Nautilus

Nature reports in News this week (453, 1149; 26 June 2008) that a Canadian graduate student dissatisfied with science coverage on online sites such as Google News and Yahoo News has created a news aggregator especially for scientists.
Michael Imbeault, an HIV researcher at the Université Laval in Quebec, launched his fully automated site called e! Science News last month. It has already attracted 300,000 different users, and averages 5,000 visits a day, he says.
News aggregators display headlines and snippets from other media sources, but don't produce their own content. Of the top five online US news sites, three are aggregators — Google News, AOL News and Yahoo News — and only two — CNN.com and MSNBC.com — generate original content. Yahoo and AOL use human editors and source almost all science stories from wire agencies, such as Reuters. Google News uses computer algorithms to aggregate headlines from thousands of news sources, ranking them by how often and on which sites stories appear. Science and technology coverage on Google News, for example, is notoriously devoid of basic science.
The above is taken from the Nature News story, where more information can be found.

Posted by Maxine Clarke on June 30, 2008
Categories: Communication, Public and media | 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.

During his first year as a graduate student, Nuruddeen Lewis at his Lab Daze blog was advised by a mentor to read at least one journal article every day. Reading a paper every day is tough, but keeping up to date with recent publications is an essential part of scientific research, writes Nuruddeen. Is the key to read as much as you can? Is there an optimal way to read the scientific literature? Nuruddeen would be interested to know your views, at Lab Daze blog.

The rENNISance woman, Cath Ennis, proposes that online networking tools such as Nature Network could be used for forge links with biologists "whose proteins of interest interact with our own". She cites a case of two people who met, discovered that one worked on an enzyme and the other on its substrate. They are now married.

Appealing to the emotion is a fundamental aspect of successful writing, says Brian Clegg at his blog PopSci. What he does not like, however, is the use of a term such as "pornography" as a substitute for this emotion. "When someone refers to a property show or a book on the impact of climate change as pornography, what they really are doing is demonstrating their own emotional insecurity, and diluting and corrupting the English language to boot", he writes. Thirty comments (at time of writing) follow, as the scientists on Nature Network respond to the concept.

Research integrity is a hotly debated topic this week, as the discussion of last week's Nature Commentary and Editorial continue at the News and Opinion forum. But "Photoshopped gels are nothing", writes Euan Adie , in a fascinating historical post about Sir John Herschel and a newspaper's stunt with bipedal beavers.

Martin Fenner continues his quest for his "paper-writing dream machine" by turning to reference management software and providing a useful brief review of what is available. "Not quite there yet", is the verdict of the post and the commenters.

Bob O'Hara describes how he is outdone by misprints. He investigates a classic paper in his field, and finds that the number of its mis-citations result in an h-index of 12, a level that the inventor of the metric, Hirsch, suggested might be a typical value for advancement to tenure.

The world's first internet balloon race is taking place, reported by Scott Keir at Mixed Miscellanies blog. In the competition, websites can be recommended by users and balloons representing subject areas race across a world map (disclaimer: I may have misunderstood the details). Scott points out that science, in the shape of Charles Darwin, is not doing very well, so nominations of science websites are required to assist. Charles Darwin himself, of course, is blogging at Nature Network, commenting on science as it is reported in the popular "prints". This week he is none too impressed at the latest genome sequencing project -- chocolate.

Finally, for those interested in how journal editors spend their days, here is an account by Henry Gee, A day in the life of a senior editor. It is impossible to summarise this eclectic account, but it is engrossing, as well as very funny, so do read it.

Previous Nature Network columns.

Posted by Maxine Clarke on June 27, 2008
Categories: Nature Network round-up | Permalink | Comments (0)

The retraction of a Nature Chemical Biology paper is a step toward a full accounting of a case of scientific misconduct, as described in the journal's July editorial (4, 381; 2008).The paper is by Won et al., "Small molecule–based reversible reprogramming of cellular lifespan" (Nat. Chem. Biol. 2, 369–374, 2006). The editorial describes the process by which the paper was considered and the process by which the problems came to light, first involving undeclared financial interests, then, some time later, lack of reproducibility of the data. From the editorial:

