On Molecules and Their Chemical Transformation

Alfred North Whitehead gave us a remarkable picture of reality in which change is the principal metaphysical category. The actualities of Whitehead’s world are not static unchanging substances, but rather dynamic processes, evolving through time, constantly becoming and perishing by a creative advance that is influenced by the relational experiences of all the other actualities of their environment. With this emphasis on change and the temporal, Whitehead’s philosophy of organism provides an especially suitable metaphysical backdrop for special sciences that concern themselves with dynamical aspects of nature. One such science is chemistry, the science of molecular change.

In previous essays, I have tried to develop accounts of chemistry from the perspective of an “all-purpose” process philosophy that is informed by a broad spectrum of process thought (Stein 2004; Stein 2005; Stein 2006). In contrast, this project is self-consciously Whiteheadian. The bulk of this paper will be devoted to answering, in Whiteheadian terms, two questions of central importance in chemistry: What are molecules, and how do they undergo chemical change? In keeping with this, I will briefly discuss the work of other scholars who have thought about chemical problems from a process perspective. Finally, I will end with a personnel assessment of the role that process thought can play in understanding, framing, and articulating chemical concepts.

1. Prolegomena to a Whiteheadian Philosophy of Chemistry

Whitehead does not give us a fully worked-out process philosophy of chemistry; that was never his intention. However, in developing his philosophy of organism, he does on occasion tell us what molecules are; thus providing important metaphysical underpinnings for a process ontology of molecules. Perhaps more important than these directly relevant arguments are his philosophical writings as a whole. From his early An Enquiry Concerning the Principles of Natural Knowledge to the mature Modes of Thought, Whitehead provides us powerful resources to develop a comprehensive philosophy of chemistry. Such a work has yet to be written. My modest goal here is to briefly develop two important topics from a Whiteheadian perspective: an ontological theory of molecules and a metaphysical theory of molecular change.

Whitehead tells us that humans have long had the intuition that “all things flow” and that it is one of the chief tasks of metaphysics to sort out the meaning of “all things flow” (PR 208). Whitehead points out that two kinds of fluency are required to explain a world in process—concrescence and transition:

One kind is the fluency inherent in the constitution of the particular existent. This kind I have called concrescence. The other kind is the fluency whereby the perishing of the process, on the completion of the particular existent, constitutes that existent as an original element in the constitution of other particular existents elicited by repetitions of process. This kind I call transition (PR 210).

Concrescence is the becoming and self-completion of the actuality; “the move towards its final cause,” while transition is the efficient causation that motivates the move from actuality to actuality (PR 150). While concrescence will be important in our development of a Whiteheadian molecular ontology, the concept of transition will help us develop a metaphysical theory of chemical change.

1.1. A Whiteheadian Theory of Molecular Ontology

In one of Whitehead’s earliest philosophical writings, An Enquiry Concerning the Principles of Natural Knowledge, he explains that “nature is ever originating its own development […] its creative advance is its fundamental characteristic” (PNK 14) and prefaces some of his thinking about molecular ontology with general statements about nature:

In biology the concept of an organism cannot be expressed in terms of a material distribution at an instant […]. Thus, a biological organism is a unity with a spatio-temporal extension which is the essence of its being […]. The fundamental assumption is that the ultimate facts of nature, in terms of which all physical and biological explanation must be expressed, are events connected by their spatio-temporal relations, and that these relations are reducible to the properties of events that can contain (or extend over) other events (PNK 3-4).

After these comments, Whitehead goes on to briefly outline his “molecular theory,” exemplifying his ideas with reference to the element iron. In a passage that I quote below, I substitute the more general “molecule” for “iron.” Here Whitehead rebukes theories that portray molecules in traditional terms of “ultimate material at an instant”:

No single characteristic property of [the molecule] can be manifested at an instant. […] What is [the molecule], is what happens during a period of time. [Molecules] and biological organisms are on a level in requiring time for functioning. There is no such thing as a [molecule] at an instant; to be a [molecule] is a character of an event (PNK 22).

