Toxic chemical space

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A screen capture from ChemMaps.com

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Created date

November 26, 2018

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, “ChemMaps.com 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, but this form of visualization dramatizes how far away we are. 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).

Design Statement:

  • 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 honestly 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).

References:

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.

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.

Source

"EnvMap," Chemmap.com, screen capture of http://www.chemmaps.com/envMap3D.html, 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, https://doi.org/10.1093/bioinformatics/bty412.

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United States