Before the scientific revolution of the last four centuries, such arguments were commonplace and widely accepted, presumably because the "gaps" were large and showing no signs of shrinking. A lightning bolt crashes down, the peasants working in the field cross themselves and say "well, we don't understand that, so it must be God."
Problems with God of the Gaps
From a philosophical point of view, the inherent problem with a God of the Gaps apologetic is that it relegates God to only a portion of creation — the portion that we don't understand yet. It places the apologist at a disadvantage by ignoring how the underlying patterns in the things we understand speak to the work of the Creator God. It also denies, in effect, the Christian view of science, which is that science is "thinking God's thoughts after him"; it does this by suggesting that we can only see God in the areas of nature which we do not understand, rather than seeing him most clearly in those which we do understand.
From a pragmatic point of view, the main problem with a God of the Gaps apologetic is that the gaps are getting smaller with every passing year. No one felt this more keenly than Isaac Newton, a religious man (in the end a Deist) who closed more gaps than any other scientist. As recorded in the General Scholium, Newton struggled to find a gap big enough for God. He eventually settled on gravity's action at a distance, unwilling to believe that a simple force could act across vast empty spaces and penetrate to matter in the center of the planets. That gap, of course, has long since diappeared from classical and relativistic physics.
Origin of the term
The earliest use of the term "God of the Gaps" was probably by Henry Drummond, a Scottish evangelist and close associate of D.L. Moody, who was renowned for his endeavours to harmonize emerging scientific theories with the gospel. Writing in 1894, Drummond was critical of those who focused on what science did not yet know:
There are reverent minds who ceaselessly scan the fields of Nature and the books of Science in search of gaps — gaps which they will fill up with God. As if God lived in the gaps? What view of Nature or of Truth is theirs whose interest in Science is not in what it can explain but in what it cannot, whose quest is ignorance not knowledge, whose daily dread is that the cloud may lift, and who, as darkness melts from this field or from that, begin to tremble for the place of His abode? What needs altering in such finely jealous souls is at once their view of Nature and of God. Nature is God's writing, and can only tell the truth; God is light, and in Him is no darkness at all.
Bonhoeffer, who may have read Drummond's book, used a similar term in a letter that he wrote in 1944:
...how wrong it is to use God as a stop-gap for the incompleteness of our knowledge. If in fact the frontiers of knowledge are being pushed further and further back (and that is bound to be the case), then God is being pushed back with them, and is therefore continually in retreat. We are to find God in what we know, not in what we don't know; God wants us to realize his presence, not in unsolved problems but in those that are solved.
God of the Gaps in theology and apologetics
Theologians and religious scientists have used God of the Gaps arguments at least since the thirteenth century, revising them in response to developments in science.
Thomas Aquinas argued that because there is order and predictability in inanimate objects, which clearly cannot create order for themselves, there must be an intelligent being ordering them:
We see that things which lack knowledge, such as natural bodies, act for an end, and this is evident from their acting always, or nearly always, in the same way, so as to obtain the best result. Hence it is plain that they achieve their end, not fortuitously, but designedly. Now whatever lacks knowledge cannot move towards an end, unless it be directed by some being endowed with knowledge and intelligence; as the arrow is directed by the archer. Therefore some intelligent being exists by whom all natural things are directed to their end; and this being we call God. 
Isaac Newton, a deist, developed equations that explained much of the order in inanimate objects, which challenged Aquinas's God of the Gaps arguments. In response, Newton turned to the variety that he saw in creation, as evidence for a creator:
We know him only by his most wise and excellent contrivances of things, and final cause: we admire him for his perfections; but we reverence and adore him on account of his dominion: for we adore him as his servants; and a god without dominion, providence, and final causes, is nothing else but Fate and Nature. Blind metaphysical necessity, which is certainly the same always and every where, could produce no variety of things. All that diversity of natural things which we find suited to different times and places could arise from nothing but the ideas and will of a Being necessarily existing. 
William Paley, writing more than a century after Newton, argued that the complexity and obvious design of God's creation, and in particular of living things, was irrefutable evidence for God's existence:
In crossing a heath, suppose I ... found a watch upon the ground, and it should be inquired how the watch happened to be in that place;... This mechanism being observed... the inference, we think, is inevitable, that the watch must have had a maker....who comprehended its construction, and designed its use. 
Not many years after Paley, Darwin offered an explanation that undermined Paley's "argument from design." Many of those who had based their faith on Paley's arguments found their faith severely challenged. It was in this context that Drummond wrote "The Ascent of Man" as quoted above.
God of the Gaps in secular discourse
One frustration for Christian apologists is the tendency for secular commentators, even well-respected ones, to assume that Christian theology is based on God of the Gaps arguments. A typical non-believing syllogism might proceed as follows:
- "I note that Christians see God's hand in the wonders of creation"
- "I can explain all observables without resorting to God-talk"
- "therefore Christians are wrong to believe in God"
The logical cum hoc ergo propter hoc error, of course, is to think that Christians have faith because they see God in creation. In general the reverse is the case: Christians see God in creation because they have faith — the veil has been lifted from their eyes and they can see God's hand in everything (2 Cor 4:3-4).
Believing that faith is based on a God of the Gaps, sceptics try to undermine faith by stitching up the gaps.
- "In the hot big bang model ... the initial state of the universe would have to have had exactly the same temperature everywhere in order to account for the fact that the microwave background has the same temperature in every direction we look."
- "It would be very difficult to explain why the universe should have begun in just this way, except as the act of a God who intended to create beings like us."
Hawking then introduces various Inflationary models of the universe, and a "no-boundary" proposal that requires no singularity at the big bang. With that cosmological gap thus closed, he concludes:
- "So long as the universe had a beginning, we could suppose it had a creator. But if the universe is really completely self-contained, having no boundary or edge, it would have neither beginning nor end: it would simply be. What place then, for a creator?"
- ↑ Isaac Newton Philosophiae Naturalis Principia Mathematica 1687
- ↑ Henry Drummond The Ascent of Man, New York: James Pott & Co. Publishers, 1894, p. 333
- ↑ Dietrich Bonhoeffer Letters and Papers from Prison edited by Eberhard Bethge, translated by Reginald H. Fuller, Touchstone, ISBN 0684838273, 1997
- ↑ Thomas Aquinas, Summa Theologica, Q. 2, Art. 3, 1270
- ↑ Newton, Principia, General Scholium, 1687
- ↑ William Paley, "Natural Theology; or, Evidences of the Existence and Attributes of the Deity", 1802
- ↑ Stephen Hawking A Brief History of Time, New York: Bantam, 1988