By the time Whitehead wrote Process and Reality, these ideas had matured and found expression in the technical lexicon of his philosophy of organism. We find molecules described in two ways: as “historic routes of actual occasions” (PR 80); and as a particular kinds of “nexus of actual occasions” (PR 73), or more specifically, as “structured societies” of actual occasions (PR 99). To understand Whitehead’s molecular ontology, we must first understand several key concepts of his philosophy of organism—namely his concepts of an actual occasion (or equivalently, actual entity), nexus, and structured society.

For Whitehead, experience defines reality for all the varied existents of the world. To be actual is to experience and be experienced. In the analysis of experience, Whitehead explains that the “ultimate facts of immediate actual experience are actual entities, prehensions, and nexus. All else is derivative abstraction” (PR 20).

Whitehead tells us that actual entities are the “final real things of which the world is made up” and “involve each other by reason of their prehensions of each other” (PR 18, 20). Here prehension is the means by which an entity objectifies another entity; the process can be likened to an “adsorption” of energy or affective tone. Involvement among actual entities can occur at several levels of increasing relational concern, or “mutual immanence,” defining a hierarchical structure. The levels we need to consider are the nexus, and two special nexus of higher order, the society and the structured society.

A nexus is the simplest association of actual occasions; a loose grouping of actual occasions that, while having a general connectedness, lack any special type of order. At the next higher level in this hierarchy of involvement we find the society. Societies of actual occasions have a social order that is defined by the existence of a common form that is reproduced again and again, giving the nexus endurance and a temporal nature. A society is self-sustaining; “it is its own reason” (AI 201-204).

Significantly, it is societies of actual occasions that comprise our world. Whitehead tell us that the “real things that endure are all societies” (AI 204). In fact, nature exists as a system of nested societies. “The Universe achieves its values by reason of its coordination into societies of societies, and into societies of societies of societies” (AI 206). These nested societies of actual occasions are “structured,” containing subordinate societies. A defining feature of structured societies is that there exist patterns of inter-relations among the subordinate societies. “Nature is a complex of enduring objects, functioning as subordinate elements in a larger spatial-physical society” (AI 206).

Working our way back to a consideration of molecules, we now start with a quote from Process and Reality in which Whitehead describes our physical universe as a vastly interconnected society of electromagnetic occasions.

Our present epoch is dominated by a society of electromagnetic occasions […]. But in its turn, this electromagnetic society would provide no adequate order for the production of individual occasions realizing peculiar “intensities” of experience unless it were pervaded by more special societies, vehicles of special order. The physical world exhibits a bewildering complexity of such societies […] the regular trains of waves, individual electrons, protons, individual molecules, societies of molecules, living cells, and societies of cells (PR 98).

Now, indicated above, Whitehead suggests two modes of analysis for molecules—temporal and structural. In the temporal mode, the molecule, as “historic route of actual occasions” is actualized through a process in which each new contemporary actual molecular occasion arises from prehension of antecedent molecular occasions. In the structural mode of analysis, the molecule, as “structured society of actual occasions,” is actualized through a social ordering of the subordinate occasions (perhaps, subordinate atomic occasions—see below) of experience that comprise it. A molecule, seen in its temporal mode, comprises a sequential train of structured societies of actual occasion.

The process of concrescence, or the “production of novel togetherness” operates in both of these modes. Concrescence is the means by which the historical route of molecular occasions is propagated as each contemporary occasion arises from the unification of prehensions of past occasions. And concrescence is the means by which each molecular occasion, as it arises, unifies subordinate societies which comprise it.

The ultimate metaphysical principle is the advance from disjunction to conjunction, creating a novel entity other that the entities given in disjunction […]. The many become one, and are increased by one. In their natures, entities are disjunctively “many” in process of passage into conjunctive unity (PR 21).

One final element needs to be considered in our development of a Whiteheadian theory of molecular ontology; the notion that Whitehead refers to as “strain” (PR 310-321). The concept of strain is a recognition of the importance of geometric or spatial elements for the constitution of the enduring objects of our world.

The geometrical facts are public facts characterizing the feelings of actual entities. It so happens that in this epoch of the universe the feelings involving them are of dominating importance. A feeling in which the forms exemplified in the datum concern geometrical, straight, and flat loci will be called a “strain” (PR 310)

Whitehead goes on to explain that strain is found only in, and indeed required for the emergence of relatively high-grade actual occasions. For such complexity to arise, highly complex processes of concrescence are necessary. “The growth of ordered physical complexity is dependent on the growth of ordered relationships among strains” (PR 311).

