Can biological complexity be reverse engineered?

Abstract

Concerns with the use of engineering approaches in biology have recently been raised. I examine two related challenges to biological research that I call the synchronic and diachronic underdetermination problem. The former refers to challenges associated with the inference of design principles underlying system capacities when the synchronic relations between lowerlevel processes and higher-level systems capacities are degenerate (many-to-many). The diachronic underdetermination problem regards the problem of reverse engineering a system when the non-linear relations between system capacities and lower-level mechanisms are changing over time. Braun and Marom argue that recent insights to biological complexity leave the aim of reverse engineering hopeless -in principle as well as in practice. While I support their call for systemic approaches to capture the dynamic nature of living systems, I take issue with the conflation of reverse engineering with naïve reductionism. I clarify how the notion of design principles can be more broadly conceived and argue that reverse engineering is compatible with a dynamic view of organisms. It may even help to facilitate an integrated account that bridges the gap between mechanistic and systems approaches.Keywords: Reverse engineering, design principles, diachronic underdetermination, systems biology, engineering approaches, dynamical systems theory The virtues and pitfalls of reverse engineeringReverse engineering methodologies are currently gaining terrain in biological fields such as systems biology and neuroscience. In response to these developments, experimental biologists have raised concerns regarding the associated quest for design principles that they take to imply an assumption of a rather static and modular design of organisms. A workshop in Konstanz brought together philosophers and biologists to discuss the implications of research methodologies in the life sciences. 2 This paper focuses in particular on concerns raised regarding reverse engineering of biological networks.The experimental biologists Erez Braun and Shimon Marom (this issue) provide fascinating insights to biological complexity by stressing how living systems are characterized by a (deep) two-way degeneracy and lack of separation of time-scales. Against this complexity, they criticize so-called reverse engineering approaches for investigating biological systems as if these were programmed and fully decomposable engineering systems, designed to conduct pre-designed functions. This paper clarifies and supports their criticism of naïve

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