Critique of "Darwin's Black Box"

Irreducible Complexity

Behe's central argument revolves around the concept of "irreducible complexity," which he defines as:

This concept is not scientifically viable for a number of reasons:

• Many "irreducibly complex" systems have been shown to have evolutionary pathways:
  • The eye: Nilsson and Pelger's (1994) research demonstrated the potential evolutionary pathway from a light-sensitive patch to a complex eye through gradual, incremental changes.
  • The bacterial flagellum: Pallen and Matzke's (2006) studies revealed structural similarities between flagellar components and the Type III Secretion System, indicating a plausible evolutionary trajectory.
  • The blood clotting cascade: Doolittle's (2009) work elucidated how the vertebrate clotting system may have evolved from simpler invertebrate systems via gene duplication and subsequent modification.
  • The immune system: Inlay's (2002) research proposed a model for the evolution of the adaptive immune system from innate immunity through a series of incremental, advantageous modifications.
• The concept ignores co-options, where parts evolve for one function and are later repurposed:
  • Feathers: Originally evolved for thermoregulation, later co-opted for flight in birds.
  • Swim bladder: Evolved from lungs in fish, repurposed for buoyancy control.
  • Crystallins: Proteins originally used in stress response, later co-opted for lens formation in eyes.
  • Antifreeze proteins: Evolved from digestive enzymes in Arctic fish, repurposed for freeze resistance.

The Bacterial Flagellum

Behe presents the bacterial flagellum as a prime example of irreducible complexity. However, extensive research contradicts this claim:

Research has shown that the bacterial flagellum likely evolved from simpler systems:

• Type III Secretion System (T3SS): This system shares many structural similarities with the flagellum, suggesting a common evolutionary origin. (Pallen and Matzke, 2006)
• Ion-driven pores: Simpler functional units that could have been precursors to the flagellum. (Liu and Ochman, 2007)
• Genetic evidence: Studies have identified core genes shared across diverse bacterial species, indicating a common evolutionary history. (Liu and Ochman, 2007)

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

• Gene duplication and divergence: Many flagellar proteins are paralogs, indicating they arose through gene duplication events. (Pallen and Matzke, 2006)
• Co-option: Parts of the flagellum may have been repurposed from other cellular functions. For example, the F-type ATPase, which shares homology with the bacterial flagellar motor, likely evolved from simpler ion channels. This suggests a plausible evolutionary pathway for the flagellar motor. (Mulkidjanian et al., 2009)
• Scaffolding proteins: Some proteins may have initially served as structural supports before being integrated into the functional flagellum. (Pallen and Matzke, 2006)

These findings demonstrate that the bacterial flagellum, far from being irreducibly complex, has a plausible evolutionary pathway supported by genetic, structural, and comparative evidence.

Blood Clotting Cascade

Another system Behe claims is irreducibly complex is the blood clotting cascade. However, extensive research contradicts this claim. Studies have shown that the blood clotting system has evolved through a series of gene duplications and modifications.

• Gene Duplication: Doolittle's research demonstrates how specific 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.
• Simpler Systems: Primitive clotting systems exist in invertebrates, demonstrating functional intermediates:
• Amphioxus has a primitive clotting system using fibrinogen-like proteins. (Hanington and Zhang, 2010)
• Horseshoe crabs use a single protein (coagulogen) for clotting. (Bergner et al., 1997)
• Crayfish use a two-step clotting process involving transglutaminase. (Hall et al., 1999)
• Fruit flies have a simplified clotting system using phenoloxidase. (Bidla et al., 2005)
• Redundancy: The vertebrate clotting system contains redundant pathways:
• Humans with factor XII deficiency still have clotting capability. (Source)
• Some mammals (dolphins, whales) lack factor XII entirely. (Source)
• Gradual Complexity: The increasing complexity of clotting systems across species supports step-wise evolution:
• Fish have a simpler system than mammals.
• Intermediate forms exist in various vertebrate lineages.

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

Scientific Consensus

The scientific community has overwhelmingly rejected Behe's arguments:

Moreover, in the 2005 Kitzmiller v. Dover Area School District trial, Behe's ideas were thoroughly examined and rejected:

Conclusion

While Behe's work has stimulated discussion, it has not withstood scientific scrutiny. The concept of irreducible complexity fails to account for known evolutionary mechanisms and ignores substantial evidence for the evolution of complex systems. As such, "Darwin's Black Box" does not present a credible challenge to the theory of evolution by natural selection.