The dramatic conflicts between Galileo and the Roman Inquisition and between Darwin and his biblicist opponents have understandably dominated the perception of the relation between science and religion in the popular imagination. But this perception is distorted because it neglects the indispensable role that religious beliefs played in the Western approach to nature that led to the rise of modern science. On the other hand, emphasis on the integration of scientific and religious beliefs has often led to facile syntheses, provoking reactions that emphasize the separation of science and religion. Even if this separation were philosophically sound, it provides little basis for understanding the historical interaction, often constructive on both sides, between science and religion.

On the relation of science to the Bible, the diversity of views and interpretations is vast, but representatives can usefully serve to indicate the variety of types of reactions found in the Judeo‐Christian tradition. In De Doctrina Christiana (DDC) and De Genesi ad Litteram (DGL), Augustine (354–430 CE) makes clear the relative insignificance of specialized sciences as compared with understanding scripture, yet Augustine does not suggest that all knowledge can be found in scripture. In DDC, Augustine provides general rules for the interpretation of ambiguous terms. It is a mistake to read figurative signs literally (a rule that covers anthropomorphisms) and literal signs figuratively. The method of determining whether a particular expression is literal or figurative is that an expression that does not literally pertain to virtuous behavior or to the truth of faith must be taken figuratively. If the meaning of an expression is absurd when taken verbally, then we must examine its figurative possibilities. It follows from these guidelines that the believer should not read the Bible to learn facts about the natural world unrelated to salvation. In DGL, however, Augustine seems to require the certain truth of a new claim about nature in order to revise the apparently plain meaning of the biblical text, but even in DGL Augustine reiterates the principle that God did not wish to teach men and women things of no relevance to their salvation. It was clear to Augustine that secular knowledge was indispensable for the correct interpretation of scripture. Although not a license for the autonomy of science, the principle in Augustine's approval of secular disciplines was expanded by later authors into arguments legitimating knowledge of the natural universe as another way of honoring God. Such authors, like William of Conches (1080–1154), presumably did not foresee the developments that would contribute to the autonomy of the sciences, but they were confident that natural science would still perform its proper role when rightly interpreted.

The revival of Aristotle in the medieval Latin West prompted scholars like Thomas Aquinas (1225–1274) to construe theology by analogy with Aristotelian science. Even so, in the context of medieval society, the definitive resolution of anomalies in the understanding of the cosmos was impossible and hence generated a resignation to the limitations of human knowledge. Nicholas Oresme (1320–1382) took seriously the hypothesis of the diurnal rotation of the earth but rejected it because no confirmation seemed possible; he fell back on the Bible in this case as providing persuasive confirmation of the greater probability of the geocentric view.

In De Revolutionibus (1543) Copernicus's arguments for the heliocentric theory rely partly on his religious point of view. Copernicus (1473–1543) shared not only the traditional beliefs about the intrinsic rationality and harmonious design of God's creation but also another traditional belief that God had made the universe for human beings; he then concluded, perhaps originally, that it therefore must be knowable. Copernicus had no reason to believe that the heliocentric theory would ever be empirically confirmed by some neutral test or observation, but he believed that criteria already existed for preferring the heliocentric hypothesis, namely, the ordering of the planets and the spheres that arose from the mathematical coherence between period of planetary orbit and distance from the sun, and the natural relation between hypothesis and some observations. In the preface dedicated to Pope Paul III (d. 1549), Copernicus denigrates those ignorant of astronomy who distort some passage of scripture in order to censure his undertaking. The biblical texts most often cited in later controversies are Joshua 10.12–14, Ecclesiastes 1.5, and Psalms 19.4–6; 93.1; 104.5.

There is evidence of early official Catholic opposition to Copernicus, but plans to censure the theory in the mid‐1540s were supposedly frustrated by the death of the master of the Sacred Palace, Bartolomeo Spina, in 1547. Lutheran reactions to the Copernican theory permitted use of the Copernican models even as the system was rejected as a literal truth. One of Tycho Brahe's (1546–1601) reasons for rejecting the Copernican theory was its incompatibility with texts of scripture, but Tycho's other reasons were astronomical and physical. Nevertheless, there is no question that Johannes Kepler (1571–1630) shared Copernicus's beliefs in divine design, the knowability of the universe, and the clues provided by mathematical coherence and commensurability for determining the order of the planets and even the true shape of their orbital paths.

