Over the course of the last three decades, computer simulations have become a major tool of doing science and engaging with the world, not least in an effort to predict and intervene in a future to come. Born in the context of the Second World War and the discipline of physics, simulations have long spread into most diverse fields of enquiry and technological application. This paper introduces a topical collection focussing on simulations in the life sciences. Echoing the current state (...) of tinkering, fast developments, segmentation of knowledge and interdisciplinary collaboration, and in an effort to bridge the science-humanities divide, the contributors to this collection come from multiple disciplinary backgrounds, including information studies, cognitive sciences, philosophy and biology. The ambiguous character of simulations, their cutting across scientific disciplines, analysis and prediction, understanding and doing, gave rise to their success in contemporary life sciences and has been the object of much scientific debate. One of the main aims of this topical collection, by contrast, is to call into question the assumption of an obvious use and easy transfer of methods between fields of knowledge as diverse as, e.g. physics and biology. The collection presents historical case studies from various biological sub-fields. The articles study how simulations are used and the ways they contribute specifically to our understanding of life. Taking up Sergio Sismondo’s description of simulations as “compromises” and “glue”, they also critically engage with the question of what exactly the life sciences have been gluing together over the last two decades. (shrink)

Where should computer simulations be located on the ‘usual methodological map’ which distinguishes experiment from theory? Specifically, do simulations ultimately qualify as experiments or as thought experiments? Ever since Galison raised that question, a passionate debate has developed, pushing many issues to the forefront of discussions concerning the epistemology and methodology of computer simulation. This review article illuminates the positions in that debate, evaluates the discourse and gives an outlook on questions that have not yet been addressed.

Continuous culture techniques were developed in the early twentieth century to replace cumbersome studies of cell growth in batch cultures. In contrast to batch cultures, they constituted an open concept, as cells are forced to proliferate by adding new medium while cell suspension is constantly removed. During the 1940s and 1950s new devices have been designed—called “automatic syringe mechanism,” “turbidostat,” “chemostat,” “bactogen,” and “microbial auxanometer”—which allowed increasingly accurate quantitative measurements of bacterial growth. With these devices cell growth came under the (...) external control of the experimenters and thus accessible for developing a mathematical theory of growth kinetics—developed mainly by Jacques Monod, Aron Novick and Leo Szilard in the early 1950s and still in use today. The paper explores the development of continuous culture devices and claims that these devices are simulators for standard cells following specific requirements, in particular involving mathematical constraints in the design and setting of the devices as well as experiments. These requirements have led to contemporary designs of continuous culture techniques realizing a specific event-based flow algorithm able to simulate directed evolution and produce artificial cells and microorganisms. This current development is seen as an alternative approach to today’s synthetic biology. (shrink)