Nautilus

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 senior scientist who already has a blog, Brian Derby, provides a vignette concerning publishing a paper. "Of the three referees, one is aginst us and does not believe that our mechanism can operate in both cases. Unfortunately he/she is a big shot with opinions that cannot be ignored (or so I was told by the editor). Because of this I spent all yesterday altering the paper so that we can publish our methodology in the appropriate journal. This is irritating because we will end up presenting the same stuff but have to finish it with the statement that goes something like – Although the accepted view is this, our evidence means that we might have to possibly consider the following, even though some people (i.e. the referee) might have thought otherwise. This is all very tedious but it is part of the publishing process." I hope he finds his USB drive soon.

Martin Fenner interviews Victor Henning of Mendeley research networks: "if you install Mendeley Desktop on your computer, you can manage and share research papers on your machine, but you can also upload your papers to your private account on Mendeley Web to access them online. Mendeley Web anonymously aggregates the metadata of these papers to generate statistics about the most popular authors and papers in your research discipline, and – in the future – generates recommendations for papers which you might like."

The relatively informal medium of blogging is well-suited to meeting reports (presenters and organizers permitting). For the reader, such meeting reports have an immediacy that is lacking in the more formal, published conference volumes; and for the scientist, meeting reports are a great way to hone authorship skills and reach new audiences. I was particularly struck by two examples from Nature Network this week from either end of the disciplinary spectrum, which show how a very wide ranging, or highly specialist, meeting can make an accessible, amusing and educational read. The first example is Sara Fletcher's fascinating report: "When I joined Diamond Light Source three years ago as a technical writer, I was really excited about having access to such a major physics toy, having spent seven years as a research scientist and then writer for the National Physical Laboratory. It’s been quite a surprise to find myself a whole host of other disciplines, from structural biology, geochemistry, environmental science, and the burgeoning area of cultural heritage. So today sees my first live-blogging attempt, coming to you from the UK Synchrotron Users meeting. I’m currently listening to a seminar on Gothic Alterpieces, part of a Cultural Heritage session. The subheading for this session is “How Time Also Paints”, and looks at how certain paints and pigments can change with time, on both macro- and microscopic layers. This has been studied by using infrared spectroscopy to look at lead carboxylates, present in the egg tempera based paints commonly used on Gothic alterpieces." Read on! Second, during the past week Bob O'Hara has been providing a daily series of posts reporting a workshop for ecologists on the distributions of butterflies in Europe, and how they will change in response to climate variations. The information "can be used for conservation planning: for endangered species: dynamic planning can even be tried, where habitat is created at times when it is needed by a species to survive, and not before when it would not be able to live on the site anyway, e.g. because it is too cold." See here for Bob's five (at time of writing this post) excellent reports of this focused workshop.

The Good Paper Journal Club discusses Liz Wager's linguistic perspective on the week's most (?) important science event, the switching on of the Large Hadron Collider: the use of qualifying adjectives in scientific papers, specifically about the subtle differences between big and large. The Journal Club is also discussing Linda Cooper's article on the quality of scientific writing. Linda writes in the discussion: "I really do believe that it’s possible to write for specialist and non-specialist audiences. It’s much more difficult to do this of course, and most researchers aren’t sure how to even try. A good place to start is with close and careful revising which certainly helps to eliminate useless words and phrases. When writers get rid of the clutter, they have more space to explain complex concepts. As well, over and over again in my classes I find that graduate students need help identifying the real focus of their papers. Once they can do that, they also figure how to tell a logical story about their important findings. And more importantly, readers – both those familiar with the field and those outside it – can more easily understand what the author is trying to communicate."

Previous Nature Network columns.

Posted by Maxine Clarke on September 12, 2008
Categories: Nature Network round-up | Permalink | Comments (0)

Stay informed about plans for Nature Chemistry, the newest journal from Nature Publishing Group, whcih will be launched in early 2009, by signing up to the journal's email alert. Register to receive both the chemistry@nature e-alert, and when the journal is published, the monthly Nature Chemistry table of contents e-alert.
Nature Chemistry is now accepting submissions through the journal's online submission and tracking system. The first print issue will be published in mid-March 2009, though some papers will probably be published online in advance of print early in 2009.
Nature Chemistry is dedicated to publishing high-quality papers that describe the most significant and cutting-edge research in all areas of chemistry, as well as covering the impact of chemistry beyond the laboratory. See here for more details of the aims and scope of the journal.
See here for the Nature Chemistry guide to authors.
Content types.
How to submit.
The editorial process.
About the editors.

