"God, in his ordinary providence, maketh use of means, yet is free to work without, above, and against them, at his pleasure."
-- Westminster Confession of Faith, Chapter 5.
This statement succinctly formulates the status of nature in Christian theology. Ordinarily, God operates into the creation through means, or second causes (that is, the ordinary regularities that we sometimes call physical laws). However, God is free: God is in no way restricted in using such means to act into the creation. In other words, miracles of direct divine intervention are always possible; the world is an open system, not a closed system of causes and effects. It is open from above.
Biologist Jacques Monod has recognized a principle of gratuity: that the structures and processes on one level of an organism do not place any restrictions on higher level processes (Chance and Necessity). Reality is stratified into many levels. The higher levels are free from determinism from below. For instance, a high level process, such as a conversation between two people, is not determined (necessarily) by what they ate for breakfast, or what their genetic makeup is. ("Gratuity in Nature and Technology", P. Arveson, J. Wash. Acad. Sci. 85(4), Dec. 1998.)
The evidence of gratuity in nature reveals an alternative to both chance and necessity (determinism) as a cause of events. Gratuity is consistent with the doctrine of providence, because it shows how even molecular systems can enable freedom or contingency in the processes of the world. Providence also opens the possibility for high-level processes to be influenced from above, not just from below. Hence we are able to accept the rational possibility that God can intervene in nature, just as persons can act into nature by their choices, without the necessity of extraordinary miracles. This relationship of God to nature shows how God can work through second causes, as well as above them or without them.