Nautilus

Monitor your performance reviews and ensure that they are showing progress, writes Paul Smaglik at the Nature Network NatureJobs forum. "Create your own set of metrics—publication, citations and patents for academics, targets met and products advanced through the pipeline for industry science. Create your own goals, set deadlines to meet them. Challenge yourself. Also, seek informal feedback from colleagues both in and outside your organization. Seek out new projects and collaborations to keep work from being route. As a science journalist, I created my own metrics
for attending meetings. And I ask people outside my organization what they think of my work. I also challenge myself to write about things I’ve never covered before (one of my scariest professional experiences was an internship at Science News; I wnated to write only about medicine, but my colleagues there encouraged me to write about a different discipline every week—truly scary!) and I try different approaches to story-telling to keep myself fresh. And I seek out healthy risks like my decision last year to leave my permanent job at Nature to hike the Appalachian Trail. Creating your own parameters for success helps exceed the metrics set by others and gives you control over the direction and progress of your own career."

Posted by Maxine Clarke on July 31, 2008
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Nature Publishing Group has several partners, highlighted in this post as most are relevant to authors and so of potential interest to readers of this blog. I have provided a direct link to each partner organization for those who wish to find out more details.
The AGORA programme, set up by the Food and Agriculture Organization of the UN (FAO) together with major publishers, enables developing countries to gain access to an outstanding digital library collection in the fields of food, agriculture, environmental science and related social sciences. AGORA provides a collection of 845 journals to institutions in 113 countries.
The HINARI programme, set up by WHO together with major publishers, enables developing countries to gain access to one of the world's largest collections of biomedical and health literature.
OARE, Online Access to Research in the Environment, an international public-private consortium coordinated by the United Nations Environment Programme (UNEP), Yale University, and leading science and technology publishers, enables developing countries to gain access to one of the world's largest collections of environmental science research.
INASP (International Network for the Availability of Scientific Publications) is a development charity that has been working to enhance worldwide access to information since 1992. As part of the Programme for the Enhancement of Research Information (PERI) INASP works with publishers and networks of libraries to enable access to scholarly information using information and communications technologies within developing and emerging countries.
CrossRef is an independent membership association, founded and directed by publishers. CrossRef’s mandate is to connect users to primary research content, by enabling publishers to do collectively what they can’t do individually.
Counter. The use of online information resources is growing rapidly. It is widely agreed by producers and purchasers of information that the use of these resources should be measured in a more consistent way. Librarians want to understand better how the information they buy from a variety of sources is being used; publishers want to know how the information products they disseminate are being accessed. An essential requirement to meet these objectives is an agreed international set of standards and protocols governing the recording and exchange of online usage data. The COUNTER Codes of Practice provide these standards and protocols and are published in full on this website.
Darwin200 is a collaboration of organizations across the United Kingdom that are celebrating Darwin’s 200th birthday in February 2009 with an exciting programme of activities.

Posted by Maxine Clarke on July 30, 2008
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From Nature 453, 969 (2008) :

Postdoctoral fellow Kristin Roovers was suspended after learning that she had manipulated and falsified data published in several papers. Roovers was hired by the institute in 2005. But in July 2007, the US Office of Research Integrity concluded that Roovers, while a graduate student and postdoctoral fellow at the University of Pennsylvania in Philadelphia, had manipulated 19 panels of western blot data. She had used Photoshop to copy a set of bands and paste them into other blots representing data from different experiments. The data ultimately appeared in 11 figures in three publications.
Two of the papers (K. Roovers and R. K. Assoian Mol. Cell. Biol. 23, 4283–4294; 2003, and K. Roovers et al. Dev. Cell 5, 273–284; 2003) have been retracted. A decision on the third (C. F. Welsh et al. Nature Cell Biol. 3, 950–957; 2001) is pending. The Office of Research Integrity barred Roovers from receiving any US government grants for five years.

