Reporting science and conflicts of interest in the lay press

Background

Forthright reporting of financial ties and conflicts of interest of researchers is associated with public trust in and esteem for the scientific enterprise.

Methods/Principal Findings

We searched Lexis/Nexis Academic News for the top news stories in science published in 2004 and 2005. We conducted a content analysis of 1152 newspaper stories. Funders of the research were identified in 38% of stories, financial ties of the researchers were reported in 11% of stories, and 5% reported financial ties of sources quoted. Of 73 stories not reporting on financial ties, 27% had financial ties publicly disclosed in scholarly journals.

Conclusions/Significance

Because science journalists often did not report conflict of interest information, adherence to gold-standard recommendations for science journalism was low. Journalists work under many different constraints, but nonetheless news reports of scientific research were incomplete, potentially eroding public trust in science.     

Beyond the genome: Reconstituting the new genetics

The mapping and sequencing of the human genome has been the 'Holy Grail' of the new genetics, and its publication marks a turning point in the development of modern biotechnology. However, the question remains: what has been the impact of this discovery on how biotechnology develops in science, and in society at large? Using concepts developed in the social studies of science and technology, the paper begins by rehearsing the historical development of the Human Genome Project (HGP), and suggests that its translation into genomics has been achieved through a process of 'black-boxing' to ensure stabilization. It continues by exploring the extent to which the move to genomics is part of a paradigm shift in biotechnology resulting from the conceptual and organizational changes that have occurred following the completion of HGP. The discussion then focuses on whether genomics can be seen as part of the development of socially robust knowledge in late modernity. The paper suggests that there is strong evidence that a transformation is indeed taking place. It concludes by sketching a social scientific agenda for investigating the reconstitution of the new genetics in a post-genomic era using a 'situated' analytic approach based on an understanding of techno-scientific change as both emergent and contingent.     

Learning about cancer genes through invertebrate genetics.

Genetic studies in yeast, nematodes and Drosophila are revealing the signal transduction pathways that regulate differentiation and cell proliferation. Some of the critical molecules involved are homologous to proto-oncogenes and others are likely to be analogous to the products of tumor suppressor genes.     

Beyond Bonferroni: less conservative analyses for conservation genetics

Studies in conservation genetics often attempt to determine genetic differentiation between two or more temporally or geographically distinct sample collections. Pairwise p-values from Fisher’s exact tests or contingency Chi-square tests are commonly reported with a Bonferroni correction for multiple tests. While the Bonferroni correction controls the experiment-wise α, this correction is very conservative and results in greatly diminished power to detect differentiation among pairs of sample collections. An alternative is to control the false discovery rate (FDR) that provides increased power, but this method only maintains experiment-wise α when none of the pairwise comparisons are significant. Recent modifications to the FDR method provide a moderate approach to determining significance level. Simulations reveal that critical values of multiple comparison tests with both the Bonferroni method and a modified FDR method approach a minimum asymptote very near zero as the number of tests gets large, but the Bonferroni method approaches zero much more rapidly than the modified FDR method. I compared pairwise significance from three published studies using three critical values corresponding to Bonferroni, FDR, and modified FDR methods. Results suggest that the modified FDR method may provide the most biologically important critical value for evaluating significance of population differentiation in conservation genetics.␣Ultimately, more thorough reporting of statistical significance is needed to allow interpretation of biological significance of genetic differentiation among populations.An erratum to this article can be found at     

Beyond genetics. Influence of dietary factors and gut microbiota on type 1 diabetes

Type 1 diabetes (T1D) is an autoimmune disease ultimately leading to destruction of insulin secreting β-cells in the pancreas. Genetic susceptibility plays an important role in T1D etiology, but even mono-zygotic twins only have a concordance rate of around 50%, underlining that other factors than purely genetic are involved in disease development. Here we review the influence of dietary and environmental factors on T1D development in humans as well as animal models. Even though data are still inconclusive, there are strong indications that gut microbiota dysbiosis plays an important role in T1D development and evidence from animal models suggests that gut microbiota manipulation might prove valuable in future prevention of T1D in genetically susceptible individuals.     

Some thoughts about genetics, differentiation, and malignancy.

This article deals with three related questions: (1) whether malignancy is determined by genetic or epigenetic mechanisms; (2) whether epigenetic mechanisms, as conventionally defined, actually exist; (3) what criteria are appropriate for defining dominance or recessiveness of the malignant state in cell fusion experiments.     

Educating health-care professionals about genetics and genomics

To biomedical researchers, this is the 'genome era'. Advances in genetics and genomics such as the sequence of the human genome, the human haplotype map, open access databases, cheaper genotyping and chemical genomics have already transformed basic and translational biomedical research. However, for most clinicians, the genome era has not yet arrived. For genomics to have an effect on clinical practice that is comparable to its impact on research will require advances in the genomic literacy of health-care providers. Here we describe the knowledge, skills and attitudes that genomic medicine will require, and approaches to integrate them into the health-care community.     

Quantifying introgression risk with realistic population genetics

Introgression is the permanent incorporation of genes from the genome of one population into another. This can have severe consequences, such as extinction of endemic species, or the spread of transgenes. Quantification of the risk of introgression is an important component of genetically modified crop regulation. Most theoretical introgression studies aimed at such quantification disregard one or more of the most important factors concerning introgression: realistic genetical mechanisms, repeated invasions and stochasticity. In addition, the use of linkage as a risk mitigation strategy has not been studied properly yet with genetic introgression models. Current genetic introgression studies fail to take repeated invasions and demographic stochasticity into account properly, and use incorrect measures of introgression risk that can be manipulated by arbitrary choices. In this study, we present proper methods for risk quantification that overcome these difficulties. We generalize a probabilistic risk measure, the so-called hazard rate of introgression, for application to introgression models with complex genetics and small natural population sizes. We illustrate the method by studying the effects of linkage and recombination on transgene introgression risk at different population sizes.