"Darwin's Black Box" by Michael Behe

Irreducible Complexity

Behe's central argument revolves around the concept of "irreducible complexity":

This concept is not scientifically viable for two main reasons:

• Many "irreducibly complex" systems have evolutionary pathways:
  • The eye: Nilsson and Pelger (1994) demonstrated the potential evolutionary pathway from a light-sensitive patch to a complex eye through gradual, incremental changes.
  • The bacterial flagellum: Pallen and Matzke (2006) revealed structural similarities between flagellar components and the Type III Secretion System, indicating a plausible evolutionary trajectory.
  • The blood clotting cascade: Doolittle (2009) elucidated how the vertebrate clotting system may have evolved from simpler invertebrate systems via gene duplication and subsequent modification.
  • The immune system: Flajnik and Kasahara (2010) proposed a model for the evolution of the adaptive immune system from innate immunity through a series of incremental, advantageous modifications.
• Parts often evolve for one function and are repurposed later (co-option):
  • Feathers: Terrill and Shultz (2023) describe how feathers initially evolved for thermoregulation before being co-opted for flight in birds.
  • Swim bladder: Daniels et al. (2004) explain how the swim bladder evolved from lungs in fish and was later repurposed for buoyancy control.
  • Crystallins: Swafford and Oakley (2019) demonstrate how crystallin proteins, originally used in stress response, were later co-opted for lens formation in eyes.
  • Antifreeze proteins: Nath et al. (2013) show how antifreeze proteins evolved from digestive enzymes in Arctic fish and were repurposed for freeze resistance.

The Bacterial Flagellum

Behe presents the bacterial flagellum as a prime example of irreducible complexity:

Behe's claim is based on the assumption that the bacterial flagellum is irreducibly complex, requiring all components to function. However, research has shown that the bacterial flagellum likely evolved from simpler systems:

• Type III Secretion System: Pallen and Matzke (2006) revealed structural similarities between flagellar components and the Type III Secretion System, indicating a plausible evolutionary trajectory.
• Ion channels: Liu and Ochman (2007) identified simpler functional units that could have been precursors to the flagellum.

Moreover, the evolution of the flagellum can be explained through well-understood evolutionary processes:

• Gene duplication and divergence: Pallen and Matzke (2006) identified many flagellar proteins as paralogs, indicating their origin through gene duplication events.
• Co-option: Mulkidjanian et al. (2009) demonstrated how parts of the flagellum, such as the bacterial flagellar motor, likely evolved from simpler structures like ion channels.
• Scaffolding proteins: Pallen and Matzke (2006) proposed that some proteins may have initially functioned as structural supports before being incorporated into the functional flagellum.

These findings demonstrate that the bacterial flagellum is not irreducibly complex, but rather an example of a complex system that evolved through a series of incremental changes.

Blood Clotting Cascade

Behe claims that the blood clotting cascade is irreducibly complex:

However, scientific research has provided evidence that contradicts Behe's claim of irreducible complexity:

• Simpler Systems: Primitive clotting systems exist in invertebrates, demonstrating functional intermediates:
• Hanington and Zhang (2010) found that Amphioxus has a primitive clotting system using fibrinogen-like proteins.
• Bergner et al. (1997) showed that horseshoe crabs use a single protein (coagulogen) for clotting.
• Hall et al. (1999) explained that crayfish use a two-step clotting process involving transglutaminase.
• Bidla et al. (2005) found that fruit flies have a simplified clotting system using phenoloxidase.
• Redundancy: The vertebrate clotting system contains redundant pathways:
• Humans with factor XII deficiency still have clotting capability.
• Some mammals (dolphins, whales) lack factor XII entirely.
• Gene Duplication: Doolittle's research demonstrates how specific gene duplication events led to the diversification of clotting factors from a common ancestral gene:
  • Doolittle (2009) demonstrates how gene duplication events led to the diversification of clotting factors from a common ancestral gene:
  • The genes for factors IX and X likely arose from duplication of a single ancestral gene.
  • Prothrombin and factor X share structural similarities, indicating a common origin.
  • Factors V and VIII, which serve as cofactors in the cascade, also appear to have evolved through gene duplication.

