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Category Archives: Editorials
Cite responsibly
In this month’s Editorial, we discuss why it is crucial for scientists to give credit to previous work by referencing responsibly. This is not always an easy task, especially in multidisciplinary research, so we provide what we hope are some helpful tips for constructing optimal reference lists.
Other Nature Research journals have also published editorials on this topic in past years (see, for example, pieces written in Nature Cell Biology and Nature Chemical Biology).
Our official policy about referencing states in very general terms that authors must appropriately cite and describe previously published relevant intellectual and technical contributions. The policy allows for citations of preprints and conference abstracts, but if such a paper has been peer-reviewed and published in a journal, the journal paper should serve as the reference. Expert reviewers often identify relevant papers that authors might have missed, and editors can help shape reference lists prior to acceptance, but ultimately, authors bear the responsibility of assigning appropriate credit to work that came before.
We are happy to answer any questions, whether general or paper-specific, about appropriate referencing.
Method of the Year 2016
As is our tradition every year we have chosen a method, or in this case a set of methods, that have experienced rapid growth in the last years. This year’s choice of epitranscriptome analysis does not comprise a single technique but is based on advances in detecting, enriching and profiling base modifications on all RNA species.
Some of these modifications are abundant and have known functions, others are rare and their role is still obscure. We believe recent methodological advances, as detailed in a Review by Chengqi Yi and colleagues, lay the groundwork for a comprehensive profiling of some of these marks that will shed light on their role in the cell.
Our selection of methods to watch highlights areas we think will experience growth in the coming year and be influential in biological research: from global metabolomics, to RNA-targeting CRISPR, to elucidating single cell function and faster brain imaging. We do not claim to provide a comprehensive list and our choices may be biased by our fields of interest. We do hope you enjoy reading this feature and if you disagree with us, or if you think we have overlooked an important area, please let us know.
An archive for raw EM data
Earlier this week we published a Correspondence describing EMPIAR, a public archive for raw 2D electron microscopy (EM) image data.
While the established Electron Microscopy Data Bank (EMDB) hosts the 3D EM map data required by most journals for publication, the EM community has long been calling for an archive to host the raw 2D image data underlying the 3D maps, as highlighted in our Method of the Year 2015 feature. EMPIAR, a pilot project from the Protein Data Bank in Europe (PDBe), now fills this need.
At Nature Methods we support this archive as a welcome development in the rapidly growing 3D EM field that will enhance transparency, reproducibility, and facilitate the development and refinement of data analysis tools. Though we do not require that our authors deposit their 2D EM image data in EMPIAR, we do encourage it. We urge researchers to make use of the archive and provide feedback to the developers in order to ensure that it is meeting the needs of the field.
Any interested readers without a subscription or site license may read the full text of the Correspondence here.
Understanding and documenting variation in human genomes
To understand disease one needs to understand the genetic variations that underlie it. Many tools exist that predict the deleteriousness of variants in the human genome; PolyPhen2, SIFT or CADD (combined annotation dependent depletion), to name only a few examples. On page 109 of our March issue Yuval Itan et al. present the mutation significance cutoff (MSC) to replace a global threshold for calling variants deleterious, often used for CADD scores, with a gene-level threshold. For MSC, as for any other variant prediction tool, it was important to validate the quality of the predictions with variants known to be deleterious. Established mutation databases are often used as ground truth to test the quality of prediction tools. MSC, for example, was validated against variants found in two large databases, HGMD and ClinVar.
The February editorial discusses the strength and limitations of large human variation databases and emphasizes the importance of sharing variant data in publicly accessible databases. We encourage our readers to share their experience with these databases and to recommend their favorite ones.
The ethics of self-organizing tissue
Reply
It becomes increasingly clear that stem cells are able to form remarkably complex structures in vitro, if they are handled right. In this month’s issue, two pieces raise the question of whether recent developments in methods for patterning embryonic stem cells in vitro raise potential ethical, regulatory or public perception concerns, or if they may do so in the future.
You can find the commentary from leading stem cell and developmental biologists here [https://www.nature.com/nmeth/journal/v12/n10/full/nmeth.3586.html] and the editorial here [https://www.nature.com/nmeth/journal/v12/n10/full/nmeth.3618.html].
We note that some of these matters were also brought up in a paper published at the end of last year (Cells Tissues Organs 2014;199(4):221-7).
DIY Biolabs – and why they matter
When proponents of Do-it-yourself Biology explain their motivation for getting involved in the movement they often resort to colorful imagery. Take for example Patrick D’haeseleer who helps organize the Counter Culture Labs in the San Francisco Bay Area. He asks, “When the first village tamed fire, the neighboring village was freaking out. Should only the village elders be allowed to make fire or should we teach everybody?” “Any new technology has risk, but it behooves us to have all citizens know how these technologies work and what the risks are. “ he continues, “ the technology needs to be democratized because it will dominate the 21th century.”
In our September editorial we encouraged people to look up DIY Biolabs in their backyard and consider getting involved.
A recent editorial in Nature also addresses the topic of Citizen scientists, focusing on sample collection and data analysis. The authors raise the question how conflict of interest should be addressed and recommend full transparency about motives and ambitions of citizen scientists.
We agree that it is important to be upfront about one’s involvement in scientific endeavors, but motives conflicting with those of established scientists need not preclude participation in the scientific process. As people learn more about methods and their potential, they may change their position on certain issues, or, if not, they will have a better grounded basis for what they belief. Either outcome is a success.
Methods comparisons are hard
Comparing methods in a fair and informative manner is often not straightforward. Benchmark data sets, thoughtfully applied metrics and clear reporting can help. Read this month’s editorial here.
Are there methodological benchmarks you think your community needs?
Funding crisis in basic research
The editorial in our November issue discusses the shortage of funding for basic science in the US and how the ramifications of funding shortfalls on society at large can be measured. But the US is not alone in facing a much tightened research budget.
Outcries over changes in funding polices can be heard also in many European countries.
In a column in Nature on October 9, Amaya Moro-Martin, a member of the governing board of Euroscience describes the problems and sums their root cause up by saying that “the policy-makers and leaders of an increasing number of nations have completely lost touch with the reality of research.” The numbers she quotes are indeed stark: Italy’s spending on basic research has dropped precipitously and recruitment of scientists has fallen by 90%. And the situation is equally dire if not more so in Spain, Greece and Portugal. She predicts that these budget cuts are triggering a brain drain from southern to northern Europe and, more seriously, lead people to leave research altogether in search for a more stable career.
The focus of the European research commissioner on applied rather than basic research will not solve this problem. Applied research does not ask the fundamental questions that underlie new discoveries, instead it improves upon what is already known.
Scientists in Canada voice similar concerns that their government puts increasing focus on funding projects that offer immediate commercial value rather than supporting basic research. A summary by the Canadian Association of University Teachers summarizes the drop in Canadian federal funding for basic Research over the last 8 years. The authors urge their government to make basic research a priority and leave the awarding of grants to peers rather than side stepping this process by determining which projects or institutions will receive money.
Ten years of Methods
Our tenth anniversary is an occasion to celebrate methods development!
In our Anniversary Issue, we highlight ten areas of methods development, among many candidates, that have had a lot of impact on biological research over the last decade. We also take the opportunity to look back at the papers we have published in some of these areas. We hope to add similar descriptions for all our ‘top-ten methods’ in coming months.
You can look back at the last ten years of Nature Methods in the following areas here: