Darwin's Black Box: The Biochemical Challenge to Evolution

Michael J. Behe, a professor of biological sciences at Lehigh University, presents a challenge to Darwinian evolution from the field of biochemistry. His central thesis is that the molecular machinery underlying life is so complex that it could not have been produced through the gradual, step-by-step process Charles Darwin envisioned. Behe argues instead that many biochemical systems show evidence of intelligent design, meaning they were purposefully arranged by an intelligent agent. The book, first published in 1996, is divided into three parts and includes a 2006 afterword.

Behe opens by distinguishing between understanding how something works and understanding how it came to be. While science has made extraordinary progress in describing molecular processes since the 1950s, he contends it has made virtually no progress in explaining how specific, complex biomolecular systems originated. He traces the history of biology as a succession of "black boxes," a term for devices whose inner workings are mysterious. From the ancient Greeks through the invention of the microscope, the discovery of cells, and the development of X-ray crystallography (a technique for determining molecular structures), each breakthrough opened one black box only to reveal another. Darwin proposed his theory when the cell was itself a black box, and Behe argues that now that biochemistry has opened it, what it reveals demands a rethinking of Darwinian theory.

To illustrate, Behe examines vision. Darwin persuasively argued that the eye could have evolved through intermediates, from a simple light-sensitive spot to a camera-type eye. At the molecular level, however, even detecting light involves a cascade of precisely interacting proteins. A photon triggers a shape change in a molecule called 11-cis-retinal, which alters the protein rhodopsin. This sets off a chain of interactions involving transducin (a signaling protein activated by rhodopsin) and phosphodiesterase (an enzyme that breaks down cGMP, a molecule that keeps ion channels open in photoreceptor cells), ultimately altering the flow of sodium ions and generating a nerve signal. Additional mechanisms then reset the system. Behe contends that this molecular complexity was invisible to Darwin and renders anatomical arguments about eye evolution insufficient.

Behe surveys scientific dissent from neo-Darwinism, a modern synthesis of evolutionary theory formulated in the mid-20th century. He cites critics including biologist Lynn Margulis, who dismisses neo-Darwinism as a "minor twentieth-century religious sect" (26); paleontologists Niles Eldredge and Stephen Jay Gould, who proposed "punctuated equilibrium" to account for the fossil record's lack of gradual transitions; and mathematicians who argued at a 1966 symposium that the theory faces insurmountable numerical problems. He then introduces his key concept, "irreducible complexity": a system composed of several well-matched, interacting parts that all contribute to a basic function, where removing any single part causes the system to stop working. He illustrates this with the mousetrap, whose five components (platform, hammer, spring, catch, and holding bar) are all necessary; remove any one and the trap fails. Such systems cannot arise through slight, successive modifications because any precursor missing a part would be nonfunctional, giving natural selection nothing to favor.

In the book's central section, Behe examines several biochemical systems. He begins with the cilium, a whip-like structure some cells use to swim. Its components include microtubules made of tubulin protein, nexin linker proteins, and dynein motor proteins. Experiments show that removing dynein paralyzes the cilium, while removing nexin causes it to unravel rather than bend. Behe concludes the cilium is irreducibly complex and notes that despite thousands of published papers on cilia, only two have attempted to model their evolution, both speculative and neither built upon by subsequent research. He applies a similar analysis to the bacterial flagellum, a rotary propeller system with a filament, hook, and motor embedded in the cell membrane.

Behe then examines blood clotting, which he compares to a Rube Goldberg machine, a contraption in which sequential steps trigger one another. The cascade involves more than a dozen proteins: fibrinogen is cut by thrombin into fibrin, which forms a clot; thrombin exists initially as inactive prothrombin, requiring activation by Stuart factor (which cleaves prothrombin) and accelerin (which boosts Stuart factor's activity); proaccelerin is itself activated by thrombin, making the system self-reinforcing. Two branching pathways feed into this cascade, with additional proteins controlling clot localization, strengthening, and dissolution. Behe argues the system is irreducibly complex and critiques a published evolutionary scenario by Russell Doolittle, a prominent biochemist at UC San Diego, in which proteins simply "appear" through gene duplication without quantitative details or realistic probability calculations.

The book also examines intracellular transport, the process by which proteins are shipped to specific compartments within the cell. Behe traces the pathway by which a protein destined for the lysosome, the cell's waste-disposal compartment, passes through labeled, tagged, and sorted steps involving the nucleus, ribosomes, the signal recognition particle (a molecule that recognizes a protein's address signal and guides it to the endoplasmic reticulum), the Golgi apparatus (a cellular processing and sorting station for proteins in transit), and specialized vesicles. He argues that both gated transport (where proteins pass through regulated openings in membranes) and vesicular transport (where proteins are packaged into container vesicles for delivery to a destination) are irreducibly complex, citing I-cell disease, a fatal genetic disorder in which a single defect causes cellular waste to accumulate, as evidence that the system must be complete to function.

Behe examines three features of the immune system. In clonal selection, the body identifies which B cell, an immune cell that produces one specific antibody type, makes the right antibody and amplifies it. Antibody diversity arises from a DNA rearrangement mechanism that generates billions of different antibodies from roughly 400 gene segments. The complement pathway is a cascade of about 20 proteins that punches holes in invading cells. Behe argues that each feature is individually irreducibly complex and that their interdependence compounds the problem: antibody diversity is useless without clonal selection, and both are useless without a killing mechanism.

Behe also examines the biosynthesis of AMP, a nucleotide building block essential for life. The 13-step pathway requires 12 enzymes and multiple energy inputs. Unlike previous examples, this system is not strictly irreducibly complex, but Behe argues the obstacles to gradual assembly are overwhelming: prebiotic chemistry has not produced the intermediates, enzymes are required to guide reactions, some intermediates are chemically unstable, and the pathway must be regulated from the start or it would function like a genetic disease.

Behe surveys the professional literature and finds that the Journal of Molecular Evolution, over its entire history, has never published a detailed model for how any complex biochemical system could have arisen gradually. A similar survey of the Proceedings of the National Academy of Sciences and of biochemistry textbooks yields the same result. He concludes that the assertion of Darwinian molecular evolution amounts to "merely bluster" (186).

Behe makes his positive case for intelligent design, defining design as "the purposeful arrangement of parts" (193). He considers and rejects two alternatives: Margulis's symbiosis theory, which explains how preexisting complex systems combined but not how they originated, and complexity theorist Stuart Kauffman's self-organization theory, which lacks experimental validation and connection to real chemistry. Behe addresses objections including arguments from imperfection and vestigial structures, contending that designers may have multiple motives and that design does not require recent creation. He identifies four reasons for science's reluctance to accept design: institutional loyalty, historical conflicts between science and religion, philosophical restrictions against invoking anything beyond nature, and some scientists' commitment to materialism. He uses the Big Bang theory as a precedent for a scientific discovery with religious implications that was accepted on the strength of observational evidence.

In a 2006 afterword, Behe contends that advances in genomics, the discovery of micro RNAs (small RNA molecules that regulate gene expression), and the elucidation of sophisticated cellular assembly mechanisms have only strengthened his argument. He reviews recent literature on the systems discussed in the book, finding them still limited to speculation and sequence comparisons, and concludes that the case for intelligent design continues to grow as biochemistry advances.