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Archive by date: September 2008

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Nature Video on the future of physics

Nature Video is proud to present five short films on the future of physics. The films comprise conversations with Nobel prizewinning physicists George Smoot, David Gross, Gerardus 't Hooft, John Hall and William Phillips, and will cover topics including dark matter, dark energy, the Large Hadron Collider, space-time and quantum computing. Recorded at the 2008 Nobel Laureate meeting in Lindau, students willingly don the role of interviewers and make the most of this one off question time.
Two of the five films will be premiered at a special screening in Second Life and you are cordially invited to attend. The screening will take place on 2 October 2008 at 10 a.m. PST, 1 p.m. EST and 6 p.m. GMT. The event is free, but it is necessary to register in advance by email , with the subject line Missions in Space-Time. Instructions are available here on how to create an account in Second Life.
Each of the five films will then be serialized weekly, on iTunes and on nature.com , starting on 3 October 2008.

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The Immunological Genome Project described in Nature Immunology

From an article by Tracy S. P. Heng of Harvard Medical School, in Nature Immunology 9, 1091 - 1094 (2008) :
"The genome-sequencing and variation-mapping projects have established essential genetic 'road maps'. In the same vein, if on a more focused scale, by generating robust expression data and metadata into a centralized and accessible location, the Immunological Genome project should provide an essential 'workbench' for delineating the intricate workings of the immunological genome.
Thanks to the broad and robust approaches allowed by gene-expression microarrays and related techniques, the transcriptome is probably the only '-ome' that can be reliably tackled in its entirety. Generating a complete perspective of gene expression in the immune system offers the potential for deciphering patterns that mirror responses at several levels. At the level of the gene, such data can give insight into how individual genes act along differentiation profiles and cellular responses. It is then possible to define modules or groups of genes whose expression is interdependent and is coordinated by shared regulatory controls. Computational methods for reverse engineering can then be applied to infer a model of the cells' underlying control system. Finally, genome-wide expression data at the highest level of integration provides an objective definition of the relations and distinctions between cells. For example, analyses of relative 'distances' in genomic space have shown that natural killer T cells are actually a subset of conventional CD4+ T cells and not an 'intermediate' between CD4+ T cells and natural killer cells, as is often believed. Thus, insights from genomic profiling may 'fine tune' or revise the classifications and mental representations of immune cells."
The Immgen (Immunologcial Genome Project) website.

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Nature Reviews Genetics supplement on genomic medicine in developing countries

In its October 2008 issue, Nature Reviews Genetics presents a Supplement on Genomic Medicine in Developing Countries. At the point when the theory is about to be translated into practice in genomic medicine, this collection of five Perspective articles describes human genome variation studies taking place in Mexico, India, Thailand, and South Africa. The articles in the Supplement discuss the challenges and opportunities facing these and other countries in the developing world as they begin to harness genomics for the benefit of their populations, and highlights areas in which the international human genomics community needs to take a more forward-thinking approach. The Supplement is free to access online.

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The week on Nature Network: Friday 26 September

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.

Pamela Ronald writes both poetically and informatively about the experience of writing a grant proposal. "I am fascinated with something no one understands and only a few of us would care to. I am consumed with the desire to think through this mystery, to know it. As Thoreau said, “to gnaw at it, bury it, unearth it and gnaw at it still”. It is exhilarating to be drawn into the deep realm of the undiscovered and it is a challenge to harness the wild power of scientific ideas by writing about them. I want to explain our research results clearly to my colleagues, propose a model and ask them “don’t you see it too?” My intellect is engaged and my heart too, because I love this work."

BobOH_citefigure.jpg Bob O'Hara has been doing some calculations to see how citations vary across some journals. Bob describes the figure thus: "The points all lay along roughly the same line. Cell is lower, i.e. there is less variation than we would expect from the other journals: no doubt this is because it covers a smaller area of biology, so the slower-moving areas are excluded, and hence the mean is higher and the variance is lower. PLoS Biology is in the same area as PNAS (not a bad journal to be compared to). Proc. R. Soc. B is at the bottom: no doubt because it tends to publish more in the slower moving areas of biology." For details of how the numbers were derived and the calculations performed, see Bob's Nature Network post.

Marco Boscolo, a science communicator, is collecting educational videos for students who are about 14-18 years old on the topics of cosmology, astronomy, geology, hydrology, oceanography, and all the other Earth sciences. Various resources are provided in the comments to his post at the Visualization and science forum; further suggestions are welcome.

