Selfish factoids

Why do editors prune appealing afterthoughts and out of focus information to leave only the highly-scrutinized core of the research paper?, asks Myles Axton, Chief Editor of Nature Genetics, in the Free Association blog post above. ‘Appealing’ is the key word, that stuff has a life of its own and can literally beg you to add it to your papers. “Add me”, the factoid pleads, “and your work will make it into the news, will get discussed”.

Myles continues: Selfish factoids can even infect Matt Ridley, probably the most accessible and informative science writer alive. I enjoyed reading his “Origins of Virtue- Human Instincts and the Evolution of Cooperation” but found this: Chapter 1, footnote 29. “I am indebted to David Haig for the information that human beings have B chromosomes at the rate of 2-3 per cent of live births.” Myles looked into this assertion, or to put it his way, performed a "reality check". Read on at the Free Association post.

Posted by Maxine Clarke on June 08, 2007
Categories: Public and media, Writing | Permalink | Comments (0)

Sam at Everyday Scientist blog writes:
We were discussing some grammar at Chemical Physics Journal Club this week: which is the (more) correct sentence?
1. It is important to deconvolute the fluorescence lifetime from the instrument-response function.
2. It is important to deconvolve the fluorescence lifetime from the instrument-response function.
I think sentence 2 is better. To me, “convolve” is to (usu. mathematically) roll together multiple things, while “convolute” means to make complex: you can convolve two mathematical functions or signals, and you can convolute a sentence. (Unfortunately, the noun form of each is “convolution.”)

The consensus in the comments at Everyday Scientist is 'option 2 probably', but dictionaries do not seem to help. Can you?

Posted by Maxine Clarke on June 08, 2007
Categories: Writing | Permalink | Comments (1)

Harry Thangaraj of the Oxford Centre for Innovation writes in Nature's Correspondence this week (Nature 447, 638; 2007):
Your News Feature 'The hard copy' (Nature 446, 485–486; 2007) accurately highlights the limited availability of information on stem-cell research methodologies — owing to competition among labs, the commercial value of such information and space restrictions in high-quality journals — which contributes to other labs' inability to replicate and verify the results.
It might sometimes repay scientists to look beyond conventional journals for information, in this or other disciplines, particularly to patents or patent applications. Thanks to the strict enablement requirements of patent law and patent offices in relation to inventions, one can often find more detailed methodology in patent documents than in journals with severe page limits.
A very good example of comprehensive detail in certain non-embryonic stem-cell methodologies is a PCT application WO/2006/028723 (Non-Embryonic Totipotent Blastomer-Like Stem Cells and Methods Therefor), which includes surgical procedures in organ removal, isolation of cells, and composition and preparation of culture media. In this instance, the level of detail and volume of text relating to methodology far exceeds that which many peer-reviewed journals can accommodate.
Some journals publish methodology and protocols online as Supplementary Information to the main paper or in separate publications (an example is Nature Protocols, which encourages user comments). Often, though, journals are only starting points in complex paper trails related to methods. In these circumstances, patent documents could contain the most methodology related to an invention in a single document.

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

Publisher Digitisation Service
The British Library has just launched its Publisher Digitisation Service (see link above), which, it says, is the first fully integrated journals digitization service on the market. One of the greatest challenges for a publisher undertaking a digitization of its archives is finding content -- one publisher had to locate 75% of the content for its programme from third parties. The British Library has an unrivalled collection of serial content and is aiming to save publishers time and money in locating material and providing it in online, searchable format. At the webpage linked to above are more details of the service, and a link to a downloadable PDF of the white paper 'Journal backfiles in scientific publishing.'
All the Nature journals have searchable online archives back to issue 1 available via each journal's website, except for the oldest, Nature. Nature's online, searchable archive currently extends back to 1950 but will be complete to issue 1 (4 November 1869) by the end of this year. In the meantime, the first issue of the journal is available online at the "about the journal" page of the Nature website.

Posted by Maxine Clarke on June 08, 2007
Categories: Access | Permalink | Comments (0)

The Nature Geoscience editorial team is now accepting manuscripts from researchers who are active at the frontiers of this diverse and multidisciplinary field. Articles for Nature Geoscience will be selected and edited to have the maximum appeal to the global geosciences community.
Nature Geoscience's online manuscript submission system.
Guide to authors and other information about the journal.