As stated in the retraction text, all nine of the paper's authors have agreed that the paper must be retracted. However, Tae Kook Kim, the principal investigator and corresponding author, did not agree to the retraction statement signed by the other authors and asserts that any scientific irregularities are limited to a subset of the paper's experiments. Although circumstances did not allow complete agreement among the paper's authors and the text does not list all of the scientific concerns that were raised in the initial inquiries, the published retraction statement and 'Editor's note' provide abundant explanation for why the paper must be removed from the scientific literature. We commend CGK scientists for raising the initial concerns with the Science and Nature Chemical Biology papers and the KAIST investigating committees for their efforts to date. It is reassuring that Korean institutions are taking a hard line on scientific misconduct. However, we do question the timing and content of the KAIST press release of February 29, 2008, which was made public without advance notice to the journal. It is not unusual for an institute to announce that an investigation is underway and to make another announcement at its conclusion. Ideally, though, investigating committees contact journals well in advance of making public statements, thereby ensuring that the information communicated is accurate at all stages. The potential negative impacts of scientific misconduct allegations on the accused and on the public perception of science cannot be underestimated. Statements to the press are useful, but first priorities should always be determining the facts quickly, giving due process to investigators under suspicion and correcting the literature.........As the KAIST committee completes its deliberations, we urge them to provide a full accounting of the case and make their findings widely available in English. This example would serve as a model for future investigations committed to maintaining the integrity of science and the scientific literature.

Posted by Maxine Clarke on June 26, 2008
Categories: Ethics | Permalink | Comments (0)

The NatureJobs Source Event career fair will be taking place in London on 26 September 2008. This dedicated science career fair combines a dynamic exhibition with conference and workshop sessions. The event will promote the UK and the rest of Europe as a great place to pursue a career in science, be it in industrial research, research organizations or academia. It will present the best opportunities from the best organizations: public, private, national and international.
Jobseekers will be able to meet with potential employers who are offering hundreds of vacancies. The plenary and workshop sessions will provide a unique opportunity to meet high-profile scientists and gain careers information and advice.
Several of the invited speakers have kindly agreed to answer career-related questions in advance of the meeting, at Nature Network. The Nature Network Question & Answer session with some of the meeting’s speakers is now "live". The NatureJobs team invites you to ask the speakers about their backgrounds, career paths, advice for getting in to a particular field or sector, relevant or important skill sets, and so on. The relevant speaker(s) will post responses, and factor the questions into their presentations at the event.

The following speakers have kindly agreed to participate:
• Jim Loftus, Research Recruitment Manager, Pfizer
• Matthais Haury, Coordinating Manager, EMBL International Centre for Advanced Training
• Zonya Jeffrey, Biomedical Scientist, Central Manchester and University Hospitals NHS Trust
• Stijn Oomes, Assistant Professor in Human–Computer Interaction, Delft University of Technology
• George Schlich, Chartered and European Patent Attorney & founder of Schlich & Co
• Jonathan Yearsley, Postdoctoral Researcher, Department of Ecology and Evolution, University of Lausanne.

Already in the Nature Network Source Event forum there are questions and answers about moving from academia to industry, what participants hope to gain from the event, which recruitment and other companies will be exhibiting, how to upload your CV, and more.
Please join this free Nature Network group to ask your questions and to obtain further careers advice from the panel of experts.
The Question and Answer sessions are here.

Posted by Maxine Clarke on June 25, 2008
Categories: Careers, Partners | Permalink | Comments (0)

Raf Aerts of the Katholieke Universiteit Leuven writes in Correspondence in Nature (453, 979; 2008):
Several Correspondences, including 'Give south Indian authors their true names' (Nature 452, 530; 2008) and 'Name variations can hit citation rankings' (Nature 453, 450; 2008), have illustrated difficulties in identifying authors and their papers, citations and h-index.
In an academic world in which decisions on promotion and funding often depend on the applicant's scientific impact, an incorrect publication or citation record in an online database can be very inconvenient. Scopus and Thomson's Web of Science, which make available abstract and citation databases, acknowledge the issue and have come up with solutions: the Author Identifier and ResearcherID, respectively.
These systems assign an identifying code to each author. Unfortunately, a single author can have more than one Author Identifier in Scopus (I am cryptically known as 7006716603 and 16551750300). And as only invited researchers can register for a number, ResearcherID is not yet used as a unique author key in the Web of Science — making it difficult to differentiate me from a highly cited ecologist from the Netherlands, despite the 'Distinct Author Sets' feature.
If it is possible to have DOIs for objects (or, so they say, enough IPv6 addresses for every molecule on Earth), why is it so difficult to implement DAIs for authors?
(See the author and reviewers' website for more about DOIs, or digital object identifers.)