Massimo Pinto reminds readers that 30 September is the deadline for appications for fellowships to ENEA, the Italian Institute for Research in Alternative Energies and the Environment, with many laboratories across the country. And Matt Brown draws attention to an award of up to £2000 to help with public engagement for researchers funded by one of the seven UK Research Councils. The awards are to encourage outreach work during National Science and Engineering Week, from 6 to 15 March 2009.

Previous Nature Network columns.

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Lasker medical research awards 2008

The Lasker Awards recognize major advances in the understanding, diagnosis, prevention and treatment of disease. This year, the Lasker Foundation honours the contributions of Victor Ambros, Gary Ruvkun, David Baulcombe, Akira Endo and Stanley Falkow. Read their freely available commentaries, written in celebration of the award, exclusively in Nature Medicine. Not only is the Lasker Foundation celebrating the contributions of these five scientists, it is also acknowledging the leadership and long-term advocacy of these prizes by Daniel Koshland and Michael DeBakey (both of whom are sadly now deceased), by naming two of the Lasker awards after them. For more information about these new tributes, the Lasker awards in general, and to access all the essays as separate PDFs or as a downloadable supplement, please visit the Nature Medicine website.

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The Source Event is on Friday of this week

A reminder that The Source Event, a free, dedicated science career fair that combines a dynamic exhibition with conference and workshop sessions, is on Friday 26 September. The event will promote Europe as a great place to pursue a career in science, be it in industrial research, research organisations 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 genuine vacancies. Our plenary and workshop sessions will provide a unique opportunity to meet high profile scientists and gain careers information and advice.
Editors from Nature journals and Nature Network will be speaking or on-hand to meet attendees, and there will be information available about Nature Publishing Group's internship scheme and other career opportunities. One presentation will be by Simon Frantz of the Nobel Foundation (previously, Simon was Chief Editor of Nature Reviews Drug Discovery). Simon's presentation is entitled Careers in science writing/editing, and he has been carrying out a 'web 2.0' experiment in advance of the event at Nature Network, encouraging his audience to help shape his talk.
The Source Event is at the Business Design Centre, London.

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Nature podcast US election special

In the third of Nature's election-themed podcasts available online, the journal looks at where US innovation policy might go under a new president. You can listen or read a trascript at the journal's podcast index page. In the latest podcast, Stephen Ezell of the Information Technology and Innovation Foundation says that "substantial amounts of research into basic science must occur before we can ever reach technology and therefore government has a substantial role to play in being a funder of basic and applied research in the United States. When you look at a great number of US companies and industries, specific companies like Google, like (UNCLEAR 14:18), like Oracle, these were all companies that got their initial funding from basic government grants for research in science and technology. Extending and increasing the amount of government funding for research is one of the most important things the next administration can do." The panel goes on to discuss how research could be funded and possible mechanisms for promoting US competitiveness in the global sphere. William Bates of the Council of Competitiveness compares the presidential candidates: "Senator Obama has been very explicit in endorsing doubling of the research budget. Senator McCain speaks about the importance of research, but I think he has been a little more hesitant to embrace a specific doubling goal of the research agencies. They're certainly talking about it and that's a big step in the right direction." Hear or read more via the Nature podcast index.

An archive of the Nature Podcasts, which are all free, can be found here. Each week, Nature authors talk about their newly published papers, on topics ranging from craters formed by asteroid collision, tsunami risk in the Bay of Bengal, the sequence of the grapevine genome, a mouse with obsessive compulsive disorder, a new species of ape, and many more.


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Launch of Protein Structure Initiative-Nature Structural Genomics Knowledgebase

Last week, Matt Day announced Nature Publishing Group (NPG)'s latest website: the Protein Structure Initiative (PSI)-Nature Structural Genomics Knowledgebase. Matt writes that the new addition to NPG's existing collection of gateways and databases is "a collaboration with the Protein Structure Initiative, a large scale NIH-funded consortium to develop and apply high-throughput techniques for protein structure determination. They've been highly successful in generating new technologies that are available for others to use, and they've shown that structure determination work can be scaled up significantly.
Now that the site is launched, we'll be providing monthly editorial updates that put developments in structural work into context for a wide range of biomedical researchers....The website is hosted at Rutgers University by the same team that hosts one of most significant and long-established databases, the Protein Data Bank".
The Structural Genomics Knowledgebase (SGKB) offers researchers and others an easy way of keeping abreast of developments both by the PSI and more generally in the fields of structural genomics and structural biology. It is a regularly updated portal to research data and other resources from the PSI, with NPG providing a monthly update with synopses of important research advances, recent additions to a categorized library of research articles, as well as news and events in structural biology. You can register to receive a monthly email newsletter and subscribe to RSS feeds. NPG resources and publications relevant to the Protein Structure Initiative can be accessed here.

