Nautilus

Access to biological databases must be guaranteed

Fri, 20 Nov 2009 07:57:18 +0000

The Arabidopsis Information Resource (TAIR) contains the most reliable and up-to-date genomic information available on the most widely used model organism in the plant kingdom. But TAIR now faces collapse: the US National Science Foundation (NSF) is phasing out funding after 10 years as the data resource's sole supporter.
According to an Editorial in Nature this week (462, 252; 2009), "TAIR's plight is emblematic of a broader crisis facing many of the world's biological databases and repositories. Research funding agencies recognize that such infrastructures are crucial to the ongoing conduct of science, yet few are willing to finance them indefinitely. Such agencies tend to support these resources during the development phase, but then expect them to find sustainable funding elsewhere. Unfortunately, that is not easy." Other funding agencies and private firms are not likely to step in to provide long-term support, even for relatively modest repositories and databases.
It is time for a whole new approach, argues the Editorial. "Front-line biology cannot function without these resources, so solutions must be found at both national and international levels.
Governments must ensure that at least one of their national funding agencies has money specifically set aside for the long-term support of bioresource infrastructures. A good model to emulate would be the United Kingdom's Biotechnology and Biological Sciences Research Council, which allows databases and other such resources to apply for ring-fenced funding, saving them from having to compete with hypothesis-driven grants, which are the agencies' mainstay.
But action is also needed on the international front. The sharing of bioresources does not and should not stop at national borders. For example, only about a quarter of TAIR users are based in the United States. China is the second biggest user at around 12%, followed by Japan at around 10%. This is not atypical. Yet it is difficult for a single national agency to justify maintaining a resource for the rest of the world. What is required is an international cost-sharing organization that could fund competitively selected infrastructures, large and small.
An international solution may be a long time coming. In the meantime, bioresource infrastructures might be wise to invest some time in public relations, giving paymasters a greater understanding of the consequences of their decisions."

See also a related News story in the same issue of Nature (462, 258-259; 2009): Japanese science faces deep cuts.

Nature reprint collection: immuno-epigentics

Thu, 19 Nov 2009 08:19:52 +0000

Epigenetic mechanisms are increasingly appreciated to have an important role in immune cell functional diversity and adaptability, and understanding these mechanisms holds considerable potential for revealing new opportunities to therapeutically modulate the immune response in a range of diseases.
This Nature Reprint Collection provides a compilation of some of the research papers that have contributed to the advances in the field of immune cell epigenetics, as well as reviews discussing aspects of this new and exciting field. The collection brings together articles from Nature, Nature Immunology, Nature Reviews Immunology and Nature Reviews Drug Discovery that have contributed to advances and discussions in the field of immune cell epigenetics.
The articles in this collection are freely available online until 30 April 2010.

More Nature Collections.
Nature Immunology supplements and focuses.

See also: Epigenetic Dynamics in the Immune System, a conference organized by Nature Immunology and Nature Reviews Molecular Cell Biology, 19 February 2010 in San Antonio, Texas.

Nature Medicine classics collection

Wed, 18 Nov 2009 08:09:29 +0000

In 2010, Nature Medicine will celebrate 15 years as the leading translational-research journal. To mark this anniversary, the journal has launched the Nature Medicine Classics Collection. This collection brings together some landmark articles published in Nature Medicine over the past 15 years, making them freely available to all readers together with a series of recent articles on different fields of biomedicine to illustrate the breadth of the journal.
The Nature Medicine editors write: Since 1995, our journal has been at the forefront of publishing translational medicine, way before the term was even coined. Our focus on publishing basic and preclinical work that has direct relevance to human disease has been a key characteristic of Nature Medicine that has helped establish the reputation of the journal in the translational research landscape.
To put together this sampler, we have chosen a series of recent articles from our pages, organized them by therapeutic area, and made them freely available in order to give you a glimpse of the breadth of Nature Medicine's coverage, as well as the quality of the science we publish.
In addition, we have chosen a few landmark articles that we had the privilege to publish over the past 15 years in an effort to illustrate why Nature Medicine is the home of translational research.
Nature Medicine Classics Collection by subject:
Classic articles
Cancer
Cardiovascular disease
Immunology
Infectious diseases
Metabolism
Neuroscience

See also:
Nature Medicine's free podcast.
Journal press releases.
Spoonful of Medicine, the journal's blog.

