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The week on Nature Network: Friday 28 November

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.

Eva Amsen calls for science fiction authors and science bloggers to opine online on the use of science fiction to communicate science. The organizers of a session at next year's ScienceOnline conference are seeking views to help in the preparation of their presentation. For more information, and for Eva's answers, see her Expression Patterns blog post.

Coming down to Earth, Paul Smaglik's latest column in the science careers advice forum is the 'new president' edition. What might be the effects of the new US administration for science careers and prospects - and indeed, are university, never mind national, presidents overpaid?

What are the right numbers for JUPITER?, asks Martin Fenner. He analyses the reporting of a clinical trial at the recent American Heart Association conference, and how the results were presented at the meeting itself, in a press release, in journal articles and on blogs. (There is a related but independent Nature From the Blogosphere column about coordination of presentation at conferences with journal publication of results.)

"What’s the most inspirational short scientific video you’ve ever seen, which everybody should watch?", asks Matt Brown. "Videos have a unique power to put across an important message in a memorable way, in a short timeframe. Are we using such videos to their full inspirational potential in classrooms and ‘public engagement’ events? I suspect not." If you've seen any suitable candidates, please post a link at Matt's Nature Network London blog.

"Science, if properly approached, is a business of setting very well-defined tests on tiny rockpools on the edge of that ocean of ignorance, whose answers can never be anything more than provisional and subject to revision. Science therefore demands a certain humility before the evidence", writes Henry Gee on 'the unknown' of science in response to Richard Grant on 'the beauty' of science: what it's all about for you.

Previous Nature Network columns.

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Call for scientists to support human-rights initiatives

This is the text of a recent Editorial in Nature (456, 2; 2008):
Six foreign medics escaped the Libyan death penalty last year thanks to intense diplomacy, supported by the advocacy and decisive expertise of scientists. But the researchers' involvement was largely a matter of luck and serendipity. Science and scientists have much untapped potential to contribute to human-rights issues, but until now there have been limited efforts to systematically consolidate the interactions between science and human-rights groups. Two new initiatives of the Science and Human Rights Program of the American Association for the Advancement of Science are intended to help fill that gap.
Its On-call Scientists program launched last month aims to create a database of scientists who will volunteer time — be it a few days or a few months — and expertise, and human-rights organizations — including non-governmental organizations and international agencies such as the United Nations — seeking practical help or advice.
'Human rights' covers a gamut of issues, from exposing abuses to disaster relief. The range of scientific advice sought is correspondingly broad — statistical or methodological help to get a more accurate picture of conflict or ethnic cleansing, advice on water issues from hydrologists, or forensic help to document mass executions or overturn false convictions.
The service faces a steep learning curve in deciphering the diverse needs of human-rights groups, and how scientists might be able to help in ways perhaps not yet imagined. But better communication between scientists and the alphabet soup of human-rights groups — and between those groups themselves on technical issues — is long overdue.
Another welcome initiative is due in January 2009. Many learned societies, as well as academic groups such as Scholars at Risk, have a long history in upholding human rights and academic freedom — for example, defending scientists under threat from oppressive governments, using satellite imagery to expose human-rights abuses and speaking out on abuse wherever it occurs. To put such efforts on a firmer footing, American organizations are to launch the US Science and Human Rights Coalition, a forum in which scientific bodies and human-rights groups can share experiences and best practice. Given the US presidential election, the timing could not be better. For the past eight years, American human-rights groups have seen their international influence undermined by the US administration's diminishing moral authority and standing in the world. Scientists can, and should, help reinstate the fundamental principles enshrined in the Universal Declaration of Human Rights in 1948.

Sign up, learn more and become a volunteer for On-call scientists here.

