Nautilus - Blog Posts

Cover competition at EMBO Journal

mclarke — 2009-11-06T10:23:13+00:00

EMBO Journal has just announced its annual competition for the best (scientific or non-scientific) cover images in 2010. The front cover of the 4 November issue (pictured) shows an assembly of many of the beautiful images that have been featured on the EMBO Journal since 2007; most of these had been submitted to previous competitions by scientists based throughout the world. Please visit the journal's competition page for details of how you can participate in this year's contest and submit your entries online. You can take a look at the gallery in the journal's online archive for an impression of what type of images might be good candidates for an EMBO Journal cover. The jury and the editors are looking forward to seeing your contributions. The closing date of the 2010 cover contest is 15 January 2010. Send a brief email to covers@embojournal.org if you wish to receive a notification when next year's contest is announced.

In another similar enterprise, the editors of The American Journal of Gastroenterology are seeking eye-catching cover images for the journal in 2010. Images can be submitted using the journal's online manuscript submission service. All readers and contributors to The American Journal of Gastroenterology are eligible. Full information on artwork submission guidelines is available (PDF).
The American Journal of Gastroenterology , the official publication of the American College of Gastroenterology, is the clinical leader in publishing highly cited articles that appeal to all practicing clinicians interested in gastroenterology, hepatology, endoscopy and other related disorders.

Nature celebrates the astonishing variety of reactions to Darwin's ideas

mclarke — 2009-11-05T08:18:58+00:00

In honour of the 200th anniversary of Charles Darwin's birth, Nature is publishing a series on the global and astounding variety of reactions to the theory of evolution. People from Egypt to Japan used Darwin's ideas to reinvent and reignite their core philosophies and religions, says Marwa Elshakry in the first of these four weekly pieces on how evolution was received around the world (Nature 461, 1200-1201; 2009). The start of the series is marked by an Editorial (Nature 461, 1173-1174; 2009) on the importance of cultural influences on science. "The lesson for today's scientists and policy-makers is simple: they cannot assume that a public presented with 'the facts' will come to the same conclusion as themselves. They must take value systems, cultural backdrops and local knowledge gaps into account and frame their arguments accordingly. Such approaches will be crucial in facing current global challenges, from recessions to pandemics and climate change. These issues will be perceived and dealt with differently by different nations — not because they misunderstand, but because their understanding is in part locally dependent.
Darwin once said: "But then with me the horrid doubt always arises whether the convictions of man's mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy." Researchers and policy-makers would do well to mimic his humility when presenting science, and remember how people's minds truly work."

Nature 's collection of all Darwin anniversary content.
The grand finale will come later this month (November), marking the 150th anniversary of On the Origin of Species. (Watch this space.)
More resources on Darwin 200 from Nature.
Nature Publishing Group celebrates Darwin 200: a round-up of commissioned content from the Nature journals.

EMBO reports asks "Is the end in cite?"

mclarke — 2009-11-04T07:43:15+00:00

In a Correspondence to EMBO reports ( 10, 1186; 2009), Mark Patterson asks how we can avoid Howy Jacobs's "light-hearted nightmare scenario" of the future of citation-based metrics. Patterson, director of publishing at the Public Library of Science (PLoS), presents his own organization's article-level metrics, as a better alternative to the journal-level metrics that are currently in most common use as research output measures. He writes: "Article-level data are not without their problems, and so it is important to interpret the data carefully. But, we believe that providing the data in the first place will inspire new ideas about how to assess research. Rather than limiting attention to the journal impact factor, it will be possible to ask sophisticated questions about the impact and influence of published research, and to obtain meaningful answers. For example, for a piece of research that is aimed at practitioners, we might want to know the extent to which it has actually changed practice—citation metrics probably would not be of much help in that case. And it should be possible to find work that only emerges with the passage of time as crucial for the development of a particular field." Noting that the PLoS journals no longer promote impact factors at their website, Patterson concludes: "As alternatives begin to emerge, the primacy of the impact factor will be challenged. But this will only happen if other stakeholders also take a stand."

Be consistent on plagiarism rules, says Nature Genetics

mclarke — 2009-11-03T07:54:19+00:00

The US Department of Health and Social Security's Public Health Service (PHS) ruled in 2005 that "Plagiarism is the appropriation of another person's ideas, processes, results, or words without giving appropriate credit." in its November Editorial 'Data divorce', Nature Genetics (41, 1157; 2009) takes the Office of Research Integrity (part of the US Department of Health and Human Services) to task for producing a different definition:

Many allegations of plagiarism involve disputes among former collaborators who participated jointly in the development or conduct of a research project, but who subsequently went their separate ways and made independent use of the jointly developed concepts, methods, descriptive language, or other product of the joint effort. The ownership of the intellectual property in many such situations is seldom clear, and the collaborative history among the scientists often supports a presumption of implied consent to use the products of the collaboration by any of the former collaborators.
For this reason, ORI considers many such disputes to be authorship or credit disputes rather than plagiarism. Such disputes are referred to PHS agencies and extramural institutions for resolution.

Nature Genetics points out that this additional definition of plagiarism was considered but not included in the PHS statement, and asks the ORI to correct its definition of plagiarism to the one published by its parent body (PHS). By "providing a channel for fair and accountable investigation, the ORI also provides an important deterrent to scientific misconduct, not only for US researchers but, by example, for the global research community. Therefore, we suggest that it is counterproductive to the reporting of misconduct—and to the deterrence of misconduct—for the ORI to be seen to be turning away a significant proportion of its cases. Indeed, these are the very cases in which thefts of data and ideas are most likely to occur."

Nature journals' policy on plagiarism. (Includes links to relevant journal editorials, free to read online.)

NIH checklist of simple rules for researchers.

Education needed more than regulation for genetic testing

mclarke — 2009-11-02T08:16:10+00:00

With sequencing costs dropping, it is likely that direct-to-consumer genetic services will soon include affordable whole-genome sequencing. Consumers who have familiarized themselves with the limitations of these data will be better equipped for the 3 gigabases of information that may soon come their way, according to the Editorial in the November issue of Nature Methods (6, 783; 2009). What is the right approach for direct-to-consumer genetic tests, asks the Editorial, given concerns about analytical validity, accuracy, clinical validity, clinical usefulness, helpfulness to consumers, and that the genetic variants tested for are actually associated with increased disease risk? Different countries are handling these issues in different regulatory and legislative ways, but the Editorial argues that a restrictive approach is not helpful, particularly given the huge range of genetic conditions and possible 'tests'. Although companies should do more in terms of providing unbiased information to the public, it is up to the consumers to educate themselves about the benefits, risks and limitations.
The Nature Methods editors invite readers to discuss this Editorial at the journal's blog, Methagora.

Nature Photonics on the Nobel prize for physics

mclarke — 2009-10-30T11:22:00+00:00

There's an interesting Editorial in Nature Photonics this month (November) about the 2009 Nobel prize for physics (Nat. Photon. 3, 605; 2009), won for two innovations in photonics that underpin society's adoption of information technology. From the Editorial: "What is particularly interesting about this year's choice of award is the strongly applied nature of the achievements and the prevalence of the technologies in today's society. Indeed, this is probably one of the rare instances where many of those working outside science are likely to have both an immediate familiarity with the topics of the award and an appreciation of their usefulness. After all, in developed countries fibre-optic communications underpin phone networks and the internet, and digital cameras are now considered a ubiquitous item in many households." The Nature Photonics editors are intrigued as to whether this year's award will set a Nobel precedent for honouring practical applications of scientific research.

