e-Social Science and Evidence-Based Policy Assessment : Challenges and Solutions

Peer reviewedPreprin

Taxonomy of grain legumes

The taxonomy; of grain legumes is relatively uncomplicated compared to that of cereals, brassicas and some other groups of plants because, in general, only limited gene pools have been available for selection and subsequent plant breeding. Then again, intergeneric legume hybrids are not known in nature and artificial crosses attempting to create them are seldom, if ever, successful [64]. Indeed, the genetic barriers between species and species groups are often substantial [86,87]. The classification' of interfertile species and infraspecific variants is inherently more difficult and the taxonomic situation in grain legumes is not exceptional. In some instances the available information would now seem to justify updating of the taxonomic framework

Social dilemmas: what if not everybody knows that everybody knows that everybody is rational?

In this paper social dilemmas are modelled as two-player games. In particular we model the Prisoner’s Dilemma, Chicken and Stag Hunt. When modelling these games we assume that players adapt their behaviour according to their experience and look for outcomes that have proved to be satisfactory in the past. These ideas are investigated by conducting several experiments with an agent-based simulation model in which agents use a simple form of case-based reasoning. It is shown that cooperation can emerge from the interaction of selfish case-based reasoners. In determining how often cooperation occurs, not only what Agents end up doing in any given situation is important, but also the process of learning what to do can crucially influence the final outcome. Agents’ aspiration thresholds play an important role in that learning process. It is also found that case-based reasoners find it easier to cooperate in Chicken than in the Prisoner’s Dilemma and Stag Hunt

Representation of decision-making in European agricultural agent-based models

The use of agent-based modelling approaches in ex-post and ex-ante evaluations of agricultural policies has been progressively increasing over the last few years. There are now a sufficient number of models that it is worth taking stock of the way these models have been developed. Here, we review 20 agricultural agent-based models (ABM) addressing heterogeneous decision-making processes in the context of European agriculture. The goals of this review were to i) develop a framework describing aspects of farmers' decision-making that are relevant from a farm-systems perspective, ii) reveal the current state-of-the-art in representing farmers' decision-making in the European agricultural sector, and iii) provide a critical reflection of underdeveloped research areas and on future opportunities in modelling decision-making. To compare different approaches in modelling farmers' behaviour, we focused on the European agricultural sector, which presents a specific character with its family farms, its single market and the common agricultural policy (CAP). We identified several key properties of farmers' decision-making: the multi-output nature of production; the importance of non-agricultural activities; heterogeneous household and family characteristics; and the need for concurrent short- and long-term decision-making. These properties were then used to define levels and types of decision-making mechanisms to structure a literature review. We find most models are sophisticated in the representation of farm exit and entry decisions, as well as the representation of long-term decisions and the consideration of farming styles or types using farm typologies. Considerably fewer attempts to model farmers' emotions, values, learning, risk and uncertainty or social interactions occur in the different case studies. We conclude that there is considerable scope to improve diversity in representation of decision-making and the integration of social interactions in agricultural agent-based modelling approaches by combining existing modelling approaches and promoting model inter-comparisons. Thus, this review provides a valuable entry point for agent-based modellers, agricultural systems modellers and data driven social scientists for the re-use and sharing of model components, code and data. An intensified dialogue could fertilize more coordinated and purposeful combinations and comparisons of ABM and other modelling approaches as well as better reconciliation of empirical data and theoretical foundations, which ultimately are key to developing improved models of agricultural systems.Swiss National Science Foundatio

Empirical agent-based modelling of everyday pro-environmental behaviours at work

We report on agent-based modelling work in the LOCAW project (Low Carbon at Work: Modelling Agents and Organisations to Achieve Transition to a Low Carbon Europe). The project explored the effectiveness of various backcasting scenarios conducted with case study organisations in bringing about pro-environmental change in the workforce in the domains of transport, energy use and waste. The model used qualitative representations of workspaces in formalising each scenario, and decision trees learned from questionnaire responses to represent decision-making. We describe the process by which the decision trees were constructed, noting that the use of decision trees in agent-based models requires particular considerations owing to the potential use of explanatory variables in model dynamics. The results of the modelling in various scenarios emphasise the importance of structural environmental changes in facilitating everyday pro-environmental behaviour, but also show there is a role for psychological variables such as norms, values and efficacy. As such, the topology of social interactions is a potentially important driver, raising the interesting prospect that both workplace geography and organisational hierarchy have a role to play in influencing workplace pro-environmental behaviours

How to keep it adequate: A protocol for ensuring validity in agent-based simulation

There has so far been no shared understanding of validity in agent-based simulation. We here conceptualise validation as systematically substantiating the premises on which conclusions from simulation analysis for a particular modelling context are built. Given such a systematic perspective, validity of agent-based models cannot be ensured if validation is merely understood as an isolated step in the modelling process. Rather, valid conclusions from simulation analysis require context-adequate method choices at all steps of the simulation analysis including model construction, model and parameter inference, uncertainty analysis and simulation. We present a twelve-step protocol to highlight the (often hidden) premises for methodological choices and their link to the modelling context. It is designed to aid modelers in understanding their context and in choosing and documenting context-adequate and mutually consistent methods throughout the modelling process. Its purpose is to assist reviewers and the community as a whole in assessing and discussing context-adequacy

The use of phylogeny to interpret cross-cultural patterns in plant use and guide medicinal plant discovery: an example from Pterocarpus (Leguminosae)

