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 lower-level processes and higher-level systems
capacities are degenerate (many-to-many). The diachronic underdetermination problem regards the
problem of reverse engineering a system where 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