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Citizendium calls for contributions to Biology week

Biology Week, an online "open house" for biologists, biology students and other interested people, begins today (22 September) on Citizendium, a 'next-generation' wiki encyclopedia started by Wikipedia co-founder Larry Sanger. (See this Peer to Peer post for a brief comparison of online encyclopaedias.)
From the Citizendium announcement: "during this week, biologists and anyone interested in the topic are invited to test the Citizendium system. Editors and authors from the project's Biology Workgroup will be on hand to meet and greet new people on the wiki. "I strongly believe that the Citizendium system will be appealing to many scientists and scholars," said Sanger. "Many of them just need to give it a try. Biology Week is an excuse for biologists to try out the system together." Gareth Leng, a professor of Experimental Physiology at the University of Edinburgh, and Citizendium author and editor, described the project: 'Our role will not be to tell readers what opinions they should hold, but to give them the means to decide, rationally, for themselves. The role of experts is critical—not to impose opinions, but to support accuracy in reporting and citing information'. "
The Citizendium, or "citizens' compendium", uses the same software as Wikipedia and is a public-expert hybrid project to produce a general reference resource. The community encourages general public participation, but makes a low-key, guiding role for experts. It also requires real names and asks contributors to sign a "social contract." As a result, the project is said to be vandalism-free and, despite its youth (its public launch was just 18 months ago), has steadily added more than 8,000 articles.
Further information:
Citizendium website and press release about this project.
Biology Week homepage.
Sample article: Life, said to demonstrate the success of the collaborative-editing system.
(Thank you to Shirley Wu for alerting me to this project.)

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The week on Nature Network: Friday 19 September

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.

Heather Etchevers urges stem-cell researchers to rally their labs "to participate in the first-ever ISSCR Educational Video Contest – explain the fundamentals of stem cells by creating an engaging and educational short video suitable for a high school audience. Your lab could win three complimentary Associate Member-level registrations to the ISSCR 7th Annual Meeting, July 8-11, 2009 in Barcelona, Spain, as well as the opportunity to have your original work featured in the Public Education section of the ISSCR Web site."

Ian Brooks initiates a lively discussion about his Correspondence in Nature last week, part of which states: "according to the US National Science Board's Science and Engineering Indicators 2008, fewer than 20% of postdoctoral scientists in the United States find tenure-track faculty positions. This suggests that, at least in the United States, we could already have a glut of trained scientists. Perhaps the solution is not financial at its core at all. A major overhaul of the academic training pathway for life-scientists is long overdue. Issues linked to today's financial and job markets are an indicator that the time is right for a serious self-appraisal on the part of academia. Are we training too many students? And what should we do with all the postdocs?" Jennifer Rohn also scrutinizes the "mythical scientist shortage", stimulating an even longer online discourse.

Stephen Curry muses (with the use of clever illustrative examples) upon works of art that have echoes of his scientific interests: reciprocal space. He would would be glad to hear any reciprocal views of others who have made similar finds.

One of the new features in the recent code release at Nature Network is the ability to embed flash movies in forum and blog posts. Hilary Spencer writes that with the new slide viewer on Nature Precedings, it is now possible to embed presentations posted on Nature Precedings in Nature Network. An example is J-C.: Bradley et al. Open Notebook Science – Falcipain-2 Preliminary Results. Available from Nature Precedings, doi:10.1038/npre.2008.2216.1 (2008).

A discussion among members of the US National Association of Science Writers on the reduction in science coverage in major newspapers is highlighted by Pamela Ronald, who sees this trend as "a call for scientists to get active and start communicating, which of course is one of the reasons we blog." She asks her readers "how can we market science better on the public square? Clearly the public does cares about global warming (if somewhat belatedly), as well as numerous other issues such as feeding the world, finding cures for diseases and enivronmental degradation- all issues intimately associated with scientific research." Michael Nestor addresses a similar theme, asking where is our forum in the mass media to discuss real science in front of millions?