Nature Chemical Biology's symposium series

Tue, 17 Nov 2009 08:14:02 +0000

Taken from the Editorial in the November issue of Nature Chemical Biology (5, 863; 2009):
In the past decade, chemical biology has expanded to embrace increasingly diverse research areas at the interface of chemistry and biology. Nature Chemical Biology has strived to highlight this aspect of chemical biology by publishing papers that apply chemical and biological approaches to achieving a greater mechanistic understanding of biological systems. The field also offers small molecules and tools that can be used to manipulate chemical and biological systems with unprecedented molecular precision. Given these basic and applied aspects, chemical biology has naturally resonated with fields that rely upon integrated chemical and biological insights. No field has been more affected than drug discovery.
This synergy was highlighted at the third Nature Chemical Biology symposium Chemical Biology in Drug Discovery, held on 19–20 September 2009 in Cambridge, Massachusetts. The organizers were Paul Workman (Cancer Research UK Centre for Cancer Therapeutics at The Institute of Cancer Research, UK), Giulio Superti-Furga (Center for Molecular Medicine, Austrian Academy of Sciences, Austria), Brian Shoichet (University of California, San Francisco, USA), and Joanne Kotz (Nature Chemical Biology, USA)
Though the symposium focused primarily on the ways that chemical biology will shape the science of drug discovery, it was clear that chemical biologists, who are equipped with a substantial toolbox of 'pathfinder compounds', chemical methods and other technologies, represent a new generation of talented interdisciplinary scientists who will bring fresh insights to the drug discovery culture. Pharmaceutical companies should make every effort to integrate chemical biology programs and scientists into their portfolios to promote innovation in chemical biology for drug discovery.
A primary aim of the Nature Chemical Biology symposium series has been to nucleate discussions among scientists who share common interests but approach these scientific areas from different perspectives or with divergent tools. We look forward to bringing together other groups at the frontiers of chemical biology, and we welcome suggestions for future symposium topics.

Nature Chemical Biology:
Journal home page.
About the journal's web site.
Focuses and supplements.
Guide for authors and peer-reviewers.
About the editors.
Contact the journal.

Nature Conferences main index.

Presubmission enquiry or entire manuscript?

Mon, 16 Nov 2009 10:51:37 +0000

Q: Dear Nature: I am considering sending a presubmission enquiry for a Letter, and in the process, noticed your comment that, "The editors would prefer to read the full paper even if it isn’t in journal format, than to read a presub." If, (hypothetically!) I had a paper written in the format of another journal which that journal has not offered to publish, is there a mechanism by which I could submit this paper, rather than a presubmission enquiry, to Nature with the understanding that it would be rewritten to conform to your format if it were to be formally submitted? Would this be preferable? It would certainly be easier for me, and presumably would give you better information.

A: Thank you for your message. Yes, you can submit a paper to Nature in the same format that you've used for another journal. We aren't too concerned about the precise details of format at the submission stage as long as the manuscript is not excessively over-length. As you say, a full manuscript that isn't quite in the journal format is more informative for the editors than a brief presubmission enquiry.
All manuscripts that are sent for peer-review go through at least two rounds of revision, so there is opportunity at the first revision stage for format issues to be addressed. The editor will send specific guidelines then.
We recommend to authors who wish to submit a manuscript that has previously been formatted for another journal that that they note in their covering letter that their manuscript is currently not in Nature's precise format as specified in our guidelines, and that they are willing to revise the manuscript to Nature's format during the peer-review process.