Posted by Maxine Clarke on July 29, 2008
Categories: Ethics | Permalink | Comments (0)

Despite a cooling of interest by the media, Tadataka Yamada, Alice Dautry and Mark Walport emphasize in a Nature Commentary (454, 162; 2008), that a vaccine stockpile may be invaluable for preventing an avian-influenza (H5N1) outbreak in humans from quickly becoming a pandemic, and urge the vaccine research and development community not to become complacent about this important issue. Although their respective institutions — the Bill & Melinda Gates Foundation, the Pasteur Institute and the Wellcome Trust — are working with other parties to develop new resources and collaborative opportunities to provide vaccines where they may be needed most (the developing world), the authors say a wider community response is also needed.
In a related Commentary in the same issue (Nature 454, 160; 2008), Steven Salzberg calls for greater transparency in the viral-strain selection process for the human influenza vaccine. The vaccine for the 2007–2008 season failed for predictable and, says Salzberg, avoidable reasons. If the process remains closed, and researchers are denied access to sequencing data used in the selection process, future vaccine failures could be more dramatic and deadly.
There is a related (free access) Editorial in the same issue of the journal, The long war against 'flu (Nature 454, 137; 2008).
What do you think? Can a pre-pandemic vaccine curb a major catastrophe? And are the cooperative attitudes that Yamada, Dautry and Walport advocate exactly the kinds of things that are lacking from efforts to develop seasonal flu vaccines? These questions and others are being discussed online at the Nature Network Opinion forum, in which Steven Salzberg, author of one of the Nature Commentaries, writes: "What our governments can and should do is launch a crash program to create vaccines using non-egg based methods. This could allow us to get a new vaccine – if a pandemic strain appears – into production in a matter of weeks. In the meanwhile, we just have to hope that a pandemic doesn’t happen." Join the conversation at Nature Network.

Posted by Maxine Clarke on July 28, 2008
Categories: Disciplines | Permalink | Comments (0)

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

The field of metabolic engineering and systems biology is rapidly growing; Jose Manuel Otero has started a forum as a resource for young and experienced scientists and engineers alike.

What was your first-ever scientific experiment? Anna Kushnir's was "designed by myself and another student (Hi Aisha!), who to this day remains a very close friend as part of a biotechnology class. We chose to assess the effect of antioxidants on the growth of cloned African violets." Read the illustrated protocol at Anna's blog, and if you can remember the momentous occasion, contribute your own first-time attempt at being a scientist.

Engaging with the public is much in the news, so here is Jennifer Rohn on judging her first science fair: "But what I and the other three judges found most interesting was the fact the projects split clearly into two camps: those that were merely descriptive and literature-research based (“What is acid rain?”) and those that actually tested a hypothesis (“Do different kinds of music affect heart-rate differently?”). We judges especially favored those that sought to answer a question, but even as I felt strongly that this should be the case, I couldn’t help remembering my own long ago blue-ribbon effort: a diorama of the solar system made out of paper mâché. It was only much later that I must have learned that science wasn’t actually about demonstrating what was already known to be there, but was about adding some new knowledge to the world."

The Science Blogging 2008 conference now has an official website. Here you can find the programme, a list of who is attending, location and accommodation advice, and, of course, register. If you want to attend, please register soon, as at time of writing the conference (which is free) is rapidly reaching capacity.

Previous Nature Network columns.

Posted by Maxine Clarke on July 25, 2008
Categories: Nature Network round-up | Permalink | Comments (0)

Scientists are apparently not as disenchanted with the media as anecdote suggests, according to a study in Science (321, 204 - 205; 2008) , and featured by Phil Ball in his Muse column in Nature News earlier this month. Phil writes: "science journalists can draw encouragement from this evidence of general goodwill but the study raises more provocative questions than it answers. It undoubtedly matters how scientists perceive the way their work is reported, but in the end the crucial question is surely how well science is communicated, not whether scientists are happy with the results. Making scientists happy is not the aim of science journalism, any more than political reporters should worry whether politicians feel good about what they write."

For more of this article, and for other Muse columns by Phil Ball, please visit Nature's News site.

Posted by Maxine Clarke on July 24, 2008
Categories: Communication | Permalink | Comments (0)

Paul Smaglik, in a Prospects article for NatureJobs, (Nature 454, 131; 2008) discussed a survey of 109 UK universities by Hampshire-based Incomes Data Services for the Universities and Colleges Employers Association, which concludes that academics are contracted to work fewer hours, have more holiday time, and better child-care policies, pension plans and sick pay than elsewhere in the public and private sectors. A related report also says that academic pay has improved in recent years, with a 30% increase between 2002 and 2007, putting the average salary at £42,588 (US$85,000) in 2007.
But Sally Hunt, general secretary of the University and College Union, said in the Times Higher Education Supplement (THES) that the report used data on contracted hours rather than actual time worked, thus painting a "misleading picture". Other surveys show that academics work some 50+ hours a week, rather than the 35 contracted hours. In a related blog, several THES readers agreed, saying that they put in far more than the contracted weekly hours and often forgo holiday time in order to catch up. And when they do take leave, they often take work with them. As far as salaries go, Hunt agrees that academics' pay has increased — but she says that it still lags behind equivalent positions in the private sector.