One solution, in part, may involve persuading eminent scientists to start blogging. As reported at the Science Blogging 2008 conference in London on 30 August, not many senior scientists have a blog, despite the usefulness of this communication tool for education and outreach. To help scientific blogging gain momentum, Nature Network is coordinating a challenge to increase the number of senior scientists who write online. Points will be awarded for the seniority and reputation of the blogger, their previous lack of experience with blogging, the quality and quantity of posts, the blog’s relevance to science and its demonstrable positive impact. Nominations can include self-nominations, and must be submitted by 5 January 2009.

Previous Nature Network columns.

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Upcoming scientific events in Second Life

On Monday 22 September, the UK Resource Centre for Women in Science, Engineering and Technology will be running their first consultation session, A Vision for Science and Society, in the virtual world of Second Life, at Second Nature Island. (Time: 1850 – 2000 GMT/1050 – 1200 PDT.) The UK Government has issued a new consultation document entitled A Vision for Science and Society. The resource centre for woman is keen to ensure that issues of gender equality are part of the agenda and are holding a series of focus groups to discuss the topic. Monday’s event will be held entirely in Second Life and all are very welcome to attend. It will be just over an hour long and will involve informal discussion in small groups on some of the issues. You do not have to have read the report, and men and women are equally welcome. The event is free, but you are asked to book in advance to give them an idea of numbers. You can book by email or telephone. See the UK Resources for Women website for further details.

Another event next week is taking place in the real world (first life) and simultaneously in Second Life. Scientific researchers and web2.0: social notworking? at the British Library in London on Wednesday 24 September from 1800 to 2030 GMT, and is organized by Sarah Kemmitt. This free event is the second in the BL’s quarterly café scientifique exploring varied topical issues in science. Timo Hannay, the Publishing Director of nature.com, will introduce the subject followed by a discussion with the audience. This provocative title aims to stimulate discussion on the following questions: is Web 2.0 all about attitudes or technologies?; what can Web 2.0 do for your research?; as a scientist, are there good reasons for getting involved beyond social ‘notworking’?; and web 3.0: another buzzword or a semantic revolution for science on the web? There is a lively discussion group on Nature Network in which aspects of these topics have been debated in the run-up to the evening. This event is free but pre-registration is required. For those interested who cannot attend in person, details of the Second Life parallel alternative are here.

Several further scientific events are scheduled in Second Life in the next few weeks. Some highlights include:
Sunday 10 February: Darwin Day Monkey Parade
Tueesday 11 February: “Nano-science and the Quantum World” talk on Nanotech Island.
Monday 18 February: “Manatee conservation and classification” talk on Second Nature
Thursday 21 February: George Monbiot talk on climate change on Second Nature.
Friday 22 February: talk by Dr David Grinspoon, an astrobiologist from the Denver Museum of Science & Nature.
Further details and links to the calendar of events can be found here.

See the website Second Nature for more information about Nature's island in Second Life, where there is a video introduction and tutorial for first-time users, and much other information about Second Nature and the events there. If you are familiar with Second Life, you can go directly to Second Nature by visiting this link.
There is a Nature Network Second Life group for those interested in using this virtual world for scientific activities.

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Meetings that changed the world

Last Thursday, Nature introduced its latest Essay series with an Editorial (Nature 455, 137-138; 2008):

"Creative ideas are not always solo strokes of genius, argues Ed Catmull, the computer-scientist president of Pixar and Disney Animation Studios, in the current issue of the Harvard Business Review. Frequently, he says, the best ideas emerge when talented people from different disciplines work together.
This week, Nature begins a series of six Essays that illustrate Catmull's case. Each recalls a conference in which a creative outcome emerged from scientists pooling ideas, expertise and time with others — especially policy-makers, non-governmental organizations and the media. Each is written by someone who was there, usually an organizer or the meeting chair. Because the conferences were chosen for their societal consequences, we've called our series 'Meetings that Changed the World'."

The first Essay, on a topical subject in the week in which the Large Hadron Collider began operation, is Paris 1951: The birth of CERN (Nature 455, 174-175; 2008), when François de Rose chaired the meeting that founded Europe's premier facility for experimental nuclear and particle research. Here he relives the five days of drama that changed the world of physics.

