The disciple thomas makes three prominent appearances in the Gospel of John, each to embody an important moral or theological principle. Nonetheless, these three episodes cohere in an interesting way that can help us to understand the different powers and procedures of science and religion. We first meet Thomas in chapter 11. Lazarus has died, and Jesus wishes to return to Judaea in order to restore his dear friend to life. But the disciples hesitate, reminding Jesus of the violent hostility that had led to a stoning on his last visit. Jesus, in his customary manner, tells an ambiguous little parable, ending with the firm conclusion that he will and must go to Lazarus—and Thomas steps forth to break the deadlock and restore courage to the disciples: "Then said Thomas . . . unto his fellowdisciples, Let us also go, that we may die with him."

In the second incident (chapter 14), Jesus, at the Last Supper, states that he will be betrayed, and must endure bodily death as a result. But he will go to a better place and will prepare the way for his disciples: "In my Father's house are many mansions ... I go to prepare a place for you." Thomas, now confused, asks Jesus: "Lord, we know not whither thou goest; and how can we know the way?" Jesus responds in one of the most familiar Bible passages: "I am the way, and the truth, and the life: no one cometh unto the Father, but by me."

According to legend, Thomas led a brave life after the death of Jesus, extending the gospel all the way to India. The first two biblical incidents, cited above, also display his admirable qualities of bravery and faithful inquiry. Yet we know him best by the third tale, and by an appended epithet of criticism—for he thus became the Doubting Thomas of our languages and traditions. In chapter 20, the resurrected Jesus appears first to Mary Magdalene, and then to all the disciples but the absent Thomas. The famous tale unfolds:

But Thomas was not with them when Jesus came. The other disciples therefore said unto him, We have seen the Lord. But he said unto them, Except I shall see in his hands the print of the nails, and put my finger into the print of the nails, and thrust my hand into his side, I will not believe.

Jesus returns a week later to complete the moral tale of a brave and inquisitive man, led astray by doubt, but chastened and forgiven with a gentle but firm lesson for us all:

Then came Jesus, the doors being shut, and stood in the midst and said, Peace be unto you. Then saith he to Thomas, Reach hither thy finger, and behold my hands; and reach hither thy hand, and thrust it into my side: and be not faithless, but believing. And Thomas answered and said unto him, My Lord and my God.

(This last passage assumes great importance in traditional exegesis as representing the first time that a disciple identifies Jesus as God. Trinitarians point to Thomas's utterance as proof for the threefold nature of God as Father, Son, and Holy Ghost at the same time. Unitarians must work their way around the literal meaning, arguing, for example, that Thomas had merely uttered an oath of astonishment, not an identification.) In any case, Jesus' gentle rebuke conveys the moral punch line, and captures the fundamental difference between faith and science:

Jesus saith unto him, Thomas, because thou hast seen me, thou hast believed: blessed are they that have not seen, and yet have believed.

Thomas, in other words, passes his test because he accepted the evidence of his observations and then repented his previous skepticism. But his doubt signifies weakness, for he should have known through faith and belief. The Gospel text emphasizes Thomas's failings through his exaggerated need to see both sets of stigmata (hands and side), and use two senses (sight and touch) to assuage his doubts.

Mark Tansey, a contemporary artist who loves to represent the great moral and philosophical lessons of Western history with modern metaphors painted in hyperrealistic style, beautifully epitomized the overly wrought character of Thomas's doubt. In 1986 he depicted a man who won't accept continental drift in general, or even the reality of earthquakes in particular. An earthquake has fractured both a California road and the adjoining cliff, but the man still doubts. So he instructs his wife, at the wheel, to straddle the fault line with their car, while he gets out and thrusts his hand into the analogy of Christ's pierced side—the crack in the road. Tansey titles this work Doubting Thomas.

I accept the moral of this tale for important principles under the magisterium of ethics and values. If you need to go through the basic argument, and to test the consequences, each time anger tempts you to murder, then your fealty to the Sixth Commandment is a fragile thing indeed. The steadfast, in such cases, are more blessed (and more to be trusted) than those who cavil and demand rationales each time. Blessed are they that have no such need, yet know the way of justice and decency. In this sense, Thomas deserved his chastening—while Jesus, through the firm gentleness of his rebuke, becomes a great teacher.

But I cannot think of a statement more foreign to the norms of science—indeed more unethical under this magisterium—than Jesus' celebrated chastisement of Thomas: "blessed are they that have not seen, and yet have believed." A skeptical attitude toward appeals based only on authority, combined with a demand for direct evidence (especially to support unusual claims), represents the first commandment of proper scientific procedure.

Poor Doubting Thomas. At his crucial and eponymous moment, he acted in the most admirable way for one style of inquiry—but in the wrong magisterium. He espoused the key principle of science while operating within the different magisterium of faith.

