It’s a familiar story, Margaret Wheeler Johnson’s account of losing her faith. As Johnson tells it, the personal integrity that religion instilled in her “made it impossible to maintain faith” in religion.

A while back, Columbia University professor Mark Lilla made a similar disclosure: Namely, the truth that led him to faith was the very thing that led him “out of faith.”

In Johnson’s case, the turn was sparked by doubts concerning her denomination’s teaching about the sacrament of Communion; in Lilla’s case, it had to do with the interpretation of a particular Bible passage that he found disagreeable. (The scriptural text in question, and its reading, Lilla does not disclose.)

Margaret Johnson and Mark Lilla are in the growing company of individuals who have left Christianity not because of core doctrines—like the Nicene Creed—but because of a sectarian peculiarity, a disagreeable scriptural interpretation, or what they deem hypocritical practices. Yet they wouldn’t think of abandoning their pet political party over an isolated plank in the platform, a questionable policy proposal, or the misdeeds of a member in the ranks.

What folks like Johnson and Lilla often don’t realize (or admit) is that they don’t lose their faith; they merely shift it from one object to another. Otherwise, they would quickly learn that without faith in something, life itself would be impossible.

What we don’t ‘know’

Faith is the bridge between what is known and what remains unknown; and that, it so happens, is a gap of cosmic proportions.

Although the scientific enterprise has led to discoveries that have been phenomenally successful in man’s manipulation of nature, it has done little to advance our understanding of nature. In some ways we are like the car owner who believes that he really knows how cars works, because when he turns the ignition key and presses the gas pedal, his car moves. Truth is, very few owners know how a car works; even among trained mechanics, few understand, much less could explain, all of the underlying physics.

And while the physics of auto mechanics could be learned, albeit with a great deal of effort, a comprehensive understanding of nature is unlikely, if not impossible.

That’s because only 4 percent of the universe is made up of things that we can see, probe, and measure. The rest (96 percent) consists of dark matter and dark energy that remain hidden from our investigative tools.* What’s more, what we know about that accessible “4 percent” is precious little.

For example, what we “know” about matter is that it is made up of atoms consisting of elementary particles which are (take your pick) localized excitations in the ubiquitous quantum field, or (as we’ll see in chapter 3) Planck-sized “strings” of energy whose “vibration patterns” produce the sensations of mass associated with matter.

But whether they are quantum blips or vibrating strings, the inescapable conclusion is that there is no “there” there—at least, any “there” that we could recognize as such.

In short, the sum total of our knowledge is infinitesimal in comparison to our ignorance, making some kind of faith an indispensable part of human existence. So the question is not whether we base our convictions and actions on faith, but on what faith we base them.

Bad faith, good faith

For example, Margaret Johnson, in eulogizing her loss of religious faith, expresses a faith that is every bit as religious as the one she left behind:

“I could no longer honestly claim that the marvels I had always named as proof of the existence of a benevolent, omniscient creator—the human body, spring—are examples of anything but the order into which, marvelously indeed but following to no master plan, evolution channels entropy.” (Emphasis mine.)

Evolution channels entropy? You mean that the mind-numbing marvel of the human body, from the complex organization of the DNA macromolecule to the integrated functionality of physiological systems, is the end product of a trial-and-error process of chance and adaptation.

Accepting that proposition requires faith of high order—so high, that everything known about the origin of functionally complex systems must be discarded for a process that is unproven and, indeed, has been shown repeatedly to exceed the creative resources of the entire universe.

This is faith, derived not from reason but rather an “escape from reason” (as the late Francis Schaeffer might have put it), leaving belief to the whims of non-rational influences (e.g., personal desire, popular opinion, or emotional affinities or aversions). It is faith that is blind to the facts, like that of the parent who believes her child will become a nuclear physicist despite his difficulty mastering his multiplication tables. Such is bad faith.

On the other hand, accepting that the highly organized structures of life (the simplest of which far exceed the complexity of the most advanced machines man has made) derive from an intelligent source—even if beyond our understanding—is to stand upon what is known to be possible. It is following the evidence and its trajectory to where it leads, weighing all explanations in the light of reason and accepting the one that best fits the facts. Based on established knowledge and exercising reason, this conclusion is the product of good faith.