Posted by Maxine Clarke on July 23, 2008
Categories: Careers | Permalink | Comments (0)

In the Nature Network discussion on 'repairing research integrity', David Lewis of the Georgia-Oklahoma Center for Reseach on the Environment, writes: "My feeling is that the only real hope of cleaning up the corruption of the scientific process that federal agencies have increasingly institutionalized and spread throughout academia lies with the editors of scientific journals. They are the Strait of Hormuz through which scientific information flows to the rest of the world". In an earlier comment in the forum, Dr Lewis wrote: "Every scientific institution that permits academic misconduct to invade its top management levels depends on science journals to publish their data and give their scientists credibility. Publishers and editors simply need to become better educated on how scientific misconduct gets institutionalized in government and academia and then develop effective ways to hold these institutions accountable when it is not corrected."

This discussion is taking place at the Nature Network Nature Opinion forum in the context of a Nature Commentary article on scientific misconduct. We welcome your views on Dr Lewis's proposition, at the Nature Network discussion, where you can read his startling account, or as a comment to this post.
The Nature journals' policies on competing interests (financial and other) are here, and other polices on the ethics of publication can be found here.

Posted by Maxine Clarke on July 22, 2008
Categories: Competing interests | Permalink | Comments (0)

Scientific meetings and conferences come in all shapes and size, and love them or loathe them, they have an important role to play in all areas of science. That's the start of Nature Nanotechnology's July Editorial (3, 371; 2008). The article goes on to discuss the size of the upcoming third International Conference on Nanoscience + Technology, a medium-scale affair compared with other mega- and nano-meetings assessed. The Editorial concludes:

In time-honoured style I have reached the end of this article without covering a very important conference topic — how to give a good conference talk. I could exceed my allotted slot by listing various do's and don'ts, but the golden rule when giving talks is to finish on time, so I will refer you to previous articles on this topic written by colleagues on other Nature journals (Nature Methods and Nature Physics). The secret, they conclude, is to rehearse and to always remember that you are speaking for the audience and not to yourself. Thank you.

Posted by Maxine Clarke on July 21, 2008
Categories: Communication | Permalink | Comments (0)

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors. The Nature Network week column is archived here.

Deanne Taylor asks what are the most important questions and problems in our respective fields? If we’re not working on them—why not? She draws attention to the transcript of a talk, ‘You and Your Research’, given by Richard Hamming at Bell Labs in 1986, who writes: "I claim that some of the reasons why so many people who have greatness within their grasp don’t succeed are: they don’t work on important problems, they don’t become emotionally involved, they don’t try and change what is difficult to some other situation which is easily done but is still important, and they keep giving themselves alibis why they don’t. They keep saying that it is a matter of luck. I’ve told you how easy it is; furthermore I’ve told you how to reform. Therefore, go forth and become great scientists!" Deanne interprets the important questions as those "that ‘go somewhere’ and address fundamental issues in the field of choice. I don’t think they all have to be ‘big questions’. I can give some good examples (bet we all could) of papers that made an impact but addressed basic research questions. " She goes on to provide an example, and the discussion continues.

How to be a success in science is another big question being discussed this week, initiated by Alexei Poliakov at the NatureJobs forum. Dr Poliakov disagrees with the position of Jonathan W. Yewdell's articles in the May and June issues of Nature Reviews Molecular Cell Biology, opining that they advocate an adaptation strategy to preserve the status quo, rather than encouraging a more philosophical approach. Some of the scientists who have responded to Dr Poliakov enthusiastically endorse Dr Yewdell's points, whereas others are less keen on them. The conversation continues, containing some pertinent opinions about survival and success for early-career scientists.

How many languages do you need for your job? Ai-Lin Chun, an editor at Nature Nanotechnology, writes: "Actually I do not speak 7 languages. I speak a total of 7 languages and dialects. So, it’s not as impressive as it sounds. I consider Cantonese a dialect but others might think otherwise. While language is not a requirement of a Nature journal editor (apart from being proficient in English of course), positions based in Asia or other offices where English is not the native language, it is a requirement and/or desirable to have these language skills. Almost everyone in our Tokyo office is minimally bilingual but most can speak more than 2 languages. These range from Korean, Japanese, Malay, Cantonese, Taiwanese to French, German and Spanish. It is indeed very enjoyable to be able to speak and understand a number of languages. For example, I’ve been able to translate questions from the audience into English during my seminars. In some cultures where English is not their first language, people tend to be a little shy. Being able to bridge this is very fulfilling for both them and myself." Comments are welcome at the Nature Nanotechnology: Asia-Pacific and beyond forum.

Richard Grant initiates a lively debate about online videos: when they are useful, and when superfluous. Is it helpful to have video "tutorials" about basic techniques, such as cell culture, or is there no substitute for personal training? Opinions differ, as can be seen. One of the comments is by Moshe Pritsker, Editor of JoVe (Journal of Visualized Experiments): "is there anything in biology today that can be considered “basic”? Biological research is becoming more and more fragmented, and researchers become more and more focused on their specific areas. Typically, as I observed in many labs, a neurobiologist would not know how to do a Western blot, and a biochemist would not know how to perform a simple cell staining. These are very “basic” techniques."

Previous Nature Network columns.

Posted by Maxine Clarke on July 18, 2008
Categories: Nature Network round-up | Permalink | Comments (0)

Danae Rebecca Dodge of the Graduate School of Archaeology, University of Sheffield, UK, writes in Nature's Correspondence pages (Nature 454, 27; 2008):

As a PhD student in archaeology and genetics, I am all too aware of the difficulties in crossing a gaping discipline divide, as well as of their effect on academic career prospects, as discussed in the Naturejobs article 'Assembly work' (Nature 453, 422–423; 2008).
For my master's degree in biomolecular archaeology, I needed a foot in two UK universities: one in the University of Manchester's biology department and the other in the University of Sheffield's archaeology department. My former lecturers later became part of the Manchester Interdisciplinary Biocentre (MIB) and the MSc course shifted to Sheffield, where eventually the programme ceased.
This closure was a disappointment for the nascent field of bioarchaeology, set to thrive only on a foundation of solid postgraduate training. Although the MIB and other new centres for interdisciplinary research are enthusiastically welcomed, they are few and far between and so able to offer only limited postdoctoral prospects.
Opening such centres and creating training programmes is not enough — it is also necessary to make interdisciplinary fields attractive to graduates and for senior academics to appreciate their significance. This would improve project turnover, bringing more funding to collaborative projects that would sustain interdisciplinary centres and allow academics from each discipline to gauge publications on an equal footing.
Perhaps then my search for a postdoctoral position in bioarchaeology would be easier. Although interdisciplinary projects are viewed as hot topics, in reality they lag behind as they await official establishment and recognition.

Posted by Maxine Clarke on July 17, 2008
Categories: Careers, Disciplines | Permalink | Comments (0)

Every field of research has influential papers that have shaped and guided future work. In the July issue of Nature Structural and Molecular Biology (15, 655-657; 2008), Reinhard Jahn gives his picks for membrane fusion and a little bit of history about how the field has developed. He writes:

Over the past 30 years, three main lines of research have made important contributions to our present understanding of the molecular mechanisms involved in membrane fusion: (i) the development and quantitative treatment of physical models describing the fusion of planar and curved bilayers at various levels of complexity and detail; (ii) the structural and mechanistic insights obtained from the investigation of fusion proteins of enveloped viruses, with research on the fusion protein of the influenza virus having made seminal contributions; and (iii) the study of fusion proteins involved in fusion events of eukaryotic cells, with the most important work being carried out on the SNARE proteins and associated regulatory proteins. In what follows, I will briefly discuss the studies that have helped form the basis for all subsequent work in the field of membrane fusion. The papers describing these studies make up my personal list of 'classics'.

Please see Nature Structural and Molecular Biology for the rest of this article, and the list of selected papers.
This issue of the journal also features a focus of articles on membrane fusion, an in-depth look at a process essential for communication within and between cells via reviews, an essay, classic papers and a library of resources.

Posted by Maxine Clarke on July 16, 2008
Categories: Disciplines | Permalink | Comments (0)

Massimo Sandal of the University of Bologna writes in Nature Correspondence (454, 158; 2008):
Raghavendra Gadagkar (Nature 453, 450; 2008) argues that the open-access 'pay to publish and read for free' model leads to a disadvantage for scientists in developing countries. I disagree. Gadagkar correctly states: "page charges may be waived for authors who cannot afford to pay." He then adds: "a model that depends on payment by authors can afford only a few such waivers." This is not necessarily true: for example, some open-access journals provide discounts to particular institutions.
I would prefer to see what little money is available to a developing country spent on helping to publish their scientists' papers rather than financing publishing houses based in First World countries. At present, open-access publication may be hard for those in the developing world to afford, but in the long run it will be advantageous, offering them free access to educational and academic resources.
Most important, the future of open access probably does not lie in journal publishing models. The huge success of online literature databases such as arXiv, free to publish and access, is significant. Such databases currently host mostly non-peer-reviewed preprints, and so are of little value for career building. But academic organizations throughout the world could, if they wished, build an equivalent archive of peer-reviewed papers.
I also disagree with Gadagkar's view: "If I must choose between publishing or reading, I would choose to publish". No one can expect to do serious science without access to the current academic literature.
Although many subscription journals are free to access online in developing countries through the HINARI, AGORA and OARE initiatives of the United Nations, the principle remains that if you cannot afford to read, you automatically cannot afford to publish. Perhaps Gadagkar will agree next time he is denied access to a fundamental paper for his research because his institution does not subscribe to it.

Posted by Maxine Clarke on July 15, 2008
Categories: Access | Permalink | Comments (0)

In the July issue of Molecular Systems Biology (4 , Article number: 201 doi:10.1038/msb.2008.39; 2008), Jonathan A Sagotsky et al. in their article "Life Sciences and the web: a new era for collaboration, write:

The World Wide Web has revolutionized how researchers from various disciplines collaborate over long distances. This is nowhere more important than in the Life Sciences, where interdisciplinary approaches are becoming increasingly powerful as a driver of both integration and discovery. Data access, data quality, identity, and provenance are all critical ingredients to facilitate and accelerate these collaborative enterprises and it is here where Semantic Web technologies promise to have a profound impact. This paper reviews the need for, and explores advantages of as well as challenges with these novel Internet information tools as illustrated with examples from the biomedical community.

Posted by Maxine Clarke on July 14, 2008
Categories: Communication, Disciplines | Permalink | Comments (1)

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

Michael Nestor writes the first of two posts on what he calls 'casual collectivism', which looks at the trend for scientific information used by students and researchers to be more commonly obtained via online resources than via conferences. Although the online Wikipedia model is that errors can be corrected and updates made quickly, there is a period of time in which information contained in the encyclopaedia is wrong. "When is casual scientific collectivism a problem?", writes Michael. "When it involves a convergence of mass distributed networks of people, being channeled and bottlenecked into faceless, anonymous, and editor-free depositories of information." For more of this fascinating argument, please visit Michael's blog. (There is a related Peer to Peer post here, about various online encyclopaedias and models of accuracy.)

John Wilbanks writes a considered post on the business models of open-access publishing. The post, together with the comment thread, provides some perspectives on the business models that can be applied to "open access" publishing, whether profit or non-profit. See also a related post about publishers' business models at Nascent, by Timo Hannay, and What is fair play in the blogo/commetosphere?, a post by Corie Lok, Nature Network Editor.

Following on from a post about technology-enabled communication between scientists, Richard Grant turns to the question of networking theories and results. This topic is also discussed at great and stimulating length, with a short diversion or two, by Jennifer Rohn and commenters, from the perspective of nomenclature and why it is important in enabling the innovative processes described by Richard.

Nature Precedings reached a milestone yesterday (9 July): the 500th document has been uploaded to the site. Read all about it in this post from Hilary Spencer.

"A lot of people seem to think that editors make a decision based on just reading the abstract and/or the covering letter, so I’d like to take this opportunity to say: THIS IS NOT TRUE!" Nature Neuroscience editor Charvy Narain takes her turn to describe her day job, at the Ask the Nature Editor forum.

Previous Nature Network columns.