Posted by Maxine Clarke on June 07, 2007
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Introducing two free-access websites for research networking and outreach to be launched this week: Nature Reports Climate Change and Nature Reports Stem Cells. Aimed at researchers and at anyone else who is interested, both provide an editorial perspective of their fields through a combination of original journalism and commissioned comment, alongside archived material from other Nature publications. Both sites also facilitate community interactions through blogs: Climate Feedback and The Niche. These sites will develop further by way of community interactions and applications in the coming months. The original content of both is freely accessible.

Posted by Maxine Clarke on June 07, 2007
Categories: Publications | Permalink | Comments (1)

The IPSEN Foundation, Nature Structural & Molecular Biology and Nature Immunology are pleased to announce the first Emergence & Convergence mini-symposium, which will focus on small RNAs in development, immunology and cancer, on 3 October 2007 at the New York Academy of Sciences, New York.
The mini-symposium will address what we know and what we have yet to understand about the molecular intricacies of the processing and production of these small non-coding RNAs, as well as the mechanistic basis underlying their physiological functions.
Speakers at this one-day meeting work in a broad array of scientific fields but share a common interest in small RNAs. The aim is to facilitate discussion and collaboration among diverse scientific disciplines to further our understanding of the function of these enigmatic RNAs.
More information is available at the conference website.

Posted by Maxine Clarke on June 07, 2007
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James A. Smith and Genna E.Carey of the University of Adelaide ask in this week's Nature Correspondence page (Nature 447, 638; 2007) how we can practically encourage and foster interdisciplinary research. They say:
Despite a shift towards an interdisciplinary research culture, we are yet to grapple with how to support a growing number of interdisciplinary researchers. As interdisciplinary postgraduate research students, we face this reality head-on.
We have found it difficult to synthesize the separate perspectives of two or more disciplines into a meaningful middle ground. Unless the scientific community identifies strategies for supporting interdisciplinary researchers to negotiate this middle ground, little progress can be made. Here we suggest two useful approaches.
First, interdisciplinary researchers are expected to develop a different skill set from that of their single-discipline colleagues. In this 'interlocker' role, they engage in a shared conversation between disciplines and work through the tensions this creates. This is more than simply negotiating the different languages and ways of working — it is about appreciating a breadth of knowledge in theory, approach and discourse.
Unfortunately, few systems accommodate this type of researcher — as is sadly demonstrated by emerging frameworks designed to assess research quality in New Zealand, the United Kingdom and Australia. Interdisciplinary committees are needed to assess research proposals, to review grant applications and to examine theses. This would be more effective than the current practice of putting interdisciplinary researchers in assessment 'silos' where they are unrealistically measured against, and by, people in a single discipline.
A second challenge is the disjunct between, on one hand, rhetoric encouraging inter-disciplinary research and, on the other, the lack of institutional structure and support for it. Although we are encouraged to work in interdisciplinary environments and to join interdisciplinary research clusters, we face numerous administrative hurdles. Cross-enrolment of interdisciplinary students is seldom acknowledged, and adequate resources and structures — such as guidance on writing for interdisciplinary audiences, or longer candidatures for postgraduate students — are rarely provided to support the interdisciplinary researcher.
It would be simple for institutional leaders to ask current interdisciplinary researchers about the challenges they face and to document these issues. These leaders could then address the issues by formalizing the interdisciplinary researcher role and reducing demands to satisfy the needs of multiple disciplines. Supportive environments must be created if we are committed to achieving interdisciplinary research goals.

See also this Recruiters article (Nature 445, 950; 2007) by A. Paytan and M.-L. Zoback.

Your views are welcome.