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

This is the text of an Editorial published in Nature on 19 June (453, 957; 2008)

Many researchers would like to believe that scientific misconduct is very rare. But news reported in this issue (see page 969), and the survey results reported by Sandra Titus and her colleagues in the Commentary on page 980, challenge that comfortable assumption. Titus's team found that almost 9% of the respondents in their survey, mainly biomedical scientists, had witnessed some form of scientific misconduct in the past three years, and that 37% of those incidents went unreported.
The results suggest a research climate in which scientific misconduct, although uncommon, is certainly not an anomaly. Titus et al. outline a number of measures to address this situation, including better protection for whistleblowers, and promotion of a 'zero tolerance' culture in which scientists have just as much responsibility to report others' misconduct as they have for their own behaviour.

Continue reading "Solutions, not scapegoats" »

Posted by Maxine Clarke on June 23, 2008
Categories: Ethics | 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 Science Blogging 2008 conference, to be held in London on 30 August, is taking shape, not least in the form of this logo, created by Euan Adie. Further updates about the meeting can be seen in the forum; where you can sign up for poster sessions or talks, and book for a science walking tour of London with Nature Network London Editor Matt Brown on Friday 29 August.

Should laptops be banned from conferences during presentations, asks Andrew Hudson-Smith of Urban Nature blog? When presenting his work, he finds it disheartening to look up "only to view a sea of laptops and people typing", using their laptops to check email, surf the web or write blog posts rather than listen to the presentation.

As part of her job, scientist and rENNISance woman Cath Ennis is receiving more and more requests from colleagues to provide lay summaries of research projects for grant submissions and websites. What bothers her is the trend towards making nouns and adjectives into verbs, for example: “please can you lay this language for me”, and “if you could just laymanise this technical abstract”. She asks Network users to suggest a better term than "lay".

The latest paper for discussion in the Good Paper Journal Club is up: Dynamics of fat cell turnover in humans. Martin Fenner's view: "What I like about this paper? The authors try to address an important problem (obesity) by asking a number of simple questions. Instead of using the traditional IMRAD format (introduction, methods, results and discussion), the different structure of the paper allows the reader to easily follow the experiments. A lot of the experimental details are put into the supplementary information and don’t distract from the key research findings."

Karesh Narasimhan, in the structural biology group, suggests that the raw data underlying experiments reported in peer-reviewed work is published online by the authors, at their institution's or laboratory's website, allowing others to "reconstruct the pieces of experiments done by a lab – the biggest beneficiaries would be graduate students – who can learn many subtler aspects of data processing and manipulation that is of publication quality."

Previous Nature Network columns.

Posted by Maxine Clarke on June 20, 2008
Categories: Nature Network round-up | Permalink | Comments (0)

New Communication Channels in Biology is the title of a workshop that takes place next week, on 26 and 27 June, at the University of California, San Diego. Hilary Spencer of Nature Precedings will be giving a talk, as well as Moshe Pritsker of JoVE (Journal of Visualized Experiments) and many others. The agenda can be viewed here. The workshop is open to the public and is free, although prior registration is required.
From the programme: "The workshop will focus on the range of emerging approaches within e-science, community engagement in dialogue knowledge input/review or assessment, science blogs, and authenticated wiki-like research discussions and analysis, as well as the potential to formalize such community level contributions. These new approaches to communication are becoming important for biology as biological scientists attempt to address the inherent complexity of life, manage both high information content and high throughput data streams, and employ the opportunities emerging from advances in e-communication/networking and information technology."

Posted by Maxine Clarke on June 19, 2008
Categories: Communication, Conferences | Permalink | Comments (0)

The Chronicle of Higher Education (29 May 2008) has published an article by Jeffrey R. Young about image "beautification", or to put it more bluntly, "fakery", in papers reporting research results. The article describes the discovery of "doctored" images by editors at the Journal of Clinical Investigation, and outlines some of the processes that it and other journals have put in place to uncover the practice, complete with some case-histories. All papers accepted for publication by the Journal of Cell Biology, for example, are subjected to an image check. Dr Linda Miller, US Executive Editor of Nature, was interviewed for the Chronicle's article:

At Nature Publishing Group, which produces some of the world's leading science journals, image guidelines were developed in 2006, and last year the company's research journals began checking two randomly selected papers in each issue for image tampering, says Linda J. Miller, U.S. executive editor of Nature and the Nature Publishing Group's research journals. So far no article has been rejected as a result of the checking, she says. Ms. Miller and other editors say that in most cases of image tampering, scientists intend to beautify their figures rather than lie about their findings. In one case, an author notified the journal that a scientist working in his lab had gone too far in trying to make figures look clean. The journal determined that the conclusions were sound, but "they wound up having to print a huge correction, and this was quite embarrassing for the authors," she says. Ms. Miller wrote an editorial for Nature stressing that scientists should present their images without alterations, rather than thinking polished images will help them get published. Many images are of gels, which are ways to detect proteins or other molecules in a sample, and often they are blurry. No matter, says Ms. Miller. "We like dirt—not all gels run perfectly," she says. "Beautification is not necessary. If your data is solid, it shines through."