Posted by Maxine Clarke on July 11, 2008
Categories: Nature Network round-up | Permalink | Comments (0)

From Nature 454; 150 (10 July 2008):
The US government may soon require, rather than just recommend, that federally funded investigators, and the ethics-board members who approve their research, receive training and education in how to protect participants in human studies.
The Office for Human Research Protections (OHRP) announced last week that it is soliciting comments on whether such training in research ethics should be mandatory — and asking for estimates of what this would cost grantee institutions.
“Over the past several years, OHRP has identified serious, systemic noncompliance with the requirements … for the protection of human subjects at a significant number of major institutions,” OHRP regulators wrote in its Federal Register announcement on 1 July.
Interested parties now have until 29 September to submit their comments.

Posted by Maxine Clarke on July 10, 2008
Categories: Ethics | Permalink | Comments (0)

Nature Publishing Group announced this week that it will provide a free service to help authors fulfil funder and institutional mandates for the archiving of primary research papers. NPG has encouraged self-archiving since 2005. The new arrangements will provide uploading for NPG authors, starting later this year. See here for NPG's press release announcing the service.
NPG will begin depositing authors’ accepted manuscripts with PubMed Central (PMC) and UK PubMed Central (UKPMC), meeting the requirements for authors funded by the Howard Hughes Medical Institute (HHMI), the US National Institutes of Health (NIH), The Wellcome Trust, the UK Medical Research Council and a number of other major funders in the United States, the United Kingdom and Canada that mandate deposition in either PMC or UKPMC. NPG hopes to extend the service to other archives and repositories in future.
"We are announcing our intention early in the process to solicit feedback from the community and to reassure authors that we will be providing this service," said Steven Inchcoombe, Managing Director of NPG. "We believe this is a valuable service to authors, reducing their workload and making it simple and free to comply with mandates from their institution or funder."
Initially, the service will be open to authors publishing original research articles in Nature, the Nature monthly journals that publish original research, and the clinical research section of Nature Clinical Practice Cardiovascular Medicine. NPG will then extend the service to society and academic journals in its portfolio that wish to participate.
For eligible authors who opt-in during the submission process, NPG will deposit the accepted version of the author’s manuscript on acceptance, setting a public release date of 6-months post-publication. There will be no charge to authors or funders for the service.
In 2005, NPG announced a self-archiving policy that encourages authors of research articles to self-archive the accepted version of their manuscript to PubMed Central or other appropriate funding body's archive, their institution's repositories and, if they wish, on their personal websites. In all cases, the manuscript can be made publicly accessible six months after publication. NPG’s policies are explained at our author and referees' website.

Posted by Maxine Clarke on July 09, 2008
Categories: Access | Permalink | Comments (0)

Nature Network's Berlin group, run by Philipp Selenko, is organizing a series of dinners during the Twentieth International Genetics Conference (to be held in Berlin from 12 to 17 July). The dinners are free to attend and are intended to provide the opportunity to meet some of the distinguished scientists who are speaking at the conference in a relaxed atmosphere.
Friday 11 July: Oliver Smithies & Mario Capecchi, winners of the 2007 Nobel prize in Medicine ’for their discoveries of principles for introducing specific gene modifications in mice by the use of embryonic stem cells.’
Monday 14 July: Elisa Izaurralde & Frank Uhlmann, respectively Max Planck Director at the MPI for Developmental Biology in Tuebingen and group leader at the Cancer Research UK Institute in London. Elisa works on various aspects of RNA biology whereas Frank is interested in the functional properties of eukaryotic cell division.
Tuesday 15 July: Eric Lander, Peer Bork & Dinshaw Patel.Eric is the Founding Director of the Broad Institute of the MIT; Peer is the Scientific Coordinator of the EMBL Stuctural Biology and Bioinformatics Program. The two are internationally known for their pioneering work in deciphering the DNA/RNA sequence space. Dinshaw runs a structural biology laboratory at the Memorial Sloan Kettering Institute in NYC where he has unraveled some key features of RNA and DNA molecules, most recently those of siRNAs.
Wednesday 16th July: Rudi Jaenisch & Barry Dickson discuss issues about model organisms in science. Rudi is at the Whitehead Institute in Boston and a distinguished expert in mouse genetics and embryonic stem-cell biology. Barry is the Scientific Director of the Institute of Molecular Pathology in Vienna, and known for his work in on axon guidance in Drosophila . He has recently embarked on a journey to unravel the molecular principles of complex animal behaviour.

