Prebiotic Chemistry: What We Know,What We Don't

How life on Earth began remains an unexplained scientific problem. This problem is nuanced in its practical details and the way attempted explanations feedback with questions and developments in other areas of science, including astronomy, biology, and planetary science. Prebiotic chemistry attempts to address this issue theoretically, experimentally, and observationally. The ease of formation of bioorganic compounds under plausible prebiotic conditions suggests that these molecules were present in the primitive terrestrial environment. In addition to synthesis in the Earth's primordial atmosphere and oceans, it is likely that the infall of comets, meteorites, and interplanetary dust particles, as well as submarine hydrothermal vent synthesis, may have contributed to prebiotic organic evolution. The primordial organic soup may have been quite complex, but it did not likely include all of the compounds found in modern organisms. Regardless of their origin, organic compounds would need to be concentrated and complexified by environmental mechanisms. While this review is by no means exhaustive, many of the issues central to the state of the art of prebiotic chemistry are reviewed here.     

What We See,What We Do Not See,and What We Do Not Want to See in HLA Class I Immunopeptidomes

The identification of peptides bound to human leukocyte antigen class I (HLA‐I) molecules—that is, the HLA‐I immunopeptidome—is a useful tool in the hunt for epitopes suitable for vaccinations and immunotherapies. These peptides are mainly generated by proteasomes through peptide hydrolysis and peptide splicing. In this issue, Nicastri and colleagues compared different methods for the elution of HLA class I‐associated peptides. It is demonstrated that the choice of HLA‐associated peptide enrichment and purification strategy affects peptide yields and creates a bias in detected sequence repertoire. The author carried out this technical brief through the analysis of canonical non‐spliced peptides. However, their study left out any analysis of post‐translationally spliced peptides, thereby missing an opportunity to shed light on the persistent debate of the frequency of these unconventional peptides.     

On Being Careful What We Wish for: Some Difficulties with Operationalizing the Precautionary Principle

An important part of the Precautionary Principle is that taking action is justified for protecting public health even when there is some scientific uncertainty. We examine here the two components of this central feature of the precautionary principle, scientific uncertainty and decision making. In order to operationalize the principle we should examine the consequences of its decision rules and how they perform under various conditions. The performance of decision rules in disease screening is measured by the sensitivity and specificity of the rule, but the consequences for the patient are given by the positive and negative predictive values, determined not only by the performance of the rule by the prevalence of the disease in the population. We look at positive and negative predictive value of the Precautionary Principle from the standopoint of the costs to one or other parts of society, show that the usual rule which tends to maximize sensitivity in favor of specificity may have unexpected consequences, and demonstrate that it is sometimes possible to trade sensitivity and specificity off against each other in a way the improves both positive and negative predictive value, or worse, degrades both.We conclude by asking if certain strategies are better for one or the other kinds of uncertainty.     

Further We Travel the Faster We Go

The average travelling speed increases in a nontrivial manner with the travel distance. This leads to scaling-like relations on quite extended spatial scales, for all mobility modes taken together and also for a given mobility mode in part. We offer a wide range of experimental results, investigating and quantifying this universal effect and its measurable causes. The increasing travelling speed with the travel distance arises from the combined effects of: choosing the most appropriate travelling mode; the structure of the travel networks; the travel times lost in the main hubs, starting or target cities; and the speed limit of roads and vehicles.     

Next-Generation Individual-Based Models Integrate Biodiversity and Ecosystems: Yes We Can,and Yes We Must

Ecosystem and community ecology have evolved along different pathways, with little overlap. However, to meet societal demands for predicting changes in ecosystem services, the functional and structural view dominating these two branches of ecology, respectively, must be integrated. Biodiversity–ecosystem function research has addressed this integration for two decades, but full integration that makes predictions relevant to practical problems is still lacking. We argue that full integration requires going, in both branches, deeper by taking into account individual organisms and the evolutionary and physico-chemical principles that drive their behavior. Individual-based models are a major tool for this integration. They have matured by using individual-level mechanism to replace the demographic thinking which dominates classical theoretical ecology. Existing individual-based ecosystem models already have proven useful both for theory and application. Still, next-generation individual-based models will increasingly use standardized and re-usable submodels to represent behaviors and mechanisms such as growth, uptake of nutrients, foraging, and home range behavior. The strategy of pattern-oriented modeling then helps make such ecosystem models structurally realistic by developing theory for individual behaviors just detailed enough to reproduce and explain patterns observed at the system level. Next-generation ecosystem scientists should include the individual-based approach in their toolkit and focus on addressing real systems because theory development and solving applied problems go hand-in-hand in individual-based ecology.