Strain brings about the “spatialization” of the enduring objects that furnish our world:

This spatialization is a real factor in the physical contribution of every actual occasion belonging to the life-history of an enduring physical object […]. The reality of the rest and the motion of enduring physical objects depends on this spatialization for occasions in their historic routes (PR 321).

In the development of a molecular ontology, Whitehead’s concept of strain explains the three-dimensionality of molecules, providing critical metaphysical underpinnings for the chemist’s talk of a molecule’s structural features such as bond lengths and angles, intramolecular steric effects, and chirality.

So, what then, is a molecule? The molecule is a process, at once an historic route of molecular occasions and a structured society of subordinate occasions. As historic routes, molecules comprise a succession of molecular occasions of experience that arise from prehensions of their antecedent occasion and then perish into objective immortality, as they are themselves prehended into subsequent occasions. As structured societies, molecules comprise subordinate occasions, inter-related in a complex spatialized manner. An intriguing question remains: What are these subordinate occasions? While they may be atomic occasions of experience, one can imagine other kinds of subordinate occasions for particular kinds of molecular occasions of experience. One can imagine “functional group” subordinate occasions comprising the sorts of complex carbon-based organic molecules of interest to chemists, as well as “domain” subordinate occasions of experience comprising protein and RNA molecules. Molecular mereology will be an area of critical importance for process philosophers of chemistry as they try to understand molecules as structured societies of actual occasions.

1.2. A Whiteheadian Theory of Molecular Change

One of the guiding principles of this project is that the insights we gain from an ontological theory of molecules should prove useful, if not essential, to the development of a metaphysical theory of molecular change. I believe we see this principle at work in a key passage about molecules in Process and Reality, where after describing molecules as historic routes of actual occasions, Whitehead goes on to explain that “changes in the molecule are the consequential differences in the actual occasions” (PR 80). The meaning of this phrase hinges on Whitehead’s use of the word “consequential.” So we start our development of a Whiteheadian theory of molecular change by trying to understand what Whitehead means here he talks about “consequential differences.”

Now, we saw above that a molecule endures by virtue of repetition of patterns. That is, as an historic route a molecule will maintain its identity if contemporary molecular occasions of experience faithfully reproduce antecedent molecular occasions. The “weight of repetition” (PR 279) insures stability of the molecule. There are no consequential differences among the actual occasions that comprise the historical route that is the molecule. On the other hand, in the process of concrescence of each new molecular occasion of experience, there is an element of freedom and self-determination, albeit freedom of a small degree for low-grade existents such electrons, atoms, and simple molecules. It is precisely this element of free novelty that has consequences for the molecule. The consequences are the creative advance of the molecule, or, in more regularly terminology, its chemical change.

The process by which these consequential differences are effected within the molecule to bring about chemical change is an example of Whitehead calls transition. Thus, within the context of Whitehead’s philosophy of organism, the chemical change of a molecule would be seen as the “transition from attained actuality to actuality in attainment.” Transition motivates the evolution of the “actual to the merely real” and provides the conditions for the attainment of novelty (PR 214, 150).

Whitehead’s concept of transition reflects that mode of molecular becoming in which the molecule as enduring object attains the potentiality for creative advance of a most radical type, in which identity is destroyed and redefined in the course of becoming (Stein 2004; Stein 2005). Such radical becoming is seen throughout the natural world. The metamorphosis of caterpillar into butterfly, the development and birth of a baby, the transformation of an ancient rainforest into the Sahara desert—all these exemplify a mode of becoming in which one identity dissolves away and is re-created in another.

2. History of Relevant Scholarship

Many scholars whom one might label “process thinkers,” have, at least tangentially, discussed chemical systems in their philosophical writings. Hegel, for example in his Science of Logic, talks about “chemical thinking” and its superiority to the “mechanistic thinking” of the physicist. Hegel wrote at the beginning of the nineteenth century and therefore did not benefit from the dramatic advance in the basic understanding of chemistry that would attend atomic and molecular theory of the late nineteenth century and quantum mechanics of the early twentieth century. With the twentieth century came a turning point for chemistry, as it moved from simple description of macro-systems to mechanistic analysis of molecular systems. It is for this reason that in this section I will only consider process thinkers, other than Whitehead, who wrote after 1900. For contrast, I have divided these scholars into two groups—”philosophers who write about chemistry” and “chemists who write about philosophy.”

