But another contemporary of Darwin’s, American botanist Asa Gray (1810–1888), was not so certain. Gray, who described himself as both a Darwinian and a convinced Christian, found room in Darwin’s depiction of natural selection for the view that God was the ultimate designer of nature; Hodge himself claimed Darwinism was contrary to the Christian faith only insofar as it denied the existence of purpose in the universe.

Historian George Marsden, writing in 1984, found that twenty years after the publication of On the Origin of Species, Bible-believing American Protestant scientists and even conservative theologians did not make opposition to all forms of evolution a necessary test of faith. But such reconciliationist positions began to lose favor in the evangelical community after the Scopes “monkey trial,” July 10–21, 1925, in Dayton, Tennessee. Though high school teacher John Scopes was found guilty of teaching evolution in the classroom (and fined $100), defense attorney Clarence Darrow held up to public ridicule the religious views of William Jennings Bryan, the prosecutor.

Revolutionary changes were sweeping American culture: surging immigration meant a breakdown of a common worldview (if one ever existed); critical biblical studies from Germany undermined the perceived authority of the Christian Bible; and a growing secularism in society loosened the ties of science and faith. Many fundamentalists, betrayed by an academy that no longer acknowledged revealed truth, retreated to a Christian subculture. Bible schools flourished, and many taught human origins from a perspective dubbed “creation-science.”

Contemporary defenders include John D. Morris of the Institute for Creation Research (ICR) in El Cajon, California, who wrote in a 1992 newsletter article that evolution “embraces strict naturalism, an anti-God philosophy, and results in a denial of the major doctrines of Scripture. . . . If no supernatural agency has been at work throughout history, then creation is dead. But if evolutionists even allow a spark of supernatural design in history, then evolution is dead, for evolution necessarily relies on solely natural processes.”

In 1999 the Kansas State Board of Education, reflecting the views of a conservative majority, wrote new state science standards that ushered creationism back into mainstream debate. The board mandated the teaching of so-called microevolution (changes within species) as illustrative of the working of natural selection. But the teaching of macroevolution (the origin of new organs or species) was made optional at the district level. In the revised document science was no longer defined as that human activity which seeks natural explanations of what can be observed, but rather one that seeks logical explanations. Proponents of the changes claimed victory for the renewed practice of legitimate science unencumbered by naturalistic (that is, materialist and by definition anti-supernatural) assumptions.

Two years later, however, on February 14, 2001, after an election which changed its composition, the Kansas School Board reversed its earlier course. Evolution was reinstated “as a broad, unifying theoretical framework in biology” and would likely have a prominent place in the development of future statewide science tests. (The new document did note that while students were required to understand evolution, they were not required to believe it.)

While the board’s decision appeared to be a loss for creationists, another development in the 1990s brought to the wider culture a more sophisticated debate over the nature of explanation. That development was the publication of three controversial books: Darwin On Trial (first published in 1991) by Phillip E. Johnson (a graduate of Harvard University who has taught law at UC Berkeley for more than three decades); Darwin’s Black Box: The Biochemical Challenge to Evolution (1996) by Lehigh University biochemist Michael J. Behe; and Intelligent Design: The Bridge Between Science and Theology (1999) by William A. Dembski, holder of a doctorate in mathematics from the University of Chicago and a doctorate in philosophy from the University of Illinois at Chicago, whose more technical treatment of the subject had been published by Cambridge University Press the year before.

Johnson, Behe, and Dembski, leaders of what has come to be called the Intelligent Design movement, rejected the “young earth” position of ICR in favor of a more academically engaged critique of Darwinian foundations. In an essay published in the New York Times in 1996, Behe wrote that the theory of evolution founders in explaining cellular development. “Many cellular systems are what I term ‘irreducibly complex.’ That means the system needs several components before it can work properly. An everyday example of irreducible complexity is a mousetrap, built of several pieces (platform, hammer, spring and so on). Such a system probably cannot be put together in a Darwinian manner, gradually improving its function. You can’t catch a mouse with just the platform and then catch a few more by adding the spring. All the pieces have to be in place before you catch any mice.”

