Peeking Inside the Black Box: A New Kind of Scientific Visualization

Michael T. Stuart*, Nancy J. Nersessian

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


Computational systems biologists create and manipulate computational models of biological systems, but they do not always have straightforward epistemic access to the content and behavioural profile of such models because of their length, coding idiosyncrasies, and formal complexity. This creates difficulties both for modellers in their research groups and for their bioscience collaborators who rely on these models. In this paper we introduce a new kind of visualization (observed in a qualitative study of a systems biology laboratory) that was developed to address just this sort of epistemic opacity. The visualization is unusual in that it depicts the dynamics and structure of a computer model instead of that model’s target system, and because it is generated algorithmically. Using considerations from epistemology and aesthetics, we explore how this new kind of visualization increases scientific understanding of the content and function of computer models in systems biology to reduce epistemic opacity.

Original languageEnglish
Pages (from-to)87-107
Number of pages21
JournalMinds and Machines
Issue number1
StatePublished - 15 Mar 2019


  • Computer simulation
  • Epistemic opacity
  • Epistemology of computer simulation
  • Epistemology of photography
  • Exemplification
  • Model-based reasoning
  • Scientific understanding
  • Scientific visualization


Dive into the research topics of 'Peeking Inside the Black Box: A New Kind of Scientific Visualization'. Together they form a unique fingerprint.

Cite this