Nature journals' image guidelines can be found here. Also on this page are links to free-access editorials in the Nature journals about our policies and why we have them, together with an invitation to authors and other scientists to comment online.

Posted by Maxine Clarke on June 19, 2008
Categories: Ethics | Permalink | Comments (0)

The 2007 Impact Factors are now out (published on 17 June 2008). The ten Nature Publishing Group journals with the highest Impact Factors are as follows:

1 NAT REV MOL CELL BIO 31.921
2 NAT REV CANCER 29.190
3 NATURE 28.751
4 NAT REV IMMUNOL 28.300
5 NAT MEDICINE 26.382
6 NAT IMMUNOLOGY 26.218
7 NAT GENETICS 25.556
8 NAT REV NEUROSCI 24.520
9 NAT REV DRUG DISCOV 23.308
10 NAT BIOTECHNOLOGY 22.848

The Impact Factors of the Nature journals that publish original research are:

1 NATURE 28.751
2 NAT MEDICINE 26.382
3 NAT IMMUNOLOGY 26.218
4 NAT GENETICS 25.556
5 NAT BIOTECHNOLOGY 22.848
6 NAT MATERIALS 19.782
7 NAT CELL BIOLOGY 17.623
8 NAT NEUROSCIENCE 15.664
9 NAT METHODS 15.478
10 NAT NANOTECHNOLOGY 14.917
11 NAT PHYSICS 14.677
12 NAT CHEM BIOLOGY 13.683
13 NAT STRUCT MOL BIOLOGY 11.085

(Nature Photonics and Nature Geoscience are not old enough to have been awarded an Impact Factor this year.)
Readers can create their own lists of journals by subject area, title, Impact Factor or publisher, at ISI Web of Knowledge.
There is a free-access account at the ThomsonISI website which explains how the Impact Factor for journals is calculated.
Discussion of the 2007 Impact Factors, and of citation in science in general, is taking place at the Nature Network Citation in Science group, which you are warmly invited to join.

Posted by Maxine Clarke on June 18, 2008
Categories: Citation analysis, Quality measures | Permalink | Comments (0)

Via Knowledgespeak press release:
Two years after a meeting calling for urgent action to preserve scholarly e-journals, the results of a survey of 1,371 library directors of four-year colleges and universities in the United States have been released.
Most library directors who responded believe their own institution has a responsibility to take action to prevent intolerable loss of scholarly records. But although larger libraries support one or more e-journal preservation initiatives, most respondents from smaller libraries are yet to support any preservation effort and secure permanent access to e-journals for their institutions.
The survey, conducted by Portico and Ithaca, raises questions about how the responsibility for preservation of critical electronic resources should be supported by the community, even as electronic resources expenditures expand substantially at libraries across the spectrum. The organizers hope that the report will be a catalyst for leaders of libraries, consortia, and other organizations to provide a mechanism for digital preservation. The full report is available for download as a PDF. (A summary is available here.) Readers are also invited to share comments and reactions in the provided online discussion space.

Posted by Maxine Clarke on June 18, 2008
Categories: Data availability, Publishing | Permalink | Comments (0)

Nature Physics, in its June Editorial (4, 429; 2008), adds its own advice to recent articles on presenting talks, summarized and referenced here. From the Editorial:

Presenting your research to an auditorium of peers can be a daunting prospect, particularly for those at the start of their careers. But with a little thought and preparation, it needn't be.
We editors go to a lot of meetings, and have listened to a lot of talks. To hear a good talk can give you a reason for being. To hear a bad talk can make you wish you'd never left your hotel room. But even if your results won't earn you a trip to Stockholm (yet), there is no reason they shouldn't be the seeds for a lively discussion. And lively discussion is what it's all about. We've put together a collection of do's and don'ts to delivering a talk that will move your audience, not put them to sleep.
Once you've cut, tightened and improved the content, deliver it again, listen to it again, and fix any remaining weaknesses, again. Then again. And again. Until you are so familiar with its structure and content that you could give it in your sleep. Familiarity fosters confidence, and a confident talk is a compelling talk.
As it is with writing papers, so it is with giving conference talks — if your research is worth being presented to your colleagues, it's worth being presented to them well.

Read the rest of the Editorial at Nature Physics.

Posted by Maxine Clarke on June 17, 2008
Categories: Communication | Permalink | Comments (0)

Steven Inchcoombe, who became Managing Director of Nature Publishing Group (NPG) last October, is interviewed in the June/July issue of Research Information. He answers questions about the main information needs of researchers, the role of peer-review, NPG's position on open access, and provides some predictions for the future.

Open access means that authors or their funders may have to pay to publish papers and I think this will make them demand a higher level of service from publishers. They will want more visibility about what is happening in the publishing process. And once papers are published, authors will want to know who has accessed them as they might want to approach them about possible collaborations. In addition, self-archiving mandates require authors to do more work. If publishers are clever they will offer authors more help to do this. Also, as more authors are not native English speakers, publishers may have to help them more in how they express themselves in their papers. There are more and more versions of content available to readers. To justify their versions, publishers must offer serious value such as in forward and backwards citation linking. Another big challenge will be bringing in rich media such as audio and video.

See the Research Information website for the full article.

Posted by Maxine Clarke on June 16, 2008
Categories: Access, Publishing | Permalink | Comments (5)

SciDevNet's Practical Guides offer very useful advice for scientists who wish to communicate their results, not only in journals but in other ways and using other media. Articles include 'How do I become a science journalist?'; 'Planning and writing a science story'; 'How do I apply for a research grant?'; 'Spotting fraudulent claims in science'; 'How do I become media-savvy?'; 'How do I make a science news story for the radio?'; and others. A full contents listing is here.

Posted by Maxine Clarke on June 16, 2008
Categories: Communication, Partners, Writing | 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.

Barbara Axt, at her blog Baxt, asks how Internet videos can be used in science communication and science journalism. The subseqent discussion ranges over podcasts, movies of protocols, and videos of experiments as training aids.

In the good paper journal club, Neil Blair Christensen describes his journal's new project, Journal of Diabetes Forum, in which an editorial team offers to help researchers formulate their study designs before they submit manuscripts to journals for peer review, providing "no strings" editorial feedback on study designs. The service aims to help a growing group of new researchers get some good paper basics right and optimize their chances of surviving triage and peer review once they do submit to a journal. After feedback, researchers are free to submit to any journal they wish. For more details, please see the Nature Network forum.

A discussion at Richard Grant's blog The Scientist has blossomed into an example of how networking using the Internet, and Nature Network in particular, can help scientists. Sebastian Gonzalez, a Masters' student from Chile, "a little country at the end of the world" containing not many scientists, entered the conversation because he is interested in web-based collaboration but thinks it doesn’t work for some stated reasons. Some inches later, he has changed his position, thanks to a Chile-Australia-UK-Finland-Switzerland five-way sharing of information and ideas.

"A paper came across my virtual desk the other day that’s got Instant Classic written all over it." Nature editor Henry Gee reacts to a rather special submission: "Without giving anything away, it’s a genuinely new and startlingly simple insight into a problem that’s been perplexing people for ages; backed up by a novel, simple and apocalyptically powerful new technique; written like a dream; and from (now get this) a single author. I’m bound not to say any more. Indeed, I might have said too much. But this is one of those papers that gave me gooseflesh and threw my editorial spidey sense into fibrillation; one of those lightning-from-a-clear-sky manuscripts that as an editor I have the opportunity and privilege to be able to read and review perhaps once in a decade, and make me feel glad to be able to do the job I do. When I look at a manuscript and can’t decide whether I should send it to review or not, I ask myself one question, in particular: does this manuscript have the potential to make me see the world in a completely new way? This one does. Oh boy, it does."

In the wake of the annual Society for Scholarly Publishing, Nature Network editor Corie Lok asks whether it is the role of a scholarly society to be setting up and running groups on Nature Network or Facebook, or even building their own networking site?

Meandering Scholar (Ian Brooks) tells us what it is really like to be a mentor, and raises a toast to a first data point.

Previous Nature Network columns.

Posted by Maxine Clarke on June 13, 2008
Categories: Nature Network round-up | Permalink | Comments (0)

According to the Editorial in the June issue of Nature Nanotechnology 3, 309 (2008), "when the papers published so far in Nature Nanotechnology are classified according to the country in which the corresponding author was based at the time, we find that 47.6% of them come from the US, followed by 8% from the UK, 7.4% from Japan and 6.7% from Germany.
Classifying papers according to the affiliation of the corresponding author is clearly an approximation, but given the fact that papers can contain ten or more authors with affiliations in three or more countries, it is necessary to make such approximations if we want to understand which areas of the world are strongest" in a particular discipline.

The Editorial goes on to explain some of its "authorship" assumptions used for its analysis of several journals that publish high-quality research in the nanotechnology, leading to the conclusion that "although the number of nanotechnology papers published by Chinese researchers is increasing rapidly, the US and Europe continue to lead in terms of quality."

