The Genome: An Outsider's View

The Buddha once told a story about a king who ordered a group of blind men to be presented with an elephant. Each man touched a different part of the animal. The king then asked them what an elephant is like. The blind men who touched the elephant’s head replied, ‘‘An elephant, your majesty, is just like a water jar.’’ The blind men who touched its ear said, ