Most contemporary scientists believe that the behavior of fundamental particles is modified by the wider physical systems of which they can form a part. This can be most easily imagined by thinking of cells in an organic body, all of which contain the same DNA. Yet, depending on where in an organism the cells are, they develop in different ways, to perform different functions. The only way to account for this is to say that the behavior of the DNA molecules and their constituent atoms is modified by the wider organic system of which they are part.
In a similar way, an organism's behavior patterns and its interactions with its environment over time can help to influence the DNA sequences that are switched on in the organism. Such environmental influence on smaller structures was termed "downward causation" or "top-down causation" by Donald Campbell (1974).
This idea was adopted by the physical biochemist Arthur Peacocke in a number of works, and he uses the related term whole—part influence "to represent the net effect of all those ways in which a system as a whole . . . is a determining factor in what happens to its parts" (2007, 16). As a scientist, Peacocke feels committed to naturalism, which he defines as the view that there are "no 'supernatural' entities, no 'miracles' that break the laws or regularities of nature discovered by science, no dualisms within the natural world" (2007, 9). All is explicable by the natural sciences, though the sciences must accept the fact of emergence in the natural world—that is, the existence of whole—part causation.
For Peacocke, complex physical systems affect the behavior of their constituent parts, but no new "extra forces or entities" are introduced. "All concrete particulars in the world (including human beings)—with all of their properties—are constituted only of fundamental physical entities of matter/energy" (2007, 12). The terms of higher-level descriptions cannot be reduced to terms of the lowest level, though all the entities there are can be found exhaustively specified at the lowest level.
Thus, we may say that particles behave differently when they are parts of a larger organic whole. To that extent, mathematical descriptions of particle behavior must include reference to whole systems as well as individual particles. But there is no reference to extra, much less immaterial, entities. The only substances (entities) that exist are physical substances, while such substances in suitably complex arrays have emergent properties and powers.
For this sort of nonreductive materialism, the nature of matter cannot be ascertained until all its potentialities, within the total structure of the physical universe, have been unfolded. That is, at least, a different sort of materialism than the classical reductionist theory. But is it really a sort of materialism at all? Peacocke accepts the existence of God, a purely immaterial consciousness, whose particular intentions influence events in the world, so that "they would not otherwise have happened had God not specifically intended them" (2007, 45). If immaterial intentions cause some material events to be as they are, when they could have been otherwise, then it looks very much as though there are material events that have an immaterial, supernatural cause after all. And purely material explanations will not, in fact, provide a fully adequate account of why things are as they are in the cosmos. A full explanation will require reference to the intentions of an immaterial Conscious Being.
Peacocke pictures this by thinking of God as "containing" the cosmos within the Divine Being (that is what panentheism means). God is, thus, the total environment within which the cosmos exists, and whole—part causation obtains not only in complex structures within the cosmos but between God and the cosmos. God is a real causal influence on events in the universe, though "without abrogating natural regularities" (2007, 46).
The fact remains that the Ultimate Reality, God, cannot be explained as a very complex arrangement of simple elementary particles. Ontological primacy must be given to consciousness and its contents. The consciousness of God exists whether or not the universe exists, so there is, at least, one supernatural cause, and a full explanation of many physical events requires reference to its intentions since those events would not have happened if those intentions had not existed. All this means that the regularities of nature must be compatible with some form of supernatural causality. And it means that there are, after all, supernatural causes—not all causes exist within the natural realm.
The theory is not quite as naturalistic as we might think. It involves the existence of quite a lot of supernatural causality and a fundamental dualism between God and the physical cosmos. What, then, is the force of talking about emergence and whole—part causation?
It is, I think, to stress that there is a continuous development in the cosmos from simple elements to complex structures and that human consciousness is the result of a gradual unfolding of the potentialities of matter. New properties and causal powers come into existence that are natural developments of matter and yet are similar in kind to the nature of the Ultimate Spiritual Reality that has initiated and sustains the whole process.
Thus, the basic nature of matter, at the most fundamental level, is what it is in order that finite embodied consciousnesses should develop. The ultimate form of explanation is teleological, the intentions of the Creator being the "whole" that influences the nature of the elementary material parts. That influence is not all-determining. It lays down natural regularities and principles of emergence, so that the cosmos has its own relative autonomy—but an autonomy intrinsically open to divine influence toward the emergence of consciousness and value.
Divine action is, thus, not occasional interference in the laws of nature. It is continuous with natural processes, present throughout the whole cosmos and entirely compatible with our mathematical descriptions of physical behavior—which, accordingly, must be rather looser and more flexible than some Newtonian physicists thought.