Box 2 | Of forelimbs and flagella

ID advocates say that their position is supported by discontinuities between the flagellum and the rest of the biological world, just as a designed entity like a watch differs from an undesigned entity, such as a stone. In support of this line of reasoning, Scott Minnich in his expert witness report claimed that "the other thirty proteins in the flagellar motor (that are not present in the type III secretion system) are unique to the motor and are not found in any other living system." As our discussion shows, this is not true. Instead, we have detected sequence homologies linking flagellar components to the rest of the biological universe (Table 1). Furthermore, a fundamental evolutionary insight underlies the very principle of homology, whether in anatomy or amino-acid sequence: there are organizational similarities in biology that cannot be explained by 'design' for a particular function. Richard Owen first made this argument with tetrapod forelimbs, pointing out that they shared fundamental organizational similarities despite being used for digging, walking, swimming, flight, and in the case of humans, tool use. Darwin reiterated the argument, this time in defence of evolution, in The Origin of Species:

"What can be more curious than that the hand of a man, formed for grasping, that of a mole for digging, the leg of the horse, the paddle of the porpoise, and the wing of the bat, should all be constructed on the same pattern, and should include the same bones, in the same relative positions?... Nothing can be more hopeless than to attempt to explain this similarity of pattern in members of the same class, by utility or by the doctrine of final causes. The hopelessness of the attempt has been expressly admitted by Owen in his most interesting work on the 'Nature of Limbs.' On the ordinary view of the independent creation of each being, we can only say that so it is; that it has pleased the Creator to construct all the animals and plants in each great class on a uniform plan; but this is not a scientific explanation."