Co-option is the quintessential evolutionary explanation for the problem of irreducible complexity. Creationists and Intelligent Design (ID) advocates point out that molecular machines and many other biological features could not evolve but have to appear complete if they were to function at all. Natural selection, they point out, cannot select for something that does not work. Thus, irreducibly complex features must have been designed. The bacterial flagellum is a well-known example of irreducible complexity.

Evolutionists reply that co-option shows that irreducible complexity is a false argument. The evolutionary arguments of Kenneth Miller on the co-option of a Type 3 Secretion System (T3SS) in the development of the bacterial flagellum, was used during a famous Dover, PA court case in 2005. (The T3SS is a tiny syringe used by some bacteria to inject damaging compounds into eukaryotic cells.  The superficial appearance of the interior part of the bacterial flagellum to the T3SS led to the co-option arguments.)

Based on his argument that the bacterial cell co-opted the T3SS to form the core of the bacterial flagellum, Miller testified that arguments that the bacterial flagellum was irreducibly complex were not just “flawed science, but instead not even science at all.” Dr. Miller reprised his arguments at a special celebratory session at the American Association for the Advancement of Science meetings in 2016. [News from Brown (University) Feb. 13, 2016]

However, there was just one problem with the AAAS celebrations. Experts in the field had long since concluded that Miller’s arguments were wrong. If anything came first in an evolutionary sense, it would have been the bacterial flagellum and not vice versa. In fact, some suggest that both systems evolved from a distant ancestor. Thus, the evolutionary arguments used by Miller have been replaced by a new interpretation: “Injectosome-T3SS derived from flagellar ancestors.” [Andreas Diepold and Judith P. Armitage. 2015. Type III Secretion Systems: the bacterial flagellum and the injectosome.  Trans. Royal Society B 370: 1-19.  http://dx.doi.org/10.1098/rstb.2015.0020

Not only is the evolutionary story turned upside down, but they also declare that the injectosome seems much more remotely connected to the bacterial cells. “[I]t became clear that flagellar components are almost always encoded on the bacterial chromosome and co-evolved with the rest of the genome to a certain degree, while the genes coding for the injectosome are often encoded on virulence plasmids or pathogenicity islands, and are more closely related to each other than to their flagellar components.” [p. 4]

A more recent article says the same thing about the reversed order: “The most recent major analysis suggests that NF-T3SS [non-flagellar-T3SS] are phylogenetically derived from the flagellum, although it appears to be a deep branch that did not originate within any particular extant bacterial flagellum.” [Nicholas Matzke et al. 2021. Flagellar export apparatus and ATP synthase: Homology evidenced by synteny predating the Last Universal Common Ancestor. BioEssays. 2021. 2100004  See p. 2.  https://doi.org/10.1002/bies.202100004 ]

Therefore, the ideas of co-option connected with irreducible complexity of the bacterial flagellum are no longer supported by evolutionists, and this fact was known in 2016 when Dr. Miller was celebrated by the AAAS for “standing up for science.” It might have helped if the participants had been more critical of the evolutionary claims made on behalf of “science.” Knowingly making false claims is not “standing up for science.” The bacterial flagellum still stands as a stellar example of intelligent design.

Evolutionists still believe in co-option as a process that drives evolutionary change. “Co-option occurs when natural selection finds new uses for existing traits, including genes, organs and other body structures.” [John R. True. 2002. Gene Co-option in Physiological and Morphological Evolution. Annual Review of Cell and Developmental Biology. Vol. 18 pp. 53-80. See p. 53]  Similarly in an essay on co-option, Deborah McLennan points out that the process of evolution can be speeded up if “characters that had evolved for one reason changed their function at a later time with little to no concurrent structural modification, at least initially. In other words, traits that had evolved under one set of conditions were co-opted to serve a different function under a second set of conditions.” [Deborah McLennan. 2008. The Concept of Co-option: Why Evolution Often Looks Miraculous. Evo Edu Outreach. Vol. 1: 247-258. See p. 247  DOI  10.1007/s12052-008-0053-8 ]

McLennan emphasizes that this process is blind, with no objective or purpose. Thus, she declares: “The only difference between human and evolutionary co-option is that we purposefully change an object’s function, while evolution simply takes advantage of an opportunity with no direction, purpose, or forethought.” So, co-option may be a useful evolutionary explanation, but figuring out how it could take place is problematic: “we may be able to answer the ‘why’ of evolution for many genetic co-option events, but we have only an incomplete picture of ‘how’ – for the moment.” [p. 251]

Keeping in mind that inventions require forethought and planning, the application of an object to a new function could not just occur spontaneously. The bottom-line is that co-option is an attempt to avoid the difficulties of explaining how natural selection could select for traits the component parts of which must be fully assembled before they are functional. Since natural selection can only select things that already work, natural selection cannot explain the appearance of irreducibly complex features. Only design, the assembling of all component parts at the same time by an intelligent designer, can explain irreducibly complex molecular machines and other parts of the cell, tissues, organs and body plans.