Science as a Social System and Virtual Research Environment

The accumulation of gradual changes in scientific landscape and research practice due to the Internet has the potential to enhance the quality of both cognitive and social aspects of science and scientists. New types of research outputs, modes of scientific communication and new circulation mechanisms, as well as enhanced opportunities for scientific re-use and measuring research impact, in combination with new approaches to research assessment and evaluation are all having profound effects on the social system of science. To be sure that these innovations will not break the social sustainability of the science community, it will be valuable to develop a model of science as a tool for computer simulation of social consequences from possible innovations within virtual research environment. Focusing on possible social problems related to these new virtual research environments this short paper provides a brief analysis of the current situation in science (challenges, problems, main actors), general views on model of science (landscape, main agents, important properties, etc.) and on areas where simulation can contribute to better understanding of possible futures for the scientific community.Virtual Research Environment, Science System Social Sustainability, Agent Based Modeling

Social Effects in Science: Modelling Agents for a Better Scientific Practice

Science is a fundamental human activity and we trust its results because it has several error-correcting mechanisms. Its is subject to experimental tests that are replicated by independent parts. Given the huge amount of information available, scientists have to rely on the reports of others. This makes it possible for social effects to influence the scientific community. Here, an Opinion Dynamics agent model is proposed to describe this situation. The influence of Nature through experiments is described as an external field that acts on the experimental agents. We will see that the retirement of old scientists can be fundamental in the acceptance of a new theory. We will also investigate the interplay between social influence and observations. This will allow us to gain insight in the problem of when social effects can have negligible effects in the conclusions of a scientific community and when we should worry about them.Comment: 14 pages, 5 figure

Learning in a Landscape: Simulation-building as Reflexive Intervention

This article makes a dual contribution to scholarship in science and technology studies (STS) on simulation-building. It both documents a specific simulation-building project, and demonstrates a concrete contribution to interdisciplinary work of STS insights. The article analyses the struggles that arise in the course of determining what counts as theory, as model and even as a simulation. Such debates are especially decisive when working across disciplinary boundaries, and their resolution is an important part of the work involved in building simulations. In particular, we show how ontological arguments about the value of simulations tend to determine the direction of simulation-building. This dynamic makes it difficult to maintain an interest in the heterogeneity of simulations and a view of simulations as unfolding scientific objects. As an outcome of our analysis of the process and reflections about interdisciplinary work around simulations, we propose a chart, as a tool to facilitate discussions about simulations. This chart can be a means to create common ground among actors in a simulation-building project, and a support for discussions that address other features of simulations besides their ontological status. Rather than foregrounding the chart's classificatory potential, we stress its (past and potential) role in discussing and reflecting on simulation-building as interdisciplinary endeavor. This chart is a concrete instance of the kinds of contributions that STS can make to better, more reflexive practice of simulation-building.Comment: 37 page

Scientific Polarization

Contemporary societies are often "polarized", in the sense that sub-groups within these societies hold stably opposing beliefs, even when there is a fact of the matter. Extant models of polarization do not capture the idea that some beliefs are true and others false. Here we present a model, based on the network epistemology framework of Bala and Goyal ["Learning from neighbors", \textit{Rev. Econ. Stud.} \textbf{65}(3), 784-811 (1998)], in which polarization emerges even though agents gather evidence about their beliefs, and true belief yields a pay-off advantage. The key mechanism that generates polarization involves treating evidence generated by other agents as uncertain when their beliefs are relatively different from one's own.Comment: 22 pages, 5 figures, author final versio

Development and Interpretation of Machine Learning Models for Drug Discovery

In drug discovery, domain experts from different fields such as medicinal chemistry, biology, and computer science often collaborate to develop novel pharmaceutical agents. Computational models developed in this process must be correct and reliable, but at the same time interpretable. Their findings have to be accessible by experts from other fields than computer science to validate and improve them with domain knowledge. Only if this is the case, the interdisciplinary teams are able to communicate their scientific results both precisely and intuitively. This work is concerned with the development and interpretation of machine learning models for drug discovery. To this end, it describes the design and application of computational models for specialized use cases, such as compound profiling and hit expansion. Novel insights into machine learning for ligand-based virtual screening are presented, and limitations in the modeling of compound potency values are highlighted. It is shown that compound activity can be predicted based on high-dimensional target profiles, without the presence of molecular structures. Moreover, support vector regression for potency prediction is carefully analyzed, and a systematic misprediction of highly potent ligands is discovered. Furthermore, a key aspect is the interpretation and chemically accessible representation of the models. Therefore, this thesis focuses especially on methods to better understand and communicate modeling results. To this end, two interactive visualizations for the assessment of naive Bayes and support vector machine models on molecular fingerprints are presented. These visual representations of virtual screening models are designed to provide an intuitive chemical interpretation of the results

From Social Simulation to Integrative System Design

As the recent financial crisis showed, today there is a strong need to gain "ecological perspective" of all relevant interactions in socio-economic-techno-environmental systems. For this, we suggested to set-up a network of Centers for integrative systems design, which shall be able to run all potentially relevant scenarios, identify causality chains, explore feedback and cascading effects for a number of model variants, and determine the reliability of their implications (given the validity of the underlying models). They will be able to detect possible negative side effect of policy decisions, before they occur. The Centers belonging to this network of Integrative Systems Design Centers would be focused on a particular field, but they would be part of an attempt to eventually cover all relevant areas of society and economy and integrate them within a "Living Earth Simulator". The results of all research activities of such Centers would be turned into informative input for political Decision Arenas. For example, Crisis Observatories (for financial instabilities, shortages of resources, environmental change, conflict, spreading of diseases, etc.) would be connected with such Decision Arenas for the purpose of visualization, in order to make complex interdependencies understandable to scientists, decision-makers, and the general public.Comment: 34 pages, Visioneer White Paper, see http://www.visioneer.ethz.c