Evolutionarily Conserved Genes or Common Design?
"From Fins to Wings" discusses many examples of similar genes controlling similar developmental processes in widely different organisms. ID-proponents have taken this re-usage of genetic coding components as indicative of common design. Pro-ID scientist Mike Gene has noted that we have to be careful when advancing arguments about common design:

I am reluctant to advance the old thesis of common design because of its nasty ad hoc flavor. Nevertheless, we are exploring the world through the Design Matrix and I simply cannot subscribe to the notion that a designer would always reinvent the wheel every time a machine is invented.

(Common Design by Mike Gene)

Gene's statement seems fair. In my view, the case for common design becomes much stronger when one finds genetic similarity expressed in the fundamental programs of many species, in places perhaps unexpected by common descent. Thus the National Geographic article reports:

The genes responsible for laying out the fly's body plan have nearly identical counterparts in many other animals, ranging from crabs to earthworms to lampreys to us. The discovery came as a surprise, since these animals have such differently looking bodies.

But "the discovery" should come as no surprise to anyone who recognizes that designers often re-use parts that work in different designs. Other examples discussed in the article which ID-proponents might argue imply common design include:

Genes that control neural cell development in larvaceans are also at work in the development of our own brains;

The same genes control eye development in organisms as diverse as insects, cats, scallops, octuposes, and ragworms;

The same genes control the growth of feathers and scales;

A similar genetic map is found on the tips of stems before flowers grow and also on early animal embryos.

Designer Analogies
Sean Carroll is quoted in the National Geographic article noting that animal development entails "variations on a theme." But the "variations on a theme" metaphor is most applicable to an intelligent composer reusing basic music segments with slight variations to design beautiful music. Similarly, the article quotes Todd Oakley saying, "It's like remodeling a house. You don't have to start from scratch; you just change certain elements." While Carroll and Oakley are staunch evolutionists, in light of Mike Gene’s comments above, composers and construction engineers are interesting choices of analogy: both are intelligent agents.

How easy is it to remodel a house through a blind, random process? The article glosses over some difficulties faced by blind evolution of developmental genes recognized in other places. These difficulties were discussed in an earlier Time magazine article:

The drawback for scientists is that nature's shrewd economy conceals enormous complexity. Researchers are finding evidence that the Hox genes and the non-Hox homeobox genes are not independent agents but members of vast genetic networks that connect hundreds, perhaps thousands, of other genes. Change one component, and myriad others will change as well—and not necessarily for the better. Thus dreams of tinkering with nature's toolbox to bring to life what scientists call a "hopeful monster"— such as a fish with feet—are likely to remain elusive.

(Where Do Toes Come From?)

Where are the detailed step-by-step explanations of how evolution "tinkered" with genes so as to create functional advantages and functional intermediates while "remodeling" species? Zimmer provides none. Successful "remodeling," it would seem, inherently implicates intelligent design.