Zimmer begins chapter three by asking how do you make a hand. Owen thought that limbs were based on a vertebrate archetype. Darwin on the other hand said that the homology of the limbs was due to the fact they came from a common ancestor. Embryos start off as limbless and the kidneys signal for cells to congregate and form limb buds. The formation of the limb occurs at the apical ectodermal ridge. The tissues are differentiated into cartilage and connective tissue and blood vessels bring bone-generating cells to the tissue. Muscles and tendons attach to the bones and stretch as the bones grow. Finally one of the most important steps occurs; cell death carves out the digits of the hand. Shubin and Alberch showed that there is a homology of growth in limbs and the size of the limb influenced the amount of digits formed. Shubin was able to study a large sample size of rough-skinned newts because of a freak freeze of a California pond. He found that almost a third of the newts had some sort of limb deformity. These variations were almost always attributed to branching limb pattern described by Shubin and Alberch.

Chapter five begins by describing Clack’s research on the development of ears. Nineteenth century embryologists found that the stapes in the human ear corresponds to the hyomandibular in fish. Clack discovered a small stapes in the Acanthostega which showed that the hyomandibular shrunk as tetrapods developed a new form of eating. Cladograms can be used to show how evolution of breathing might have occurred. Lungfish used a double mouth pump, amphibians used the double mouth pump in addition to ribs for exhalation, and amniotes used ribs for inhalation and exhalation. In order for amniotes to be able to come on to land several things needed to happen. Instead of the egg being made of jelly and being susceptible to drying out, it needed membranes. It was also necessary for the amniotes to be able to conserve water through its intestines. Amniotes also needed to evolve grinding teeth and large jaws in order to eat plants, as well as allowing bacteria into its gut to extract as many nutrients as possible from the plants and to break down cellulose. It was also an advantage for these early herbivores to grow large in order to be less threatened by predators. It thought that the amniotic eggs are the reason that terrestrial herbivores were able to evolve, without them they would be stuck in the water.