Likewise, Galileo (1564–1642) shared the views of Copernicus and Kepler on mathematical coherence, but he also felt the need to demonstrate the truth of the Copernican theory, and his personal relations with several theologians, cardinals, popes, and political leaders introduced further complications into the story.

The text in which Galileo most directly and fully addresses questions about the Bible and science is the Letter to the Grand Duchess Christina (1615). Galileo cites Augustine several times, and he initially adopts the traditional view, emphasizing the principle of accommodation and arguing that it is not the purpose of the Bible to teach science. Where Joshua 10.12–14, then, reports the sun standing still, we are not to read the text as a literal description of the motions of the heavenly bodies.

Almost immediately, however, Galileo apparently accepts the criterion proposed by Cardinal Robert Bellarmine (1542–1621) earlier in 1615 in a letter to Paolo Antonio Foscarini (1580–1616), a theologian who supported the Copernican theory, that only in cases in which a scientific conclusion is demonstrated, and not merely probable, are we authorized to reinterpret the plain meaning of the biblical text. Later in his letter Galileo presses the attack further. If geocentrists insist on the literal interpretation of scripture, the passage from Joshua requires that the motion of the sun be stopped. According to the Ptolemaic theory, however, the proper motion of the sun is its annual motion on the ecliptic. Stopping the sun's annual motion would shorten the day, not lengthen it, argues Galileo. Then Galileo suggests a literal interpretation of the text of Joshua consistent with the Copernican theory. The very idea is astounding; it is hardly surprising that theologians were shocked, and even less surprising that they misinterpreted the point of Galileo's critique.

Although Galileo's intention was to demonstrate the absurd consequence of insisting on using scripture for proof of a scientific hypothesis, it does appear that Galileo got carried away by his telescopic observations, his discovery of the sunspots, the cleverness of his own literal reading of the text of Joshua, and by his conviction that he could demonstrate the truth of Copernican theory. If Galileo intended to forestall official restrictions being placed on the Copernican theory, then his acceptance of Bellarmine's challenge and the introduction of the second reading seems to have provoked the very reaction he was trying to deflect.

In 1616 the Congregation of the Index condemned Foscarini's work supporting the Copernican theory, and it suspended Copernicus's De Revolutionibus and Diego de Zuniga's (1536–1597) Copernican interpretation of texts of scripture until they were corrected. The decree followed the decision of the Congregation of the Holy Office, which accepted the arguments propounded by Bellarmine, who in a letter to Foscarini had expanded the Augustinian criterion about faith and morals to include under faith any natural assertion declared by the Holy Spirit. Hence, the text of Joshua had to be interpreted plainly as asserting the geocentric view, and because it was declared by the Holy Spirit, the conclusion had to be accepted as pertaining to faith. Bellarmine's reasoning was faulty, and through adoption by the Holy Office it set a dangerous precedent. Galileo was issued a warning, but one that also confirmed that his views had not been censured.

By the end of 1616, however, the premises for the eventual case against Galileo were in place: the Copernican theory was under censure and it appears that Galileo had been warned against defending it. From a narrow, legal point of view, Galileo's Two Chief World Systems (1632), even with the license that he was granted, violated the spirit, if not the letter, of the earlier injunction. Historians tend to excuse the Inquisition's mistake in condemning Galileo in 1633 on the grounds that the Roman Catholic church felt itself under pressure from some Protestant critics to guard against individual interpretations of scripture, thus abandoning its traditional, sound view for a narrower, literalist interpretation of the biblical text. In spite of Pope John Paul II's public acknowledgments in 1983 of Galileo's mistreatment at the hands of church authorities in 1633, and in 1992 of the correctness of Galileo's views, the Vatican continues to refuse scholars complete access to the Vatican archival records on the Galileo case, fueling further speculation about the case.

