To buttress the false claim that developmental pathways regulated by Hox genes cannot evolve Explore Evolution engages in a major error of omission by failing to address the issue of modularity. This is concept is not obscure - a PubMed search of "modularity and evolution" yields over 140 publications in the last ten years. Modularity describes the independent control of hierarchical levels in development and evolution ranging from anatomical structures to signaling pathways to genetic switches.
The authors of Explore Evolution raise another issue, that of variations of clock rates along lineages due to "environmental factors", which if true would be more problematic because they would be harder to control for.
Explore Evolution's arguments against molecular clocks are a bungled mishmash of actual facts, misinterpretations and completely spurious claims. First, the authors raise the issue of calibration of the molecular clock. This is an acknowledged potential problem in using the clock to date certain evolutionary events, especially those in the very deep past. Nevertheless, when appropriate methodology and controls are used, molecular clock dating has been shown to be reliable and consistent.
Molecular homology, genes shared due to common ancestry, is a powerful tool for reconstructing the history of life. A small fraction of the research in molecular phylogeny is concerned with tracing all life to a common ancestor, or population of ancestors. Explore Evolution ignores the bulk of research in molecular evolution to focus on this narrow topic.
The vision of biogeography in Explore Evolution is shockingly narrow. The examples of biogeography discussed are: the Galá Islands, the Hawaiian Islands, and island continents Australia and ancient South America. The discussion of marsupial biogeography across South America and Australia bizarrely omits any discussion of plate tectonics, a central theme in any discussion of biogeography over long time scales. No discussion at all is offered of many crucial biogeographic concepts that bear on evolutionary biology.