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Time to act on vaccination

Vaccination is one of the greatest achievments of modern science. Yet despite accumulating evidence that vaccines are safe, uptake is falling. This month's (December) superb Editorial in Nature Immunology (9, 1317; 2008) asks why more outbreaks of mumps and measles have occurred this year (2008) in the United States, Canada, the United Kingdom and other Western countries, when both diseases had been almost completely eradicated in the Western hemisphere before the 1990s because of the introduction of the measles mumps and rubella (MMR) vaccine in 1979.
From the Editorial: "A decrease in 'uptake' of the MMR vaccine fuelled by vaccine skeptics is the main cause behind the resurgence of these diseases in recent years. In 1998, Andrew Wakefield and colleagues published a paper in The Lancet linking the MMR vaccine to autism. This coincided with a growing belief that environmental cues were causing the increase in autism. The anti-vaccine movement jumped on this, and the ensuing media frenzy continues to this day.
Many studies have refuted Wakefield's claims. Furthermore, Wakefield had a serious conflict of interest, as his research was secretly funded by personal-injury lawyers whose clients were suing MMR vaccine makers. The paper was retracted and Wakefield is being tried for professional misconduct. Despite this, the rumors that the MMR vaccine causes autism persists."
The Editorial goes on to outline other vaccine scares dating back to the early nineteenth century, showing that arguments used by vaccine skeptics both past and present have changed relatively little. "They often suggest that vaccination is motivated by profit and is an infringement of personal liberty and choice; vaccines violate the laws of nature and are temporary or ineffective; and good hygiene is sufficient to protect against disease. Governmental conspiracy theories also abound."
The facts are that to achieve herd immunity and avoid disease outbreaks on a mass scale, mandatory vaccination is needed. "Huge numbers of scientific papers support the safety and efficacy of vaccination. If governments were determined to 'cover up' side effects, then why was the rhesus monkey–derived rotavirus vaccine immediately withdrawn once a side effect was noted?"
From the Editorial: "The internet is increasingly used as a source of health information. Unfortunately, vaccine skeptics have recognized this, and anti-vaccine websites have proliferated. Some are filled with anti-vaccine quotes from physicians linked financially to autism research. They use scare-mongering tactics with pictures of children allegedly injured by vaccines to feed on parents' concerns. Alongside such pictures, stories written by other parents who feel their child's disability was caused by vaccination, on the basis of temporal rather than causal evidence, abound. Risks associated with vaccination are exaggerated and the scientific literature is 'cherry picked' to deceptively support their bogus views.
In the West, where vaccine scares are more common, parents with unvaccinated children tend to be well educated with ready access to information sources. Fed misinformation by vaccine skeptics, such parents prefer not to immunize their children because they percieve the risk of vaccination to be greater than that of a disease they have never encountered. What vaccine skeptics fail to mention is that diseases such as measles can be lethal or can cause life-long disabilities. Another pro-vaccine argument often ignored is that healthy children perform better at schools, and healthy adults are more productive at work."
Irresponsible and ill-informed media coverage is partly responsible for this state of affairs, but according to the Editorial, governments are not blameless. The Editorial recommends that they should "be more proactive, funding mass-education campaigns to relay the facts simply and emphasize the many advantages of vaccination. Immunologists themselves should stand up and publicly promote the history, successes, safety and efficacy of the world's vaccination program."
Read the full Editorial here.

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Conference on the processes of aging

The Salk Institute, Nature, Nature Reviews Molecular Cell Biology and the Fondation IPSEN are holding Processes of Aging, the third annual Symposium on Biological Complexity, from 8 to 10 January 2009, at the Salk Institute for Biological Studies, La Jolla, California. The organizers are: Yves Christen (Fondation IPSEN); Sue Deeley (Nature Publishing Group); Andrew Dillin (Salk Institute); Ron Evans (Salk Institute) Marie-Therese Heemels (Nature); Arianne Heinrichs (Nature Reviews Molecular Cell Biology); Fred Gage (Salk Institute); and Inder Verma (Salk Institute) - Chair.
The aging process is a multi-faceted process, where cellular aging, metabolism, the DNA damage machinery and stem cell dynamics interact to influence aging of an entire organism. Single genes can greatly alter the aging process in organisms as diverse as yeast and mice. Furthermore, it has become increasingly clear that distinct activities — which act on dividing and nondividing cells alike — protect organisms from age-related deterioration and decline. The focus of this meeting will be to decipher the mechanistic details that surround age onset, disease onset and perturbation within the aging population.
For more information and to register, please see the conference website.

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Signaling Gateway publishes 500th molecule page

The UCSD-Nature Signaling Gateway has recently published HB-EGF, its 500th Molecule Page. Each week, the gateway publishes several of these concise, free review articles on a diverse range of signalling molecules, from transcription factors to membrane receptors. In addition to these published pages, the Molecule Pages database also includes key information about the biological, biochemical and functional activities of thousands of signalling molecules. There is now a new 'getting started guide' for a quick overview of the anatomy of a Molecule Page.

Sign up for the Signaling Update e-alert, a one-stop overview of current cell signalling research for specialists and interested non-specialists.
All published Molecule Pages.
Archive by date of Signaling Updates.
Signaling Gateway research library (organized by subject).

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The week on Nature Network: Friday 21 November

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.

In the light of a recent announcement that Conservative MPs in the UK are to "increase their science awareness", Brian Derby asks some pertinent questions, including why there are so few scientists in politics. "Are scientists uninterested in politics (outside the need to lobby for greater research funding of course) or are the skills required for both occupations so different that crossover never occurs?" He also asks whether scientists are so bad at communicating that politicians ignore what they say; and whether people wishing to go into politics for a career do not think science is an important topic for study.