Posted by Maxine Clarke on June 06, 2007
Categories: Careers, Disciplines | Permalink | Comments (2)

The current issue of EMBO Reports features a Talking Point collection of articles on the use of animals in scientific research. Frank Gannon writes in his introduction:
The balance between the rights of animals and their use in biomedical research is a delicate issue with huge societal implications. The debate over whether and how scientists should use animal models has been inflammatory, and the opposing viewpoints are difficult to reconcile. Many animal-rights activists call for nothing less than the total abolition of all research involving animals. Conversely, many scientists insist that some experiments require the use of animals and want to minimize regulation, arguing that it would impede their research. Most scientists, however, try to defend the well-established and generally beneficial practice of selective experimentation on animals, but struggle to do so on an intellectual basis. Somehow, society must find the middle ground—avoiding the cruel and unnecessary abuse of animals in research while accepting and allowing their use if it benefits society.
In any debate, one should first know the facts and arguments from each side before making an educated judgement.
The article continues here.
The other articles in the Talking Point are:
Animal research: a moral science by Bernard E. Rollin.
The ethics of animal research by Simon Festing and Robin Wilkinson.

Posted by Maxine Clarke on June 06, 2007
Categories: Animal experiments, Policies | Permalink | Comments (0)

Molecular Systems Biology is the journal partner of the International Conference on Systems Biology (ICSB), Long Beach, California, from 1 to 8 October 2007. Authors of the best abstracts from the conference will be invited to submit full research articles to Molecular Systems Biology. If accepted, articles will be featured in a special online issue of the journal devoted to ICSB 2007. You can submit your abstract online now.
From the conference website: cells, tissues, organs, organisms and ecological niches are systems of components whose interactions have been defined and refined by evolution. There is a resurgence of interest in achieving a systems-level understanding of biology. Systems biology seeks answers to the following key questions by integrating experimental and computational approaches: (1) What are the basic structures and properties of biological networks? (2) How do biological systems behave over time under various conditions? (3) How does a biological system maintain its robustness and stability? (4) How can we modify or construct biological systems to achieve desired properties?
Answers to these questions require breakthroughs in fields as varied as biology, chemistry, computer science, engineering and mathematics, together with an evolution of our social and educational structures so that members of different disciplines can effectively bridge conceptual, and experimental boundaries. The International Conference on Systems Biology is the premier annual meeting for everyone interested in pursuing these goals.

Molecular Systems Biology journal homepage.

Posted by Maxine Clarke on June 06, 2007
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From Philip Campbell, Editor of Nature and Editor-in-Chief of Nature publications:

David Cyranoski, Nature's Asia-Pacific correspondent, has won the 2007 Michel E DeBakey journalism award from the Washington-based Foundation for Biomedical research, for his article ‘Primates in the frame’ (Nature 444, 812-813; 2006). This was part of last year’s special issue on debates about animal research within the biology community.

Every year the Association of British Science Writers gives a set of much-coveted awards, and Nature has received a bunch of shortlisted nominations.For ‘the best feature on science subject in a specialist periodical' the following three articles were nominated out of a total of four:

Jo Marchant, for ‘In search of lost time' published in Nature 30 November 2006
The ancient Antikythera Mechanism doesn't just challenge our assumptions about technology transfer over the ages — it gives us fresh insights into history itself.
Helen Pearson, for ‘What is a gene?' published in Nature 25 May 2006
The idea of genes as beads on a DNA string is fast fading. Protein-coding sequences have no clear beginning or end and RNA is a key part of the information package.
Quirin Schiermeier, for ‘A sea change' published in Nature 19 January 2006.
A collapse in ocean currents triggered by global warming could be catastrophic, but only now is the Atlantic circulation being properly monitored.

For ‘the best science journalism on the World Wide Web’, one of the three shortlisted nominations is Michael Hopkin and the news team for ‘World Cup 2006 Special', published on news@nature.com on 9 June 2006.

Please join me in congratulating all of them, as well as Oliver Morton (Nature's Chief News and Features Editor) and the news team as a whole for fostering such outstanding work.

(The articles can be seen at the links provided, subscription or site licence required.)

