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==The flagellum and the argument for Intelligent Design==

==The flagellum and the argument for Intelligent Design==

The flagellum has frequently been presented as a counter-example to evolution. <ref>Dembski, W. 2002a, No Free Lunch: Why specified complexity cannot be purchased without intelligence. Lanham, Maryland: Rowman & Littlefield.</ref> <ref>Behe, M. 1996a. Darwin's Black Box. New York: The Free Press.</ref> Anti-evolutionists argue that it could not possibly have been produced by an evolutionary pathway.  However, similarity with other bacterial processes indicates that it is not irreducibly complex.

The flagellum has frequently been presented as a counter-example to evolution. <ref>Dembski, W. 2002a, No Free Lunch: Why specified complexity cannot be purchased without intelligence. Lanham, Maryland: Rowman & Littlefield.</ref> <ref>Behe, M. 1996a. Darwin's Black Box. New York: The Free Press.</ref> Anti-evolutionists argue that it could not possibly have been produced by an evolutionary pathway.   

===The argument from irreducible complexity===

===The argument from irreducible complexity===

Studies of the genes and proteins associated with the flagellum and other cellular structures have now established that there are precursors to the flagellum that are fully functional despite "missing a part."   

Studies of the genes and proteins associated with the flagellum and other cellular structures have now established that there are precursors to the flagellum that are fully functional despite "missing a part."   

Disease-causing bacteria threaten the organisms they infect in many ways, one of which is to inject poisons into a host cell's cytoplasm. Once inside, these toxins break down and destroy the host cells, producing illness, tissue damage, and sometimes even death. They do this by employing a Type III secretory system (TTSS)<ref>Heuck, C. J., 1998. Type III protein secretion systems in bacterial pathogens of animals and plants, Microbiol. Mol. Biol. .</ref> The proteins transferred this way are how these bacteria make people sick.

Disease-causing bacteria threaten the organisms they infect in many ways, one of which is to inject poisons into a host cell's cytoplasm. Once inside, these toxins break down and destroy the host cells, producing illness, tissue damage, and sometimes even death. They do this by employing a Type III secretory system (TTSS)<ref>Heuck, C. J., 1998. Type III protein secretion systems in bacterial pathogens of animals and plants, Microbiol. Mol. Biol. Rev. 62: 379-433.</ref> The proteins transferred this way are how these bacteria make people sick.

Molecular studies of proteins in the TTSS show that they have the same relative structure as proteins in the basal portion of the bacterial flagellum. A detailed comparison of the proteins associated with both systems <ref>Aizawa, S.-I., 2001. Bacterial flagella and type III secretion systems, FEMS Microbiology Letters </ref> notes that the two systems "consist of homologous component proteins with common physico-chemical properties". This demonstrates that a smaller subset of the full complement of proteins in the flagellum makes up the functional transmembrane portion of the TTSS.  

Molecular studies of proteins in the TTSS show that they have the same relative structure as proteins in the basal portion of the bacterial flagellum. A detailed comparison of the proteins associated with both systems <ref>Aizawa, S.-I., 2001. Bacterial flagella and type III secretion systems, FEMS Microbiology Letters 202: 157-164</ref> notes that the two systems "consist of homologous component proteins with common physico-chemical properties". This demonstrates that a smaller subset of the full complement of proteins in the flagellum makes up the functional transmembrane portion of the TTSS.  

It is normal for evolutionary processes to mix and match proteins opportunistically to produce new functions. According to the doctrine of irreducible complexity, however, this should not be possible. If the flagellum is irreducibly complex, then removing just one part, let alone 10 or 15, should render what remains nonfunctional. Yet the TTSS is fully-functional, even though it is missing most of the parts of the flagellum. Since the function of the TTSS is favoured by natural selection, it is obviously incorrect to argue that the flagellum must be fully assembled before any of its parts can be useful.  

It is normal for evolutionary processes to mix and match proteins opportunistically to produce new functions. According to the doctrine of irreducible complexity, however, this should not be possible. If the flagellum is irreducibly complex, then removing just one part, let alone 10 or 15, should render what remains nonfunctional. Yet the TTSS is fully-functional, even though it is missing most of the parts of the flagellum. Since the function of the TTSS is favoured by natural selection, it is obviously incorrect to argue that the flagellum must be fully assembled before any of its parts can be useful.