As a rule, both in Protestant and Catholic countries instruction in chemistry and physics was for a long time discouraged by Church authorities; and, when its suppression was no longer possible, great pains were taken to subordinate it to instruction supposed to be more fully in accordance with the older methods of theological reasoning.

I have now presented in outline the more direct and open struggle of the physical sciences with theology, mainly as an exterior foe. We will next consider their warfare with the same foe in its more subtle form, mainly as a vitiating and sterilizing principle in science itself.

We have seen thus far, first, how such men as Eusebius, Lactantius, and their compeers, opposed scientific investigation as futile; next, how such men as Albert the Great, St. Thomas Aquinas, and the multitude who followed them, turned the main current of medieval thought from science to theology; and, finally, how a long line of Church authorities from Popes John XXII and Innocent VIII, and the heads of the great religious orders, down to various theologians and ecclesiastics, Catholic and Protestant, of a very recent period, endeavoured first to crush and afterward to discourage scientific research as dangerous.

Yet, injurious as all this was to the evolution of science, there was developed something in many respects more destructive; and this was the influence of mystic theology, penetrating, permeating, vitiating, sterilizing nearly every branch of science for hundreds of years. Among the forms taken by this development in the earlier Middle Ages we find a mixture of physical science with a pseudo-science obtained from texts of Scripture. In compounding this mixture, Jews and Christians vied with each other. In this process the sacred books were used as a fetich; every word, every letter, being considered to have a divine and hidden meaning. By combining various scriptural letters in various abstruse ways, new words of prodigious significance in magic were obtained, and among them the great word embracing the seventy-two mystical names of God—the mighty word "Schemhamphoras." Why should men seek knowledge by observation and experiment in the book of Nature, when the book of Revelation, interpreted by the Kabbalah, opened such treasures to the ingenious believer?

So, too, we have ancient mystical theories of number which the theological spirit had made Christian, usurping an enormous place in medieval science. The sacred power of the number three was seen in the Trinity; in the three main divisions of the universe—the empyrean, the heavens, and the earth; in the three angelic hierarchies; in the three choirs of seraphim, cherubim, and thrones; in the three of dominions, virtues, and powers; in the three of principalities, archangels, and angels; in the three orders in the Church—bishops, priests, and deacons; in the three classes—the baptized, the communicants, and the monks; in the three degrees of attainment—light, purity, and knowledge; in the three theological virtues—faith, hope, and charity—and in much else. All this was brought into a theologico-scientific relation, then and afterward, with the three dimensions of space; with the three divisions of time—past, present, and future; with the three realms of the visible world—sky, earth, and sea; with the three constituents of man—body, soul, and spirit; with the threefold enemies of man—the world, the flesh, and the devil; with the three kingdoms in nature—mineral, vegetable, and animal; with "the three colours"—red, yellow, and blue; with "the three eyes of the honey-bee"—and with a multitude of other analogues equally precious. The sacred power of the number seven was seen in the seven golden candlesticks and the seven churches in the Apocalypse; in the seven cardinal virtues and the seven deadly sins; in the seven liberal arts and the seven devilish arts, and, above all, in the seven sacraments. And as this proved in astrology that there could be only seven planets, so it proved in alchemy that there must be exactly seven metals. The twelve apostles were connected with the twelve signs in the zodiac, and with much in physical science. The seventy-two disciples, the seventy-two interpreters of the Old Testament, the seventy-two mystical names of God, were connected with the alleged fact in anatomy that there were seventy-two joints in the human frame.

Then, also, there were revived such theologic and metaphysical substitutes for scientific thought as the declaration that the perfect line is a circle, and hence that the planets must move in absolute circles—a statement which led astronomy astray even when the great truths of the Copernican theory were well in sight; also, the declaration that nature abhors a vacuum—a statement which led physics astray until Torricelli made his experiments; also, the declaration that we see the lightning before we hear the thunder because "sight is nobler than hearing."

In chemistry we have the same theologic tendency to magic, and, as a result, a muddle of science and theology, which from one point of view seems blasphemous and from another idiotic, but which none the less sterilized physical investigation for ages. That debased Platonism which had been such an important factor in the evolution of Christian theology from the earliest days of the Church continued its work. As everything in inorganic nature was supposed to have spiritual significance, the doctrines of the Trinity and Incarnation were turned into an argument in behalf of the philosopher's stone; arguments for the scheme of redemption and for transubstantiation suggested others of similar construction to prove the transmutation of metals; the doctrine of the resurrection of the human body was by similar mystic jugglery connected with the processes of distillation and sublimation. Even after the Middle Ages were past, strong men seemed unable to break away from such reasoning as this—among them such leaders as Basil Valentine in the fifteenth century, Agricola in the sixteenth, and Van Helmont in the seventeenth.

The greatest theologians contributed to the welter of unreason from which this pseudo-science was developed. One question largely discussed was, whether at the Redemption it was necessary for God to take the human form. Thomas Aquinas answered that it was necessary, but William Occam and Duns Scotus answered that it was not; that God might have taken the form of a stone, or of a log, or of a beast. The possibilities opened to wild substitutes for science by this sort of reasoning were infinite. Men have often asked how it was that the Arabians accomplished so much in scientific discovery as compared with Christian investigators; but the answer is easy: the Arabians were comparatively free from these theologic allurements which in Christian Europe flickered in the air on all sides, luring men into paths which led no-whither.

Strong investigators, like Arnold of Villanova, Raymond Lully, Basil Valentine, Paracelsus, and their compeers, were thus drawn far out of the only paths which led to fruitful truths. In a work generally ascribed to the first of these, the student is told that in mixing his chemicals he must repeat the psalm Exsurge Domine, and that on certain chemical vessels must be placed the last words of Jesus on the cross. Vincent of Beauvais insisted that, as the Bible declares that Noah, when five hundred years old, had children born to him, he must have possessed alchemical means of preserving life; and much later Dickinson insisted that the patriarchs generally must have owed their long lives to such means. It was loudly declared that the reality of the philosopher's stone was proved by the words of St. John in the Revelation. "To him that overcometh I will give a white stone." The reasonableness of seeking to develop gold out of the baser metals was for many generations based upon the doctrine of the resurrection of the physical body, which, though explicitly denied by St. Paul, had become a part of the creed of the Church. Martin Luther was especially drawn to believe in the alchemistic doctrine of transmutation by this analogy. The Bible was everywhere used, both among Protestants and Catholics, in support of these mystic adulterations of science, and one writer, as late as 1751, based his alchemistic arguments on more than a hundred passages of Scripture. As an example of this sort of reasoning, we have a proof that the elect will preserve the philosopher's stone until the last judgment, drawn from a passage in St. Paul's Epistle to the Corinthians, "We have this treasure in earthen vessels."

The greatest thinkers devoted themselves to adding new ingredients to this strange mixture of scientific and theologic thought. The Catholic philosophy of Thomas Aquinas, the Protestant mysticism of Jacob Boehme, and the alchemistic reveries of Basil Valentine were all cast into this seething mass.