Scientists should resist the temptation to hype their results

mclarke — 2009-10-29T12:51:40+00:00

According to an Editorial in today's Nature ( 461, 1174; 2009 - free to read online), "the temptation for scientists and their institutions to spin their research to the media, or to go publicity-mongering, is always there. And — as illustrated by the excessive public-relations campaign surrounding "Ida", a fossil presented as a missing link in human evolution (see Nature 459, 484; 2009 and Nature 461, 1040; 2009) — too many in the media will buy into the initial hype. Such behaviour is corrosive to the process of scholarly scientific communication. Research institutions must not allow it to become the norm."
The Editorial discusses the recent announcement of results from an HIV vaccine trial in Thailand, in which the trial's sponsors announced that it had been a success in that the vaccine had a statistically significant effect on preventing infection. But the full data for the claim were not made available for almost a month after the announcement - and included two other data sets in which the effects were not statistically significant.
Fortunately, states the Editorial, such stories are still rare in science. "Witness the way scientists have behaved since the beginning of the current H1N1 flu pandemic, in which the urgent threat to health creates legitimate tensions between getting results out fast and respecting peer review. Most researchers have negotiated this tension well, through a combination of fast-track publication by journals and online pre-publication sharing of preliminary data — but not through hyping their results."

Nature Neuroscience speaks up for young researchers

mclarke — 2009-10-28T08:10:58+00:00

The Editorial in the November issue of Nature Neuroscience (12, 1351; 2009) emphasizes the importance of the US National Institutes of Health (NIH) policy of funding an increasing number of grants to young investigators with merit scores below the 'payline'. Early-stage investigators are "especially vulnerable to funding crisis and are often at a disproportionate disadvantage when competing with more established laboratories for R01 grants. Such actions that protect some of these young investigators are critical if we are to retain young scientists and encourage our future research base", states the journal. This problem may have been exacerbated by recent efforts to streamline the grant peer-review process, which may mean that evaluators are putting even more store on previous track-record, hence putting young researchers at a greater disadvantage. The Editorial identifies other factors that could be hindering young researchers in the cold funding climate. Although affirmative actions to help younger, less established, researchers are seen by some as unfair, Nature Neuroscience concludes: "Given the dismal projections for NIH budget growth, a step of this magnitude is necessary to support young investigators and to preserve the future of the scientific community as a whole."

Nature Neuroscience journal website.
About Nature Neuroscience.
Nature Neuroscience guide to authors.

Two views of the Lindau Nobel chemistry laureates' meeting

mclarke — 2009-10-27T08:06:38+00:00

Each year since 1951, young researchers and Nobel laureates have gathered on the shores of Lake Constance for a unique scientific conference. In 2009 the meeting was dedicated to chemistry, and laureates and students all came away enriched by their experiences. Martin Chalfie, one of the three recipients of the 2008 Nobel prize in Chemistry, reports what they learned from each other in the November issue of Nature Chemistry (1, 586-587; 2009) He writes:
"From their reading or from simply listening to my talk, the students generated a large number of fascinating questions. They wanted to know details of the experiments and they wanted to discuss potential future experiments. Conclusions about my research that had taken me years to realize (and which I have not written about or described in my talk) were instantly suggested by several of the students at the session. Seeing their excitement and quickness was humbling, but also invigorating.
The meeting allowed the students (as well as the laureates) to broaden their horizons, to have a chance to meet, exchange ideas, and learn about new areas of research from investigators from all over the world (the conference participants came from 67 different countries). The word 'exchange' is important here, because I don't believe that the real benefits were associated with hearing advice from a bunch of older scientists who had been fortunate enough to get some recognition for their work." The meeting's significance is "the acknowledgement it gives to young scientists, especially at a time when they do not get much recognition, that they are on their way to succeeding in science, and that we think that they are important. Although they really do not need any seal of approval, everyone likes to get the occasional pat on the back."
In a companion article in the same issue of Nature Chemistry (1, 587-590; 2009), Jeffrey R. Lancaster, a fourth-year graduate student in the Department of Chemistry, Columbia University, looks back at what he got out of the Lindau meeting: "two subtle points have ultimately distinguished the Lindau meeting for me as a unique event of which I was honoured to have been a part.
First, conversation and the sharing of ideas were fostered not solely between scientists with comparable levels of experience, but also across scientific generations and geographies. I had worthwhile discussions with my peers from Australia, China, India, the Netherlands, Poland and Spain (to name but a few), and was able to speak to scientists at various stages of their careers, from undergraduate to graduate students, postdocs, professors, governmental scientists and, of course, Nobel laureates. Second, the activities pursued by scientists outside of publishable, academic research also featured prominently at the meeting. That scientists might have a life apart from, and in addition to, their research is most often a topic best reserved for conference happy hours, not keynote addresses."

