Knowledge in the dark: scientific challenges and ways forward

A key dimension of our current era is Big Data, the rapid rise in produced data and information; a key frustration is that we are nonetheless living in an age of ignorance, as the real knowledge and understanding of people does not seem to be substantially increasing. This development has critical consequences, for example it limits the ability to find and apply effective solutions to pressing environmental and socioeconomic challenges. Here, we propose the concept of “knowledge in the dark”—or short: dark knowledge—and outline how it can help clarify key reasons for this development: (i) production of biased, erroneous, or fabricated data and information; (ii) inaccessibility and (iii) incomprehensibility of data and information; and (iv) loss of previous knowledge. Even in the academic realm, where financial interests are less pronounced than in the private sector, several factors lead to dark knowledge, that is they inhibit a more substantial increase in knowledge and understanding. We highlight four of these factors—loss of academic freedom, research biases, lack of reproducibility, and the Scientific tower of Babel—and offer ways to tackle them, for example establishing an international court of arbitration for research and developing advanced tools for research synthesis

Loss of G–A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif

Upon binding to the 15.5K protein, two tandem-sheared G–A base pairs are formed in the internal loop of the kink-turn motif of U4 snRNA (Kt-U4). We have reported that the folding of Kt-U4 is assisted by protein binding. Unstable interactions that contribute to a large opening of the free RNA (‘k–e motion’) were identified using locally enhanced sampling molecular dynamics simulations, results that agree with experiments. A detailed analysis of the simulations reveals that the k–e motion in Kt-U4 is triggered both by loss of G–A base pairs in the internal loop and backbone flexibility in the stems. Essential dynamics show that the loss of G–A base pairs is correlated along the first mode but anti-correlated along the third mode with the k–e motion. Moreover, when enhanced sampling was confined to the internal loop, the RNA adopted an alternative conformation characterized by a sharper kink, opening of G–A base pairs and modified stacking interactions. Thus, loss of G–A base pairs is insufficient for achieving a large opening of the free RNA. These findings, supported by previously published RNA structure probing experiments, suggest that G–A base pair formation occurs upon protein binding, thereby stabilizing a selective orientation of the stems

Reanalysis of the FEROS observations of HIP 11952

Aims. We reanalyze FEROS observations of the star HIP 11952 to reassess the existence of the proposed planetary system. Methods. The radial velocity of the spectra were measured by cross-correlating the observed spectrum with a synthetic template. We also analyzed a large dataset of FEROS and HARPS archival data of the calibrator HD 10700 spanning over more than five years. We compared the barycentric velocities computed by the FEROS and HARPS pipelines. Results. The barycentric correction of the FEROS-DRS pipeline was found to be inaccurate and to introduce an artificial one-year period with a semi-amplitude of 62 m/s. Thus the reanalysis of the FEROS data does not support the existence of planets around HIP 11952.Comment: 7 pages, 8 figures, 1 tabl

Western Wheatgrass Recovery From Drought

Native grasses are predictably taller in wet years than in dry years and their density also increases with favorable precipitation. These responses of western wheatgrass are more dramatic on mechanically treated rangeland when precipitation is adequate. Measurements taken in July 1991 confirmed that western wheatgrass was slightly taller and density at least two times greater on mechanically treated claypan soils compared with untreated soils 13 and 18 years following treatment. Increases of this magnitude constitute a potentially greater carrying capacity which livestock producers should be prepared to utilize. This report briefly summarizes the effects of mechanical treatment on height and density of western wheatgrass 13 and 18 years following treatment and in a wet year following several dry years

Preassociative aggregation functions

The classical property of associativity is very often considered in aggregation function theory and fuzzy logic. In this paper we provide axiomatizations of various classes of preassociative functions, where preassociativity is a generalization of associativity recently introduced by the authors. These axiomatizations are based on existing characterizations of some noteworthy classes of associative operations, such as the class of Acz\'elian semigroups and the class of t-norms.Comment: arXiv admin note: text overlap with arXiv:1309.730

Spatial and topical imbalances in biodiversity research

The rapid erosion of biodiversity is among the biggest challenges human society is facing. Concurrently, major efforts are in place to quantify changes in biodiversity, to understand the consequences for ecosystem functioning and human wellbeing, and to develop sustainable management strategies. Based on comprehensive bibliometric analyses covering 134,321 publications, we report systematic spatial biases in biodiversity-related research. Research is dominated by wealthy countries, while major research deficits occur in regions with disproportionately high biodiversity as well as a high share of threatened species. Similarly, core scientists, who were assessed through their publication impact, work primarily in North America and Europe. Though they mainly exchange and collaborate across locations of these two continents, the connectivity among them has increased with time. Finally, biodiversity-related research has primarily focused on terrestrial systems, plants, and the species level, and is frequently conducted in Europe and Asia by researchers affiliated with European and North American institutions. The distinct spatial imbalances in biodiversity research, as demonstrated here, must be filled, research capacity built, particularly in the Global South, and spatially-explicit biodiversity data bases improved, curated and shared