Readjusting observational grids in dragonfly field guides.

Wildlife field guide books present salient features of species, from colour and form to behaviour, and give their readers a vocabulary to express what these features look like. Such structures for observation, or observational grids, allow users to identify wildlife species through what Law and Lynch have called 'the difference that makes the difference'. In this article, we show how these grids, and the characteristics that distinguish species, change over time in response to wider concerns in the community that use and make the field guides. We use the development of Dutch field guides for dragonflies to show how the ethics of observing wildlife, the recreational value of dragonfly observation, the affordances of observational tools, and biodiversity monitoring and conservation goals all have repercussions for how dragonflies are to be identified. Ultimately, this affects not only how dragonflies are to be observed and identified, but also what is taken to be 'out there'. The article is based on a transdisciplinary cooperation between a dragonfly enthusiast with emic knowledge and access, and an STS researcher. We hope the articulation of our approach might inspire analyses of other observational practices and communities.

Misidentified biomedical resources: Journal guidelines are not a quick fix.

Biomedical researchers routinely use a variety of biological models and resources, such as cultured cell lines, antibodies and laboratory animals. Unfortunately, these resources are not flawless: cell lines can be misidentified; for antibodies, problems with specificity, lot-to-lot consistency and sensitivity are common; and the reliability of animal models is questioned due to poor translation of animal studies to human clinical trials. In some cases, these problems can render the results of a study meaningless. As a response, some journals have implemented guidelines regarding the use and reporting of cell lines, antibodies and laboratory animals. In our study we use a portfolio of existing and newly created datasets to investigate identification and authentication information of cell lines, antibodies and organisms before and after guideline introduction, compared to journals without guidelines. We observed a general improvement of reporting quality over time, which the implementation of guidelines accelerated only in some cases. We therefore conclude that the effectiveness of journal guidelines is likely to be context dependent, affected by factors such as implementation conditions, research community support and monitoring and resource availability. Hence, journal reporting guidelines in themselves are not a quick fix to repair shortcomings in biomedical resource documentation, even though they can be part of the solution.

Reducing versus Embracing Variation as Strategies for Reproducibility: The Microbiome of Laboratory Mice.

Irreproducibility is a well-recognized problem in biomedical animal experimentation. Phenotypic variation in animal models is one of the many challenging causes of irreproducibility. How to deal with phenotypic variation in experimental designs is a topic of debate. Both reducing and embracing variation are highlighted as strategies for reproducibility. In this theoretical review, we use variation in mouse microbiome composition as an example to analyze this ongoing discussion, drawing on both animal research and philosophy of science. We provide a conceptual explanation of reproducibility and analyze how the microbiome affects mouse phenotypes to demonstrate that the role of the microbiome in irreproducibility can be understood in two ways: (i) the microbiome can act as a confounding factor, and (ii) the result may not be generalizable to mice harboring a different microbiome composition. We elucidate that reducing variation minimizes confounding, whereas embracing variation ensures generalizability. These contrasting strategies make dealing with variation in experimental designs extremely complex. Here, we conclude that the most effective strategy depends on the specific research aim and question. The field of biomedical animal experimentation is too broad to identify a single optimal strategy. Thus, dealing with variation should be considered on a case-by-case basis, and awareness amongst researchers is essential.

Innovating editorial practices: academic publishers at work.

BACKGROUND: Triggered by a series of controversies and diversifying expectations of editorial practices, several innovative peer review procedures and supporting technologies have been proposed. However, adoption of these new initiatives seems slow. This raises questions about the wider conditions for peer review change and about the considerations that inform decisions to innovate. We set out to study the structure of commercial publishers' editorial process, to reveal how the benefits of peer review innovations are understood, and to describe the considerations that inform the implementation of innovations. METHODS: We carried out field visits to the editorial office of two large academic publishers housing the editorial staff of several hundreds of journals, to study their editorial process, and interviewed editors not affiliated with large publishers. Field notes were transcribed and analysed using coding software. RESULTS: At the publishers we analysed, the decision-making structure seems to show both clear patterns of hierarchy and layering of the different editorial practices. While information about new initiatives circulates widely, their implementation depends on assessment of stakeholder's wishes, impact on reputation, efficiency and implementation costs, with final decisions left to managers at the top of the internal hierarchy. Main tensions arise between commercial and substantial arguments. The editorial process is closely connected to commercial practices of creating business value, and the very specific terms in which business value is understood, such as reputation considerations and the urge to increase efficiency. Journals independent of large commercial publishers tend to have less hierarchically structured processes, report more flexibility to implement innovations, and to a greater extent decouple commercial and editorial perspectives. CONCLUSION: Our study demonstrates that peer review innovations are partly to be understood in light of commercial considerations related to reputation, efficiency and implementations costs. These arguments extend beyond previously studied topics in publishing economics, including publishers' choice for business or publication models and reach into the very heart of the editorial and peer review process.

The effect of journal guidelines on the reporting of antibody validation.

