The flagella of certain bacteria constitute a molecular motor requiring the interaction of about 40 complex protein parts, and the absence of any one of these proteins causes the flagella to fail to function. Behe holds that the flagellum "engine" is irreducibly complex because if we try to reduce its complexity by positing an earlier and simpler stage of its evolutionary development, we get an organism which functions improperly.
There are many examples of molecular machines, such as the bacterial flagellum, that are composed of numerous elements. Behe rightly points out that such machines are irreducibly complex in that if any one part were removed, the function in question would be instantly lost. How then could such a machine be built up gradually if it will not work to any selectable degree until all its parts are present in their proper order?
Kenneth Miller, a well-known evolutionary biologist from Brown University, points out that certain subsystems of the bacterial flagellum would still be in working order if other parts were removed. The overall flagellar motility system requires around 50 different types of proteins (and underlying genes to code for them). However, it is quite interesting to note that 10 of these genes and the resulting structure within the flagellar motility system also code for what is known as a type III secretory system (TTSS). The TTSS is used as a toxin injector by some especially nasty bacteria that attack both animals and plants. Therefore, Kenneth Miller argues that it is mistaken to use the flagellar system as an example of a truly irreducibly complex machine since around 40 different parts could be removed from the machine without a complete loss of function. Miller also points out that the majority of the protein parts of the flagellar system have other functions as parts of other systems within bacteria.
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