Francis Collins’s bestselling The Language of God turned 15 this year, and with the author back in the news, it’s a good time to review his case for theistic Darwinism and consider what 15 years of subsequent research have done to strengthen or undermine those arguments. 

He became a household name in 2000 when he and Craig Venter announced that their teams had together successfully mapped the 3.1 billion letters of the human genetic code. The Language of God appeared six years later, making a case for both Darwinian evolution and a transcendent Creator.

The evolution Collins argues for involves no direct intelligent input after the origin of the universe until the origin of humans, and yet he also makes a case for a specifically Christian theism, arguing not only for a Creator but also for the possibility of miracles, the deity of Christ, and a literal resurrection. He insists that a scientist can believe these articles of Christian doctrine without checking his brain at the door.

The mainstream media emphasized the book’s insistence that Darwinism is no threat to Christianity and that Darwinism explains a range of physical evidence better than does either creationism or intelligent design. But what has gone begging for ink is a feature of the work hidden in plain sight: Francis Collins makes a scientific case for intelligent design.

According to the theory of intelligent design, which extends from the origin of matter to the origin of mind, an intelligent cause is the best explanation for certain features of the natural world. In chapter nine Collins argues against intelligent design in biology, a point the media duly emphasized; but elsewhere he argues that an intelligent cause is the best explanation for certain other features of the natural world.

Collins’s Case for Cosmic Design

He begins Chapter 3, “The Origins of the Universe,” by reviewing 20th century discoveries in physics and cosmology, many of which reinforce Christian teaching. For example, whereas scientists of the 19th century generally believed that the universe was eternal, a growing body of evidence in the 20th century convinced them that the universe began about 14 billion years ago, a theory, Collins notes, nicely in harmony with the biblical doctrine of creation ex nihilo — that is, creation out of nothing.

The chapter then summarizes the fine-tuning problem. This is the growing body of evidence suggesting that the physical constants of nature (including gravity, electromagnetism, and the mass of the universe) are exquisitely calibrated to allow for complex and even advanced life. A very tiny difference in any of these and life in the universe would be impossible.

Collins lists the three live explanations for fine tuning: (1) There are a multitude of universes in addition to our own, perhaps an infinite number, and at least one, ours, was bound to have the right physical constants for advanced life; (2) We’re just incredibly lucky; and (3) The physical constants look fine tuned because they were fine tuned. That is, they were designed.

He put his money on the third one, the design hypothesis, and he supports that conclusion by appeals to physical evidence and standard methods of scientific reasoning. Regarding the two non-design options, 1 and 2, he says, “On the basis of probability, option 2 is the least plausible. That then leaves us with option 1 and option 3. The first is logically defensible, but this near-infinite number of unobservable universes strains credulity. It certainly fails Occam’s Razor.”

Lest his guarded language obscure the fact that he’s chosen door number three, he adds, “It could be argued … that the Big Bang itself seems to point strongly toward a Creator.”

His appeal to the Big Bang and the fine-tuned cosmos serves as one of his main design arguments in the book. We should pause and register the significance of this. In our present intellectual climate, where scientists have been harassed and even fired for advocating intelligent design, and the idea is routinely attacked in news stories and popular books by “new atheists” such as Richard Dawkins and Daniel Dennett, it’s no small matter that a bestselling book by the former head of the Human Genome Project, and subsequently the head of the National Institutes of Health, makes a scientific case for intelligent design.

Collins’s Flaw

Why hasn’t this garnered more media attention? In part because Collins accepts the misleading description of ID that many of its critics employ. According to them, intelligent design is a purely negative argument aimed primarily against biological evolution, and is coupled to a fallacious God-of-the-gaps theology.

These ID critics insist that design theorists poke holes in Darwinism and then, in a rush to judgment, insist that the holes prove that God designed life. More broadly, they claim that ID proponents supposedly argue from our present ignorance of any adequate material cause of certain natural phenomena directly to intelligent design.

But this isn’t so. Design theorists in biology do offer an extensive critique of Darwinian theory, including various contemporary variations on it, but they also offer positive evidence for intelligent design. They argue from our growing knowledge of the natural world (in biology, chemistry, physics, and cosmology), and from our knowledge of the only kind of cause known produce information or irreducibly complex machines (both found at the cellular level): intelligent agents.