The Catholic reaction partly provoked by Protestant literalistic criticisms lent the more open approaches of yet other Protestants an air of free inquiry. Scholars still debate the concreteness of supposed Puritan or Anglican influences on scientific activity, but there seems little question that, in England and Holland, religious ideology played a role in the advancement of empirical science. Francis Bacon's (1561–1626) appeal to the recovery of the garden of Eden in a technological paradise, Robert Boyles's (1627–1691) efforts to Christianize Epicurean atomism, the development of a natural theology supportive of scientific activity, the legitimation of science as a profession, and other similar consequences, however diverse and however loosely connected with any official doctrine, cannot be dismissed as irrelevant. Isaac Newton's (1642–1727) religious beliefs, even if not orthodox, and his extensive biblical commentaries attest to the importance that he himself attached to the Bible and to the partly religious foundations of his own conception of the universe. The later separation of the legitimation of science from religious motivations does not argue against the importance of religion for science prior to the eighteenth century.

In the nineteenth century, the controversies provoked by Charles Darwin's (1809–1882) theory of evolution were viewed as the focal point for a much broader perception of conflicting loyalties—to the belief in a universe divinely created with purpose or to the belief that the universe is the result of chance. The notion that the human eye could be the result of millions of years of evolution seems as improbable to those who believe in a special divine creation as the biblical story of Eve's creation from Adam's rib seems to the paleontologist. The official Roman Catholic response of the late nineteenth century was subordinated to the church's antimodernist reaction, constituting a position between liberal Protestantism and fundamentalism. In 1950 Pope Pius XII declared the belief in monogenesis as a foundation for the biblical account of original sin and its universal consequences. The a priori proscription of polygenesis on theological grounds has restricted Catholic evolutionists' options. Liberal Protestants have not seen fit to restrict God's options on this question. The impact of the theory of evolution on biblical interpretation is undeniably clear from the further developments in historical‐critical method and the emphasis on the social‐ethical message of scripture. Literalistic creationists have rightly pointed out problems with the theory of evolution, but to most scientists the theory remains the best available and is strongly supported by evidence from physics and astronomy. Some scientists speak of evolution dogmatically as a fact, but such a dogmatic stance seems partly provoked by the educational threat posed by fundamentalists efforts in America to legislate the teaching of religious alternatives to the theory of evolution and the effect of such efforts on textbook publishers—demonstrate the reality of such threats. Ironically, in the case of Teilhard de Chardin (1881–1955), the French Jesuit paleontologist, the Roman Catholic church was concerned with tying Christian dogma to scientific theory and hence advocated more circumspect theological discussions of evolution, thus demonstrating the caution it had painfully learned from the Galileo case.

There is always a theoretical background to empirical research, but the danger for theology lies in the use of science to advance a particular interpretation of the Bible and the danger for science lies in the use of dogma to obstruct scientific theorizing; it does not lie in the use of dogma or the Bible to promote scientific research or to question a specific interpretation of the Bible. The advance of science depends to some extent on skeptical questioning of established views. The recognition of the contingency of nature is consistent with the belief in creation and in the dependence of nature on God's sustaining and controlling presence. Contemporary theologians who advocate the revival of traditional natural theology seem unaware of its earlier fate. The preference of some cosmologists for the anthropic principle requires the theological assumption that human beings are the goal of God's creation in order for the anthropic principle to be regarded as explanatory. But even from a theological point of view, such an account is unsatisfactory for it places a priori limitations on how God could have accomplished the divine purposes. The principles enunciated by Augustine seem susceptible of a broad interpretation with modern amendments: the Bible does not teach natural science; theology makes legitimate knowledge claims; our understanding of the meaning of the Bible has changed with our growth in knowledge of the physical universe; belief in the divine origin of the universe has often motivated and sustained confidence in the ability of humans to penetrate the secrets of the universe; the failures of science and the excesses of human intervention alert us to the relevance of values for decisions in science and technology; historical experience enjoins us to admit the possibly ultimate futility of human achievements; biblical homage to the sacredness of nature and human responsibility is harmonious with the awe and wonder expressed by cosmologists and environmentalists; and the search for meaning in human existence supports the limited aim of consonance between theological and scientific interpretations of the cosmos.

André L. Goddu