Toxic chemical space (revised)


A screen capture from




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Contributed date

January 21, 2019 - 5:20pm

Critical Commentary

Substantive Caption:

Screen capture from the web app ChemMaps, depicting a view of “chemical space” from the perspective of PFOA. Each “star” in this map represents a chemical compound of a distinct molecular identity. The relative positions of these stars indicate structural similarity, according to “a complex compendium of 1D, 2D and 3D pre-computed molecular descriptors to generate the chemical space in three dimensions” (Borrel, Kleinstreuer, and Fourches 2018). Based on the assumption that chemical properties are correlated with molecular structure—a bedrock of modern organic chemistry—the proximity of substances in this map is supposed to be an index of chemical and toxicological similarity. Like most work in cheminformatics, ChemMaps was originally designed to expedite drug discovery. However, “ aims to become the go-to website for anyone wanting to search, mine or visualize chemical space” (Borrel, Kleinstreuer, and Fourches 2018). This includes those concerned about environmental toxicity of chemicals like the PFASs.

Here, hovering just over the shoulder of PFOA, the viewer floats in a purely molecular galaxy. This chemical holism purports to represent the constituents of the material world of Teflon and Scotchgard and cancer. However, this form of visualization unintentionally dramatizes how far removed this holism of molecules is from the world of materials. It is one realization of a trend that the philosopher François Dagognet associated with the representation of chemical substances in abstract molecular terms: “whereas the poets have always suffered from the gap between things and signs, chemistry tranquilly effects the miracle of their coincidence. The neologisms, however, lose their attachment with sensible reality, qualities, and appearances. In order to be able to go to the depths of substances, on the ocean of their relationships, it’s necessary to break the moorings. The learned words, kinds of algebraic polynomials, cease then to touch us. Uprooted, they address themselves only to the intelligence of structures.” (Dagognet 2002 [1969], 158).

Framing the problem of environmental toxicity as a problem of information overload tends to suggest computational solutions. Molecules are extremely well adapted to computer modeling and large-scale comparisons. But the intensification of computational methods is suspiciously analogous to the intensified production of new, putatively safer chemicals as a solution to environmental toxicity. It may be that the computational tractability of molecules is an index of their intractability as toxic subjects. Perhaps here, as in other domains, “the simplification of ontology has led to the enormous complication of epistemology,” (Viveiros de Castro 2004).

Design Statement:

This image is a data visualization expressing calculated estimates of toxicity-relevant properties of chemical substances. Like most (all?) visualizations, it is a visual metaphor: here, chemical substances are stars, and spatial proximity is toxicological similarity. As Lily Kay (2000) points out, scientific metaphors have ontological force – the ways they render the world may beget ways of interacting with and remaking it. Molecular structures are abstractions, not material substances; one might define chemical identity in many other ways. The visual metaphor of the star map enforces a conception of chemical individuality that strongly privileges the molecular structure – each molecule, forever alone and itself, in the chemical heavens.

Two methodological points: first, ethnographers may wish to reflect on the implications of the visual metaphors they employ in data visualization and other image-making practices. Second, if we wish to create ethnographic images that contest and situate putative views from nowhere, we should be careful to avoid (or at minimum ironize) data visualizations practices that reproduce such a view.


Borrel, Alexandre, Nicole C. Kleinstreuer, and Denis Fourches. 2018. “Exploring Drug Space with ChemMaps.Com.” Bioinformatics 34 (21): 3773–75. doi: 10.1093/bioinformatics/bty412.

Dagognet, François. 2002 [1969]. Tableaux et langages de la chimie : essai sur la représentation. Seyssel: Champ Vallon.

Kay, Lily E. 2000. Who Wrote the Book of Life?: A History of the Genetic Code. Stanford: Stanford University Press.

Viveiros de Castro, Eduardo Batalha. 2004. “Exchanging Perspectives: The Transformation of Objects into Subjects in Amerindian Ontologies.” Common Knowledge 10 (3): 463–484. doi: 10.1215/0961754X-10-3-463.

(Revision of May 9, 2019)


"EnvMap,", screen capture of, 25 November 2018. See Alexandre Borrel, Nicole C. Kleinstreuer, and Denis Fourches, “Exploring Drug Space with ChemMaps.Com,” Bioinformatics 34, no. 21 (November 1, 2018): 3773–75,




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Cite as

Alexandre Borrel, Nicole C. Kleinstreuer and and Denis Fourches, "Toxic chemical space (revised)", contributed by Evan Hepler-Smith, Center for Ethnography, Platform for Experimental Collaborative Ethnography, last modified 9 May 2019, accessed 25 September 2023.