@swamidass I do not find anything substantial in that article, it repeats arguments presented by Kenneth Miller (2004)
«Kenneth Miller (2004) beautifully demonstrated the structural similarities between one component of the flagellum and the socalled type III-secretory system. He convincingly argued that the former is a very plausible evolutionary precursor of the latter, which has been co-opted by evolution to perform a new function. In response to this embarrassing demonstration, Behe (2001:689-690) simply shifted his attention to the complexity of the newly discovered system by itself , and at the same time stubbornly insisted that the assemblage of these precursors into the flagellum system is still impossible without the helping hand of a Designer (Behe, 2004:359)»- Maarten Boudry, Stefaan Blancke, and Johan Braeckman, “Irreducible Incoherence and Intelligent Design – a look into the conceptual toolbox of a pseudoscience,” Quarterly Review of Biology , Vol. 85
However, Phylogenomic and comparative analyses show that Type III Secretion System is devolved from bacterial flagellum, not otherwise.
«Phylogenomic and comparative analyses of these systems argue that the NF-T3SS arose from an exaptation of the flagellum»-Sophie S. Abby and Eduardo P.C. Rocha, “The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems”
Nguyen L, Paulsen IT, Tchieu J, Hueck CJ, and Saier MH Jr. Phylogenetic analyses of the constituents of the Type III protein secretion systems. J. Microbiol. Biotechnol. 2:125-144.
what is more, Type III Secretion Systems argument does not explain the following questions
«Тhe other thirty proteins in the flagellar motor (that are not present in the TTSS) are unique to the motor and are not found in any other living system, From whence, then, were these protein parts co-opted? [E]ven if all the protein parts were somehow available to make a flagellar motor during the evolution of life, the parts would need to be assembled in the correct temporal sequence similar to the way an automobile is assembled in factory. Yet, to choreograph the assembly of the parts of the flagellar motor, present-day bacteria need an elaborate system of genetic instructions as well as many other protein machines to time the expression of those assembly instructions. Arguably, this system is itself irreducibly complex. In any case, the co-option argument tacitly presupposes the need for the very thing it seeks to explain—a functionally interdependent system of proteins»։ Scott A. Minnich & Stephen C. Meyer (2004). “Genetic Analysis of Coordinate Flagellar and Type III Regulatory Circuits in Pathogenic Bacteria.” Second International Conference on Design & Nature, Rhodes Greece, Wessex Institute of Technology, September 1, 2004. DOI: 10.2495/DN040301
a more elaborate questions that chanage the co-option argument presented here Advances in Biology Discredit Argument that Cooption Can Explain Irreducible Complexity | Evolution News
so, I do not understand why should the same already refuted arguments presented by Kenneth Miller be responded over and over again