Posted by Maxine Clarke on September 11, 2008
Categories: Disciplines, Publications | Permalink | Comments (0)

Andreas Trabesinger, a senior editor at Nature Physics, writes in News and Views this month (Nature Physics 4, 677; 2008):

"The past is by no means definite. It is rather open", wrote the German historian of science Ernst Peter Fischer in Die Welt on 24 July 2006. In his column, Fischer introduced the "zeroth theorem of the history of science"; a discovery named after a person, the theorem says, did not originate from that person.
Take, for example, Avogadro's number, named after Amedeo Avogadro, who asserted that there is the same number of molecules contained in a given volume of any gas at the same temperature and pressure. However, it was not the Italian savant who first estimated that number, but the Austrian scientist Johann Josef Loschmidt. Indeed, German-language texts sometimes refer to the number 6.022 1023 as 'Loschmidt's number'. Much depends on who tells a story, and where and when. Fischer sees his zeroth theorem as an invitation to look with fresh eyes at the history of science, and in particular at how discoveries got their names.
That thought has now been picked up by J. David Jackson (Am. J. Phys. 76, 704–719; 2008). He has explored five examples from physics that illustrate Fischer's zeroth theorem, and discusses the broader issue of credit-giving, and where it gives rise to inappropriate attributions. Jackson's five examples take in various areas of physics, from the Dirac delta function to the Weizsäcker–Williams method of virtual quanta, to the Bargmann–Michel–Telegdi equation of spin dynamics. The journey includes encounters with big names such as Enrico Fermi or Nikola Tesla, but also with physicists whose biographies are far less commonly known, such as Oliver Heaviside, Llewellyn Thomas or Emil Wiechert. Their names are famous in some specific contexts, but little is known about their complete works.
Read more of the article at this link.

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

Linda Cooper of McGill University, Montreal, writes in Correspondence (Nature 455, 26; 2008):

The World-Wide Web is remarkable as a vehicle for communicating scientific discoveries. Online journals unite distant researchers and inspire worldwide collaborations. However, despite these advantages, there is a growing risk that papers published today are less successful in meeting their objectives than in the past.
To ensure clear communication, most journals encourage authors to write for a broad audience. But most published papers still compress too much information into uncomfortably short articles, leading to convoluted sentences, specialized terminology and a proliferation of abbreviations. Errors in grammatical style result in impenetrable and ambiguous texts that seriously undermine the scientific literature. This need not be the case.
Electronic publishing could offer authors limitless space to explain their ideas and discuss their new findings. Surprisingly, though, online manuscripts are often bound by the same space constraints as print manuscripts.
Authors are instructed to conform to print-journal guidelines, leading many to redirect essential material to online Supplementary Information. The recent explosion in Supplementary Information is problematic: it seems to have no standard format among different journals, and there is a common misperception that data in Supplementary Information have escaped peer review. It can be a nuisance for readers too. For example, if they want to peruse articles away from their computers and haven't downloaded the related Supplementary Information, it may be impossible for them to understand or fully evaluate the papers' merits.
The scientific article in 2008 is on the cusp of change, with one foot in the past and one in the future. Science journals should shed the constraints of the old media and exploit the advantages of the new, to offer readers easy and enjoyable access to the scientific literature.
Even if journals are successful at reinventing themselves, it won't be adequate unless the quality of writing in scientific manuscripts improves. Paradoxically, the deterioration in science writing seems to coincide with the swell in e-publications — at a time when the need to communicate advances in science is more urgent than ever. The quality of writing needs to match the power of today's e-publishing technology.

Posted by Maxine Clarke on September 10, 2008
Categories: Writing | Permalink | Comments (1)

The use of model organisms in research will continue despite their shortcomings, writes Philip Hunter in the September issue of EMBO Reports (9, 717-720; 2008). From his article:

During the 1940s and 1950s, in the early days of molecular biology, biologists tackled the enormous problem of explaining how cells work at the molecular level by applying the tried and tested tools of reductionism. They reduced the complexity of the task in two ways: they focused on a few central molecular mechanisms—replication, transcription, protein synthesis and the control of gene activity—and they chose to use the simplest organisms—bacteria and bacteriophages—in which to study these phenomena. Over time and with more knowledge to hand, biological research expanded to the study of more complex systems, which required the increasing use of higher organisms, including Caenorhabditis elegans, Drosophila, Arabidopsis, zebrafish and rodents.
These model organisms became the irreplaceable tools of fundamental biological and clinical research, and helped scientists to amass an enormous amount of knowledge. However, several high-profile clinical trials in which the use of model organisms failed to predict the serious side effects of some drugs, coupled with the prospect of using human stem-cell lines in trials and the growing sophistication of in silico methods, have all cast doubt on the future use of model organisms. This is the case at least for research into human diseases, which, after all, drives much of the research in molecular biology.
Animal rights activists have seized on this argument, but show little interest in appreciating the huge contribution that model organisms have made to molecular biology. Indeed, it is not an exaggeration to say that research on animals has taught us nearly all we know about cell biology—be it transcriptional control, RNA quality control or the structure of chromatin.

