The Stanford School generally opposed the Unity of Science movement, characterized by the claims "chemistry can be reduced to physics, and biology can be reduced to chemistry."

A decade before the founding conference of the Stanford School, Dupré's 1993 book, The Disorder of Things, proposed a refutation of reductionism and determinism. He was skeptical about the idea of causal closure, that every physical event has a necessary and sufficient physical cause. This leads Dupré to reject reductionism, for example Jaegwon Kim's physicalism, which Kim calls the "causal closure of the world."

Dupré wrote...

The best way to introduce the position against which this book will argue is to consider the continuing influence of one particularly notorious founding metaphor of modern science, the idea that the universe should be considered as a gigantic machine. Traditionally the favored machine has been a clock... Anyone who thinks that such mechanical metaphors have faded in significance might reflect on the amount of scientific effort that has been devoted in recent years to investigation of the hypothesis that the human brain — and generally also the human mind — is really a kind of calculating machine, or computer.

The philosophical thesis most intimately connected with this mechanistic metaphor is determinism. The cosmic clock, we must assume given its provenance, has always told the correct time and always will. To achieve such precision its components must exhibit the same unvarying reliability as the whole. Once the clock is wound up and set in motion, its behavior and that of all its parts are determined for all eternity.

...the current vogue for chaos theory suggests that certain aspects of this complexity may be in principle beyond the reach of certain kinds of comprehension, notably prediction. Nevertheless, the metaphysical conceptions of order that originated in the picture of the mechanical universe seem to have been little threatened, if sometimes modified, by such developments. The case of chaos theory nicely illustrates this resilience. Prediction, though long conceived as a very central excellence of scientific understanding, is a goal that has tended to recede rather than approach as various scientific disciplines have increased their understanding of the complexity of the phenomena within their domains. Chaos theory appears to confront prediction not merely with an insuperable practical difficulty, but with a logically impassable obstacle. Yet paradoxically determinism, the metaphysical underlay of :he possibility of prediction, is strengthened rather than threatened by this development. For the central mathematical functions of chaos theory are quite deterministic...Even the increasing prevalence of probabilistic rather than deterministic hypotheses and methods from quantum mechanics up through the scientific hierarchy has not, I shall argue, led to the rejection of some of the most fundamental features of the deterministic world view.

(The Disorder of Things, pp.2-3)

To begin with, it will help to introduce what is perhaps both the clearest and the strongest version, which I shall call classical reductionism. Assume, first, a hierarchical classification of objects in which the objects at each level are complex structures of the objects com- prising the next-lower level. Paul Oppenheim and Hilary Putnam propose the following levels: elementary particles, atoms, molecules, living cells, multicellular organisms, and social groups. The investigation of each level is the task of a particular domain of science, which aims to discern the laws governing the behavior of the objects at that level. Reduction consists in deriving the laws at each higher (reduced) level from the laws governing the objects at the next-lower (reducing) level. Such reduction, in addition to knowledge of the laws at both the reducing and reduced levels, will also require so-called bridge principles (or bridge laws) identifying the kinds of objects at the reduced level with particular structures of the objects at the reducing level. Given the transitivity of such deductive derivation, the endpoint of this program will reveal the whole of science to have been derived from nothing but the laws of the lowest level and the bridge principles. The lowest level will be the physics of elementary particles. Thus, finally, truly basic science need concern itself only with the objects described by particle physics.

(The Disorder of Things, p.88)

In 2012, Dupré offered the book Processes of Life: Essays in the Philosophy of Biology

In 2018, with his Exeter colleague D.J. Nicholson, he published Everything Flows: Towards a Processual Philosophy of Biology

In 2022, Dupré delivered a Gifford Lecture on A Brief History of Form at the University of Aberdeen. In 2023 he delivered the Gifford Lectures at the University of Edinburgh on A Process Perspective on Human Life, based on the book Everything Flows.

Dupré's "process perspective" argues

"that it is a mistake to suppose that processes require underlying things, or substances... Instead of thinking of processes as belonging to things, we should think of things as being derived from processes. This does not mean that things do not exist, even less that thing-concepts cannot be extremely useful or illuminating. What it does imply is that things cannot be regarded as the basic building blocks of reality. What we identify as things are no more than transient patterns of stability in the surrounding flux, temporary eddies in the continuous flow of process."

Everything Flows, p.12

Dupré's Processual Philosophy of Biology identifies an essential difference between the atomic and molecular processes of physics and chemistry and the organic processes of the macromolecules of biology.

By contrast, information philosophy identifies a single cosmic creation process from the first few minutes of the universe, when elementary particles like protons and neutrons formed from the primordial quarks, gluons, electrons, and photons. It took hundreds of thousands of years before the universe cooled down and stable atoms could form atoms from protons, neutrons, and electrons. It was hundreds of millions of years before atoms could collapse under gravitational forces to produce planets, stars, and galaxies, and billions of years before life formed on one of those planets.

The first information structures formed in the early universe, elementary particles, atoms and molecules, galaxies, stars, and planets, are all the result of microscopic quantum cooperative phenomena and macroscopic gravitational forces. These "things" are not acting. They are being acted upon by the forces of Nature

But with the emergence of life, information replication, information communication, and information processing begin. Only then is information itself used in the creation of new - living - information structures. Living things are biological information processors, forms through which matter and energy flows, with capabilities far beyond the electronic digital computers that cognitive scientists think provide a “computational theory of mind.”

Most important, living things have “purposes.” They engage in communications of information with other living things and with their environment. Their messaging is meaningful, allowing them to be active users of information - which makes them agents, compared to passive material things, whose structural information is largely inert and meaningless in itself.

Since the total of matter and energy in the universe is a conserved constant, it's the arrangement of the matter and energy that is the information. Information philosophy (and science) tells us who or what is doing the arranging. In physics and chemistry, the forces in processes creating more complex objects are purely passive. In all of biology the active forces creating more complex organisms deploy information templates (e.g., the "central dogma" of DNA to mRNA to proteins). At animal and human levels these active creative processes become intentional, "mind over matter."

As Dupré's former colleague Anne Sophie Meincke stressed in a recent Vienna conference, living things are "agents." They introduce purpose into the universe.

We should note that where Dupré argues that "things cannot be regarded as the basic building blocks of reality," philosopher Trenton Merricks argues the exact opposite, defending "mereological nihilism, the idea that there are no composite objects, only "simples" arranged to look like objects. Or as Peter van Inwagen said in his 1990 book Material Beings, There are "no tables, only simples arranged tablewise."