All dinners will start at 7 p.m. and take place at the Meierei, Kollwitzstrasse 42, Prenzlauer Berg.
Philipp writes "We hope that you are as excited as we are about the program and that many of you will show up for those special events!" For further information (including travel directions), please see the Nature Network Berlin forum; if you have any additional questions, you can contact Philipp via email.
Nature Network Berlin has set up a shared Google calendar for these and other Berlin-related events.

Posted by Maxine Clarke on July 08, 2008
Categories: Author benefits, Conferences | Permalink | Comments (0)

Nature Cell Biology wishes Nature Precedings a happy birthday in its July Editorial (Nature Cell Biology 10, 753; 2008), in the process taking stock of the usefulness of "web 2.0" publishing ventures to cell biologists (and other scientists).
Nature Precedings allows rapid posting of unpublished (and unreviewed) manuscripts, conference posters and slide presentations. Entries are subject-tagged, searchable and citable. Postings are screened by curators for scientific legitimacy, plagiarism and scope, but not peer-reviewed for novelty or data quality; commenting and voting by readers is encouraged.
The immediate question for most cell biologists and other scientists is whether posting material on a preprint sever is worth the risk of being scooped. Nature Cell Biology concludes that although many cell biologists are still wary of preprint servers, they could consider posting solid data that are not likely to be published in traditional journals because they are confirmatory or negative. Well-controlled negative data are immensely useful to colleagues, so documenting them in a citable form on a preprint server is a valuable community service.

Related posts:
Peer to Peer on the first year of Nature Precedings.
Nature Network post by Hilary Spencer of Nature Precedings.
Nature Network online discussion forum for the Nature Cell Biology editorial.
Futher information about Nature Precedings is available here.

Posted by Maxine Clarke on July 07, 2008
Categories: Communication, Data availability | Permalink | Comments (0)

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

For those interested in consistency of nomenclature, Jennifer Rohn (Mind the Gap) posts about some of the challenges, after discoverinng that a particular "gene’s ‘official’ symbol was ZNF265 according to OMIM, but ZRANB2 according to NCBI Entrez and HGNC." As well as the challenge of researchers agreeing on common nomenclatures for entities such as genes and viruses with many variants (subtypes, polymorphisms and so on) and depositing the information in an appropriate database, the databases themselves sometimes do not update frequently. It does not get better, as Jennifer writes: "Looking up your new gene of interest in PubMed is not an easy way to grasp a coherent idea of what’s been published in the literature. Abstracts are littered with synonyms (and some pairs of different genes have the same synonym), but there is no unique gene identifier, as far as I can see, associated with the abstracts." And, as Euan Adie remarks in the comment thread: "even if you used database identifiers instead of HGNC names you could run into trouble – in the abstract did you mean the gene as we knew it in 2000, or in 2002, after we discovered those extra exons? In the position it was in on the initial genome assembly, or a million basepairs further down in the latest version? The same gene in different contexts needs different identifiers (or at least version numbers), but you still need to be able to pull all that together somehow and pull out the information you need." Further discussion continues, to which you are welcome to contribute. Views from authors (past, present and future) on topics such as this one are invaluable to journals in helping them to shape their policies.

So you use Nature Network, but what do you really think of the impact of Web 2.0 (the 'social' web) on research? The TalkScience team at the British Library has set up a group Scientific researchers and Web 2.0, posing a few questions about why busy scientists should invest in Web 2.0; using the web to share data and preprints; whether concern about confientiality will lead groups to set up "gated communities"; relevance of taxonomies, folksonomies, semantic web and other Web 3.0 concepts; and user-participation, necessary to keep these new web services alive. There are already discussions on scientific method in the era of big data, advertising by stealth, open notebook science, Web 2.0 in neuroscience, and more. Please join the group, which will be providing details of the TalkScience evening at the British Library in London in September, where some of these issues will be debated. Keep an eye out for the notice on this group to attend this free event.