For Dembski, irreducible complexity is a specific case of a more general understanding of how to detect intelligent, as opposed to mere natural, causes: “Whenever we infer design, we must establish three things: contingency, complexity and specification. Contingency ensures that the object in question is not the result of an automatic and therefore unintelligent process that had no choice in its production. Complexity ensures that the object is not so simple that it can readily be explained by chance. Finally, specification ensures that the object exhibits the type of pattern characteristic of intelligence.”

This pattern, he adds, has to be “detachable” from the particular set of data. Given a set of scrambled numbers, any mathematician could develop a formula to generate those numbers. But the pattern, the formula, is not detachable; it uniquely applies only to that set of numbers. But a string of numbers such as 011011100. . . can be broken into the binary pattern 0, 1, 10, 11, 100, . . . (that is, 1, 2, 3, 4 . . .) that exhibits a specifiable pattern that is meaningful apart from that set of numbers; if the set is complex enough, and not the result of an automatic generating process, one could infer design or intelligence produced the sequence. Dembski argues that the same procedure is used in the Search for Extraterrestrial Life project in its analysis of far distant electromagnetic emissions. Numbers aside, however, the question Dembski must answer is whether the genetic code itself meets his design inference criteria.

Evolutionary biologist Richard Dawkins, in The Blind Watchmaker (1986) and other works, argues that any appearance of purpose in biological systems is merely the result of time and chance. “To ‘tame’ chance means to break down the very improbable into less improbable small components arranged in series. No matter how improbable it is that an X could have arisen from a Y in a single step, it is always possible to conceive of a series of infinitesimally graded intermediates between them. However improbable a large-scale change may be, smaller changes are less improbable.”

Johnson, ever the political scourge of the evolutionists, also focuses on a critique of evolutionism’s materialist assumptions, what he calls “methodological naturalism.” The chemical or physical laws of nature, he writes, “produce simple repetitive order, and chance produces meaningless disorder. When combined, law and chance work against each other to prevent the emergence of a meaningful sequence. In all human experience, only intelligent agency can write an encyclopedia or computer program.” Dawkins’ blind watchmaker (natural selection and mutation) cannot, Johnson insists, create complex new genetic information.

Yet the issue of complexity seems a red herring in the inference of intelligent design. Dembski’s analysis requires the presence of complexity to eliminate chance occurrence; Dawkins counters that chance can produce marvelous complexities. It is also the case that non-complex patterns can carry meaning, such as a pile of rocks indicating a grave site, which Dembski’s formula overlooks. The attempt by Dembski and Dawkins to find the presence or absence of purpose based solely on empirical examination seems a fruitless quest if the status of materialism has not first been established. And that’s a philosophical question.

Johnson presents a version of the claim that naturalism is self refuting. (The argument was popularized by the British writer C. S. Lewis and adopted by the American analytic philosopher Alvin Plantinga.) He asks sarcastically: “If unthinking matter causes the thoughts the materialists don’t like, then what causes the thoughts they do like?” This takes us back to the problem of explanation. The materialist must explain human reason, and indeed the existence of anything at all, in terms of “unthinking matter.” If for Dawkins the appearance of purpose in evolution is merely an illusion, then what is the status of purposive human reason? If that, too, is an illusion, then there is no good reason to accept the argument. If it is not illusion, how can Dawkins explain the rise of genuine purpose or meaning from a purposeless flow of cause and effect? For those in the intelligent design movement, the most important metaphysical question, “Why is there something rather than nothing?” must go unanswered by the scientific materialist.

The same point is made in a joke told about a group of super-scientists who probed the secrets of life. One day they challenged the Deity in a contest to make a human being. “We can make a human out of the dust of the earth, just like you did!” they said, as they began gathering their materials. “Hold on!” exclaimed the Deity. “Get your own dirt!”