The Editorial continues: "When we began to think about commissioning this series, several difficulties arose. First, we were looking for more than the traditional scientific conference, and it was notable how few of the twentieth century's world-changing meetings had involved scientists taking a lead. As a list emerged, we were faced with another problem: time had sadly depleted the pool of writers. This week's author, for example, is among the few surviving members of a group that met 57 years ago.
The six events that made the final cut took place on three continents and span five decades, from 1951 to the dawn of the new millennium. They represent the twentieth century's promise, and two of its greatest threats. And they illustrate a period in history when scientists felt they should raise a collective voice to advance the public good. The six meetings have something else in common. In wanting to change their world, the scientists involved needed and obtained the support of governments and, in some cases, the media."

There are, of course, other candidates for the title of Meetings that Changed the World. And our illustrious attendees' opinions are, of course, personal and often provocative. Readers are invited to have their say, and suggest their own favourite Earth-shaking meeting, at Nature Network. One, or rather two, suggestions have been made by Daniel Greenberger: "a very important conference just after the second world war was the Shelter Island conference on high energy physics, which discussed the newly discovered elementary particles, and such new phenomena as the Lamb shift. This conference determined the direction of high energy physics for a generation. A similar, first-ever, conference that took a field that did not even exist yet to the point where the principals started seriously considering it, and subsequently started a revolution, was the MIT conference on quantum computing, held in 1980."

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Consent for research on biological material

An increasing research trend is to pool collections of biological samples in international scientific studies, thereby amplifying their potential scientific value. The pooling of samples in such 'biobanks' poses several ethical and legal challenges, which various authors have attempted to meet by proposing guidelines for researchers (see G. Helgesson et al. Nature Biotechnol. 25, 973-976; 2007). One suggestion made by these authors is that "when the study is not particularly sensitive, and on the condition that (i) strict coding procedures are maintained, (ii) secrecy laws apply to any handling of sensitive information and (iii) vital research interests are at stake ...that genetic analyses of identifiable samples should be permitted without (new) consent."
Bjørn M Hofmann takes issue with this view in the September issue of Nature Biotechnology (26, 979-980; 2008), arguing that the earlier proposals would be "detrimental to the public's trust". He writes: "If one applies a lax interpretation of "not particularly sensitive" research, any study can be justified as long as it serves research interests. Their lax interpretation of consent to "future cancer research" as being consent to any kind of future research endorses this. For the above reasons, instead of minimizing risk to research participants, the framework they suggest actually enhances the risk by not addressing basic challenges with biobank research."
In the same issue of the journal (Nature Biotechnol. 26, 980-981; 2008), Helgesson replies that there is no risk of direct physical harm to research subjects once biobank samples have been collected, because "a core characteristic of biobank research is that it is the inappropriate distribution of information that has a potential to harm research subjects. This is why we stressed the importance of strict routines for coding, storage and use of biobank samples and related data as the first central feature of our ethical framework for research on previously collected samples."
The core of the debate is the fact that "some people might be included in biobank research who would have said no if they had been informed and asked", writes Helgesson. Although it is important to exclude people who do not wish to participate, excessively cautious informed-consent procedures might cause many more peple to drop out and hence to reduce the quality of the research.
Further information: World Medical Association Helsinki Declaration on ethical principles for medical research involving human subjects.
The Nature journals' policies on these topics are here.

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Regulation of dual-use research

The September Editorial in Nature Medicine (14, 891; 2008) addresses the difficulty of monitoring biosecurity research, in the context of the increase in biosecurity spending in the US to $41 billion per year, almost ten times larger than the amount spent before 9 September 2001. In the wake of the Bruce Ivins affair, the Editorial notes that a consequence of the increased funds available for biodefense is that there are now so many people working in this field (perhaps 14,000 individuals) that monitoring their activities is not adequate. From the Editorial:

Aiming to fill this void, the BWC [biological weapon convention] countries have held annual meetings since 2003 to promote "common understanding and effective action" on a series of biosecurity issues agreed upon in advance. For example, as this issue of Nature Medicine went to press, the 2008 meeting was taking place in Geneva, with a focus on measures to promote biosafety and on oversight, education and development of codes of conduct to prevent misuse of advances in biotechnology. Regrettably, again at the insistence of the US, the participants of these annual meetings do not have decision-making authority, raising serious doubts about their real influence. Deciding on the right level of regulation for dual-use research, both at the national and international levels, is a difficult problem. Scientists should continue to get involved in the decision-making progress to make sure that their point of view is heard until clear guidelines are in place. If the outcome of this domestic discussion is successful, it may provide a blueprint for a global regulatory scheme—a sorely needed opportunity for the US to lead by example.