BACKGROUND: Despite the widespread use of antibodies as a research tool, problems with specificity, lot-to-lot consistency and sensitivity commonly occur and may be important contributing factors to the 'replication crisis' in biomedical research. This makes the validation of antibodies and accurate reporting of this validation in the scientific literature extremely important. Therefore, some journals now require authors to comply with antibody reporting guidelines. METHODS: We used a quasi-experimental approach to assess the effectiveness of such journal guidelines in improving antibody reporting in the scientific literature. In a sample of 120 publications, we compared the reporting of antibody validation and identification information in two journals with guidelines (Nature and the Journal of Comparative Neurology) with two journals without guidelines (Science and Neuroscience), before and after the introduction of these guidelines. RESULTS: Our results suggest that the implementation of antibody reporting guidelines might have some influence on the reporting of antibody validation information. The percentage of validated antibodies per article slightly increased from 39% to 57% in journals with guidelines, whereas this percentage decreased from 23% to 14% in journals without guidelines. Furthermore, the reporting of validation information of all primary antibodies increased by 23 percentage points in the journals with guidelines (OR = 2.80, 95% CI = 0.96-INF; adjusted p = 1, one-tailed), compared to a decrease of 13 percentage points in journals without guidelines. Fortunately, the guidelines seem to be more effective in improving the reporting of antibody identification information. The reporting of identification information of all primary antibodies used in a study increased by 58 percentage points (OR = 17.8, 95% CI = 4.8-INF; adjusted p = 0.0003, one-tailed) in journals with guidelines. This percentage also slightly increased in journals without guidelines (by 18 percentage points), suggesting an overall increased awareness of the importance of antibody identifiability. Moreover, this suggests that reporting guidelines mostly have an influence on the reporting of information that is relatively easy to provide. A small increase in the reporting of validation by referencing the scientific literature or the manufacturer's data also indicates this. CONCLUSION: Combined with the results of previous studies on journal guidelines, our study suggests that the effect of journal antibody guidelines on validation practices by themselves may be limited, since they mostly seem to improve antibody identification instead of actual experimental validation. These guidelines, therefore, may require additional measures to ensure effective implementation. However, due to the explorative nature of our study and our small sample size, we must remain cautious towards other factors that might have played a role in the observed change in antibody reporting behaviour.

On the Willingness to Report and the Consequences of Reporting Research Misconduct: The Role of Power Relations.

While attention to research integrity has been growing over the past decades, the processes of signalling and denouncing cases of research misconduct remain largely unstudied. In this article, we develop a theoretically and empirically informed understanding of the causes and consequences of reporting research misconduct in terms of power relations. We study the reporting process based on a multinational survey at eight European universities (N = 1126). Using qualitative data that witnesses of research misconduct or of questionable research practices provided, we aim to examine actors' rationales for reporting and not reporting misconduct, how they report it and the perceived consequences of reporting. In particular we study how research seniority, the temporality of work appointments, and gender could impact the likelihood of cases being reported and of reporting leading to constructive organisational changes. Our findings suggest that these aspects of power relations play a role in the reporting of research misconduct. Our analysis contributes to a better understanding of research misconduct in an academic context. Specifically, we elucidate the processes that affect researchers' ability and willingness to report research misconduct, and the likelihood of universities taking action. Based on our findings, we outline specific propositions that future research can test as well as provide recommendations for policy improvement.

The ghosts of HeLa: How cell line misidentification contaminates the scientific literature.

While problems with cell line misidentification have been known for decades, an unknown number of published papers remains in circulation reporting on the wrong cells without warning or correction. Here we attempt to make a conservative estimate of this 'contaminated' literature. We found 32,755 articles reporting on research with misidentified cells, in turn cited by an estimated half a million other papers. The contamination of the literature is not decreasing over time and is anything but restricted to countries in the periphery of global science. The decades-old and often contentious attempts to stop misidentification of cell lines have proven to be insufficient. The contamination of the literature calls for a fair and reasonable notification system, warning users and readers to interpret these papers with appropriate care.

The Academic Manifesto: From an Occupied to a Public University.

Universities are occupied by management, a regime obsessed with 'accountability' through measurement, increased competition, efficiency, 'excellence', and misconceived economic salvation. Given the occupation's absurd side-effects, we ask ourselves how management has succeeded in taking over our precious universities. An alternative vision for the academic future consists of a public university, more akin to a socially engaged knowledge commons than to a corporation. We suggest some provocative measures to bring about such a university. However, as management seems impervious to cogent arguments, such changes can only happen if academics take action. Hence, we explore several strategies for a renewed university politics.

Is Inequality Among Universities Increasing? Gini Coefficients and the Elusive Rise of Elite Universities.

One of the unintended consequences of the New Public Management (NPM) in universities is often feared to be a division between elite institutions focused on research and large institutions with teaching missions. However, institutional isomorphisms provide counter-incentives. For example, university rankings focus on certain output parameters such as publications, but not on others (e.g., patents). In this study, we apply Gini coefficients to university rankings in order to assess whether universities are becoming more unequal, at the level of both the world and individual nations. Our results do not support the thesis that universities are becoming more unequal. If anything, we predominantly find homogenisation, both at the level of the global comparisons and nationally. In a more restricted dataset (using only publications in the natural and life sciences), we find increasing inequality for those countries, which used NPM during the 1990s, but not during the 2000s. Our findings suggest that increased output steering from the policy side leads to a global conformation to performance standards.