Posted by Maxine Clarke on June 12, 2008
Categories: Authorship | Permalink | Comments (0)

Debbie Chaves of Wilfrid Laurier University, Waterloo, Ontario writes in Correspondence in the current issue of Nature (Nature 453, 719; 2008):

In his Correspondence 'Hall and Keynes join Arbor in the citation indexes' (Nature 452, 282; 2008 - see also Nautilus), Daniel Postellon describes the distinguished careers of Milton Keynes, Walton Hall and Ann Arbor. In the last case, I note that Professor Arbor has an h-index of 1 from the Web of Science database provided by Thomson Scientific's ISI Web of Knowledge. This is based on her five citations for the year 2007: two articles, two letters and one abstract.
An author search in the Web of Science reveals that Chevy Chase MD (not to be confused with Chevy Chase, Maryland) has co-authored a letter with Howard Kaplan (H. Kaplan Am. Sci. 96, 3; 2008). My own institution, Wilfrid Laurier University, is also an author (S. Cadell et al. J. Palliat. Care 23, 273–279; 2007).
Irrespective of how these errors are created, the rising use of systems in which citation information moves directly from the search of a database or citation index to a bibliographic management system, and then into a reference list, means that inexperienced students and researchers who are not savvy enough to detect these errors will propagate them further.
Vigilance is required by all users of citation indexes and databases.

Posted by Maxine Clarke on June 11, 2008
Categories: Citation analysis | Permalink | Comments (0)

Nature reporter Quirin Schiermeier is spending June 5-12 aboard the Canadian research icebreaker CCGS Amundsen, as part of a project to study climate change in the high Canadian Arctic. His dispatches can be read at In The Field . At the start of his voyage, Quirin writes:

After an epic journey, on four planes and one helicopter, I have at last arrived on board the CCGS Amundsen. The final leg of my trip, the short transfer from Inuvik to Cape Parry at the northern tip of Canada’s Northwest Territories, was easily the most spectacular flight of my whole life. The tiny aircraft flew at very low altitude, so that every barren hill and every glittering lake in the tundra below seemed almost seizable. Then we were out on the frozen Franklin Bay, an inlet of the Amundsen Gulf, and headed towards the edge of the fast ice. We went down on a gravel airstrip next to an abandoned cold-war early warning station. From there a helicopter took us on board the icebreaker which is currently staying put in the fast ice at only a few ship lengths distance to the ice edge.

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

In its June 2008 issue, Nature Methods presents a free-access focus on single-molecule techniques. Biologists are becoming increasingly interested in methodologies that can examine the mechanism of action of fundamental biological processes at the molecular level. The Nature Methods focus consists of four review articles that provide practical guidance for some of the techniques that are most integral to in vitro single-molecule experiments. These cover single-molecule fluorescence methods; microfluidic flow cells to manipulate experimental conditions during experiments; and force-spectroscopy techniques such as atomic force microscopy (AFM) and optical traps to manipulate individual molecules themselves.
From the focus's Editorial: The ability to analyse biological systems at the single-molecule level opens avenues of investigation that are not possible using techniques that measure aggregate properties of molecular populations. This new vantage point can yield important insights. A textbook example is that of molecular motors. Although classical biological assays for motor function show that these molecules support constant-velocity movement, studies of individual molecules revealed that they take discrete individual steps. The technique that allowed these crucial biological observations came from the physics field in 1986—a momentous year that saw the first demonstration not only of the optical tweezers technique used in the subsequent molecular motor study but also of the atomic force microscope. Created by physicists, these force-spectroscopy methods form much of the backbone of the field of research now devoted to studying biological systems at the single-molecule level."

Please read on at the Nature Methods focus website. Comments from readers are welcome at Methagora, the Nature Methods blog.

Posted by Maxine Clarke on June 10, 2008
Categories: Author services, Disciplines | Permalink | Comments (0)