Parts & purpose

Bad faith deems the machine-like features of nature beneficial, useful, or detrimental, but bereft of any intended purpose. Good faith sees it differently, like Hugo Cabret, the title character in the 2011 Oscar-winning film “Hugo.”

Hugo, a young mechanical savant, lives alone in a secret hideaway in a train station. There, unbeknownst to anyone save his friend Isabella, Hugo services and maintains the elaborate station clock.

One day while working on the intricate clockwork, Hugo turns to Isabella and poses a question:

“Did you ever notice that all machines are made for some reason? They make you laugh, like Papa Georges’ toys, or they tell time, like the clocks. . . . Maybe that’s why broken machines always make me sad, because they can’t do what they’re meant to do. . . . Maybe it’s the same with people. If you lose your purpose . . . it’s like you’re broken.”

Hugo presses his insight further as he takes Isabella to a majestic overlook of the bejeweled Paris nightscape:

“Right after my father died, I would come up here a lot. . . . I would imagine that the whole world was one big machine. Machines never have any extra parts, you know. They always have the exact number they need. So I figured if the entire world was a big machine I couldn’t be an extra part, I had to be here for some reason. . . . And that means you have to be here for some reason, too.”

In two short passages, Hugo turns the tables on materialism. For the materialist, broken parts (think: vestigial organs and junk DNA) are evidence that the “machine,” however complex and functional, is merely the unguided, unintentional product of atomic collisions. But for Hugo Cabret, the “machine” is evidence of intention, such that parts, no matter how deformed and defective, point to purposes which are intrinsic, if obscured in the present by their condition.

Heart matters

With each passing year, the pile of surplus parts used to bolster the claims of Darwinian evolution has been dwindling, as researchers continue to discover functions previously hidden. For example, inert segments of DNA dismissed as “junk” are increasingly being found essential in gene expression, either through direct action as a chemical “switch” or indirectly as a “space” or “punctuation mark” in a molecular command string.

In 2012 the ENCODE Project, a five-year study involving 30 peer-reviewed papers, concluded that 80 percent of the human genome has a biological function. The Human Genome Project, completed in 2003, had put that number at 2 percent.

Good faith, in light of nature’s architecture, would lead us to expect that trend to continue.

And yet, there is no denying the brokenness of nature, as evidenced in “parts,” which while not superfluous, cannot, or cannot completely, fulfill their intended purpose: the blighted tree that can’t bear fruit; the omega wolf that can’t find a mate; the defective appendage or organ inimical to health and well-being… or the collective “we,” who, because of varying degrees of bad faith, are weighed down from ascent to our supreme end—communion with God. And Margaret Johnson seems to know that.

After describing her former life as one of “magical thinking,” she closes with some telling disclosures. She describes her current life (that committed to reason) as a “wasteland in comparison, a frolic in the land of false idols”—upscale bistros, fine cuisine, and a tribe of urban professionals; she admits to a gnawing emptiness that she “can’t name and can’t begin to fill,” and she confesses, “When I’m at my wits’ end, I find myself sending up a plea for help. And afterwards, in the face of all reason, I sometimes feel relief.”

Margaret Wheeler Johnson has not lost faith. She is just oscillating between two faith objects: one pulling her further into the wasteland, and the other nudging her gently out. One, autonomous reason; the other, reason’s Source.

*In 1929 Edwin Hubble discovered redshifts in the light emissions from stars, indicating that the universe was not static, but expanding. Nearly seventy years later, light spectra measurements of supernovae indicated that the universe is not only expanding, but accelerating! Mystified by this unknown cosmic power source, physicists dubbed it “dark energy.” Subsequent measurements revealed that dark energy accounts for 70 percent of all the stuff in the universe. What’s more, gravitational anomalies observed in stellar objects indicated a sizeable source of invisible (“dark”) matter affecting their movements. When “dark matter” is added to dark energy, it turns out that dark stuff makes up 95 percent of the cosmos. But what it is, no one knows; and the answer is as elusive as ever. For that reason, a number of leading physicists, including Krauss, have called it the biggest mystery in physics.

(Adapted from “Why There Is a God and Why It Matters,” available in paperback and e-book formats. A version of this article was published in Salvo.)

Regis Nicoll is a fellow of the Colson Center who writes commentary on faith and culture for a number of print and online publications including Touchstone, BreakPoint.org, Salvo, Crosswalk, and Crisis.