text: The "black box" in the title refers to the conceptual tool in which, for one reason or another, the internal workings of a device are taken for granted, so that its function may be discussed.  The philosophical tool is commonly used in scientific discourse, and Behe notes that understandings of cellular structure and other aspects of microbiology were not much understood when Charles Darwin was alive.  He then states that he plans to delve into the issue.
  Behe begins by reminding the general reader of paradigm shifts in the history of science, in which the foundations and assumptions of theories are examined, sometimes resulting in the rejection of an entire past theory.  Behe suggests that such a paradigm shift in biology (and particularly in evolution) is imminent due to recent discoveries (circa 1996) in biochemistry.  Behe acknowledges acceptance of the theory of evolution by "the great majority" of scientists, and he states that "most (though not all) do so based on authority."
  Behe states that elucidations of the evolutionary history of various biological features typically assume the existence of certain abilities as their starting point, such as Charles Darwins example of a cluster of light-sensitive spots evolving into an eye via a series of intermediate steps. He then points out that Darwin dismissed the need to explain the origin of the simple' light-sensitive spot, summarizes the modern understanding of the biochemistry of vision and claims that many other evolutionary explanations face a similar challenge.
  Behe next introduces and defines the concept of irreducible complexity as a system with a series of parts in which the removal of any part causes the entire system to cease functioning, offering a spring-loaded bar mousetrap as a familiar example.  In the following chapters, Behe discusses the apparent irreducible complexity of several biological systems, including the cilium, the bacterial flagellum, blood clotting, the immune system, and vesicular transport.  Behe claims the underlying complexity and biochemical mechanisms of the systems are vastly under-appreciated, and identifies other, similar systems.
  Behe identifies one of the primary counter-arguments of irreducible complexity, gradual adaptation—that certain systems may have been co-opted from an original, unrelated role to assume a new function as an irreducibly complex system.  He counter-argues that though it is impossible to consider all possible roles for any component, it is extremely implausible that components can fortuitously change function within a complex system and that the focus of the theory changes from making to modifying components and recounts unsuccessful attempts to discover evolutionary pathways for complex systems within scientific journals.  Behe states that though he did identify assertions that evolution had occurred, he found none that had been supported by experiment or calculation, and concludes the book by offering intelligent design as a solution to irreducible complexity.