Simon Buckingham Shum draws attention to ESSENCE: E-Science/Sensemaking/Climate Change, the world’s first global climate collective intelligence event — designed to bring together scientists, industrialists, campaigners and policy makers, and the emerging set of web-based sensemaking tools, to pool and deepen our understanding of the issues and options facing the UN Climate Change Conference in Copenhagen in December 2009. The event starts online in January 2009 and culminates in a conference at the National e-Science Institute in Edinburgh, in April 2009. See here for further details.

While on the topic of events, on 2 December there is a free workshop to provide information on the Wellcome Trust's Engaging Science grant schemes, including an overview of the grants programme, the aims and objectives of the awards, and details of the application and review process. As well as finding out how to produce an appropriate grant application, there will be opportunities to exchange ideas and develop partnerships and collaborations. More details at Nature Network events.

One grant catetory is for the arts, which came to mind when viewing Christie Wilcox's favourites from the entries to the 2008 Olympus Bioscapes photo contest, an international competition that honours "the world’s most extraordinary microscope images of life science subjects".

A different kind of visualization is reported by Hilary Spencer, who posts Pawel Szczesny's c.v., shown as a scatter plot in which the y-axis represents time and the x-axis is roughly 'skillset' (ranging from artistic endeavours to scientific ones). A neat way to see at a glance what a job candidate has to offer.

Last week's roundup reported on the interpid task of Matt Brown, to find the most popular science cliche (if that isn't an oxymoron). This week, Matt provides the reckoning - here according to Google, and here, Google Scholar. Check out the lists for your favourites - and for hints about what to eliminate from your own prose.

Previous Nature Network columns.

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Nature celebrates Darwin and his work

Next year will be the 200th anniversary of the birth of Charles Robert Darwin, perhaps the most influential scientist of modern times. In this week's issue (20 November), Nature presents a special collection of news, features, research and analysis of Darwin, his life, his science and his legacy. This special will be updated throughout 2009 with essays, podcasts and free educational resources, as well as news from the Darwin200 consortium of organizations celebrating this landmark event. The first installment is here. From the current issue (20 November 2008), all of which can be accessed from Nature's Darwin main page:
Editorial: Beyond the origin (free to access online). As Nature anticipates next year's bicentenary of Darwin's birth and the 150th anniversary of On the Origin of Species, we begin our coverage with a look 50 years into the future.
News features:
The needs of the many (free to access online this week). The idea that natural selection acts on groups, as well as individuals, is a source of unending debate. Marek Kohn reports on what the two sides disagree about — and why it matters to them.
Systems biology: Beneath the surface Biologists see living systems like mechanical clocks: optimally tuned and prone to failure if one component goes wrong. But, as Tanguy Chouard reveals, this is not what happens in the real world.
Let's make a mammoth (free to access online for one month from pubication date). Evolution assumes that extinction is forever. Maybe not. Henry Nicholls asks what it would take to bring the woolly mammoth back from the dead.
Online slideshow: An eye for the eye. Darwin knew that the eye — so brilliantly 'designed' — might represent an obstacle to the acceptance of natural selection. We now know that the eye is one of evolution's crowning glories.
Commentary: Great expectations. A new path for evolution? A truce in the culture wars? Here's what a selection of readers told Nature they expect from Darwin 200. Add your own suggestions at Nature Network's online discussion forum.
Events: Darwin: Heading to a town near you (free to access online for one month). The theory of evolution challenges artists and philosophers as much as scientists. Joanne Baker rounds up the many forthcoming events worldwide that examine Darwin's life, his work and reactions to it.
Books in brief: A Down House bookshelf. An archipelago of books to celebrate Darwin's anniversaries is about to hit the shelves. On the Origin of Species will be reissued, and new biographies and analyses will examine the man behind the ideas. Joanne Baker reports.
Essay: Birthdays to remember. Anniversaries of Charles Darwin's life and work have been used to rewrite and re-energize his theory of natural selection. Janet Browne tracks a century of Darwinian celebrations.
Podcast: The next 50 years (free). Simon Ings and Gáspár Jékely on the evolving eye, and Marek Kohn on group selection. Henry Nicholls and Stephan Schuster discuss making mammoths — and the online trade in mammoth hair. Presenters: Adam Rutherford and Charlotte Stoddart.
Among the other articles and research in the Darwin special is the Letter Sequencing the nuclear genome of the extinct woolly mammoth by Webb Miller et al.. This Letter is free to access online.
See here for the full list of articles and features in the Darwin special collection, and find direct online links to all material.

