Haeckel Just Won't Die
After over 100 years, biologists are still making mistakes reminiscent of Haeckel's distortions. This article asserts that "[t]he early embryos of three different vertebrates--a fish, a chicken, and a human--look much the same." To his credit, Zimmer doesn't endorse Haeckel, however his statement is misleading because vertebrate embryos start off very different and then converge upon a similar stage partway through development--the stage that Zimmer selectively displays in his article. This "hourglass" pattern of development is shown in the graphic below:

This diagram by Jody Sjogren from page 100 of Jonathan Wells’s book, Icons of Evolution, shows that vertebrate embryos start off quite differently. Zimmer's diagram selectively displays embryos from the encircled stage where they are most similar.

These facts don't so fit neatly with Zimmer's claim that "[e]volution often reshapes organisms by tinkering with the genes that control development" because the hourglass pattern of development shows that transitions from fishlike development ultimately into other forms of development would require radical restructuring (not "tinkering") from the earliest stages of development.

The Simple Evolution of Complexity
The article called evolution a "simple" process. In our experience, does a "simple" process generate the type of vast complexity found throughout biology? The article tackles the evolution of the flagellum, but the only evidence hard it provides is the Type 3 Secretion System. Dembski refuted this argument long ago:

[F]inding a subsystem of a functional system that performs some other function is hardly an argument for the original system evolving from that other system. One might just as well say that because the motor of a motorcycle can be used as a blender, therefore the motor evolved into the motorcycle. Perhaps, but not without intelligent design. Indeed, multipart, tightly integrated functional systems almost invariably contain multipart subsystems that serve some different function. At best the TTSS represents one possible step in the indirect Darwinian evolution of the bacterial flagellum. But that still wouldn't constitute a solution to the evolution of the bacterial flagellum. What's needed is a complete evolutionary path and not merely a possible oasis along the way. To claim otherwise is like saying we can travel by foot from Los Angeles to Tokyo because we've discovered the Hawaiian Islands. Evolutionary biology needs to do better than that.

(Still Spinning Just Fine: A Response to Ken Miller by William Dembski)

Here is Zimmer's attempt to meet Dembski's call to "do better":

It all started with a pump-and-syringe assembly like those found on pathogens. In time, the syringe acquired a long needle, then a flexible hook at its base. Eventually it was linked with a power source: another kind of pump found in the cell membranes of many bacteria. Once the structure had a motor that could make it spin, the needle turned into a propellor, and microbes had new mobility.

Like one of Rudyard Kipling's just-so-stories, there are no details here, just assertions which don't address any of the actual biochemical complexities of acquiring flagellar motility. Zimmer quotes Mark Pallen on the origin of the flagellum, but Zimmer would have been most accurate to inform the public what Pallen recently wrote in Nature Reviews Microbiology: "the flagellar research community has scarcely begun to consider how these systems have evolved." (Mark J. Pallen and Nicholas J. Matzke, "From The Origin of Species to the origin of bacterial flagella," Nature Reviews Microbiology, [Sept. 5, 2006].)

With its irreducibly complex nature and machinelike properties, perhaps the simplest explanation for the origin of the flagellum is intelligent design.