As a former collaborator in Eleonore Pauwels' research on the misuse of metaphors by synthetic biologists, I agree with many of her points but find her perspective too restrictive (Nature 500, 523–524; 2013). In my view, the use of analogies, concepts and metaphors is crucial for advancing scientific research.

Pauwels tends to merge metaphors with analogies and theoretical concepts. Her examples of oscillators, switches and logic gates, which have a precise meaning in engineering, are better viewed as the analogical transfer of a scientific concept (see also B. Calcott Nature 502, 170; 2013). To treat them as though they were on a par with expressions such as 'selfish gene', 'software of life' or 'household of nature' does not capture the ways in which they are used in scientific practice.

Metaphors and analogies have long driven cross-disciplinary exchange. For example, the early mathematization of biology and economics in the nineteenth and twentieth centuries was largely built on analogies with physics. Analogies and metaphors have also contributed substantially to ideas developed in cognitive science and in the philosophy and history of science (reviewed in J. Maienschein et al. Isis 99, 341–349; 2008).