Nature Nanotechnology on public attitudes and responses

Fri, 13 Nov 2009 07:38:39 +0000

The proportion of the public that knows about nanotechnology has reached a plateau, which means that it is now necessary to develop new approaches to explore public perceptions in greater detail than before, according to the November Editorial in Nature Nanotechnology (4, 695; 2009). The Editorial draws attention to "the publication of the first meta-analysis of survey data on public attitudes towards the risks and benefits associated with nanotechnology (see page 752 of this issue). Terre Satterfield and colleagues looked at 22 publications reporting the results of surveys and found that the public response to nanotechnology has, so far, been different to the responses to previous new technologies in a number of ways. In particular, and contrary to expectations, unfamiliarity with nanotechnology is not strongly associated with risk aversion. The meta-analysis also reveals that twice as many people think that the benefits will outweigh risks as vice versa, but the authors caution that "a large minority of those surveyed (44%) is unsure, suggesting that risk judgments are highly malleable." Satterfield and colleagues also call for the development of new methods to understand public responses to nanotechnologies. In an accompanying News & Views on page 705 Dan Kahan concludes that "the meta-analysis suggests that public attitudes toward nanotechnology remain open to the guidance of sound science, but that it would be a serious error to take such receptivity for granted.".... It is important that the nanotechnology community — researchers, funders, regulators and others — continues to work hard to ensure that nano does not become the next GM, all the time accepting that there might always be new questions to answer and new challenges to address."

Nature Medicine's wake-up call on intellectual property rights

Thu, 12 Nov 2009 07:33:17 +0000

Intellectual-property protection is a key driver of innovation, and researchers are always keen to file patents to shield their discoveries. Yet scientists often have an uninformed view of the value of their intellectual property. This naiveté slows down translational research. So concludes the November Editorial in Nature Medicine (15, 1229; 2009).
An informal poll conducted by the Nature Medicine editors revealed that "about two-thirds of scientists, particularly in Europe, don't know who owns the intellectual rights to the discoveries made in their labs. A similarly high proportion don't know if there are any provisions in their job contracts assigning them any rights over their discovery. And roughly half don't even know whether they are legally entitled to open a company based on their research." Ironically, states the Editorial, these are the very same scientists who dream of patenting their work and reaping the financial benefits. Before thinking about licenses (the essential first step), the Editorial continues, "it's important to realize that the decision to file a patent seldom rests with the scientists, but rather with the technology transfer office (TTO) of their institution. Strangely enough, although most of the scientists we surveyed were interested in patenting their work and knew about the importance of the TTO to this end, over 60% admitted to never having interacted with that office." After highlighting some of the problems concerning technology transfer offices and investor caution, the Editorial concludes:
"Translational researchers never shy away from the chance to present their science to anyone who might want to invest in it. But they would be well advised to start listening to companies, investors and their own TTOs to develop a better understanding of what they must bring to the table in order to attract financial support. Admittedly, there are very few places where scientists can learn how to engage in this dialogue, but the excuse that provides should be cold comfort given how important this is to the progress of translational research. The creation of forums of this sort should therefore become a priority for universities and research centers alike. A high-profile paper may allow you to get your foot in the door, but it won't be enough to open it."

See also the free Nature Medicine podcast, this month looking at the law in the context of the "patent cliff" which pharmaceutical companies are facing.

In other Nature Medicine news, the journal is organizing a colloquium on Systems Biology and HIV Vaccine Development on 8-10 February 2010 in Peachtree City, Georgia, USA. Participants will include HIV researchers and scientists using systems approaches in other areas of biomedical research, who will address how systems biology has provided insight into the immune response and into other areas of medicine, such as cancer and autoimmunity. Also on the agenda for discussion are the technical and bioinformatic challenges associated with using systems biology approaches; the gaps in HIV immunology that need to be resolved to develop an HIV vaccine; whether systems approaches can help to address these questions; and how 'systems vaccinology' approaches can be implemented in HIV vaccine development and clinical trial monitoring.

Authors warned to keep their online identities secure

Wed, 11 Nov 2009 08:15:07 +0000

This is the text of a Correspondence in Nature (462, 35; 2009) by Irene Hames , an editor at The Plant Journal.
Goudarz Molaei is right to express concern in his Correspondence about simultaneous submission of manuscripts to different journals (Nature 461, 723; 2009). As a professional journal editor with more than 20 years' experience, I would like to highlight here a worrying new problem I recently encountered: duplicate submission arising from author impersonation.
Unfortunately, online submission and review systems inadvertently encourage this unwelcome activity. For example, a co-author or colleague may be given the corresponding author's account password in order to submit his or her manuscripts — perhaps because of the corresponding author's lack of time or unfamiliarity with file creation and uploading. These people are then able to change the author's accounts, including the passwords, and submit manuscripts in that person's name without their knowledge.
So, authors, be wary of who has access to your account. Keep a check on what's happening and change your password after files have been submitted.

