Non-Standard Errors

In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty: Non-standard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for better reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants

Genome analysis of E. coli isolated from Crohn’s disease patients

Abstract Background Escherichia coli (E. coli) has been increasingly implicated in the pathogenesis of Crohn’s disease (CD). The phylogeny of E. coli isolated from Crohn’s disease patients (CDEC) was controversial, and while genotyping results suggested heterogeneity, the sequenced strains of E. coli from CD patients were closely related. Results We performed the shotgun genome sequencing of 28 E. coli isolates from ten CD patients and compared genomes from these isolates with already published genomes of CD strains and other pathogenic and non-pathogenic strains. CDEC was shown to belong to A, B1, B2 and D phylogenetic groups. The plasmid and several operons from the reference CD-associated E. coli strain LF82 were demonstrated to be more often present in CDEC genomes belonging to different phylogenetic groups than in genomes of commensal strains. The operons include carbon-source induced invasion GimA island, prophage I, iron uptake operons I and II, capsular assembly pathogenetic island IV and propanediol and galactitol utilization operons. Conclusions Our findings suggest that CDEC are phylogenetically diverse. However, some strains isolated from independent sources possess highly similar chromosome or plasmids. Though no CD-specific genes or functional domains were present in all CD-associated strains, some genes and operons are more often found in the genomes of CDEC than in commensal E. coli. They are principally linked to gut colonization and utilization of propanediol and other sugar alcohols

An emerging international network focused on permafrost coastal systems in transition

Perennially frozen ground and sea ice are key constituents of permafrost coastal systems, and their presence is the primary difference between temperate and high-latitude coastal processes. These systems are some of the most rapidly changing landscapes on Earth and, in the Arctic, are representative of the challenges being faced at the intersection between natural and anthropogenic systems. Permafrost thaw, in combination with increasing sea level and decreasing sea-ice cover, exposes arctic coastal and nearshore areas to rapid environmental and social changes. Based on decadal timescales, observations in the Arctic indicate an increase in permafrost coastal bluff erosion and storm surge flooding of low-lying ice-rich permafrost terrain. However, circum-arctic observations remain limited and the factors responsible for the apparent increase in arctic coastal dynamics are poorly constrained. A better understanding of permafrost coastal systems and how they are responding to changes in the Arctic is important since a high proportion of Arctic residents live on or near coastlines, and many derive their livelihood from terrestrial and nearshore marine resources. An expanding industrial, scientific, and commercial presence in the Arctic Ocean will also require advanced knowledge about permafrost coastlines as terrestrial access points. Since the issues involved span political, cultural, geographical, and disciplinary borders, an international network focused on permafrost coastal systems in transition is needed. An integrative network focused on permafrost coastal systems is required to realize and address the scale and complexity of the processes, dynamics, and responses of this system to physical, ecological, and social change. A primary focus of such an effort would be guided by the fact that the issues and impacts associated with permafrost coastal systems in transition are far greater than any single institution or discipline is capable of addressing alone. Future permafrost coastal system dynamics will challenge conventional wisdom as the system enters a new state impacting human decision making and adaptation planning, cultural heritage resources and ecosystems, and likely resulting in unforeseen challenges across the Arctic