See also a related News story in the same issue of the journal Nature Medicine 14, 893 (2008).
The Nature journals' policy on biosecurity is here, with links to associated (free to access) Editorials providing context for the policy.

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The week on Nature Network: Friday 12 September

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.

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Register for Nature Chemistry e-alerts

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.

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The zeroth theorem of the history of science

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.

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Better writing and more space needed online

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.

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Paradox of model organisms in biology

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.

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Video journal to be indexed in Medline and PubMed

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).

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Nature's special issue on 'big data'

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.

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The week on Nature Network: Friday 5 September

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.

Steffi Suhr, Editor of the journal Ethics in Science and Environmental Politics , invites scientists and science writers to submit a manuscript for a planned theme section on the ’Ethics of science journalism’ . Further details can be found here: the aim is for the theme section to bring together all viewpoints of those involved in bringing science to the ‘public’ – writers (freelance and staff), editors, publishers, and – not least – scientists themselves.

One of the stimulating views expressed at last week's Science Blogging 2008 conference (a collection of photographs is here) was that scientists do a far better job than science journalists (and other professional communicators) at describing science accurately to a wide audience. Brian Clegg begs to disagree, citing some pertinent counter-examples to those provided at the conference, which were from the area of medical "quackery" . What do you think? Although it is far too sweeping to dismiss as a group either scientists themselves or "science communicators", there is plenty of scope for development of effective communication skills, as well as ensuring accuracy without hype.

Also stimulated by the Science Blogging conference, Martin Fenner summarizes where we are today with science blogging, pointing to several evolving subdisciplines which are being refined in the online discussion to his post:
-conference blogging (also includes event blogging)
-edublogging (education of students or users, careers advice, academic culture)
-metablogging (blogging about blogging, by far the largest discipline)
-research blogging (blogging about scientific experiments)
-investigational blogging (exposing incorrect or misleading science)
- issue (or 'political') blogging (for example evolution, climate change, vaccines)
-news blogging (blogging about science news)
-watercooler (or 'fun') blogging (small pieces of interesting or funny thoughts/pictures)
-summary (or 'meta') blogging (summarizing other blog posts and linking to them)
-diary blogging (blogging as a personal diary of self-expression).

See also David Bradley's post on improving science blogging, which asks for reactions to his idea of a "plug-in" to "monitor your latest blog post, and on the basis of the names and keywords it sees as you type suggest likely literature references. It would be a straightforward matter to display the titles of all relevant papers and as you blog you could add a star to the main paper about which you’re righting and tick any others that might be worth citing in the post."

In a discussion about information and reference management online, Frank Norman writes that Karen Blakeman and Phil Bradley run expert internet courses on search tools and resources. He writes: "Karen comes up with some amazing tips at her talks at IOLIM each December. Try browsing her blog for internet search tips".

The next talk on "Science 2.0: the future of online tools for scientists" will take place this Sunday, 7 September, in the form of a panel and discussion with Timo Hannay, Cameron Neylon, and Michael Nielsen, hosted by Nature Network Toronto. What does the future hold for the way we do science? Are online repositories such as GenBank and the physics preprint ArXiv, or social tools such as Nature Network, about to change science profoundly? To find out, join Nature Network Toronto for an interactive panel discussion over drinks at the pub (see Jen Dodd's Nature Network post for more details of the panellists and the venue).

Previous Nature Network columns.