The study of traditional knowledge of medicinal plants has led to discoveries that have helped combat diseases and improve healthcare. However, the development of quantitative measures that can assist our quest for new medicinal plants has not greatly advanced in recent years. Phylogenetic tools have entered many scientific fields in the last two decades to provide explanatory power, but have been overlooked in ethnomedicinal studies. Several studies show that medicinal properties are not randomly distributed in plant phylogenies, suggesting that phylogeny shapes ethnobotanical use. Nevertheless, empirical studies that explicitly combine ethnobotanical and phylogenetic information are scarce.In this study, we borrowed tools from community ecology phylogenetics to quantify significance of phylogenetic signal in medicinal properties in plants and identify nodes on phylogenies with high bioscreening potential. To do this, we produced an ethnomedicinal review from extensive literature research and a multi-locus phylogenetic hypothesis for the pantropical genus Pterocarpus (Leguminosae: Papilionoideae). We demonstrate that species used to treat a certain conditions, such as malaria, are significantly phylogenetically clumped and we highlight nodes in the phylogeny that are significantly overabundant in species used to treat certain conditions. These cross-cultural patterns in ethnomedicinal usage in Pterocarpus are interpreted in the light of phylogenetic relationships.This study provides techniques that enable the application of phylogenies in bioscreening, but also sheds light on the processes that shape cross-cultural ethnomedicinal patterns. This community phylogenetic approach demonstrates that similar ethnobotanical uses can arise in parallel in different areas where related plants are available. With a vast amount of ethnomedicinal and phylogenetic information available, we predict that this field, after further refinement of the techniques, will expand into similar research areas, such as pest management or the search for bioactive plant-based compounds

Varying Herbivore Population Structure Correlates with Lack of Local Adaptation in a Geographic Variable Plant-Herbivore Interaction

Local adaptation of parasites to their hosts due to coevolution is a central prediction of many theories in evolutionary biology. However, empirical studies looking for parasite local adaptation show great variation in outcomes, and the reasons for such variation are largely unknown. In a previous study, we showed adaptive differentiation in the arctiid moth Utetheisa ornatrix to its host plant, the pyrrolizidine alkaloid-bearing legume Crotalaria pallida, at the continental scale, but found no differentiation at the regional scale. In the present study, we sampled the same sites to investigate factors that may contribute to the lack of differentiation at the regional scale. We performed field observations that show that specialist and non-specialist polyphagous herbivore incidence varies among populations at both scales. With a series of common-garden experiments we show that some plant traits that may affect herbivory (pyrrolizidine alkaloids and extrafloral nectaries) vary at the regional scale, while other traits (trichomes and nitrogen content) just vary at the continental scale. These results, combined with our previous evidence for plant population differentiation based on larval performance on fresh fruits, suggest that U. ornatrix is subjected to divergent selection even at the regional scale. Finally, with a microsatellite study we investigated population structure of U. ornatrix. We found that population structure is not stable over time: we found population differentiation at the regional scale in the first year of sampling, but not in the second year. Unstable population structure of the herbivore is the most likely cause of the lack of regional adaptation

Oxidative/Nitrative Stress and Inflammation Drive Progression of Doxorubicin-Induced Renal Fibrosis in Rats as Revealed by Comparing a Normal and a Fibrosis-Resistant Rat Strain

Chronic renal fibrosis is the final common pathway of end stage renal disease caused by glomerular or tubular pathologies. Genetic background has a strong influence on the progression of chronic renal fibrosis. We recently found that Rowett black hooded rats were resistant to renal fibrosis. We aimed to investigate the role of sustained inflammation and oxidative/nitrative stress in renal fibrosis progression using this new model. Our previous data suggested the involvement of podocytes, thus we investigated renal fibrosis initiated by doxorubicin-induced (5 mg/kg) podocyte damage. Doxorubicin induced progressive glomerular sclerosis followed by increasing proteinuria and reduced bodyweight gain in fibrosis-sensitive, Charles Dawley rats during an 8-week long observation period. In comparison, the fibrosis-resistant, Rowett black hooded rats had longer survival, milder proteinuria and reduced tubular damage as assessed by neutrophil gelatinase-associated lipocalin (NGAL) excretion, reduced loss of the slit diaphragm protein, nephrin, less glomerulosclerosis, tubulointerstitial fibrosis and matrix deposition assessed by periodic acid-Schiff, Picro-Sirius-red staining and fibronectin immunostaining. Less fibrosis was associated with reduced profibrotic transforming growth factor-beta, (TGF-beta1) connective tissue growth factor (CTGF), and collagen type I alpha 1 (COL-1a1) mRNA levels. Milder inflammation demonstrated by histology was confirmed by less monocyte chemotactic protein 1 (MCP-1) mRNA. As a consequence of less inflammation, less oxidative and nitrative stress was obvious by less neutrophil cytosolic factor 1 (p47phox) and NADPH oxidase-2 (p91phox) mRNA. Reduced oxidative enzyme expression was accompanied by less lipid peroxidation as demonstrated by 4-hydroxynonenal (HNE) and less protein nitrosylation demonstrated by nitrotyrosine (NT) immunohistochemistry and quantified by Western blot. Our results demonstrate that mediators of fibrosis, inflammation and oxidative/nitrative stress were suppressed in doxorubicin nephropathy in fibrosis-resistant Rowett black hooded rats underlying the importance of these pathomechanisms in the progression of renal fibrosis initiated by glomerular podocyte damage