He specifically investigated the manner in which experience itself is a dynamic structure (or web) woven of triadic relations (signs in the strict sense) whose elements or terms (representamens, significates and interpretants)[4] interchange positions and roles over time in the spiral of semiosis.

[6] John Deely first became aware of semiotics as a distinct subject matter during the course of his work on language at the Institute for Philosophical Research in Chicago as a senior research fellow under the direction of Mortimer J. Adler, through reading Jacques Maritain and John Poinsot, which led to his original contact with Thomas Sebeok in 1968 with a proposal to prepare a critical edition of Poinsot's Tractatus de Signis (1632) as the earliest full systematization of an inquiry into the being proper to signs.

In 1980, Sebeok asked Deely to take charge of the development of the SSA annual proceedings volumes, to which end Deely developed the distinctive SSA Style Sheet,[7] which takes as its principle foundation the fact that no one writes after he dies, as a consequence of which primary source dates should always come from the lifetime of the cited source—the principle of historical layering—because it reveals the layers of discourse just as the layers of rocks reveal the history of the Earth to a trained geologist.

Thus the argument whether the manner in which the action of signs permeates the universe includes the nonliving as well as the living stands, as it were, as determining the "final frontier" of semiotics.

The full return to semiotic consciousness, Deely argued, was launched by the work of Charles S. Peirce, beginning most notably with his New List of Categories.

In his work on René Descartes and Poinsot, Deely highlights how Charles Sanders Peirce drew on Jeremy Bentham who proposed understanding on the basis common to all as cenoscopy and science which wishes to discover new phenomenon as ideoscopy.

John Deely writes: Indeed, one way of understanding that historical period or epoch in European history called "the Enlightenment" is precisely as that period when ideoscopy began to take hold and demand institutionalization within the framework of the developing "communities of inquirers" inspired by the idea of the university, even though that idea as so-far-institutionalized fell short of the needs for adequately and appropriately supporting the emergent growth of ideoscopy.