DiscussionSystems biology, synthetic biology and data-driven research: A commentary on Krohs, Callebaut, and O’Malley and Soyer
Section snippets
Krohs on convenience experimentation
Krohs’ paper argues that there is a strong reliance on what he calls convenience experimentation in top-down systems biology, a branch of systems biology that studies ‘omic’ interactions at the whole cell scale. (As Krohs himself points out, top-down systems biology is only one strand of systems biology). Krohs summarizes his argument: “in convenience experimentation many experiments are done in the way they are actually done for the reason that they are so extraordinary convenient to perform”
O’Malley and Soyer on integration
I think a helpful way of understanding Krohs notion of exploratory experimentation is by linking it to O’Malley and Soyer’s discussion of ‘exploratory questions’. They describe these as being broad general questions rather than specific hypotheses. O’Malley and Soyer give some examples of these, including ‘what if’ questions (p. 63), and questions like ‘what’s going on here, and what happens when we construct things differently?’ (p. 64).
According to O’Malley and Soyer, exploratory questioning
Callebaut on scientific perspectivism
The key concept in Callebaut’s paper on big-data biology is scientific perspectivism.2 This is an idea I cannot do justice to here, but crudely put it is a philosophical position that recognises that we always perceive the world from a particular point of view because of factors such as our observational vantage point, our theoretical position, and even the language that we speak. Scientific
Engineering life
Scientific perspectivism is the central concept in Callebaut’s paper, but another important strand of the paper is exhibited in the idea of ‘engineering life’ as ‘changing the living world without trying to understand it’. This is a view that Callebaut draws from Woese’s (2004) famous article ‘A new biology for a new century’, where Woese laments about the current lack of a ‘guiding vision’ for the life sciences, saying that without such a vision science becomes an engineering discipline. This
Conclusions: new ways of thinking about scientific practice
All three of the papers discussed here started from an interest in the transformations in biology that are associated with data-driven research, particularly those manifested by systems biology. Something which underlies all the papers is the importance of technological changes in driving scientific research. All the papers show how technological developments can result in conceptual ones, although Krohs and Callebaut are rather concerned about the results of these developments, while O’Malley
References (24)
Scientific perspectivism: a philosopher of science’s response to the challenge of big data biology
Studies in History and Philosophy of Biological and Biomedical Sciences
(2012)- et al.
Calculating life: Duelling discourses in interdisciplinary systems biology
Studies in History and Philosophy of Biological and Biomedical Sciences
(2011) Convenience experimentation
Studies in History and Philosophy of Biological and Biomedical Sciences
(2012)- et al.
The roles of integration in molecular systems biology
Studies in History and Philosophy of Biological and Biomedical Sciences
(2012) - et al.
Synthetic biology: New engineering rules for an emerging discipline
Molecular Systems Biology
(2006) - et al.
Logics of Interdisciplinarity
Economy and Society
(2008) A partnership between biology and engineering
Nature Biotechnology
(2004)Comments on complexity and experimentation in biology
Philosophy of Science
(1997)Systems biology, interdisciplinarity and disciplinary identity
Foundations for engineering biology
Nature
(2005)