In the last discourse of Idea of a University Newman wishes to explain why many scientists are unbelievers or skeptics. He does this by reference to history and to the methods used by science and theology.

First Newman refers to the “positive or negative unbelief of Laplace, Buffon, Franklin, Priestley, Cuvier, and Humboldt.” In the Middle Ages there was antagonism towards Bacon, Pope Sylvester II, and St. Virgil of Saltzburg. The antagonism between experimental science and theology, however, goes as far back as the ancient Greeks.

According to Bacon, physics must be excluded from religious investigations and vice-versa. Newman writes about this autonomy of the sciences: “If the theologian, in tracing the ways of Providence, were stopped with objections grounded on the impossibility of physical miracles, he would justly protest against the interruption; and were the philosopher, who was determining the motion of the heavenly bodies, to be questioned about their Final or their First Cause, he too would suffer an illogical interruption.”

For Bacon, science is in a certain sense atheistic. He objected to the metaphysical considerations Aristotle and later Galen gave to physical matters. Newman describes the prejudice of scientists (physical philosophers) towards theologians: “on the one hand, their deep satisfaction in the laws of nature indisposes them towards the thought of a Moral Governor, and makes them sceptical of His interposition; on the other hand, the occasional interference of religious criticism in a province not religious, has made them sore, suspicious, and resentful.”

With regards to methods Newman writes: “Induction is the instrument of Physics, and deduction only is the instrument of Theology.” God revealed himself and many other truths to man, giving the Apostles a unique role in the transmission of these truths and giving the Church the sole authority to sanction the interpretation of these truths. The method used in theology is that of deduction. The school of Bacon, superseded this method with regards to the physical sciences with the method of induction and thus it was “no wonder that the very force and dazzling success of their own method in its own departments should sway or bias unduly the religious sentiments of any persons who come under its influence.”

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