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Nature China: nanotechnology and beyond

Every week, the Editors of Nature China survey the scientific literature to identify the best recently published papers from mainland China and Hong Kong and provide a summary of the results. If you are interested in, say, nanotechnology, here are some recent highlights posted on Nature China:
Carbon nanotubes: Domino drive
The potential energy stored in a carbon nanotube can be harnessed to power tiny devices.
Nanofibres: Bright belts
Rare-earth-based nanofibres and microbelts can produce an entire rainbow of colours for electronic displays.
Fullerenes: Symmetry breakers
Researchers in Xiamen are close to making symmetry-breaking buckminsterfullerenes.
Carbon nanotubes: From stress to strength
Prestressed multiwalled carbon nanotubes have enhanced mechanical properties that are ideal for building space elevators.

Register for Nature China e-alerts, and stay abreast of the latest research in your field from mainland China and Hong Kong.
Nature China main index page.
Nature China subject archive.
About Nature China.

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Research rewards are worth the effort

Tracey L. Rogers of the University of New South Wales, Sydney 2052, Australia writes in Correspondence (Nature 456, 29; 2008):
The reasons women drop out of science are complex, and Timothy Roper and Larissa Conradt have hit on an important factor in their Correspondence 'Childcare not enough to make a science career family-friendly' (Nature 455, 1029; 2008). However, I don't see encouraging more women into science as either pointless or unethical.
Careers in science can offer enormous rewards to women. Moving into an academic environment has provided great opportunities for me as a mother, owing to its flexibility. I am now measured largely on my productivity, and my ability to multitask — honed by motherhood — is an asset as I juggle research, administrative duties and teaching.
I have worked in the male-dominated field of Antarctic research for the past 15 years, and I run a research programme looking at climatic warming impacts on the top predators, leopard seals. This work has been successful, thanks to my scientific team — which, incidentally, is mainly composed of women. As the mother of two children under the age of six, I suspect that a large part of my success has been due to the enduring support of my partner. I'm not going to pretend that it has been plain sailing, but I wouldn't have done it any differently.
Let's stop asking why there are so few women in science. Instead, let's turn the question round to ask how those who made it actually got there.
As scientists, we are skilled strategists, overseeing the conception of a new research initiative, then the project's gestation and its birth as a peer-reviewed article. These planning skills also sustain our lives outside the lab.
To those women embarking on the journey, I would say that it is not a road for everyone — but if, like me, you have a burning passion for your research, I would encourage you whole-heartedly to pursue it. It's a long journey, so pace yourself and plan — including your home life and time with your family in your plan. Sometimes you need to step back a little in order to move forwards.

Readers are invited to discuss these issues at Nature Network.

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Authors on authorship, collaboration and output measures

Publishing a paper in a journal has traditionally marked the end of a research project, but increasing numbers of academics are becoming interested in the publication process itself, according to the Editorial in the November issue of Nature Nanotechnology (3, 633; 2008). Many of these 'papers about papers' are concerned with citations and impact factors — researchers looking to get more citations for their papers are advised to write longer papers, work in teams or write the first paper on a topic (references in the Editorial). However, other authors have started to look behind the scenes at issues such as the changing nature of collaboration. The Editorial goes on to discuss some of these issues, including the h-index, a relatively recent yet controversial method of assessing a scientist's output.
Previous Nautilus posts about the h-index.
Previous Nautilus posts about authorship.
Previous Nautilus posts about citation analysis.

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Is your meeting really necessary?

This is the text of a Correspondence from Nature (455; 1175; 2008) by David Grémillet of the Centre d'Ecologie Fonctionnelle et Evolutive, Montpellier, and the University of Cape Town:
"Scientists are becoming increasingly concerned about the environmental impact of their work. For example, in the latest of many recent reflections on the subject, bioinformatician Hervé Philippe urges us to uncouple scientific progress from economic growth (Trends Genet. 24, 265–267; 2008). He adds his voice to those advising us to reduce our carbon footprint by attending fewer scientific conferences (see also the free-access Editorial 'Meeting expectations', Nature 455, 836; 2008).
Regular long-distance flying can easily triple an academic's carbon footprint. During the past year, I have 'spent' about nine tonnes of carbon, two-thirds of this on plane trips. Yet I am a good consumer otherwise, and I don't even own a car. Such figures are particularly hard for field ecologists to stomach, as we hope our long-term work will highlight the environmental consequences of climate change and may ultimately influence the public and policy-makers.
Take, for instance, the dynamic field of conservation biology. Most of its best researchers are based at universities in the Northern Hemisphere, but most of their field sites are located in developing countries in the south. These hotshots and their students use up tonnes of fuel each year in commuting trips. In fact, those who are particularly renowned and most involved in environmental politics become 'constant fliers' who are always jetting off to field sites and meetings.
I estimate that such behaviour can potentially increase an individual's carbon footprint to ten times their national average. Of course, plenty of businessmen have similar or larger carbon footprints, but few of them would claim that their journeys are good for the environment. One is left wondering whether the carbon footprints of ecologists outweigh the environmental benefits of their findings and of their lobbying.
One way around this problem is to promote conservation biology on site, with improved local academic training (see here, for example), local research leaders and fewer but longer stays by foreign visitors. With regard to environmental politics, one faces the classic dilemma between personal restraint (I stay at home and work in the garden) and energy-demanding public involvement (I fly daily to help ban overfishing).
The outcome is a personal decision that may be dictated more by ambition than by environmental awareness. Nevertheless, as a German environmental campaigner told me 15 years ago, "Industry would be all too pleased if we did not attend distant meetings because we refuse to board aeroplanes."
Further online discussion of this topic is continuing at the Nature Network Opinion forum and in the Nature Network forum 'Getting science to go green'. Readers are warmly welcomed to contribute their views.