2.1. Philosophers who write about Chemistry

John B. Cobb, Jr. takes a thoroughly Whiteheadian approach to molecular ontology in his early work, where he writes that a molecule

is nothing more than a succession of molecular happenings or occasions [and] is typical of enduring objects in the extreme similarity of the successive occasions that make it up […]. Each occasion feels and reenacts the preceding occasion’s feeling and reenactment of its predecessor, and so on indefinitely. The successive occasions are comparatively little affected by other past occasions and the novelty of the new occasion is both trivial in itself and ineffective for the future. Enduring objects provide the things of the world with stability (Cobb 1965, 41).[1]

Later, in an essay published in 1988, Cobb makes an important observation: “The importance of arrangement of atoms in the determination of [molecular] properties is so great that ‘structure’ is now a fundamental category of analysis. This fact would not be so if the world were really composed of material substances” (Cobb 1988, 107; my italics). Cobb’s recognition of this property of molecular systems prompted him to then provocatively suggest that “instead of viewing molecules as machines, we should view them as ecosystems” (Cobb 1988, 108). “Molecule-as-ecosystem” is a powerful and evocative metaphor and while it may initially strike us as odd, it is consistent with what we know to be the case in chemistry. Chemists know that the properties of molecules are environmentally conditioned and determined by relation (Woolley 1978; Bogaard 1993).

David Ray Griffin develops a molecular ontology that draws inspiration from panexperientialism, the metaphysical proposition that all actual entities are experiencing entities. Panexperientialism describes a view of reality in which entities at all levels of complexity are capable of enjoying some degree of subjective experience. We saw that Cobb’s “molecule-as-ecosystem” is defined by relation, both internal and external. Thus molecular entities should not be viewed as mere objects, “vacuous entities,” but rather as subjects, with a nature that allows them to experience and respond to their environment (Stein 2004; Stein 2005; Stein 2006). Such an ontology is necessarily based on a panexperientialist understanding of nature in general, and of molecules in particular. This is expressed by Griffin when he insists that a molecule should not be thought of as a simple aggregate of atoms but rather, that “insofar as the molecule shows signs of responding to its environment with a unity of action, it can be thought to have a unity of experience” (Griffin 1988, 158).

2.2. Chemists who write about Process Thought

Ilya Prigogine won the Nobel Prize in Chemistry in 1977 for his work on dissipative chemical systems; he can be considered a process thinker, though not in the Whiteheadian sense. In a major work entitled Order Out of Chaos, Prigogine and coauthor Isabell Stenger address what they regard as “the central problem of Western ontology: the relation between Being and Becoming” (Prigogine and Stengers 1984, 310). They do so from a new rendering of chemistry and the natural sciences that emphasizes “the multiple, the temporal, and the complex” (Prigogine and Stengers 1984, xxxvii). Prigogine teaches us that the ordered phenomenon of our world have emerged through chemical and physical processes that are irreversible (i.e., “involve an arrow of time”) and non-deterministic.

Joseph E. Earley, Sr. has been working at the interface of chemistry and philosophy for over twenty five years. In much of his work, he uses Prigogine’s dissipative structures as models for his metaphysical investigations. In some of these studies, he has interpreted dissipative structures and other chemical phenomenon in a context that is influenced by Ivor Leclerc’s concept of “fully reciprocal acting,” as well as by Whitehead (Earley 1981; Earley 1993; Earley 1998). In his development of a process-influenced chemical ontology, Earley explains that we should “count as existing any patterned set of interrelationships that, under specific historical condition, yielded coherence sufficiently persistent to have effects as one unified whole rather than as a mere aggregate.” He applied this concept not only to chemical dissipative systems but also to human civilizations, where “each of these are properly considered units with ontological significance” (Earley 1998).

Markus Reiher (2003a, 2003b) has begun to develop a systems approach to chemistry that is broadly modeled after the general systems theory of Ludwig von Bertalanffy (Bertalanffy 1968) and the systems philosophy of Ervin Laszlo (Laszlo 1972). Though not exactly a process approach to chemistry, Reiher’s systems approach is similar in the sense that it interprets the transformation of molecules as contextual and environmentally conditioned.

