Working totally from the Wikipedia article, it appears he took a bizarre position: In the quasi-deist Victorian theistic intellectual stance, God was the legislator who created the natural laws governing how physical objects interact, the ones that human scientists discover and formulate definitions of. In other words, we discover and define that the gravitational pull between two objects varies proportionately as the square of their distance; God in His wisdom was the one who ordained that that relationship should obtain.
Given this proposition, then, a belief that miracles occur was a denial of God’s role as the Supreme Legislator of Natural Law – and hence a denial of His power, and thus atheistic.
It is not, frankly, an argument I would care to defend, even against a bright five-year-old. But I follow the “logic” of what he was asserting.
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In this regard, it’s interesting to note one proposition advanced by C.S. Lewis, a follower in the same intellectual tradition, in his Miracles. (And this one has the benefit of slightly more plausibility.) To wit: None of the recorded miracles in Scripture, save the Resurrection itself, is strictly contrary to natural law, but instead represents an acceleration of natural processes. Water (with other ingredients) is turned into wine naturally by the growth and fruiting of grape vines, and then the action of viniferous microbes. A paralyzed limb properly treated medically eventually regains the ability to function. Under the forces of wind and weather, a fig tree eventually will wither and die. CPR and defibrillation will return to life someone who was briefly clinically dead. And so on. What the Biblical miracles do, according to Lewis, is to “short-circuit” the natural process by the equivalent of forced growth, to produce immediately the same results as might occur naturally over time.
Given the amount of third-party retellings, legend, and such that appear to have permeated the Biblical accounts, the debunking of this theory is easy enough. But if you accept for the sake of argument the premise that the Biblical accounts are accurate if naive retellings of real occurrences, Lewis’s point becomes very strong: The Biblical miracles are not **anti-**natural, things that never happen in nature,but supernatural, things that do not happen normally in the manner described, but do happen naturally under variant conditions. Jesus at Cana did nothing a vintner could not accomplish over years of effort; any basilisk lizard or water-strider bug can walk on water by using tricks with surface tension. The “E” account of the Parting of the Reed Sea (oddly, the English names of the Red Sea and the former marsh just north of the site of Suez mimic the close Hebrew parallels in the two names) even attributes the “miraculous” event to a strong wind forcing the shallow water back from the desired passage across.
I am not interested in promoting the idea as probable-fact, but I do find it a very intriguing point.