Discussion
Systems biology, synthetic biology and data-driven research: A commentary on Krohs, Callebaut, and O’Malley and Soyer

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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

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