The official programme for Science Blogging 2008 is now up. Whether you are a blogger and regular user of the Internet, or whether you have never written an online comment but are interested to learn more, this meeting is for you, so please head on over to the Nature Network group to find out more about the programme, contribute to the make-up of the sessions, discover where to find cheap accommodation, and sign up for some science-themed outings. As a taster, here is the abstract for one panel: "Mistrust of scientists is common, and misinterpretation of scientific results rampant. Science blogs can serve as a bridge between scientists and the general public. Blogs build a community of scientists in which they can discuss the peculiarities of their jobs, their work, and their results. More than that, science blogs have the power to demystify the scientific process for the public and to reverse deeply held stereotypes of scientists. In this session, we will discuss how science blogs can change the public’s perception of scientists and provide a support framework for scientists themselves."

Previous Nature Network columns.

Posted by Maxine Clarke on July 04, 2008
Categories: Nature Network round-up | Permalink | Comments (0)

Nature Geoscience publishes a regular feature called BackStory, at the back of the journal or on the journal's website, in which the authors of a paper in the current issue of the journal answer questions about their field work -- providing an unusual perspective on the region of the world that contributed to the paper. The Backstory in the July issue (Nature Geoscience 1, 482; 2008), Sailing for a stretched lithosphere, describes how Jenny Collier and colleagues, having managed to get themselves and all their instruments on board a ship not too far away from an imminent war zone, enjoyed the serenity of life at sea as they investigated the rifted continental margin of India.

How long did it take to plan the fieldwork?

Two years elapsed between getting the project approved and setting sail. We wanted to use a particular vessel, the RRS Charles Darwin, which was already in the Indian Ocean and had the scientific capability that we needed. Unfortunately, we had to join a rather long waiting list. Coordination was a nightmare — our scientific instruments were all in different parts of the world, taking part in experiments that were also subject to scheduling changes. When we finally had our chance, the build-up to the Iraq invasion resulted in several changes to our port of embarkation. It was a huge relief when we finally set sail with all the equipment onboard!

See Nature Geoscience's website for the rest of the Backstory.
The paper featured is: The relationship between rifting and magmatism in the northeastern Arabian Sea, by Timothy A. Minshull, Christine I. Lane, Jenny S. Collier & Robert B. Whitmarsh (Nature Geoscience 1, 463-467; 2008).

Posted by Maxine Clarke on July 03, 2008
Categories: Communication, Disciplines | Permalink | Comments (0)

The International Mathematical Union has released a report on the use of citations in assessing research quality. The report, Citation Statistics, is written from a mathematical perspective and strongly cautions against the over-reliance on citation statistics such as impact factor and h-index. The belief that these parameters are accurate, objective and simple, is unfounded.
It states that the objectivity of citations is illusory because the meaning of citations is not well-understood. Its meaning can be very far from ‘impact’. Although having a single number to judge quality is indeed simple, it can lead to a shallow understanding of something as complicated as research. Numbers are not inherently superior to sound judgments.
The report, written by mathematicians, promotes the sensible use of citation statistics in evaluating research and points out several common misuses of this widespread application of mathematics. The authors of the report recognize that assessment must be practical and that easily-derived citation statistics will be part of the process, but caution that citations provide only a limited and incomplete view of research quality. Research is too important, they say, for its value to be measured with only a single coarse tool.
(This is a precis of the press release accompanying publication of the report, see links above.)
Further discussion of the report, together with other matters related to citation and quality metrics, is taking place online at the Nature Network Citation in Science group, which all are welcome to join.

Posted by Maxine Clarke on July 02, 2008
Categories: Citation analysis | Permalink | Comments (0)

The availability of whole-genome association studies has redefined the genetic architecture of genetically complex disorders, and genotyping and resequencing will reveal new susceptibility genes for a wide range of common human diseases. The emphasis of the field is thus changing from focusing on the identification of susceptibility genes towards an understanding of mechanisms and potential applications.
Following the successful inaugural conference in Hinxton, Cambridge, UK in July 2007, this second meeting, organised by Nature Genetics and the Wellcome Trust, will take place from 6 to 9 September 2008, at The Broad Institute of MIT and Harvard, Cambridge, MA, USA aims to address the following topics, across a range of common diseases:
--The state of the art in gene-identification strategies
--The transition from knowledge of susceptibility genes to understanding of mechanisms
--Population genetics and genome evolution in common-disease genetics
--The utility of risk prediction based on genetic and other available tests
--Ethical, legal and social implications of personal genetic information.
Please see the conference website for further details of the organizers, speakers, abstract submission, accommodation and more.

Posted by Maxine Clarke on July 01, 2008
Categories: Conferences | Permalink | Comments (0)