Frontiers of cellular, developmental and molecular biology, Nice; 30 August – 2 September 2008.
The seventh international congress of the European Life Scientist Organization (ELSO) returns this year to Nice on the French Cote d’Azur. Promoted for the first time in collaboration with the European Molecular Biology Organization (EMBO), the ELSO meeting offers a broad palette of top-notch international molecular life science mixed with informative and practical events to promote the career development of young researchers.
From the conference information pages: Plenary session speakers this year include: systems biologist Ursula Klingmueller; cell biologist Graham Warren; stem cell biologist Andreas Trumpp; developmental biologist Magdalena Zernicka-Goetz; tissue engineer Donald Ingber, and proteomics expert Matthias Mann. The 21 minisymposia and the poster sessions cover topics ranging from entry of pathogens into cells, through epigenetics to computational biology and all stops en route. Around 180 speakers, 600 posters and 80 commercial exhibitors will provide four full days of exciting and topical life science. Abstract submission deadline is 15 June.
If you are looking for advice on what to do next, whether it be a postdoc or a junior group leader position in another country or a move into a career outside academia, ELSO’s career development events can give you the inspiration to try something new and challenging and the practical help to put your plans into practice. At this year’s meeting there will be mentoring and mobility sessions, first-hand accounts of careers outside academia, as well as a new career enhancement workshop looking at your own personality, CV, interview techniques, and so on. Not to be missed if you are planning a career move soon!

Posted by Maxine Clarke on June 09, 2008
Categories: Careers, Conferences, Partners | 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.

A necessarily brief round-up this week, due to lack of time.

Ai Lin Chun, at Nature Nanotechnology: Asia-Pacific and beyond, explains how the journal's Research Highlights come into being . "Every week, each editor reads a list of journals in their area. We scan through all the articles published within the past week and pick out the most interesting two articles. A picking session occurs mid-week and we spend about 1-2 hours to read and write about the selected article. The criteria for Research Highlights are not as stringent as selecting papers for publication. They are meant to highlight a new idea or interesting preliminary findings published in other journals. Sometimes they are papers that we would publish and sometimes they are not. So, if you want to get into our radar, post your most recent publication on our network group. We will most definitely see it!"

Why would a researcher who has access to most journals himself be bothered to submit a paper to an open access journal and pay the publication costs when there are similarly ranked “closed” journals that are supported by subscriptions and cheaper to submit to? So asks Eva Amsen at Expression Patterns blog. The question has led, inevitably, to a lively comment thread.

Andrew Hudson-Smith, one of the newer bloggers at Nature Network, writes at his blog Urban Nature: "Blogging research thoughts and outcomes to me at least seems the most natural thing in the world, after all the current buzz around universities is outreach and breaking down silos. As such, Web 2.0, with its shared videos via services such as YouTube; its virtual environments such as Second Life; and real-time research updates via Twitter have all been welcomed and indeed become central to my work. The embracing of Web 2.0 by academics is not however universal and by many it can be viewed as trivialising research." (Some pros and cons have been discussed recently at Peer to Peer.)

Previous Nature Network columns.

Posted by Maxine Clarke on June 06, 2008
Categories: Nature Network round-up | Permalink | Comments (0)

The June editorial in Nature Neuroscience (11, 619; 2008) discusses the relationship between web traffic and citations. The journal’s preliminary analysis indicates that the number of downloads a paper receives immediately following its appearance online correlates very well with its citation frequency years after publication. Noah Gray, one of the Nature Neuroscience editors, has written a post at Action Potential, the journal’s blog, to provide more of the details behind the data and analysis, and to initiate discussion. He writes (edited for length):
Everyone has their own pet problem with impact factors, but despite these concerns, these numbers are typically used to rate the importance or prominence of a particular journal, and thus by proxy, the importance of the individual papers published within. This is a seriously flawed use of association, leading scientists to often equate the total number of citations with scientific impact, which can be fraught with problems. Searching for an alternative measure of impact that is perhaps free of the “bias of authority” (citing a paper because it is from a famous lab) or the “lemming bias” (citing a paper just because everyone else seems to do so whenever broaching a particular subject) led us to explore readership….
The “number of downloads” measure potentially provides a piece of an alternative solution for deciphering the impact of an individual paper. In this current scientific climate where tenure and grant funding decisions are influenced by flawed metrics like impact factor, it is important to make good use of all available technology in an attempt to realize a better system of measuring the scientific impact of any particular paper. This analysis is obviously preliminary and flawed in its own ways, but perhaps metrics such as paper downloads can find a place in a compilation of aggregated stats, painting a more accurate and informative picture of manuscript influence.
The Nature Neuroscience editorial.
The Action Potential post and discussion.
Nature Network Citation in science forum discussion.
Nature Network Citation in science group homepage.
Futher reading: Connotea bookmarks "citation"
Further reading: Connotea bookmarks "impact factor" : thanks to Bob O'Hara for this library.

Posted by Maxine Clarke on June 05, 2008
Categories: Citation analysis, Quality measures | Permalink | Comments (0)

Nature Publishing Group presents a Collection on Neurotechniques, which includes original Research, Progress and Review articles as well as Research Highlights from Nature Methods and Nature Reviews Neuroscience. This collection aims to inspire and provoke thought by drawing attention to groundbreaking advances in technology that hold great promise for the pursuit of answers to long-standing questions, such as how brain regions are connected, what contributions single neurons and populations of neurons make to behaviour and cognition, and what role cell dysfunction has in neurological disorders. This collection is freely available until November 2008. It also contains a library of links to articles published by Nature Publishing Group journals on the topic.

