Nature’s past and future after 140 years

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.

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

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.

Free poster on the transcriptome at Nature Reviews Genetics

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.

Nature special issue on human genetics

The flow of human genetic information is growing into a deluge: from high throughput sequencing to genome wide association studies to copy number variation to personal genetic tests. In today’s (8 October 2009) issue, Nature assesses their biological and medical value so far and asks – where should the field go next?

Nature ’s special issue on human genetics can be found here.

Selected content is free to access online for one month from date of issue:

Opinion: An agenda for personalized medicine

Nature 461, 724-726 (2009).

Pauline C. Ng, Sarah S. Murray, Samuel Levy and J. Craig Venter find differences in results from two direct-toconsumer genetics-testing companies. They therefore give nine recommendations to improve predictions.

News Feature: Human genetics: Hit or miss?

Nature 461, 712-714 (2009).

Genome-wide association studies have identified hundreds of genetic clues to disease. Kelly Rae Chi looks at three to see just how on-target the approach seems to be.

Review Article: Finding the missing heritability of complex diseases

Teri A. Manolio et al. Nature 461, 747-753 (2009).

An examination of the potential sources of missing heritability and possible research strategies to enhance the potential of genetics of complex diseases for effective prevention or treatment.

And this week’s Nature podcast features an interview with Pauline Ng in which she discusses personal genomics and other highlights from the special issue.

More from Nature’s human genomics special issue.

Join Nature at the American Society of Human Genetics, 20-24 October 2009 in Honolulu. Visit booth #803 to pick up your free copy of the special human genetics themed issue and ask a representitive at the booth about our special 30% conference discount rate.

Other Nature news special collections.

Nature web focuses.

Nature Methods celebrates methods (and being 5)

Nature Methods is five years old. To celebrate this anniversary, the journal looks at methodological development and its role in scientific inquiry in its October Editorial, In celebration of methods (Nat. Meth. 6, 687; 2009) and a special focus of commentaries discussing the impact and progress of methodological developments in the life sciences. The focus also includes a fun selection of papers and covers from the past five years.

Nature Methods’ Chief Editor, Daniel Evanko, writes on Methagora, the journal’s blog: "It’s hard to believe that five years have gone by since Veronique Kiermer, Nicole Rusk and myself saw the first issue of Nature Methods go out the door. In some ways it doesn’t feel like it was that long ago while in others it feels like much, much longer. But it has certainly been a rewarding and stimulating five years and we are thrilled with the success that Nature Methods has enjoyed. To help celebrate, Veronique asked a local pastry shop run her friend called “How Sweet It Is” to bake a cake using the cover image of our inaugural issue. It turned out spectacularly and tasted just as good. I’m hoping to convince Veronique to post a blog entry describing the undertaking with accompanying pictures." Check out Methagora for the mouth-watering cover images and updates about the anniversary celebrations.

Nature Milestones in Light Microscopy

Nature Milestones in Light Microscopy is published today, 1 October 2009. Nature Milestones in Light Microscopy is a collaboration from Nature Methods, Nature Cell Biology and Nature Reviews Molecular Cell Biology, focusing on ground-breaking advances in light microscopy research. The field of light microscopy has revolutionized our understanding of cell biology and is continuing as new imaging tools and techniques are developed. The Nature Milestones in Light Microscopy supplement contains a series of short articles, called Milestones, presenting key developments in the field, written by editors from the Nature Publishing Group. In addition, selected content from Nature Milestones in Light Microscopy are freely available online.

Print copies of the supplement will be available at the NPG stand at the Society for Neuroscience (SFN) conference in October 2009 and the American Society for Cell Biology (ASCB) conference in December 2009.

Also of interest is Nature‘s recent News special on microscopy, consisting of a slideshow, News Features, opinion and various other articles. Microscopes are biologists’ window to life — and advances in microscopy over recent years are revealing some breathtaking new views. The Nature special profiles five microscopes that are changing the ways that researchers see the world, and examines the challenges involved in collecting and interpreting the microscopic image.

Nature Genetics focus on copy number variation

Individual genomes vary, not only in sequence, but in both their structural organization and in the number of sequence copies they contain. The technology now exists to understand the mechanisms by which genomes diverge, so we can investigate the consequences of copy number variation for gene expression and clinical phenotypes. This month (September), Nature Genetics presents a Focus of articles published in Nature and Nature Genetics, free to read online, on copy number variation, which highlights the complementary roles of paired-end sequencing and oligonucleotide array technology in research discovery.

As well as an Editorial (‘Making diversity count’) and an NPG library of relevant past articles, the Focus consists of the following research articles:

A highly annotated whole-genome sequence of a Korean individual

Jong-Il Kim et al.

The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans

Feng Zhang et al.

Increased LIS1 expression affects human and mouse brain development

Weimin Bi et al.

Mapping and sequencing of structural variation from eight human genomes

Jeffrey M Kidd et al.