See also the News Feature in Nature 454, 682-685 (2008), which reports on questions raised about the appropriateness of mouse and other animal models in some neurodegenerative diseases.

Posted by Maxine Clarke on September 09, 2008
Categories: Animal experiments, Ethics | Permalink | Comments (0)

The Journal of Visualized Experiments (JoVE) has announced that its online video protocols will be indexed in the popular US National Library of Medicine repositories MEDLINE and PubMed.
Founder and chief executive Moshe Pritsker views the MEDLINE–PubMed listing as a sign that the scientific community has accepted video-based publications. "It was a very important decision for us, and for scientific publishing," he says.
Since JoVE was founded in 2006 with support from an angel investor, the journal has published more than 200 videos, most produced by professional videographers. It aims to improve the reproducibility of scientific results by using videos to clarify subtle experimental details. The journal was itself an experiment in video publishing and remains the only video-based scientific journal.
From Nature 455, 13 (2008).

Posted by Maxine Clarke on September 08, 2008
Categories: Data availability, Format, Publications, Quality measures | Permalink | Comments (0)

The Big Data special package of articles in this week’s issue of Nature (4 September 2008) looks at how massive influxes of data are changing the way science is done in many fields, and includes a feature story on ‘Wikiomics’ that might be of particular interest to the scientists who work with "web 2.0" tools. Coping with floods of data is now one of science's biggest challenges, so the Nature special issue assess the need to complement smart science with smart searching; looks at what the next Google will be; interviews the pioneering biologists who are trying to use wiki-type web pages to manage and interpret data; and recalls that the first mass data crunchers were not computers, but the remarkable women of Harvard's Observatory. All the articles, as well as downloadable PDFs of the print versions, are free online for two weeks from the publication date. We encourage you to download everything you are interested in—and then to spread the word to friends and colleagues about what you like (and don’t like!) via email, blog, by commenting online at the Nature website, or other means. And of course, Nature always welcomes Correspondence submissions.
The contents of the Big Data 'special' in full:
Editorial: Community cleverness required
Researchers need to adapt their institutions and practices in response to torrents of new data — and need to complement smart science with smart searching.
Special Report: The next Google
Ten years ago this month, Google's first employee turned up at the garage where the search engine was originally housed. What technology at a similar early stage today will have changed our world as much by 2018? Nature asked some researchers and business people to speculate — or lay out their wares. Their responses are wide ranging, but one common theme emerges: the integration of the worlds of matter and information, whether it be by the blurring of boundaries between online and real environments, touchy-feely feedback from a phone or chromosomes tucked away on databases.
Party of One column: Data wrangling
Collecting and releasing environmental data have stirred up controversy in Washington, says David Goldston, and will continue to do so.
Features: Welcome to the petacentre
What does it take to store bytes by the tens of thousands of trillions? Cory Doctorow meets the people and machines for which it's all in a day's work.
Features: Wikiomics
Pioneering biologists are trying to use wiki-type web pages to manage and interpret data, reports Mitch Waldrop. But will the wider research community go along with the experiment?
Commentary: How do your data grow?
Scientists need to ensure that their results will be managed for the long haul. Maintaining data takes big organization, says Clifford Lynch.
Books & Arts: Distilling meaning from data
Buried in vast streams of data are clues to new science. But we may need to craft new lenses to see them, explain Felice Frankel and Rosalind Reid.
Essay: The Harvard computers
The first mass data crunchers were people, not machines. Sue Nelson looks at the discoveries and legacy of the remarkable women of Harvard's Observatory.
Review: The future of biocuration
To thrive, the field that links biologists and their data urgently needs structure, recognition and support. Doug Howe, Maria Costanzo, Petra Fey, Takashi Gojobori, Linda Hannick, Winston Hide, David P. Hill, Renate Kania, Mary Schaeffer, Susan St Pierre, Simon Twigger, Owen White & Seung Yon Rhee
Podcast Extra: Big Data
As Google celebrates its 10th anniversary, we find out how science is coping with massive datasets generated by unprecedented computing power. BoingBoing blogger Cory Doctorow tells us about his visits to the LHC data storage facility and the genome sequencing Sanger Centre.

Posted by Maxine Clarke on September 08, 2008
Categories: Access, Author services, Data availability | Permalink | Comments (0)