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The week on Nature Network: Friday 14 November

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.

When writing your paper, or any scientific document, how inventive are you with your prose? Lapsing into the over-familiar phrase can now be easily avoided via a definitive list of scientific clichés put together by Matt Brown and many users of Nature Network. Entering hackneyed terms into Google reveals the extent of their use: 'implications for therapy’ (230,000 hits); ‘it has not escaped our notice’ (14,200 hits); and ‘this raises more questions than it answers’ (1,030 hits) are three popular examples, but nowhere near ‘further research needed’ (520,000 hits). A fairer test of the scientific, as opposed to any other form of, literature would be to use Google Scholar. There, ‘the next ice age’ has 313 returns compared with 4,300,000 on Google itself. See plenty more suggestions at the Nature Network discussion - and for those even more interested in this type of esoterica, note Nature's recent News feature (455, 1023-1028; 2008) 'Disputed definitions', containing plenty of useful tips on what not to write and how not to write it.

Moving on to the more uplifting, the 2009 Subtle Technologies Festival is currently seeking submissions for its festival on the theme of “networks”, writes Jim Ruxton. The festival takes place in Toronto from 11 to 14 June 2009. "It is time to critically discuss the network metaphor and how it affects the direction of various disciplines and our societies at large. Under this theme, we will be curating a symposium, exhibition, workshops and performances." Biological networks, virtual worlds and social networking are three of the areas covered, but there are other science-related themes, so do check out the post.

Branwen Hide draws attention to a meeting in December 'The journal article: what does it cost and who really pays?', under the auspicies of the Research Information Network. The meeting is based on a report by the organization in which they examined the costs and funding mechanisms of 'scholarly communications' - publishers' costs, the cost to academic libraries, and the hidden costs to researchers in producing and accesing journal articles. Branwen writes that "it would be great to get some researchers there to talk about it, and discuss the types of changes reseachers would like to see happen in the area." It promises to be a stimulating meeting, and I hope to be there.

Two posts about scientists' public engagement featured at Nature Network during the week. Sara Fletcher reported on a visit to Diamond, the UK's new synchrotron facility by science minister Lord Drayson, asking whether whether Diamond (her choice) or Lewis Hamilton (Lord Drayson's) is a better example to help demonstrate the attractions of a scientific education and career to young people. And Stephen Curry proposes a new form of 'lay summary' for articles and grant proposals:
"Shall I compare thee to a summers day?
No! A nonsensical hypothesis!
Your DNA sequence will show the way
And give a much truer diagnosis."
There is, as may be imagined, plenty of discussion of this idea, but perhaps the Brian Derby Roxy music tribute is the most melodious attempt to make science accessible.

The peer-review process comes under scrutiny in a post by Mike Fowler, 'Peering at the review process', which addresses the question of whether peer-review is a conservative process that is biased against new ideas and paradigms, as well as various other issues about the interactions between authors, editors and peer-reviewers. There is an informative discussion at the Nature Network post.

Michael Durney calls attention to yet another social networking site for scientists, ResearchGate - which aims to help share resources and data. In the discussion to this post are links to lists of other social networking sites and brief reviews of those (see David Bradley's, for example), as it seems that there are rather many of them in existence or almost-existence. How many repeat what already exists, and how many offer useful new services to scientists interested in online collaboration and other types of open sharing of information and ideas?

Previous Nature Network columns.