These findings contradict Behe's claim of irreducible complexity, demonstrating instead a gradual, evolutionary pathway for the blood clotting cascade.

Irreducible Complexity on Trial

The concept of irreducible complexity, as presented by Michael Behe in "Darwin's Black Box," faced significant scrutiny in the landmark 2005 court case Kitzmiller v. Dover Area School District.

• Background: The Dover Area School District attempted to teach Intelligent Design (ID) in science classrooms as an alternative to evolution. Behe was an expert witness for the defense, arguing for the validity of ID.


• Behe's Testimony:
  • Behe claimed that the bacterial flagellum, with its intricate motor-like structure, could not have evolved gradually and must have been designed.
  • Behe argued that the blood clotting cascade, with its multiple interdependent factors, was too complex to have evolved through natural selection.
  • He asserted that these systems would cease to function if any part were removed, making gradual evolution impossible.


• Behe's Cross-Examination:
  • Behe acknowledged that his definition of science, if applied consistently, would also include astrology as a scientific theory.
  • Behe conceded that there were no peer-reviewed scientific articles supporting his concept of irreducible complexity.
  • He admitted to not having read much of the scientific literature on the evolution of the immune system, despite claiming it was irreducibly complex.


• Scientific Rebuttal:
  • Biologist Kenneth Miller demonstrated how the bacterial flagellum could have evolved from simpler precursor systems:
    • He showed that the Type III Secretion System (T3SS) shares many proteins with the flagellum, suggesting a possible evolutionary pathway.
    • Miller explained that the T3SS functions as a molecular syringe in some bacteria, demonstrating a useful intermediate structure.
  • Regarding the blood clotting cascade:
    • Evidence was presented showing simpler clotting systems in other organisms, such as the horseshoe crab's single-protein system.
    • The court heard about gene duplication events that could explain the evolution of multiple clotting factors.
  • The court was presented with numerous peer-reviewed studies on the evolution of complex systems that Behe claimed were irreducibly complex:
    • Studies on the evolution of the immune system, which Behe had admitted to not having thoroughly reviewed.
    • Research demonstrating the step-by-step evolution of biochemical pathways through gene duplication and modification.


• Ruling: Judge John E. Jones III issued a comprehensive 139-page decision, ruling that:
  • Intelligent Design is not science, but a form of creationism repackaged to avoid legal challenges.
  • Teaching ID in public school science classes violates the Establishment Clause of the First Amendment.
  • The concept of irreducible complexity is an argument from personal incredulity, not a scientific argument.
  • Behe's claims were thoroughly refuted by scientific evidence and peer-reviewed research presented during the trial.
  • The Dover School Board's ID policy was enacted for religious reasons, not scientific ones.
  The judge's decision was particularly scathing, describing the defendants' actions as "breathtaking inanity" and noting that several board members had lied under oath to conceal their religious motivations.

Other Issues

Beyond the scientific criticisms, Behe's concept of irreducible complexity and the broader Intelligent Design movement face significant philosophical challenges:

God of the Gaps: Intelligent Design is a "God of the gaps" argument, where gaps in scientific knowledge are filled with divine intervention. Isaac Newton, for example, used the intelligent design argument to explain the motion of the planets:

"This most elegant system of the sun, planets, and comets could not have arisen without the design and dominion of an intelligent and powerful being. And if the fixed stars are the centers of similar systems, they will all be constructed according to a similar design and subject to the dominion of the One ... And so that the system of the fixed stars will not fall upon one another as a result of their gravity, he has placed them at immense distances from one another."
Isaac Newton, Principia Mathematica (1687)

Testability: There are no testable mechanisms for how ID is implemented. The identity, methods, and limitations of the proposed designer are undefined. What mechanisms does God use to create the complex systems that He has designed in the natural world? How does this compare with evolution by natural selection? ID offers no clear answer to these questions.

"Creationism, intelligent design, and other claims of supernatural intervention in the origin of life or of species are not science because they are not testable by the methods of science. These claims subordinate observed data to statements based on authority, revelation, or religious belief."
National Academy of Sciences, Science and Creationism (1999)