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Summary of problems:
The approach toward learning actually used in EE is directly at odds with the inquiry-based approaches developed by leading science educators. EE gives students incomplete and/or misleading information and provides canned questions and answers, rather than providing students with appropriate background information and allowing them to formulate testable hypotheses.
In the inquiry-based approaches which are gaining acceptance in science education, the student is provided with appropriate background data, and then encouraged to generate a testable hypothesis, test it, and decide if the hypothesis should be accepted or rejected. These approaches reinforce the student's knowledge of the power and the limitations of the scientific method, and allow the student to arrive at a novel (to them) answer via their own efforts. Such "Eureka moments" can strongly reinforce the facts and concepts that are deemed pedagogically important by the instructors, and can even lead to insights that are unrelated to the immediate facts and observations. The power of this approach rests entirely on the notion that the student understands the background, poses the hypothesis, tests the hypothesis, and makes his/her own conclusions. The role of the instructor is very different in this model. As noted on the Duke University Center for Inquiry-based Learning site: "When using inquiry, teachers must bite their tongues. Too many hints, too many questions, and too many answers take all the learning out of the process. And all the fun, too."
Unfortunately, this description is completely at odds with the approach used in Explore Evolution. In every instance, students are led through exercises where the authors provide the questions. In every instance, the student is given incomplete or even misleading information in the sections labeled "Case For", and then this incomplete or misleading information is rebutted by the authors (not by the student) in the "Reply" sections. Even in the "Further Debate" sections, there is no attempt to add critical information (e.g. citations of recent publications), which might allow the student to generate hypotheses and test those hypotheses. There is no opportunity for the Eureka moment; the students are merely led down the path that the authors desire them to tread. So the claim that this book is "inquiry-based" fails on at least two counts. First, the information needed to promote genuine inquiry is never given; the authors set up strawman arguments rather than provide the necessary complete information. Secondly, the students do not generate their own questions, do not test their own hypotheses, and never get a chance to experience the joy of discovery that has been found to be critical in any truly inquiry-based endeavor.
The approach taken in this book is old-fashioned in terms of pedagogy, and radically different from the innovative and effective inquiry-based approaches developed in recent years. EE's method most closely resembles legal argumentation. The jurors (the students) are subjected to two presentations of opposite sides in a dichotomy, and asked to make up their minds. Jurors are not allowed to ask questions in a courtroom, and students are not allowed to ask questions in this book. Furthermore, just as might be the case in a courtroom, the jurors do not have access to all of the facts.
The phrase "inquiry-based learning" is exploited to promote the view that students should "debate Darwinism" in order to learn it. This is simply the Discovery Institute's latest strategy for insinuating and reinforcing doubts about the evolutionary sciences.
"Our goal in using this approach is to expose you to the discoveries, evidence, and arguments that are shaping the current debates over the modern version of Darwin's theory, and to encourage you to think deeply and critically about them."
No good teacher or scientist is against scientific debate or critical thinking. The authors of EE, however, use this ideal as a guise for promoting misleading, incorrect, and incomplete information about evolution. Unfortunately, anti-evolutionists have time and time again called for "critical thinking" or "critical analysis" of evolution, as a way to encourage students to criticize evolution and doubt its validity.
This statement is skillfully written to sound like good pedagogy. In reality, it deceptively uses the phrase "debates over the modern version of Darwin's theory" to insinuate doubt about the validity of evolution.
It is quite telling that Dave Springer, one of the administrators of Uncommon Descent, the blog of ID-proponent William Demsbki, recently wrote this on one of the threads there.
Why is it that chance worshipping (sic) biologists are continually surprised at what they discover but design advocates aren’t surprised at all?
This question clarifies a distinction between the authors/publishers of EE and the scientific enterprise. The surprise of discovery is one of the best things about science. The smugness implicit in "I knew it all along", captured in this comment and fostered by the DI in this book, disdains surprises, and is the antithesis of inquiry-based learning. Scientists doing research actually do make unexpected discoveries; they are the lifeblood of real science. Surprises, discovery, and the joy of discovery are the incentives in inquiry-based learning. Explore Evolution is neither scientific nor inquiry-based. Instead, it reveals its revelation-based roots of neo-creationism, in stark contrast to the inquiry-based roots of modern science and modern science education.