EE's Claim: Some scientists claim that features "that could not have been formed by the natural selection/mutation process have been found." (p.116)
Problems with claim: This claim is wrong and/or deceptive in 3 ways. First, no structures have been found in living things that cannot in principle be explained by evolutionary processes. Ongoing research in evolutionary biology is continuing to develop our understanding of the evolution of cell structures. Second, modern evolutionary theory encompasses much more than just mutation and natural selection. Evolutionists have made this point numerous times, but ID promoters and other creationists continue to ignore that fact. Third, EE uses the phrase "some scientists" in a misleading manner. The only scientists who doubt evolution are members of a fringe group of intelligent-design promoters and other creationists who reject evolution.
EE's claim: Molecular biology has shown that cells contain "machines" which can't be explained by evolution. (p. )
Problems with claim: EE highlights a quotation from the distinguished biological scientist Bruce Alberts in which he refers to "protein machines" and "assemblies with highly coordinated moving parts" inside cells (quoted on p. 116). EE uses this quote to imply that cell structures are just like human-made machines which break down if a part is taken out or broken. EE's use of the quote also suggests that Alberts shares ID-creationist doubts about evolution. What does Albert's really think about evolution? In a letter to the New York Times, Alberts objected to the way ID-promoters quote him, writing:
...the majestic chemistry of life should be astounding to everyone. But these facts should not be misrepresented as support for the idea that life's molecular complexity is a result of "intelligent design." To the contrary, modern scientific views of the molecular organization of life are entirely consistent with spontaneous variation and natural selection driving a powerful evolutionary process. In evolution, as in all areas of science, our knowledge is incomplete. But the entire success of the scientific enterprise has depended on an insistence that these gaps be filled by natural explanations, logically derived from confirmable evidence. Because "intelligent design" theories are based on supernatural explanations, they can have nothing to do with science. Bruce Alberts Letter to the New York Times, February 12, 2005
EE's claim: The flagellum is irreducibly complex. It requires 40 proteins -- 30 structural, 10 regulation. "[A]ll 30 parts have to be present together" to function
This claim is factually incorrect. The latest published review, apparently ignored by the authors of EE, showed that only 23 of the 42 proteins found in the bacterium E. coli are universally required in the flagella of all bacteria. This error has occurred repeatedly in ID literature.Research has shown that the motor only functions after all 30 of the motor's protein parts are in place. All 30 are required for motor function. When experimenters in the laboratory take away even one part of the motor, it stops working. (EE, p. 118, italics original)
Unfortunately, the authors of Explore Evolution do not acknowledge a directly relevant paper by Pallen and Matzke (2006), which specifically debunked this point and was published online in September 2006. The paper debunked directly the ID movement's claims about the bacterial flagellum, for example as made by ''EE'' author Scott Minnich during his testimony on behalf of ID in the Kitzmiller v. Dover case.
Table 1 of Pallen & Matzke (2006) gave a systematic review of the literature on each protein of the bacterial flagellum, examining whether or not the protein was universally required in all functional flagella. The analysis showed that of the 42 flagellar proteins in the standard lab strains E. coli and Salmonella typhimurium only 23 (55%) were actually universally required in all functional flagella. Some proteins can be removed experimentally without removing flagellar function, and other proteins simply aren't found in all flagellated bacteria.
References
W. Ford Doolittle, Olga Zhaxybayeva, Evolution: Reducible Complexity -- The Case for Bacterial Flagella, Current BiologyVolume 17, Issue 13, , 3 July 2007, Pages R510-R512. (http://www.sciencedirect.com/science/article/B6VRT-4P3MFYD-G/2/7acab142…)
Pallen MJ, Matzke NJ. (2006). From The Origin of Species to the origin of bacterial flagella. Nature Reviews Microbiology, 4(10), 784-790. October 2006. Advanced Online Publication on September 5, 2006