Use a big hammer and sell sand.
More info:
Connecting the Type III Secretory System to Bacterial Flagellum:
"Miller's whole argument that the bacterial flagellum evolved by Darwinian means rests on the existence of the type III secretory system (TTSS). The TTSS is coded for by about ten genes, each of which is homologous to genes in the bacterial flagellum. Thus Miller sees the TTSS as embedded in the bacterial flagellum, capable of being selected for on its own, and as a possible evolutionary precursor to the flagellum. He writes: "The TTSS does not tell us how either it or the flagellum evolved. This is certainly true, although Aizawa has suggested that the TTSS may indeed be an evolutionary precursor of the flagellum (Aizawa 2001)."
Accordingly, the TTSS may be thought of as a possible subsystem of the flagellum that performs a function distinct from the flagellum. Nevertheless, finding a subsystem of a functional system that performs some other function is hardly an argument for the original system evolving from that other system. One might just as well say that because the motor of a motorcycle can be used as a blender, therefore the motor evolved into the motorcycle. Perhaps, but not without intelligent design. Indeed, multipart, tightly integrated functional systems almost invariably contain multipart subsystems that serve some different function. At best the TTSS represents one possible step in the indirect Darwinian evolution of the bacterial flagellum. But that still wouldn't constitute a solution to the evolution of the bacterial flagellum. What's needed is a complete evolutionary path and not merely a possible oasis along the way. To claim otherwise is like saying we can travel by foot from Los Angeles to Tokyo because we've discovered the Hawaiian Islands. Evolutionary biology needs to do better than that.
There's another problem here. The whole point of bringing up the TTSS was to posit it as an evolutionary precursor to the bacterial flagellum. The best current molecular evidence, however, points to the TTSS as evolving from the flagellum and not vice versa (Nguyen et al. 2000). This can also be seen intuitively. The bacterial flagellum is a motility structure for propelling a bacterium through its watery environment. Water has been around since the origin of life. But the TTSS, as Mike Gene (see citation at end) notes, is restricted "to animal and plant pathogens." Accordingly, the TTSS could only have been around since the rise of metazoans. Gene continues: "In fact, the function of the system depends on intimate contact with these multicellular organisms. This all indicates this system arose after plants and animals appeared. In fact, the type III genes of plant pathogens are more similar to their own flagellar genes than the type III genes of animal pathogens. This has led some to propose that the type III system arose in plant pathogens and then spread to animal pathogens by horizontal transfer.... When we look at the type III system its genes are commonly clustered and found on large virulence plasmids. When they are in the chromosome, their GC content is typically lower than the GC content of the surrounding genome. In other words, there is good reason to invoke horizontal transfer to explain type III distribution. In contrast, flagellar genes are usually split into three or more operons, they are not found on plasmids, and their GC content is the same as the surrounding genome. There is no evidence that the flagellum has been spread about by horizontal transfer."
It follows that the TTSS does not explain the evolution of the flagellum (despite the handwaving of Aizawa 2001). Nor, for that matter, does the bacterial flagellum explain in any meaningful sense the evolution of the TTSS. The TTSS is after all much simpler than the flagellum. The TTSS contains ten or so proteins that are homologous to proteins in the flagellum. The flagellum requires an additional thirty or forty proteins, which are unique. Evolution needs to explain the emergence of complexity from simplicity. But if the TTSS evolved from the flagellum, then all we've done is explain the simpler in terms of the more complex.
The scientific literature shows a complete absence of concrete, causally detailed proposals for how coevolution and co-option might actually produce irreducibly complex biochemical systems In place of such proposals, Darwinists simply observe that because subsystems of irreducibly complex systems might be functional, any such functions could be selected by natural selection. Accordingly, selection can work on those parts and thereby form irreducibly complex systems. All of this is highly speculative, and accounts for cell biologist Franklin Harold's (2001, 205) frank admission: "There are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations."
When I challenged Ken Miller with this quote at the World Skeptics Conference organized by CSICOP summer 2002 (for a summary of the conference see http://www.csicop.org/si/2002-09/conference.html), Miller did not challenge the substance of Harold's claim. Rather, he merely asserted that Harold had been retired a number of years. The implication I took was that Harold was old and out of touch with current biological thinking and therefore could be ignored (in which case one has to wonder what the editors at Oxford University Press were thinking when they agreed to publish Harold's book). I wish that at the skeptics conference I had followed up more forcefully on Miller's glib dismissal of Harold. Perhaps Miller will see my response here and clarify why Harold's retirement has anything to do with the substance of Harold's claim.
To sum up, the Darwinian mechanism requires a selectable function if that mechanism is going to work at all. Moreover, functional pieces pulled together from various systems via coevolution and co-option are selectable by the Darwinian mechanism. But what is selectable here is the individual functions of the individual pieces and not the function of the yet-to-be-produced system. The Darwinian mechanism selects for preexisting function. It does not select for future function. Once that function is realized, the Darwinian mechanism can select for it as well. But making the transition from existing function to novel function is the hard part. How does one get from functional pieces that are selectable in terms of their individual functions to a system that consists of those pieces and exhibits a novel function? The Darwinian mechanism is no help here. Darwin himself conceded this point. Writing in the Origin, he noted: "Unless profitable variations do occur, natural selection can do nothing." To say that those profitable variations are random errors is to beg precisely the point in question.