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Science students need artistic skills

This is the text of a Correspondence from Nature 455, 1175 (2008) by Kenneth R. Jolls of Iowa State University:

In your 'Big data' issue, Felice Frankel and Rosalind Reid call for an "investment in visual communication training for young scientists" to prepare them for modern methods of data representation ('Distilling meaning from data' Nature 455, 30; 2008). But the problem goes deeper than that.
Graphic artists who collaborate with scientists have often been shaped by the other of C. P. Snow's 'two cultures'. Although well-intentioned, many artists' understanding of basic science is inadequate for meaningful participation in high-level technical work. Cognitive art is like commercial art and technical writing: it has never garnered respect from the artistic establishment, and its practitioners are left to fend for themselves.
From the start of schooling, distinctions are made between students with a talent for science and those with leanings towards the arts. In our technology-focused society, science receives more attention and an emphasis that does not include visual-thinking skills. Calculus, for example, is learned through symbolic operations, but portraying those procedures by using curves and surfaces and tangents and intercepts is typically considered to be an unnecessary frill.
Thus the two cultures diverge, and if we try to reassemble them later to let one benefit the other, we have serious difficulties: the world views don't match. Subjective ideas can be stifled by objective thought but, by the same token, physical reality can be mismanaged by well-meaning attempts at creativity.
We must indeed invest in visualization skills for science-bound students, but there should be a parallel path for science-illustrators-to-be to learn the basics of physics, chemistry and mathematics. Collaborators who understand each other's language have a much better chance of finding the common ground they need for the cooperation they seek.

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Molecular biology approaches to energy research

Frank Gannon writes an Editorial in the November EMBO Reports (9, 1055; 2008) about the importance of molecular biology to energy research. From the Editorial:
"Despite appearances, this is not an editorial about politics. It is about how biologists—more specifically, molecular biologists—can contribute to solving these problems. The obvious first step is to make energy production and conservation a prime focus of research, placing it on the same pedestal as curing cancer or developing therapies for HIV/AIDS and malaria. In fact, reducing our reliance on fossil fuels while preserving the environment might arguably be more important than other essential causes; an increasingly uninhabitable planet will affect both current and future generations, not only those who suffer from disease today.
We must therefore revisit our attitude towards certain avenues of research and accept that some of the solutions can only come from molecular biology. For example, after a brief period of enthusiasm, biofuels are now in the 'bad books' for various reasons, but mostly because their increasing production and the associated tax benefits are having an impact on the cost and availability of staple foods. Of course, sustainable food production is another important challenge that requires more research; yet, biologists could engineer energy crops to grow in poor soils and in harsh environments where it does not make sense to grow food crops. I suspect that such crops would eventually be welcomed even if they were genetically engineered. Similarly, we could also invest more into studying natural processes such as photosynthesis; bio-mimicry might help us to engineer more efficient ways for converting sunlight into energy."
Molecular biologists are going to face the problems of an ill-prepared scientific community at a time when the public increasingly expects science to solve our current energy and environmental problems, concludes Gannon. "This is complicated further by public skepticism about the science such solutions will require. Clearly, molecular biologists have to focus their attention on this huge challenge; it is no longer a question of 'if we should' but one of 'how we must'."

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Personal genomics: Nature web focus

As the number of human beings with their genomes fully sequenced ticks higher and direct-to-consumer gene profiling companies push the limits of what medical genetics can do, the once fantastical notion that any given human can walk into a doctor’s office with his or her genome on a hard drive looks more and more like a reality.
Still the question remains to be answered: how do we use this wealth of information? A Nature web focus presents the challenges this approaching reality poses for technology, the legal and ethical confines of research, and the ability of genomics to translate into clinical utility. Here you’ll also find the latest additions to the human genome menagerie: sequenced individuals from Africa and Asia. Access selected content fro the web focus free online, and listen to the special features on personal human genomes in the free Nature Podcast.
Discuss the Commentaries on personal genomics (free to access online until 6 December) at Nature Network.
The Nature Human Genome Collection
Nature Web Focus: Hap Map
Read on as Nature blogs from the 58th Annual Meeting of the American Society of Human Genetics in Philadelphia from 11(today) to 15 November 2008.

Continue reading "Personal genomics: Nature web focus" »

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Nature Methods, looking back and moving forward

The fourth anniversary of Nature Methods' arrival on the publishing scene and a change in leadership offer an opportunity for reflection and editorial fine-tuning, as described in the journal's November Editorial (5, 911; 2008).
From the Editorial: "When Nature Methods made its debut in October 2004, just over 4 years ago, it was an anxious but exciting time for our founding chief editor Veronique Kiermer and manuscript editors Nicole Rusk and Daniel Evanko. We were all novices at scientific publishing and more comfortable calibrating a pipette than editing a fledgling journal." The Editorial goes on to outline developments and other changes at the journal since then. Veronique is taking on the role of publisher for Nature Methods and Nature Protocols, and Daniel is taking over as Chief Editor of Nature Methods. Reviews, Perspectives and Research Highlights are to be expanded, while the Protocols section is closing. (Authors are encouraged to submit their protocols to the online publication Nature Protocols.) The Editorial concludes: "We hope that our journal has helped dispel the notion that methods are less important than results and deserving only of small print at the end of a paper. Debunking this myth has been and will continue to be our main mission. We will persist in our efforts to bring you, every month, a journal that allows methods to be featured prominently in their own right—as the cornerstones upon which results are based."
Nature Methods guide to authors.
How to submit to Nature Methods.
Aims and scope of the journal.
Methagora, the Nature Methods blog.