Collins accuses design theorists of making arguments from ignorance, but actually it is Collins and other critics of intelligent design who do so when they make certain bad-design argument for blind evolution over against intelligent design. Collins does so, for instance, when he argues that the presence of “junk DNA” strongly suggests a blind evolutionary process rather than anything a divine engineer would have created. That argument rested on scientists’ ignorance of what purpose might be served by DNA that doesn’t code for proteins. But in the intervening years researchers have discovered numerous functional roles for this non-coding DNA. 

To his credit Collins eventually conceded that his use of the term “junk DNA” was misguided. “I’ve stopped using the term,” he told Wired magazine. And as biologist Jonathan Wells notes, “Since then, the evidence for function in non-protein-coding DNA has vastly increased. The first line of one recent article in a scientific journal is, “The days of ‘junk DNA’ are over.”

Chapter 3 of The Language of God contains another argument from ignorance. Collins refers to the “backward wiring” of the vertebrate eye, characterizing it as flawed from an engineering perspective because it forces light to pass through the nerves and blood vessels on its way to the eye’s light sensors. He says this bungled design is evidence for neo-Darwinism’s catch-as-catch-can evolutionary process, and evidence against the idea that a wise designer optimally engineered this organ. “The design of the eye does not appear on close inspection to be completely ideal,” he writes, and its imperfection seems “to many anatomists to defy the existence of truly intelligent planning of the human form.”

This is a favorite argument of Dawkins’s, and of Darwinists generally. However, geneticist Michael Denton and others have shown that the wiring improves oxygen flow, an important advantage not achievable by the tidier approach demanded by Dawkins. They have called attention to this point repeatedly, but The Language of God shows no evidence that Collins is aware of it. He neither addresses it nor so much as mentions it. (Dawkins and other Darwinists generally avoid discussing it.) In this case, then, it’s an argument from ignorance of why the vertebrate eye might benefit from “backward wiring,” and the ignorance appears almost willful.

Collins’s Flagellum

Collins also betrays unfamiliarity with the work of leading design theorists in the way he handles the scientific controversy surrounding a microscopic rotary engine called the bacterial flagellum. The flagellum is a favorite of design theorists because they are convinced that attempts to explain its origin apart from design are manifestly inadequate, and because images of the flagellum practically scream design.

In his book Darwin’s Black Box, Lehigh University biochemist Michael Behe made this sophisticated molecular machine famous by arguing that it was “irreducibly complex” and therefore evidence of design. He used the simple mechanism of a mousetrap as an example of irreducible complexity. If any part of the mousetrap is missing (the base, spring, hammer, holding bar, or catch), the trap cannot work. The mousetrap, then, is irreducibly complex. It is either complete, or it is not a functioning mousetrap.

In the same way, the bacterial flagellum, composed of dozens of protein machines, needs every one of them in place or it doesn’t work.

Here is how irreducible complexity relates to evolutionary theory: A conscious designer can pull together several non-functioning parts and assemble them into a functional whole, but blind evolution — which excludes intelligent guidance — must progress by one slight, random functional mutational improvement at a time. So how could such a process build an irreducibly complex motor one part at a time if the motor cannot propel at all until all its parts are in place?

Using the arguments of leading evolution apologist Kenneth Miller and others, Collins suggests that nature could have co-opted simpler molecular machines to create the bacterial flagellum, and he points to the “type three secretory apparatus” as evidence of such an indirect pathway (p. 192). But as it turns out, and as design theorists have emphasized, there are three crucial problems with this explanation.

One, the micro-syringe at best accounts for only ten proteins, leaving thirty or more unaccounted for; and these other thirty proteins are not found in any other living system. Second, as a wider body of literature suggests, the system probably developed after the more complicated flagellum, not the other way around.

Third, even if nature had on hand all the right protein parts to make a bacterial flagellum, something or someone would still need to assemble them in the precise temporal order the way cars are assembled in factories. How are such tasks presently accomplished? As biologist Scott Minnich and philosopher of science Stephen Meyer explain, “To choreograph the assembly of the parts of the flagellar motor, present-day bacteria need an elaborate system of genetic instructions as well as many other protein machines to time the expression of those assembly instructions.”

Collins never mentions any of this. In these and other instances, he comes across as having never engaged the best arguments for intelligent design in biology. To briefly note one other example, he muffs the issue of testability, mistakenly asserting that ID arguments are not testable.

These constitute significant weaknesses in Collins’s case against intelligent design, but as I will show tomorrow, perhaps the most glaring one is this: he flatly contradicts himself at crucial points.

(Go here for Part 2 of this review.)

Editor’s note: This essay is a substantially revised and updated version of a book review that first appeared in Touchstone Magazine.