God is sovereign. This means God is the supreme, ultimate cause of everything that happens in the universe (which includes angels, humans, animals, plants, rocks, and all else). It is His creation.
But this does not imply the exaggeration that nature is merely an extension of the essence of God, in which God is identified with the processes of the world. These are the exaggerations of pantheism, panenthism or panpsychism.
On the contrary, natural history is real. God's activity in nature is usually through second causes, but God relates to a real universe that he created.
But this does not imply the exaggeration that the universe is the only reality; that there is no sovereign God Who transcends the autonomous universe. In that case all things would happen by accident, chance or fate. Christianity rejects these exaggerated conceptions of nature (naturalism, materialism etc.).
Providence and Sovereignty: So Christian doctrine acknowledges God as the sovereign Ruler over all things, but on the other hand, the nature that God created is real, and contains processes that operate as secondary causes. Nature is not merely an embodiment of God. On the other hand, "there is no chance back of God." (Francis Schaeffer's phrase).
In the concept of providence, the emphasis of Christian theology is on the active presence of God. While Christian doctrine emphasizes the reality of the world, this is not at the expense of the transcendent reality of God. Naturalism excludes God; pantheism identifies nature with God. But pantheism in so doing does not exalt God. Rather, if God is everything, then God is nothing. The net effect in both cases is to exclude a real, living and active God from nature. When God is thus excluded as a real Power to be reckoned with, nature itself becomes meaningless. As Steven Weinberg, the particle physicist stated in The First Three Minutes, "The more the universe seems comprehensible, the more it seems pointless."
In dealing with such a profound subject as God's relationship with the universe, "we see through a glass darkly" (I Cor. 13:12). Perhaps the most satisfactory understanding has been by means of an analogy: as we, with our minds, we can freely move our bodies, so God can freely act into the universe. This view recognizes that mind and matter are both real, but complementary aspects of the whole picture.
John Polkinghorne offers an intriguing suggestion:
"The picture beginning to form encourages the thought of man as a psychosomatic unity, with the material and mental as complemenentary poles of his nature. In that way he is able to participate in a noetic world of ideas and purposes, as well as being able to act within the physical world. Such a view seeks to avoid an incomprehensible Cartesian dualism by its appeal to the complementary linkage of the material and mental as aspects of the world in different degrees of organizational complexity and flexibility. Here seems to be a promising location for the causal joints by which both we and God interact with the universe."
John Polkinghorne, Science and Providence: God's Interaction with the World. (New Science Library, 1989).
Perhaps Polkinghorne's suggestion could be described briefly as: God:world :: mind:body. (God is to world as mind is to body).
But this is not a perfect analogy, because God is not dependent on matter, as the human mind (brain) is. There just doesn't appear to be a picture that we creatures can find to understand this mystery.
"The most ardent literalist has no idea of the process by which God still performs miracles, nor indeed how the King of creation brought the universe into being. Thus the Bible does not defend any particular picture or 'world-view'. The story of creation must therefore be distinguished from all the theogonies, cosmogonies or cosmologies -- ancient or modern. Genesis one is not a primitive account of how the universe began, but about who brought all things into being. The attitude of 'how-it-all-began' is the product of deistic views that would speculate about how the phenomenal world began and then was left alone to run its own course. Rather, the kingship of God is that He still rules. He still 'upholds all things by the Wor of His power'. In His general as well as His special providence, God has not abdicated the moral governorship of the universe to the hypotheses of men."J. Houston, I Believe in the Creator, pp. 46-47.
God is no King if He only originated creation and then has left it to unwind like a clock. The Creator is behind all physical processes, all reproductive capacities, all principles of harmony in the universe. God's activity therefore does not come in as an extra. As Professor MacKay has said, 'If God is active in any part of the physical world, He is in all. If the divine activity means anything, then all the events of what we call the physical world are dependent on that activity. [D. MacKay, The Clockwork Image, p. 57]. If so, then in principle there can be no conflict between faith and science. Conflict will arise only if God is assumed to be merely the God-of-the-gaps, whose activities are circumscribed to the miraculous while science studies the 'normal' or 'natural' events. If the Creator is Lord of all events, taking ultimate responsibility for everything, even evil, then the term 'natural' will not mean self-explanatory, but that fixed and stable set of processes in the universe of which God is the Ruler and Maintainer."