So if Thomas the Apostle defended the norms of science in the wrong magisterium of faith, let us consider another Thomas usually (but falsely) regarded as equally incongruous in the other direction—as a man of dogmatic religion who improperly invaded the magisterium of science. The Reverend Thomas Burnet (1635-1715), although unknown outside professional circles today, wrote one of the most influential books of the late seventeenth century—Telluris theoria sacra, or The Sacred Theory of the Earth, a work in four sections, with part one on the deluge of Noah, part two on the preceding paradise, part three on the forthcoming "burning of the world," and part four "concerning the new heavens and new earth," or paradise regained after the conflagration. This book not only became a "best-seller" in its own generation, but gained lasting fame as a primary inspiration (largely, but not entirely, in criticism) for two of the greatest and most comprehensive works of eighteenth-century intellectual history—the Scienz a nuova (New Science) of Giambattista Vico in 1725, the foundation for historical studies of cultural anthropology, and the Histoire naturelle of Georges Buffon, the preeminent compendium of the natural world, begun in 1749.

But modern scientists dismiss Burnet as either a silly fool or an evil force who tried to reimpose the unquestionable dogmas of scriptural authority upon the new paths of honest science. The "standard" early history of geology, Archibald Geikie's Founders of Geology (1905 edition) featured Burnet's book among the "monstrous doctrines" that infected late-seventeenth-century science. One modern textbook describes Burnet's work as "a series of queer ideas about earth's development," while another dismisses the Sacred Theory as a "bizarre freak of pseudo-science."

Of course, Burnet did not operate as a modern scientist, but he faithfully followed the norms of his time for proper residence within the magisterium of scientific inquiry. Burnet did begin by assuming that the Bible told a truthful story about the history of the earth, but he did not insist on literal accuracy. In fact, he lost his prestigious position as private confessor to King William III for espousing an allegorical interpretation of creation as described in the Book of Genesis—for he argued that God's six "days" might represent periods of undetermined length, not literal intervals of twenty-four hours or physical episodes of one full rotation about an axis.

Burnet accepted the scriptural account as a rough description of actual events, but he insisted upon one principle above all: the history of the earth cannot be regarded as adequately explained or properly interpreted until all events can be rendered as necessary consequences of invariable natural laws, operating with the knowable regularity recently demonstrated for gravity and other key phenomena by his dear friend Isaac Newton. Ironically, the most bizarre features of Burnet's particular account arise from his insistence upon natural law as the source and explanation of all historical events in the earth's history—a difficult requirement given the peculiar and cataclysmic character of several biblical tales, including universal floods and fires.

Burnet begins, for example, by seeking a source for the water of Noah's flood. (He greatly underestimated the depth and extent of the earth's oceans, and therefore believed that present seas could not cover the mountains. "I can as soon believe," he wrote, "that a man could be drowned in his own spittle as that the world should be deluged by the water in it.") But Burnet then rejects, as outside his chosen magisterium of "natural" (i.e., scientific) explanation, the easiest and standard solution of his age: that God simply made the extra water by miraculous creation. For miracle, defined as divine suspension of natural law, must lie outside the compass of scientific explanation. Invoking the story of Alexander and the Gordian Knot, Burnet rejected this "easy way" as destructive of any scientific account. (According to legend, when Alexander the Great captured Gordium, the capital of Phrygia, he encountered a famous chariot, lashed to a pole with a knot of astonishing complexity. He who could untie the knot wo uld conquer all Asia. So Alexander, using raw power to circumvent the rules of the game, took his sword and severed the knot clean through. Some call it boldness; I, and apparently Burnet as well, call it anti-intellectualism.) Burnet wrote:

They say in short, that God Almighty created waters on purpose to make the deluge, and then annihilated them again when the deluge was to cease; and this, in a few words, is the whole account of the business. This is to cut the knot when we cannot loose it.

Instead, Burnet devised a wonderfully wacky theory about a perfectly spherical original earth with a smooth and solid crust of land covering a layer of water below (the natural and eventual source of Noah's flood). This crust gradually dries and cracks; waters rise through the cracks and form clouds; the rains arrive and seal the cracks; the pressure of water rising from below finally bursts through the crust, causing the deluge and producing the earth's present rough topography. Wacky indeed, but fully rendered by natural law, and therefore testable and subject to disproof under the magisterium of science. Indeed, we have tested Burnet's ideas, found them both false and bizarre, and expunged his name from our pantheon of scientific heroes. But if he had simply advocated a divine creation of water, such a conventional and nonoperational account could never have inspired Buffon, Vico, and a host of other scholars.

Burnet followed the common view of a remarkable group of men, devout theists all, who set the foundations of modern science in late-seventeenth-century Britain—including Newton, Halley, Boyle, Hooke, Ray, and Burnet himself. Invoking a convenient trope of English vocabulary, these scientists argued that God would permit no contradiction between his words (as recorded in scripture) and his works (the natural world). This principle, in itself, provides no rationale for science, and could even contradict my central claim for science and religion as distinct magisteria—for if works (the natural world) must conform to words (the scriptural text), then doesn't science become conflated with, constrained by, and subservient to religion? Yes, under one possible interpretation, but not as these men defined the concept. (Always look to nuance and actual utility, not to a first impression about an ambiguous phrase.) God had indeed created nature at some inception beyond the grasp of science; but he also established invariant laws to run the universe without interference forever after. (Surely omnipotence must operate by such a principle of perfection, and not by frequent subsequent correction, i.e., by special miracle, to fix some unanticipated bungle or wrinkle—to make extra water, for example, when human sin required punishment.)