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The week on Nature Network: Friday 7 November

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.

"What can print copies offer that online access cannot?", asks Nature Nanotechnology editor Ai Lin Chun. Wen Jiang provides one answer in an online reply: "When I grasped the last printed copy of the March 2008 Nature Nanotechnology issue at the MRS conference in San Francisco this year, I felt that I had won the jackpot! Although more and more scientific journals are becoming fully digitalized, the printed format holds a longer-lasting sentimental value for the student authors publishing in the journal, similar to having a “Collector’s Edition”."

Richard Grant is the latest to address the complex question of the motivation of scientists to communicate their work to the public, sometimes "to encourage children to become scientists—or at least convince them that science is important—other times it’s to secure our funding, or explain why there’s no link between the measles vaccine and autism, or why GM crops are better for us and the environment. Other times it’s because we want to persuade people with treatable diseases to take this drug and live, rather than go to a homeopath and die." And have those encouraging clear writing in scientific papers thought about issues such as the one Richard provides in his post? "Here’s an example: [Butterflies] were subjected while being held by hand to hindwing removal. (The hindwing was severed with scissors along a line just distal to the point of articulation of the hindwings with the thorax, so that only a small triangular flap of each hind wing remained). Here’s the same sentence, rewritten so that my daughters can understand it: We cut the back wings off butterflies." Please join the discussion if you can help address this conundrum.

Eva Amsen, on the other hand, provides some good news about scientific papers, specifically the performance of the students on her science-writing course. Although one of the welcome pieces of news is that students are using the active voice in preference to the passive, Linda Cooper comments that "[teaching assistants] at my university still deduct marks from lab reports when students use the active voice. Such a pity because in addition to draining the life out of a sentence, the passive construction encourages writers to overuse weak linking verbs (variations on the verb “to be”), nominalizations (noun forms of verbs), prepositional phrases, and imprecise terms. While the passive voice is useful in making transitions between sentences, scientific articles written largely in the passive voice are often boring to read (and to write, i imagine!). My guess is that many researchers have difficulty transforming passive sentences into active ones – one more good reason for them to take science writing courses!"

Writing aside, "how do you read scientific papers?" asks Anna Kushnir, after reading a blog entry by Chris Lasher. "How do you read papers? Only look at the figures? Skip the intro? Have you read (really read, comprehended, and retained) every paper you have cited in your own publications?" As the number of papers and other reading material inexorably increases year-on-year, a reading strategy is essential to keep up to date without being swamped.

Joerg Heber, a senior editor at Nature Materials, asks whether, in the light of current economic concerns, there "will be an impact for some web 2.0 initiatives in science, where funding might become more difficult in the near future. For example, should we worry about long-term funding for initiatives such as open notebook science, where data volumes might be rather high? Or is there no reason for concern at all?" Bob O'Hara responds: "I can’t see that the recession will hit Web 2.0 initiatives in science, partly because we’re buffered (to some extent) against the “real” economy, but also because we’re generally not using Web 2.0 to make money, our motivation is to improve the way we do science." Further views are welcome at the Nature Network publishing forum.

Every Thursday at 11am PDT, writes Joanna Scott, the Nature Podcast will be broadcast at the rooftop cafe on the Elucian Islands, Nature’s home in Second Life. "It is completely free and anyone is welcome to come and listen to the Podcast and chat with other science enthusiasts......I’m also wondering about having a later listening as well, perhaps in the evening PDT. I know some people are missing out on everything – anyone with any comment to make about timezones or scheduling, please do get in touch" via her Nature Network Second Life blog.

Previous Nature Network columns.

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A world of science in the developing world

Nature Publishing Group has just published its second free access custom publication, A World of Science in the Developing World. Published on behalf of TWAS (the academy of sciences for the developing world) to celebrate their 25th anniversary, this publication is a reflection of the insights and expertise of TWAS members and scientists who have been closely associated with the academy and is part of a broader effort to explore the rapidly changing state of science and technology in the developing world.
You can view the supplement online as well as an accompanying editorial in Nature (455, 1149-1150; 2008). If you would like your own printed copy of the collection, please request a free copy here.

