Project relevance and research goals
                       
Systems biology (SB) is in need of theoretical and philosophical grounding. It is a relatively new discipline, both when it comes to its object of study (complex systems), its methods (in silico modelling and simulations, large scale experiments), and its theoretical and practical approaches. SB aims to obtain a comprehensive and systematic understanding of life through investigating how a wide range of functional properties of living organisms are brought about by systems behavior and by the interactions of system constituents (Alberghina and Westerhoff 2005; Ideker et al 2001; Kitano 2002; Ge et al 2003). SB depends on interdisciplinary work engaging both biologists, mathematicians, statisticians, computer scientists and biophysicists. In stead of focusing on the behavior of single factors such as genes or proteins, it assesses a vast amount of data aiming at investigating system properties by simulating the interaction between multiple parts, domains and levels of dynamic biological processes. The new discipline is often seen as a successor to molecular biology and genomics as well as mathematical biology and biophysics, and it is in the process of taking over the scene of cutting edge biology. It is often described as shifting the focus in biology from the behavior of single molecules to higher-level systems behavior (Boogerd et al 2007, 3). SB is predicted to transform our understanding of biology as well as influencing other sciences, such as physics, mathematics, engineering and social science (Ehrenberg et al 2003). This novelty in focus and methods brings to the fore important questions that can best be answered with the tools of philosophy. It will be a key task for philosophers to point out and clarify theoretical issues and implications of this discipline, and such an undertaking will present an opportunity to stake out the direction of systems biology built on the results of both biological and philosophical investigations.

Furthermore, empirical results and research frameworks of SB additionally have a clear potential for feeding back to philosophy, stimulating and influencing the development of several lines of inquiry in the philosophy of science, metaphysics and philosophy of mind.  There is an array of questions in SB that are linked up with questions in contemporary philosophy, such as questions of reduction, relationships between scientific levels, downward causation, modelling, and integration of disciplines and theories. Facilitating philosophical work on SB will therefore have the potential of benefiting both disciplines greatly.

Biological research has an increasing impact on society through for instance biomedical investigations, food research and biotechnology, and SB approaches will constitute more and more of this research in the future. SB also has the potential to influence how we look at life and how human beings perceive their identity as biological beings. This large potential impact ought to be reflected in the amount of philosophy of systems biology being conducted. Although a couple of international workshops have been organized and some literature has been published on philosophy of SB, the research is scarce and should be expanded.

The PSBio researchers will work with the following aims and questions organized under one main goal and three sub-themes including the following specific research questions:

Main goal: Developing Philosophical Foundations for Systems Biology

Theme 1: Systems and parts

1. How should we understand the ontology of systems? Are systems a genuine ontological category, or can they be described only as a collection of parts? What is the relation between systems and their parts? How can a system influence the behavior of its parts?
2. How does the role and concept of genes change from molecular genetics to systems biology? Is there room for attribution of causal priority to genes, or should genes be viewed as just one among many equally important system constituents?
3. How should the functional organization, plasticity, robustness, redundancy and modularity of systems be understood in relation to their parts?

Theme 2: Levels and Causes

1. Should systems biology aspire to be either anti-reductionist or reductionist, and if so, in what sense? Is systems biology a science of emergent phenomena?
2. How does the so-called ‘causal exclusion debate’ in philosophy relate to systems biology? Does systems biology investigate cases of downward causation?
3. How are scientific levels or domains interrelated in systems biology? How does the interdisciplinarity of systems biology influence the sciences and scientific theory?

Theme 3: Methods and epistemological issues

1. What is the relationship between systems biology models and real systems? What are the limitations of systems biology modelling?
2. How can we access information about real systems by simulating systems using sophisticated computer programs? To what degree can ‘in silico’ testing replace in vivo testing?