3. Process Thought and Chemistry

At the beginning of this essay, I said that chemistry is the science of molecular change. Of course, this description is a caricature of a much broader field of investigation and captures only a piece of what chemistry is. But for that segment of the chemical and biochemical sciences that is concerned with how molecules are transformed into other molecules, process thought can provide important and relevant metaphysical underpinnings. Furthermore, for chemists (such as myself) for whom the chemical transformation of a molecule is always transformative process in context, process thought is not merely relevant, but necessary.

In published work, I have been concerned with seeing how process thought can further our understanding of enzymes (Stein 2004; Stein 2005; Stein 2006). Enzymes are protein molecules that greatly accelerate the rates of critical biochemical reactions. Without the catalysis of these inherently slow reactions, key metabolic processes would proceed far too sluggishly to sustain life. The catalytic efficiency of enzymes is truly remarkable and can frequently exceed a factor of a billion.[2] Understanding how enzymes attain such enormous catalytic efficiencies is an area of intense investigation in contemporary biochemistry. Recent advances in experimental enzymology, including some from my own laboratory (Case and Stein 2003; Hengge and Stein 2004), suggest that a complete understanding of enzyme catalysis can only be achieved if we view the enzyme in its biological context. This point was emphasized twenty years ago by biophysicist G. Ricky Welch who told us that “enzymology [must] graduate from its present reductionist status to a more holistic posture” (Welch 1986, ix).

I emphasize in my philosophical writings that these new results in enzymology will require new thinking in metaphysics for their complete integration into the broader picture of biological reality. Whitehead’s philosophy of organism clearly provides one way to approach these issues. But there are, of course, other ways to think about process, and it would be a mistake for chemists, as they try to probe the process metaphysics of molecular change, to restrict their thinking to one school of thought. In the twentieth century alone, a number of process thinkers with distinctive ontologies have appeared, including Buchler’s “natural complexes” (Buchler 1990), Leclerc’s “reciprocally acting compound substances” (Leclerc 1972), Rescher’s “processes within processes” (Rescher 1996), Laszlo’s “natural systems” (Laszlo 1972), and Koestler’s “holons” (Koestler 1978).

All of these resources will be necessary to construct a comprehensive metaphysical system that stresses becoming (over being) and environmentally-responsive transformation. In such a system, molecules are not static, unchanging substances, but rather dynamic entities that negotiate complex energy landscapes. Process thought gives us the language to express what we believe to be the case when we think about molecules and molecular change.


[1] Cobb’s description of molecules as “enduring objects” initiated a debate which continues to this day. This debate centers around what exactly Whitehead meant by terms such as “actual occasion,” “society,” and “enduring object.” Which of these, if any, can be used to describe a molecule and still be faithful to what Whitehead intended? Donald Sherburn argues strongly that a molecule cannot be an enduring object, but is only a society (1971, 314-19). Some of this controversy has been reviewed and analyzed by Paul Bogaard (1992). An unorthodox, but perhaps accurate, interpretation of Whitehead was written by F. Bradford Wallack for whom “the actual entity is any concrete existent whatsoever” (1980, 7; her italics).

[2] “Catalytic efficiency” relates the rate of the catalyzed chemical reaction to that of the uncatalyzed reaction and is always defined as a ratio. Thus, a catalytic efficiency of a billion means that the catalyzed reaction occurs 109 times faster than the reaction in the absence of catalyst. Perhaps the most striking example occurs in the enzymatic decarboxylation of amino acids where the catalytic efficiency has been estimated to exceed 1020 (Snider and Wolfenden 2002). In the absence of enzymatic catalysis, these reactions would require billions of years for their completion, while in the presence of the correct enzyme (i.e., amino acid decarboxylases) these reactions are complete in less than a tenth of one second!

Works Cited and Further Readings

Bertalanffy, L. v. 1968. General Systems Theory—Foundations, Development, Applications (New York, George Braziller).

Bogaard, P. A. 1992. “Whitehead and the Survival of “Subordinate Societies””, Process Studies, 21, 219-226.

Bogaard, P. A. and Treash, G. 1993. The Philosophical Content of Quantum Chemistry (Albany, NY, State Univesity of New York Press).