Posted by Maxine Clarke on June 04, 2008
Categories: Disciplines, Publications | Permalink | Comments (0)

Biji T. Kurien of the Oklahoma Medical Research Foundation writes (Nature 453; 450; 2008):
The Correspondence 'Give south Indian authors their true names' (Nature 452, 530; 2008) and earlier News Feature 'Identity crisis' (Nature 451, 766–767; 2008) are highly relevant to calculations of PubMed citations and h-index (the number n of a researcher's papers that have received at least n citations).
For example, I used to use the south Indian form of my name: T. Biji Kurien, with Biji being my personal name. I have seven publications cited incorrectly in PubMed as being by 'Kurien, T. B.', 'Bijikurien, T.' or 'Kurien, B.'. Four of these entries were cited often enough to be counted towards my h-index computation. As I had by then changed my name to conform with Western style, these publications unfortunately do not appear in the Web of Science or PubMed under my current name format. Consequently, my h-index ranking has fallen by 25% .
It is of paramount importance to adhere to a consistent name pattern right from the start, in order to maintain a correct list of publications in the public databases as well as the right h-index rankings.

Prabhu B. Patil, of the Centre for Cellular and Molecular Biology, Hyderabad, writes in the same issue of Nature (453, 450; 2008):
The Correspondence 'Give south Indian authors their true names' (Nature 452, 530; 2008), incorrectly states that people from the south do not traditionally have surnames.
I am from southern India and have a proper surname — as do all the families in my region. Besides Patil, surnames such as Naidu, Reddy, Rao and Gouda are common in the different states of southern India. One of the authors of the Correspondence has the surname Kutty.
Surnames have widely fallen into disuse because our fathers and forefathers avoided using them to prevent discrimination on grounds of caste.
It doesn't make sense in this case to use only an author's first name in scientific publications and to devise a special system to accommodate a different naming format. Instead, editors should encourage these authors to revive the use of their surnames.

Comments are welcome here and at Indigenus, the blog of Nature India.

Posted by Maxine Clarke on June 04, 2008
Categories: Authorship, Citation analysis | Permalink | Comments (0)

Jérôme Murienne, Alexander Ziegler & Bernhard Ruthensteiner write in a Correspondence to Nature (453, 450; 2008):
Since the release of Adobe Systems' Portable Document Format (PDF) version 1.6 in 2004, it has become possible to view interactively three-dimensional models that are embedded into PDF files. This attribute will dramatically increase information content as well as data transparency in scientific papers. Additionally, replacing multiple two-dimensional figures of a three-dimensional structure with one integrated interactive three-dimensional model will reduce the need for supplementary material.
The potential of this technological advance for all science is obvious. Because of the foreseeable rise in demand by the scientific community, publishers and scientific institutions need to work hand in hand to support the implementation of this highly desirable technique.

Posted by Maxine Clarke on June 03, 2008
Categories: Publishing, Writing | Permalink | Comments (0)

In many countries funding agencies have set up dedicated funding schemes to help the plight of young principal investigators. But is the playing field level for all qualified scientists? This question is asked in the June Editorial of Nature Cell Biology (10, 629; 2008), and we welcome your views here.

In many countries it is possible to obtain one's first position as principal investigator within five years of a first postdoc, and funding policies that encourage this fast-track route are all the rage. In the UK, for example, the Medical Research Council and the Wellcome Trust offer generous Career Development Awards of up to £1 million — enough to effectively kick-start a successful independent career. However, both specify a narrow time-frame (three to six years' postdoctoral experience), which markedly restricts the number of candidates. This reflects the international funding landscape; for example, in Germany the 'Junior Professor' scheme is also capped at nine years of postgraduate research.
Some of the most promising candidates who follow a less linear career path run the risk of disqualifying themselves from vital funding. An investigator who has gone through multiple postdocs to learn different skills in diverse disciplines may be better equipped for innovative and independent research than fast-track, inexperienced principal investigators. Clearly, it is good to encourage early independence, but not at the expense of researchers who delay the move for the right reasons. Such principal investigators may actually find themselves between a rock and a hard place: they may have been awarded a coveted university position but be unable to apply for start-up funding and have to compete for programme grants with senior researchers who have established groups of a dozen people.

Continue reading "Is there a loophole in start-up funding?" »

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