Nature Cell Biology joins call for microattribution of datasets

Tue, 10 Nov 2009 07:25:45 +0000

Nature Cell Biology (11,1273; 2009) joins in the call for 'microattribution' in its November Editorial, stating that reference datasets should be accessible independently of scientific papers in a citable form. The problem, from a cell biological perspective:

"Scholarly publication remains essential for describing and contextualizing findings, but it is inadequate as the only document of research activity. Most journals require a significant conceptual advance, and format constraints typically allow only for the presentation of representative qualitative, or statistically processed quantitative data. Consequently, the majority of raw data never emerges from lab hard drives, and a wealth of information, hard work and funding is wasted. High throughput platforms generate reams of data that cannot be captured in traditional papers. Moreover, methods sections fail to adequately describe metadata essential for the comparison and reproduction of experiments. Databases are essential for comprehensively archiving both published and unpublished data, but have only become fully integrated into the scientific process in a few cases, such as DNA sequencing and microarray data. For many types of data, including light microscopy, no databases exist at all. "

Prepublication deposition into databases is relatively new to biology, but is essential, according to the Editorial, whether or not some embargo condition is imposed by authors, funders or publishers. Journals, in their turn, need to systematically link online to data and other material in databases, in order to remain relevant. The Editorial concludes that "Large reference datasets that benefit the wider community and that cannot be analysed efficiently by the data producers should enter the public domain without delay, as long as appropriate attribution and credit can and is given. Scientific culture has to change so that data is valued alongside publications."

See also: 'Accreditation and attribution in data sharing' by Gudmundur A. Thorisson of the Department of Genetics, Leicester, UK (Correspondence to Nature Biotechnology 27, 984-985; November 2009).

Nature's past and future after 140 years

Mon, 09 Nov 2009 10:04:21 +0000

From an Editorial in Nature (462, 12; 5 November 2009):
Nature's first issue appeared on Thursday 4 November 1869. 7,269 issues later, a little bit of satisfaction may be in order given that the journal has survived wars and, so far, the Internet's onslaught on traditional models of publishing. Nature's papers are highly cited for what seem to us to be good reasons. Lots of people (millions online every month) want to read the journal. So where do we need to be self-critical? Readers will no doubt have many answers, but here are a few.

> Others sometimes put more weight on our judgement than it can justifiably bear. Large grants, philanthropic donations and personal chairs have been awarded on the strength of a paper in Nature — in effect, using editors' decisions as a surrogate for independent judgement. This is an abdication of the decision-makers' responsibility, and is a pitfall to be avoided.

> We endorse efforts to create systems that reach beyond the crudeness of the impact factor — systems that make transparent the citations and other effects of papers, and that record impacts of scientists' other work, such as their contributions to databases and the hard slog of peer review.

> We have enhanced our journalism and externally authored opinion in recent years, and readers can anticipate further developments ahead.

> Nature has to reflect the values of its authors and readers. The core values of science — objectivity, independence, self-critical thinking and a relentless urge to observe, experiment and explore — are also important principles of good journalism and editing. As an unusual hybrid of magazine and journal, Nature can only retain readers' respect if it follows those principles while adding substantial value to the lives and work of researchers and others seriously interested in science. Our commitment to fulfil these ambitions is as strong as it has ever been.

More about Nature.
Nature's own history website.

Cover competition at EMBO Journal

Fri, 06 Nov 2009 10:23:13 +0000

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

Thu, 05 Nov 2009 08:18:58 +0000

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?"

Wed, 04 Nov 2009 07:43:15 +0000

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

Tue, 03 Nov 2009 07:54:19 +0000

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

Mon, 02 Nov 2009 08:16:10 +0000

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.