Closing gaps in the human genome with fosmid resources generated from multiple individuals

Donald Bovee et al.

Nature Reviews Neuroscience web focus on CNS evolution

Charles Darwin’s theory of descent with modification by means of natural selection has stood the test of time, with new discoveries in genetics and the mathematical basis of natural selection providing ever growing evidence for the theory. The October issue of Nature Reviews Neuroscience — contains an online focus, free to access online for six months from the issue date, celebrating the contribution of Darwin’s ideas to our current understanding of the evolution of the nervous system. The articles in this special issue discuss the molecular, cellular and structural changes that have contributed to CNS (central nervous system) evolution and their functional consequences. The focus consists of reviews and perspectives on:

The origin and evolution of synapses

Tomás J. Ryan & Seth G. N. Grant

Considering the evolution of regeneration in the central nervous system

Elly M. Tanaka & Patrizia Ferretti

Evolution of the neocortex: a perspective from developmental biology

Pasko Rakic

Chordate roots of the vertebrate nervous system: expanding the molecular toolkit

Linda Z. Holland

Sleep viewed as a state of adaptive inactivity

Jerome M. Siegel

MicroRNAs tell an evo–devo story

Kenneth S. Kosik

Editors’ summary of these articles.

NPG library of articles on CNS evolution.

Nature celebrates Darwin 200.

Nature Publishing Group celebrates Darwin 200 with a range of articles from its journals.

Fifteen evolutionary gems from Nature’s archives.

More about Nature Reviews Neuroscience.

New NPG journal: Cell Death & Disease

Via press release: Nature Publishing Group (NPG) and the Associazione Differenziamento e Morte Cellulare (ADMC) have announced a new open access journal, Cell Death & Disease. Launching in January 2010, Cell Death & Disease will explore the area of cell death from a translational medicine perspective. The journal is now accepting submissions.

Cell Death & Disease is a sister journal to the well-established and highly respected journal Cell Death & Differentiation. Together, the two journals provide a unified forum for scientists, clinicians and members of the pharmaceutical and biotechnology industry.

Cell Death & Disease is devoted to the biology of cell death in the pathogenesis of human diseases or relevant animal models. The journal aims to publish papers that present novel observations in the field of cell death, with pathophysiological or medical implications. Particular emphasis will be given to clinical, translational and applied research through its five sections: experimental medicine, cancer, immunity, internal medicine and neuroscience.

Cell Death & Disease will be online only and will make all content freely available to all researchers worldwide. There will be an processing charge of £2,000 / $3,000 / €2,400 for each article accepted for publication.

The editorial team is led by Gerry Melino, Guido Kroemer and Pierluigi Nicotera, and will include a highly respected international editorial board.

Cell Death & Disease preliminary website.

Cell Death & Disease: journal scope.

Submit your manuscript to Cell Death & Disease.

The journal’s guide to authors.

Summary of author benefits.

Data sharing discussed at Nature and Nature Network

Sharing data is good. But sharing your own data? That can get complicated. As two research communities who held meetings on this question in Rome and in Toronto in May report their proposals to promote data sharing in biology, a special issue of Nature (10 September 2009) examines the cultural and technical hurdles that can get in the way of good intentions. Some of the authors of these proposals are participating in two online forums (Rome and Toronto) at Nature Network – so please accept our invitation to visit and have your say on these questions.

More details:

The two research communities held meetings with a broad range of stakeholders to discuss ways to promote data sharing in biology. Data producers and users met at a workshop in Toronto to discuss the benefits and best practices of rapid data release prior to publication. Ewan Birney, Tom Hudson and colleagues report the main conclusions of these discussions in a community statement, free to access here.

The Toronto group propose that the principles for early release of genomics data should be extended to other large datasets in biology and medicine. A grace period should be allowed, if requested, to enable data producers to analyse and publish their dataset, but this should be limited to one year. The authors also suggest a set of best practices for funding agencies, scientists and journal editors.

The recommendations are intended to spark community discussion on this subject. Ewan Birney, Tom Hudson and others will be responding to reader comments in our Nature Network forum. Be sure to have your say.

Mouse researchers, along with funding agencies and publishers, met in Rome to address the barriers preventing more effective sharing of data and biomaterials — particularly mouse strains and embryonic stem cells. Their agenda, free to access here, suggests guidelines to enable sharing of materials under the least restrictive terms, avoiding material transfer agreements where possible.

The Rome participants argue that funding organizations, journals and researchers need to work together to encourage better use of public repositories and to promote a ‘research commons’ in mouse biology.

The recommendations are intended to spark community discussion on this subject. Paul Schofield and others will be responding to reader comments in our Nature Network forum. Be sure to have your say.

See also the Editorial (free to access online) in the same issue of Nature (461, 145; 2009): ’Data’s shameful neglect’, opining that research cannot flourish if data are not preserved and made accessible. All concerned must act accordingly.

Nature’s special issue on data sharing.