Posted by Maxine Clarke on June 06, 2007
Categories: Awards | Permalink | Comments (0)

A Nature Reviews Immunology Focus on Cytokines & Cytokine Therapies published this month (June 2007) is freely accessible online for six months. Cytokines act as key communicators for immune cells; maintaining a delicate balance in the level of these communicators is vital for health — in many chronic diseases, this balance is disrupted. Thus, therapeutic targeting of cytokine pathways promises great hope for patients suffering from chronic diseases such as rheumatoid arthritis.
This Focus issue of Nature Reviews Immunology highlights the latest advances in cytokine research and the application of these findings for clinical intervention. It includes the following articles by leaders in the field:
Cytokines in the pathogenesis of rheumatoid arthritis
Iain B. McInnes and Georg Schett
TGFb signalling in control of T-cell-mediated self-reactivity
Yuri P. Rubtsov and Alexander Y. Rudensky
SOCS proteins, cytokine signalling and immune regulation
Akihiko Yoshimura, Tetsuji Naka and Masato Kubo
These reviews, other articles and related material can be found at the Focus website.

Posted by Maxine Clarke on June 05, 2007
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Via news @ nature.com

Computer scientists at Columbia University in New York have used a mathematical model to estimate the number of flawed scientific papers that go unretracted, and its relation to journal impact factors.In correspondence published in EMBO Reports (M. Cokol et al. EMBO Rep. 8, 5, 422–423; 2007), the researchers find that fewer papers are retracted by journals with low impact factors. But their model raises as many questions as it answers, say specialists in scientific publishing, some of whom argue that it greatly oversimplifies the issues.

From the Nature story: "scientists and editors familiar with retraction issues are sceptical of the quality of the model's input data. Theoretical modelling exercises will generate bad results if the input data are flawed, says Drummond Rennie, deputy editor of the Journal of the American Medical Association, and a medical researcher at the Institute for Health Policy Studies, at the University of California, San Francisco.
Although the number of retracted articles is probably only the tip of the iceberg in terms of the number that should have been retracted, the model — based on journal impact factor and number of retractions — is too simplistic to capture the complex reality of the issues affecting the size and nature of the hidden part, Rennie says."

The full news @ nature.com story is here (site licence or subscription required).

Posted by Maxine Clarke on June 05, 2007
Categories: Ethics, Quality measures | Permalink | Comments (1)

EMBO Award for Communication in the Life Sciences
Call for entries: DEADLINE 30 JUNE 2007
The award is for scientists who have, while remaining active in laboratory research, risen to the challenge of communicating science to a non-scientific audience. The winners of the EMBO Award are nominated for the EU Descartes Prize for science communication. The prize is Euro 5,000, accompanied by a silver and gold medal inscribed with the winner's name.
Eligibility. Scientists working in Europe or Israel at the time of application, who have made an outstanding contribution to the public communication of science via any medium or activity. Candidates must be working in active research at the time of application, and should have done most of their communication work in Europe or Israel. Scientists who are already widely regarded as professional communicators will not be considered for the award. Applications must be written in English.
See the EMBO website for further details and official application forms.
Nature Publishing Group publishes the EMBO Journal and EMBO Reports, journals of the European Molecular Biology Organisation.

Posted by Maxine Clarke on June 05, 2007
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This month's Editorial in Nature Physics (3, 363; 2007) is entitled Take the lead, and is about how to tackle the under-representation of women at all career levels in physics research.
From the Editorial:
Last month, a workshop entitled Gender Equity: Strengthening the Physics Enterprise in Universities and National Laboratories took place at the headquarters of the American Physical Society in Maryland, with the stated aim of facilitating a doubling of the number of women in physics over the next 15 years. The under-representation of women in research careers in physics is proving a tough nut to crack. Why would this workshop, ahead of many other well-meaning efforts, come any closer to a solution?
What was remarkable about the Maryland workshop was its participants: chairs from 50 major physics departments across the USA, 14 division directors of national laboratories units, and leaders from the National Science Foundation and the Department of Energy. After all, if there is to be change, it has to come from the top.
In the list of preliminary recommendations from the workshop, many begin with the words "leaders should". Leaders should "set a code of conduct", "make expectations clear", "be aware of subtle biases" and so on. Many of these recommendations are easily recognizable as good management practice. A good manager creates the appropriate atmosphere in which all team members can thrive, each being encouraged to play to their strengths, and, through their collective effort, carry the interests of the team forwards. That picture doesn't necessarily describe the average physics research group — although it probably should.