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Citation patterns in geoscience

Nature Geoscience's September editorial (1, 563; 2008) broaches the subject of impact measures. From the editorial:

The ripples of the revolution in science evaluation have long reached the relatively uncompetitive backwaters of the geosciences. Indeed, Nature Geoscience received questions regarding its likely future impact factor before it was even accepted into Thomson Scientific's Web of Science in April this year. So here are a few thoughts on the topic from us, long before our own impact factor (due in 2010) may skew our perspective. Citation patterns vary hugely between disciplines. The impact factors of Nature and Science have ranged between 26 and 32 in the past few years. But a quick estimate, based on a sample of papers, suggests that geoscience papers in these journals score an impact factor of around 15 when evaluated on their own. This is high considering that the impact factors of journals publishing exclusively geoscience research have not exceeded 5 in the past several years. But far higher citation counts in the biological sciences drive up the statistics of journals that publish across disciplines. The timescales of the publication cycle in a field determine a journal's impact factor. These are defined as all citations in one year to citable content published in the two preceding years, thereby excluding all references more than two years from publication. This can be problematic for the slower-moving sciences. For example, the ten most cited papers in Geology in 2004 were collectively referred to about 1.5 times more often in 2007 than in 2006 — citations that have never entered the index. For geoscientists, taking guidance from impact factors alone would mean favouring interdisciplinary journals (whereas many biologists would, for the same reasons, favour their own disciplines). It would also lead to reading preferentially short-lived, quickly cited papers over those that develop more slowly — not necessarily a good idea. Other more time-consuming ways of assessing quality are therefore needed to supplement the quick and easy number check.
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Method of the Year 2008: cast your vote!

When the Nature Methods editors sat down last year to select a Method of the Year for 2007, it was with the firm intention of initiating a yearly tradition. This year, the editors are are asking for your opinion, so please nominate candidate methods as well as vote and comment on posted suggestions.

From the editorial in the September issue of Nature Methods (5, 749; 2008):
The Method of the Year event is a celebration of methods development and innovation because we think that methods developers should have their share of the limelight. It is also a fun opportunity to assemble Commentaries, technical information and news items about a method we consider particularly important among the developments that we, as editors, continuously observe across a broad range of disciplines. But we also wanted to take the pulse at the bench and see what you, with firsthand experience, think of recent methods developments. This online one-click voting and nomination process is your opportunity to speak up.
We are interested in methods that have come into their own in 2008 and have had a proven impact, but also in your views on burgeoning methods which, while they are not quite ready for prime time, are worth watching.

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Connecting the cultures of science and society

In an article in the September issue of EMBO Reports (9, 709-713; 2008), Bart Penders, Klasien Horstman and Rein Vos of Maastricht University propose "crafting a new profession at the intersection of science and society". They write that "the new field of research into the ethical, legal and social aspects of scientific and technological developments (ELSA) is rapidly becoming a professional field with grants, research programmes and university departments devoted to it." Can ELSA succeed in reacquainting science with society, and the natural sciences with the humanities and the social sciences when, according to these authors, previous attempts have failed? The authors argue that both natural scientists and social scientists are keen to bridge the gap that exists between their respective approaches, but conclude that "only time will tell" if these new attempts will be successful.

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Cultural media at Nature Reviews Microbiology

Chris Condayan, manager of the Public Education Outreach Initiative at the American Society for Microbiology, writes an Editoral in the September issue of Nature Reviews Microbiology (6, 646; 2008) about how self-created audio and video content enable more microbiologists to share knowledge and news online. From his article:

As the science audiences for newspapers, radio and television decline, the future for audio and video podcasts, blogs and social networking looks bright. On the horizon we are starting to see the emergence of science-related social networks and a movement towards 'open science' that allows scientists and researchers to collaborate on projects, communicate results, share data and publish papers with the same recognition that is afforded to colleagues who publish in print journals. Specific details of how open science will work are still murky, and concerns over citation, peer review, accuracy, scooping and accountability resound even among its strongest supporters. But this has not stopped microbiologists from engaging with one another on wikis, such as EcoliWiki, TOPSAN or Proteopedia, or prevented thousands of scientists from sharing their poster presentations, lectures or laboratory methods through iTunes or video destination sites, such as YouTube, SciVee and JoVE. Podcasting for audio or video is generally defined as episodic content that listeners or viewers can subscribe to for free and which they can consume at any time and on any device, whether it be a computer, iPod, mobile telephone or television set. Audio podcasts are easy and affordable to create, and can be used to make a radio-style show or to make lectures available to a wider audience. Uploading and sharing videos on websites such as YouTube, or creating a video podcast show, is more time consuming and requires more equipment and a video-editing software program.

Chris Condayan goes on to provide some examples of microbiologists who produce online resources to educate and promote microbiological research, and the MicrobeWorld sevice of the American Society for Microbiology, which includes the popular resources MicrobeWorld Radio and MicrobeWorld Video.