Buchler, Justus. 1966. Metaphysics of Natural Complexes (New York, Columbia University Press). Reprinted 1990 (Albany, State University of New York Press).

Case, A. and Stein, R. L. 2003. “Mechanistic Origins of the Substrate Selectivity of Serine Proteases”, Biochemistry, 42, 9466-9481.

Cobb, J. B. 1965. A Christian Natural Theology (Philadelphi, Westminster Press).

Cobb, J. B.—Griffin, D. R. 1988. Ecology, Science, and Religion: Toward a Postmodern Worldview (Albany, State University of New York Press).

Earley, J. E. 1981. “Self-Organization and Agency: In Chemistry and In Process Philosophy”, Process Studies, 11, 242-258.

Earley, Joseph E. 1993. “The Nature of Chemical Existence,” in Metaphysics as Foundation: Essays in Honor of Ivor Leclerc, edited by Paul A. Bogaard and Gordon Treash (Albany, SUNY Press).

Earley, J. E. 1998. “Modes of Chemical Becoming”, Hyle—International Journal for the Philosophy of Chemistry, 4, 105-115.

Griffin, D. R.—Griffin, D. R. 1988. Of Minds and Molecules: Postmodern Medicine in a Psychosomatic Universe (Albany, State Univesity of New York Press).

Hengge, A. and Stein, R. L. 2004. “Role of Protein Conformational Mobility in Enzyme Catalysis—Acylation of a-Chymotrypsin by Specific Peptide Substrates”, Biochemistry, 43, 742-747.

Koestler, A. 1978. Janus—A Summing Up (New York, Random House).

Prigogine, I. and Stengers, I. 1984. Order Out of Chaos—Man’s New Dialogue with Nature (New York, Bantam Books).

Laszlo, E. 1972. Introduction to Systems Philosophy—Toward a New Paradigm of Contemporary Thought (New York, Harper & Row Publishers).

Leclerc, I. 1972. The Nature of Physical Existence (London, George Allen & Unwin Ltd.).

Reiher, M. 2003a. “A Systems Theory of Chemistry”, Foundations of Chemistry, 5, 23-41.

Reiher, M. 2003b. “The Systems-Theoretical View of Chemical Concepts”, Foundations of Chemistry, 5,

Rescher, N. 1996. Process Metaphysics—An Introduction to Process Philosophy (Albany, State University of New York).

Sherburne, D. W.—Brown, D., James, R. E. and Reeves, G. 1971. Whitehead Without God (Indianapolis, Merrill Educational Publishing).

Snider, M. and Wolfenden, R. 2002. “The Rate of Spontaneous Decarboxylation of Amino Acids”, Journal of the American Chemical Society, 122, 11507-11508.

Stein, R. L. 2004. “Towards a Process Philosophy of Chemistry”, Hyle—International Journal for the Philosophy of Chemistry, 10, 5-22.

Stein, R. L. 2005. “Enzymes as Ecosystems—A Panexperientialist Account of Biocatalytic Chemical Transformation”, Process Studies, 34, 62-80.

Stein, R. L. 2006. “A Process Theory of Enzyme Catalytic Power—The Interplay of Science and Metaphysics”, Foundations of Chemistry, 8, 3-29.

Wallack, F. B. 1980. The Epochal Nature of Process in Whitehead’s Metaphysics (Albany, State University of New York Press).

Welch, G. R. 1986. The Fluctuating Enzyme (New York, John Wiley & Sons).

Woolley, R. G. 1978. “Must a Molecule Have a Shape?”, Journal of the American Chemical Society, 1073-1078.

Author Information

Ross L. Stein
Laboratory for Drug Discovery in Neurodegeneration
Harvard NeuroDiscovery Center, 65 Landsdowne St., Cambridge, MA 02139

How to Cite this Article

Stein, Ross L., “On Molecules and Their Chemical Transformation”, last modified 2008, The Whitehead Encyclopedia, Brian G. Henning and Joseph Petek (eds.), originally edited by Michel Weber and Will Desmond, URL = <http://encyclopedia.whiteheadresearch.org/entries/thematic/sciences/on-molecules-and-their-chemical-transformation/(opens in a new tab)>.