Thus, nature works by invariant laws subject to scientific explanation. The natural world cannot contradict scripture (for God, as author of both, cannot speak against himself). So—and now we come to the key point—if some contradiction seems to emerge between a well-validated scientific result and a conventional reading of scripture, then we had better reconsider our exegesis, for the natural world does not lie, but words can convey many meanings, some allegorical or metaphorical. (If science clearly indicates an ancient world, then the "days" of creation must represent periods longer than twenty-four hours.) In this crucial sense, the magisteria become separate, and science holds sway over the factual character of the natural world. A scientist may be pious and devout—as all these men were, with utmost sincerity—and still hold a conception of God (as an imperial clockwinder at time's beginning in this version of NOMA) that leaves science entirely free in its own proper magisterium.

I choose Thomas Burnet to illustrate this central principle for three reasons: (1) he was an ordained minister by primary profession (thereby illustrating NOMA if he truly kept these worlds distinct); (2) his theory has become an unfair source of ridicule under the fallacious notion that science must be at war with religion; and (3) he upheld the primacy of science in a particularly forceful way (and with even more clarity than his friend Isaac Newton, as we shall see on page 87). Recognizing the primacy of science in its proper magisterium, Burnet urges his readers not to assert a scriptural interpretation contrary to a scientific discovery, but to reexamine scripture instead—for science rules the magisterium of factual truth about nature:

'Tis a dangerous thing to engage the authority of scripture in disputes about the natural world, in opposition to reason; lest time, which brings all things to light, should discover that to be evidently false which we had made scripture assert.

In a lovely passage equating an independent magisterium for science with a maximally exalted concept of God, Burnet develops a striking metaphor for contrasting explanations of the earth's destruction in Noah's flood: do we not have greater admiration for a machine that performs all its appointed tasks (both regular and catastrophic) by natural laws operating on a set of initial parts, than for a device that putters along well enough in a basic mode, but requires a special visit from its inventor for anything more complex:

We think him a better artist that makes a clock that strikes regularly at every hour from the springs and wheels which he puts in the work, than he that so made his clock that he must put his finger to it every hour to make it strike: and if one should contrive a piece of clock-work so that it should beat all the hours, and make all its motions regularly for such a time, and that time being come, upon a signal given, or a spring touched, it should of its own accord fall all to pieces; would not this be looked upon as a piece of greater art, than if the workman came at that time prefixed, and with a great hammer beat it into pieces?

As a professional clergyman and a leading scientist, Burnet practiced in both magisteria, and kept them separate. He allocated the entire natural world to science, but he also knew that this style of inquiry could not adjudicate issues beyond the power of factual information to illuminate, and in realms where questions of natural law do not arise. Using an image from his own century (we would define the boundaries differently today), Burnet grants the entire history of the earth to science, but recognizes that any time before the creation of matter, and any history after the Last Judgment, cannot be encompassed within the magisterium of natural knowledge:

Whatsoever concerns this sublunary world in the whole extent of its duration, from the Chaos to the last period, this I believe Providence hath made us capable to understand ... On either hand is Eternity, before the World and after, which is without [that is, outside of] our reach: But that little spot of ground that lies betwixt those two great oceans, this we are to cultivate, this we are masters of, herein we are to exercise our thoughts [and] to understand.

I may be reading too much into Burnet's words, but do I not detect a preference, or at least a great fondness, for the factuality of science when, in the chronological narrative of his Sacred Theory of the Earth, Burnet must bid adieu to reason as his guide, as he passes from the factually knowable history of an earth fully governed by natural law to a radically different future at the Last Judgment, when God will institute a new order, and can therefore only inform us (if at all) through the revelation of his words? Burnet speaks to the muse of science:

"Farewell then, dear friend, I must take another guide: and leave you here, as Moses upon Mount Pisgah, only to look into that land, which you cannot enter. I acknowledge the good service you have done, and what a faithful companion you have been, in a long journey: from the beginning of the world to this hour ... We have travelled together through the dark regions of a first and second chaos: seen the world twice shipwrecked. Neither water nor fire could separate us. But now you must give place to other guides."

I told this tale of two Thomases to sharpen the distinctions between two entirely different but equally vital magisteria of our rich and complex lives—the two rocks of ages in my title. One must not assume that a book (the Bible in this case) or a day job (as a clergyman in this example) defines a magisterium. We must look instead to the subject, the logic, and the particular arguments. Our goal of mutual respect requires mutual understanding most of all. But I must complete this intuitive and particular case for NOMA by telling another story—with a similar message, but from the moral side this time—before presenting the more formal argument in chapter 2.