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Costs (and benefits?) of financial crisis to research

Nature Immunology , in its November Editorial (9, 1199; 2008), asks what the cost will be for science of the turmoil in the world financial markets that has forced the US government to spend huge amouts of money.
The US government has now committed more than $700 billion to ease the financial crisis, following the $85 billion to support AIG and $200 billion for the mortgage companies Fannie Mae and Freddie Mac, which together will raise the US debt ceiling to approximately $11.3 trillion. For perspective, $700 billion is roughly 3.4 times the 2008 budget of the European Union and 24 times the 2008 budget of the entire US National Institutes of Health (NIH).
The 2009 NIH budget proposed by the Bush administration was already set to stall biomedical research with its zero increase. Even before the present financial crisis, ineffective political lobbying and disengagement of the public on the importance of biomedical research may have contributed to the present state of anemic science funding. Now that combination may join forces with a debt of at least $11.3 trillion to form what could become a prolonged stalemate for government-supported biomedical research.
Nature Immunology suggests that biomedical researchers take a proactive stance: "those who have the ability and knowledge to influence politicians and the public to invest in scientific research must make every effort to be heard loud and clear to ensure the continued advance of the present amount of scientific research, at the very least."

Nature is running a special feature on science in the financial crisis. As the world faces its biggest financial crisis in decades, Nature keeps you updated on what it all means for science. Will your research funding be cut? How secure is your company or research institution? And can the meltdown actually create opportunities for science? Articles, including Editorials, News stories, Essays and other features, can be accessed from this main feature page. See also the journal's regularly updated financial crisis blog.

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Two million hours of science

G. N. Greaves of Aberystwyth Univesity and co-authors write in a Commentary in Nature Materials 7, 827-839 (2008):
"The world's first dedicated X-ray synchrotron radiation storage ring, the Synchrotron Radiation Source or SRS (Fig. 1), is closing down this autumn after 27 years of operation. Designed, built and commissioned at Daresbury Laboratory in less than four years, it thrust the United Kingdom into a world-leading position in 19801, delivering the first uninterrupted beams of intense X-rays. Since then, the use of synchrotron X-rays has led to major advances in both fundamental and applied science, which at the SRS has ranged from the structure of glass to catalysts in operation, from the crystallography of proteins to elements at high pressure, and from semiconductor surfaces to the magnetism of atomic layers, to take just a few examples. The SRS has had a substantial role in what has truly become a revolution in characterization science. With over 5,000 papers published, research and instrumentation from the SRS continues to influence facilities across the world."
The authors review the range of fields of science in which the SRS has made significant contributions, calculating that since 1981 "the SRS has served a staggering 11,000 individual users from 25 countries, and been the training ground of over 4,000 doctorate students and 2,000 post-doctorate researchers. With materials research making up around 40% of this research programme, the legacy of the SRS in this field is enormous. We have picked out examples where the international impact of the SRS has been particularly impressive, but there are many more: developments in industrial materials, biomaterials, electrochemical materials and, very recently, heritage materials. The international conference series, 'Synchrotron Radiation in Materials Science', which began in Chester, UK, in 1994, charts this progress and involvement of the SRS over the years. Indeed, many of the new concepts, experiments, theory and instrumentation in X-ray science owe their origins to research at Daresbury, starting 27 years ago when the SRS heralded the age of dedicated synchrotron radiation.
It is worth reflecting on the relatively short time taken for authorization to build the SRS by the then Science Research Council. The decision in the late 1970s followed the briefest of approval procedures compared with the current process-driven practice of seeking the widest consultation before dipping into the public purse. If the gut-reaction decision to build the SRS had taken any longer, it would have jeopardized its place as a world-first and, more importantly, the confidence to build new science over the next generation — much of which has been internationally leading and continues to influence the synchrotron radiation community worldwide."

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Web Focus on cell polarity

Cell polarity relies on the asymmetric organization of cellular components and functions. It is implicated in the differentiation, proliferation and morphogenesis of unicellular and multicellular organisms, and its dysregulation can cause developmental disorders and cancer. This month (November), Nature Reviews Molecular and Cell Biology presents a Focus on Cell Polarity, free to access online for the month of November, which aims to capture the current state of cell polarity research in a range of different systems by dissecting the underlying principles. The Focus includes five Review articles by leaders in the field, and the topics range from organelle positioning, cytoskeletal dynamics and mechanisms of protein sorting, targeting and distribution in polarized cells, to crosstalk between small GTPases and polarity proteins, and the mechanisms that coordinate the assembly of cells into polarized tissues.
Cell polarity Focus, including table of contents.
Nature Reviews Molecular and Cell Biology Editorial summarizing the Cell polarity Focus.
Library of articles from Nature Publishing Group journals on the topic of cell polarity.