According to the online critique of Explore Evolution by the National Center for Science Education (NCSE):
The authors of EE "omit the recent research showing evolutionary conservation of the genetic pathways regulating animal development." Biologists "now know there is an evolutionarily conserved 'genetic toolkit'--a set of genes responsible for constructing all animals, from sea anemones to fruit flies to humans (Carroll et al. 2005, Davidson, 2005). The only mention [in EE] of the genetic regulation of development refers to the outdated macromutation theory from the 1940's by Richard Goldschmidt." 
The NCSE Critique's claim that except for mentioning Richard Goldschmidt, EE fails to discuss" the genetic regulation of development" is false. Such a discussion is found on pages 101-111 of EE.
Unlike Neo-Darwinists, however, EE challenges the idea that DNA controls embryo development. Among other things, the "conserved genetic toolkit" mentioned by the NCSE Critique poses a problem for Neo-Darwinism: If the "genetic toolkit" is "responsible for constructing all animals, from sea anemones to fruit flies to humans"--as the NCSE Critique claims--then why are animals with such similar toolkits so different from each other? As Italian geneticist Giuseppe Sermonti asked in 2005, "Why is a fly not a horse?" 
The NCSE critique states in a different section that the four-winged fruit fly is important because "it established that there were genes which could control developmental pathways and helped to lead to the discovery of many of the members of the genetic toolkit." But the four-winged fruit fly is also important in two other respects. First, the fruit fly embryo is a fruit fly before the genetic toolkit is even turned on; its basic body plan is laid out beforehand. Second, a four-winged fruit fly is severely disabled; since the second pair of wings has no muscles, the mutant fly can survive only in the laboratory.
Neo-Darwinists claim on theoretical grounds that genes control development and that gene mutations provide the raw materials for anatomical evolution, but Berkeley geneticist Richard Goldschmidt was not the only biologist to question this. In actuality, a growing number of biologists now question this aspect of Neo-Darwinian dogma, and students deserve to learn about the controversy. 
 NCSE, Critique of Explore Evolution. Sept. 30, 2008. "Haeckel's Drawings." http://ncseweb.org/creationism/analysis/haeckels-drawings.
 Giuseppe Sermonti, Why Is a Fly Not a Horse? Seattle, WA: Discovery Institute Press, 2005. More information available online (2008) at http://www.discovery.org/a/3607.
 NCSE, Critique of Explore Evolution. October 14, 2008. "The Four-Winged Fly." Available online (2008) at http://ncseweb.org/creationism/analysis/four-winged-fly; J. Fernandes, S. E. Celniker, E. B. Lewis & K. VijayRaghavan, "Muscle development in the four-winged Drosophila and the role of the Ultrabithorax gene," Current Biology 4 (1994): 957-964; Wells, Icons of Evolution, Chapter 9.
 Gerry Webster and Brian Goodwin, Form and Transformation: Generative and Relational Principles in Biology. Cambridge: Cambridge University Press, 1996; Gerd B. Muller and Stuart A. Newman, Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology. Cambridge, MA: MIT Press, 2003; Jonathan Wells, The Politically Incorrect Guide to Darwinism and Intelligent Design. Washington, DC: Regnery Publishing, 2006, Chapter 3. More information available online (2008) at http://www.darwinismandid.com/.