See here for the full text of the Editorial (subscription or site licence required).
See here for the conference website, from which you can download most of the talks as PDFs as well as obtain other resources.

Posted by Maxine Clarke on June 04, 2007
Categories: Careers | Permalink | Comments (0)

Nature Nanotechnology is currently calling for papers. Nature Nanotechnology is a multidisciplinary journal that publishes papers of the highest quality and significance in all areas of nanoscience and nanotechnology. The journal covers research into the design, characterization and production of structures, devices and systems that involve the manipulation and control of materials and phenomena at atomic, molecular and macromolecular scales. Both bottom-up and top-down approaches - and combinations of the two – are covered. Research areas covered in the journal include:

Nanomaterials and nanoparticles
Carbon nanotubes and fullerenes
Organic-inorganic nanostructures
Structural properties
Electronic properties and devices
Nanomagnetism and spintronics
Photonic structures and devices
Quantum information
Molecular self-assembly
Molecular machines and nanoelectromechanical devices (NEMS)
Surface patterning and imaging
Nanofluidics, nanosensors and other devices
Nanobiotechnology and nanomedicine
Computational nanotechnology
Nanometrology and instrumentation
Synthesis and processing

Posted by Maxine Clarke on June 04, 2007
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Molecular Therapy is the official journal of the American Society for Gene Therapy (ASGT). Available in print and online, the journal is dedicated to publishing important peer-reviewed research and cutting-edge reviews and promoting the sciences in genetics, medicine and biotechnology. You can read an issue free online by visiting the journal's website. An announcement about Nature Publishing Group's publishing partnership with the ASGT, and plans for the journal, is available at this link.

Posted by Maxine Clarke on June 04, 2007
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Nature's Avian Flu e-newsletter for June is just out. If you'd like to sign up for monthly updates from Nature Reports Avian Flu, our extensive archive of news about and research articles reporting the most significant developments on avian flu, please go to the Avian Flu website. Each newsletter brings you free updates -- this month including an account of how researchers are gaining a stronger appreciation of the effect of human behaviour on the course of epidemics, as well as about the origins of influenza and other major infectious diseases. Other developments include the prospects of new antibody-based treatment for H5N1 infection, and a resolution by WHO to stockpile vaccines against influenza viruses with pandemic potential. The Nature Reports Avian Flu website carries a regularly updated timeline, FAQs, and Nature's award-winning interactive Google Earth map that enables users to see the spread of the H5N1 avian flu virus over time around the world. Share your views on the Nature Reports Avian Flu blog.

Posted by Maxine Clarke on June 04, 2007
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south by southwest festivals conferences

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

Posted by Maxine Clarke on June 02, 2007
Categories: Communication, Publishing | Permalink | Comments (0)

Oncogenes and Human Cancer: The Next 25 Years. Nature and Centro Nacional de Investigaciones Oncolgicas (the Spanish National Cancer Research Centre) are pleased to announce a conference focusing on the future of cancer research on the 25th anniversary of the isolation of oncogenes from human tumours, from 3 to 6 October 2007, in Madrid. The isolation of cancer genes from human tumours represented a landmark in the understanding of the molecular mechanisms responsible for human neoplasia. We now have a more detailed understanding of the molecular changes within transformed cells and how these and the tumour microenvironment influence cancer development. Oncogenes and Human Cancer: The Next 25 Years will emphasize future directions for cancer research and treatment.
For organisers, venue and further details, visit the conference website.

Posted by Maxine Clarke on June 01, 2007
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Photonics at NPG is a round-up of recent papers in the photonics field published by the physical sciences division of the Nature Publishing Group. This month's selection includes twisted photons, unidirectional nanoslit couplers for surface plasmons, Bloch gain in quantum cascade lasers, mapping surface plasmons on a single metallic nanoparticle, extrafluorescent electroluminescence in light-emitting devices, and finally, multimaterial fibres that see, hear, sense and communicate.

See Photonics at NPG for more details.
Nature Photonics June issue is now available.

Posted by Maxine Clarke on June 01, 2007
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