Goodbye from Nature Reports Stem Cells

mclarke — 2009-10-26T13:15:15+00:00

We are sad to announce that this month brings the last update of Nature Reports Stem Cells.
When we launched in June 2007, we wanted to support the stem cell field and the interested public by providing freely available content. Stem cell research was then - and is still - exciting and expanding. It requires highly varied experts to think and work together, and it requires the support and understanding of non-scientists. We believe we have been successful in creating a venue that highlights and explores the many facets and implications of stem cell science. It is now time for us to move on to fresh publishing challenges.
We have been helped by many contributors and experts who have generously given their time and insight. We give a heartfelt thanks to everyone who wrote articles or gave interviews, advice, and words of encouragement.
NRSC and its blog, the Niche, will continue to remain online as an archive. Nature and its sister titles remain committed, as ever, to publishing new research and news about stem cells.
Monya Baker, Editor
Natalie DeWitt, Editor at Large

Nature special: Climate of compromise

mclarke — 2009-10-23T07:16:17+00:00

The road to Copenhagen. With the UN Climate Change Conference just six weeks away, Nature this week (22 October issue) assesses how much - or little - progress is being made on tackling climate change in a set of Opinion articles and News Features, all free to read online for one month from the date of issue, as well as an Editorial (free to read online). The latest round of negotations shows that the gulf between rich and poor nations is as great as ever, and hopes of a strong agreement are rapidly fading. Raúl Estrada-Oyuela, a diplomat who guided the Kyoto negotiations, argues that success in Copenhagen will depend on the skills of the lead negotiator (Nature 461, 1056-1057; 2009) Meanwhile, Rajendra Pachauri, chairman of the Intergovernmental Panel on Climate Change, comments on the Indian negotiation stance (p. 1054), while Jiahua Pan, of the Chinese Academy of Social Sciences, examines the Chinese perspective on reducing global emissions (p. 1055) . A pair of news features take us around the world to look at efforts to adapt to climate change in Bhutan (pp 1042- 1046), and a project in Peru to monitor forest carbon (pp 1048-1052).
Successful international negotiations share some important characteristics with scientific research, argues an Editorial this week (Nature 461, 1027-1028; 2009). Both are iterative processes, in which results from one step help to determine the path forward. They require time and perseverance. And they rarely travel in a straight line. Countries should endeavour to build on the positive actions of the past year, both before and after the Copenhagen summit.
See also: more articles, the free Nature podcast and more online extras.

Five years on for the Allen Brain Atlas

mclarke — 2009-10-22T07:24:47+00:00

In their Perspective 'The Allen Brain Atlas: 5 years and beyond' (Nat. Rev. Neurosci. 10, 821-828; 2009), Allan R. Jones, Caroline C. Overly and Susan M. Sunkin of the Allen Institute describe an experiment on a massive scale: a web-based, genome-wide atlas of gene expression in the adult mouse brain The development of this atlas faced a combination of great technical challenges and a non-traditional open research model, they write, and it encountered many hurdles on the path to completion and community adoption. Having overcome these challenges, it is now a fundamental tool for neuroscientists worldwide and has set the stage for the creation of other similar open resources. Nevertheless, there are many untapped opportunities for exploration.
The Perspective, in the November issue of Nature Reviews Neuroscience, looks back on the 5 years from the inception of the Allen Brain Atlas to the present, highlighting challenges and the contributions that it has made to neuroscience. The authors discuss the advantages and caveats of using this unique resource, how it is currently being used and point to opportunities for further exploration. They conclude by describing the ever-expanding suite of related resources that have become available since the atlas was launched, and comment on those that will be coming in the next few years.

Allen Brain Atlas portal.
Allen developing mouse brain map.
Allen Institute human cortex study.
NeuroCommons project.
Mutant mouse regional resource centers.
Nature Reviews Neuroscience.
About Nature Reviews Neuroscience.

