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Line 23: − ===Counter arguments to the argument from irreducible complexity=== − The argument for intelligent design has received many detailed rebuttals have appeared in scientific literature <ref>Coyne, J. A., 1996. God in the details, Nature 383: 227-228.</ref><ref> Miller, K. R. 1999. Finding Darwin's God. New York: Harper Collins</ref><ref> Depew, D. J. (1998), Intelligent design and irreducible complexity: A rejoinder. Rhetoric and Public Affairs 1: 571-578.</ref><ref> Thornhill, R. H., and D. W. and Ussery, 2000. A classification of possible routes of Darwinian evolution, The Journal of Theoretical Biology 203: 111-116</ref> including counter-examples to the assertion that evolution cannot explain biochemical complexity. <ref>Miller, K. R. 1999. Finding Darwin's God. New York: Harper Collins.</ref> Researchers have also investigated the means by which evolutionary mechanisms allow biological systems to increase in information content <ref>Schneider, T.D. (2000), Evolution of biological information. Nucleic Acids Research 28: 2794-2799.</ref> <ref>Adami, C., C. Ofria, and T. C. Collier, 2000. Evolution of biological complexity, Proceedings of the National Academy of Sciences 97: 4463—4468</ref> − − 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. 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 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 self-contradictory to argue that one irreducibly-complex system might contain another. The flagellum cannot be irreducibly complex if it contains a smaller functional set of components like the TTSS.
→Counter arguments to the argument from irreducible complexity
The argument is that because a minimum number of protein components are needed for a working biological function, evolution could not have selected to produce those components a few at a time, since they do not have functions that natural selection would favor. The logic of irreducible complexity dictates that these individual components should have no function until all 30 are put into place, at which point the function appears. Behe wrote: " . . . natural selection can only choose among systems that are already working" <ref>Behe, M., 2002. The challenge of irreducible complexity, Natural History 111 (April): 74.</ref>. An irreducibly complex system does not work unless all of its parts are in place. The flagellum is irreducibly complex, and therefore it must have been designed.
The argument is that because a minimum number of protein components are needed for a working biological function, evolution could not have selected to produce those components a few at a time, since they do not have functions that natural selection would favor. The logic of irreducible complexity dictates that these individual components should have no function until all 30 are put into place, at which point the function appears. Behe wrote: " . . . natural selection can only choose among systems that are already working" <ref>Behe, M., 2002. The challenge of irreducible complexity, Natural History 111 (April): 74.</ref>. An irreducibly complex system does not work unless all of its parts are in place. The flagellum is irreducibly complex, and therefore it must have been designed.
===The Combinatorial argument===
===The Combinatorial argument===