In his book, Endless Forms Most Beautiful, Sean Carroll makes this point very clear:

Comparative and evolutionary biology had long assumed that different groups of animals, separated by vast amounts of evolutionary time, were constructed and had evolved by entirely different means. "¦So prevalent was this view of great evolutionary distance that in the 1960s the evolutionary biologist (and architect of the Modern Synthesis) Ernst Mayr remarked:

"Much that has been learned about gene physiology makes it evident that the search for homologous genes is quite futile except in very close relatives. If there is only one efficient solution for a certain functional demand, very different genes complexes will come up with the same solution, no matter how different the pathway by which it is achieved. The saying, "Many roads lead to Rome" is as true in evolution as in daily affairs."

This view is entirely incorrect. The late Stephen Jay Gould, in his monumental work The Structure of Evolutionary Theory, saw the discovery of the Hox clusters and common body-building genes as overturning a major view of the Modern Synthesis. Gould state, "The central significance of our dawning understanding of the genetics of development lies not in the simple discovery of something utterly unknown,"¦but in the explicitly unexpected character of these findings, and in the revisions and extensions thus required of evolutionary theory."

Always remember a crucial part of science history. With evolutionary theory in hand and guiding research, scientists were SURPRISED, for example, to find that the same genes involved in the development of the fly eye were also involved in the development of the mammalian eye.