The Nature Autumn '09 Debate - Science in Cinema

mclarke — 2009-10-21T07:58:00+00:00

From the prescient visions of space travel in 2001: A Space Odyssey, through to the apocalyptic warnings presented in The Day After Tomorrow, science fiction cinema has examined many of the theoretical possibilities and consequences of science and technology. But just how plausibly does the genre interpret such possibilities and how accurately can it predict what the future holds? Have the futuristic celluloid visions of film-makers inspired scientists to fulfil some of these visions? And are movies the best way of promoting environmental awareness to contemporary societies? Join a lively debate organized by the weekly science journal, Nature.

Speakers
Adam Rutherford (chair) is an audio video editor at Nature, science writer and presents television and radio programmes, most recently Cell for BBC4.
Henry Gee (panellist) is a senior biology editor at Nature. He also edits the ‘Futures' science fiction column in Nature, and has written several non-fiction and fiction books.
Mark Henderson (panellist) is science editor of The Times and a double winner of the Norwich Union / Medical Journalists' Association awards. He is the author of 50 Genetics Ideas You Really Need to Know.
Gia Milinovich (panellist) is a technology writer and broadcaster as well as a new media consultant for the film industry. She has worked on various films, including Sunshine, 28 Weeks Later, X Files: I Want To Believe and Indiana Jones and the Kingdom of the Crystal Skull.

The Nature Autumn '09 Debate - Science in Cinema is at Kings Place, London on Monday 9 November at 19:00. For further details and to book, see the Kings Place website.

Being communicative but careful with the media

mclarke — 2009-10-20T07:30:11+00:00

Bad journalism is best met not with red-faced indignation, but with good journalism. The truth is the best revenge. So concludes an Editorial in the current issue of Nature (461, 848; 2009) about an email campaign to a US climate scientist who backed out of participating in a documentary when he realized that the film-makers had not been clear with him about their intentions. Occasionally, scientists have been hoodwinked by the media, but these are rare events compared with the vast majority of programmes and other media articles. From the Editorial:
"Most journalists and documentarians are honestly trying to report the facts, and scientists have a responsibility to tell the public about their work — especially if it is supported by public money.
Fortunately, scientists can do much to protect themselves. When someone asks for an interview, for example, a scientist should enquire about starting assumptions, the intended audience and the identity of the project's backers. And, if possible, researchers should check the earlier work of the journalists and any companies behind the film for a partisan tone, or unacceptable levels of sensationalism.
But if these efforts fail, and it is discovered too late that the film-makers are bent on using an on-tape interview to promote a view that seems unscientific, the question becomes what steps to take. There is rarely a way to withdraw an interview that was given on the record, for good reason. In any case, making a fuss can be a gift of publicity to film-makers. Schneider admits that he might have spared himself the deluge of e-mails had he just ignored the makers of Not Evil Just Wrong.
A better approach might well be to complain to the television channels and broadcasting regulators, many of which have standards for their programming. The Great Global Warming Swindle was censured by Ofcom, Britain's broadcasting regulator, for breaking several rules in its broadcasting code. And when the same documentary was aired by the Australian Broadcasting Corporation, it was followed by a point-by-point debate and rebuttal."

Free poster on the transcriptome at Nature Reviews Genetics

mclarke — 2009-10-19T07:53:28+00:00

Nature Reviews Genetics presents a free poster, 'The pervasive and interlinked transcriptome', in its November 2009 issue. Our knowledge of the eukaryotic transcriptome is being transformed as we come to realize that the proportion of the genome that is transcribed is far greater than expected. New insights into the diversity of transcriptional products are rapidly emerging. Technological advances, such as RNA deep sequencing, are driving an increased knowledge of how transcripts are encoded in intricate and overlapping ways and are processed into myriad RNAs.
Using snapshots at different levels of resolution – from chromosomes down to a few nucleotides – this poster provides a window into the layers of complexity and introduces transcriptional phenomena and types of RNA that are key topics in current research.
More about Nature Reviews Genetics.
Featured articles on genetics from across the Nature Publishing Group journals.
NPG '-omics' gateway.