Summary of problems with claim:
This is a case of "shifting the goal posts," much as we saw in the chapter on fossils. The fact that we do not fully understand everything is not a problem for science. An inquiry-based textbook would not hold these lacunae in our knowledge out as problems, it would hold them out as exciting opportunities for students to explore.
Explore Evolution, having presented a misleading and even erroneous case against the evolution of one particular structure, responds to the evidence showing that the structure would not be impossible to evolve by simply choosing a new target for their anti-intellectual pseudo-criticism":
In other words, even assuming the presence of all the necessary genes and protein parts, the only way co-option can explain the origin of one irreducibly complex system (the bacterial motor) is by assuming the pre-existence of another irreducibly complex system (the system of protein machines that reads and processes genetic information). Critics of co-option say this is rather like explaining the origin of machines by saying that a machine that makes machines makes them.Explore Evolution , p. 122
Actually, it is like responding to a question about where heavy elements come from and being told that they are produced from reactions between lighter elements inside of suns. Explore Evolution's "critics of co-option" are doing the equivalent of demanding to know where suns come from before they will accept that nuclear fusion can occur. When three-year-olds ask "why?" until their parents can't (or decide not to) answer, it is cute. It is less cute when grown men attempt the same game.
As shown above, the flagellum is not actually irreducibly complex — it could have been assembled through a stepwise evolutionary process. Research into the evolution of protein synthesis is an ongoing area of research, and progress is indeed being made. If there were a model for that process, the authors of Explore Evolution would undoubtedly inquire about areas where our knowledge was less complete, and present those blank spots as if they were evidence that no knowledge of those subjects was even possible. In doing so, they follow their intellectual godfather, Philip Johnson, who once wondered "why the scientists won't admit that there are mysteries beyond our comprehension," and that phenomena like the origins of protein synthesis, the bacterial flagellum, or the origins of complex multicellular organisms might be among those mysteries (Philip Johnson, 1990. "Evolution as Dogma: The Establishment of Naturalism," First Things 6:15-22, reprinted in Robert Pennock, ed. 2001. Intelligent Design Creationism and its Critics, The MIT Press, Cambridge, MA, ch. 2).
Scientists do not work by that process. Scientists employ a process for asking questions and testing the answers to those questions which is comfortable with uncertainty and does not require that the currently unknown be branded as eternally unknowable. As discussed elsewhere (for instance, Chapter 3), areas once presented as insurmountable problems for evolutionary theory are now well-understood examples of evolution at work. The model of science that the authors endorse here (and elsewhere) is hopeless — and hopelessly wrong.
The idea of inquiry-based learning is to encourage scientific exploration. By getting students to propose their own experiments to test the hypotheses they develop about the world around them, they learn not just the facts of science (e.g., how protein synthesis works), but the process scientists employ (e.g., how scientists test hypotheses about the evolution of protein synthesis). The approach Explore Evolution adopts does not describe that scientific process, and in passages like this, it actively discourages students from those scientific pursuits. This inquiry-averse approach to science is inaccurate and inappropriate.