A proposal for validation of antibodies. The International Working Group on Antibody Validation (IWGAV) is an independent group of international scientists with diverse research interests in the field of protein biology. Thermo Fisher Scientific provided financial support to the IWGAV in 2015 to spearhead the development of industry standards and help combat the common challenges associated with antibody specificity and reproducibility.
In this commentary, published in Nature Methods, the IWGAV proposed a set of standard guidelines for validating antibodies, guidelines that may be used in an application-specific manner and that in part take advantage of technologies recently introduced by the genomics and proteomics communities. The IWGAV suggests five conceptual pillars for validation of antibodies: (i) genetic strategies, (ii) orthogonal strategies, (iii) independent antibody strategies, (iv) expression of tagged proteins, and (v) immunocapture followed by mass spectrometry (MS).
The ultimate goal is that through continued engagement of all stakeholders, comprehensive guidelines will be established that improve the reproducibility of biomedical studies and reduce the amount of time and resources spent on inappropriate immunoreagents.
Truth in Science Publishing: A Personal Perspective. In this perspective article, published in PLoS Biology, Nobel laureate Thomas C. Südhof described some of the current challenges to the peer review system that have endangered public acceptance of science and mentioned possible avenues to address these issues, e.g. establishing basic rules that render peer review more transparent, such as publishing the reviews.
Furthermore, he also discussed ‘the other pillar of scientific truth, reproducibility’, and presented multiple problems increasingly imperil reproducibility. Here, Südhof calls for checklists that ensure that proper controls and reagent validations are present when a paper is submitted, and such validations should be required for the supplementary materials. Ideally, scientists should recruit other groups to independently reproduce key results. Although his ideas are not new, with this article, he strongly emphasizes that the need for action has never been more urgent than now and that ‘we should speak up, express our concerns and demand rules that inject accountability into the system.’
Gene name errors are widespread in the scientific literature. The spreadsheet software Microsoft Excel, when used with default settings, is known to convert gene names to dates and floating-point numbers. In this study by Ziemann et al., a programmatic scan of leading genomics journals was conducted which revealed that approximately one-fifth of papers with supplementary Excel gene lists contain erroneous gene name conversions.
Although the automatic conversion of gene symbols to dates and floating-point numbers in Excel were first highlighted over a decade ago, inadvertent gene name conversion errors persist in the scientific literature. However, these should be easy to avoid if researchers, reviewers, editorial staff and database curators remain vigilant.
Citation Metrics: A Primer on How (Not) to Normalize. It is well documented that citation metrics vary considerably with the area of knowledge, the publication age, the type of document and the coverage of the database where citations were collected. However, Citation metrics are increasingly used to appraise published research. In this PLoS Biology article by John P.A. Ioannidis et al., the authors evaluate the advantages and disadvantages of metrics normalization using different approaches, as well as the challenges of this bibliometric exercise. Diverse citation metrics may offer complementary insights, and, once their limitations are properly recognized, judicious use of these metrics can be very useful, especially when applied in a robust and transparent manner.
Scientific integrity resource guide: Efforts by federal agencies, foundations, nonprofit organizations, professional societies, and academia in the United States. Scientific integrity is at the forefront of the scientific research enterprise. This paper, published in Food Science and Nutrition, provides an systematic overview of key existing efforts to increase scientific integrity by federal agencies, foundations, nonprofit organizations, professional societies, and academia in the United States from 1989 to April 2016. It serves as a resource for the scientific community on scientific integrity work and helps to identify areas in which more action is needed. As the authors correctly state: ‘All the same, scientific integrity needs to remain visible in the scientific community and evolve along with new research paradigms. High priority in instilling these values falls upon all stakeholders.’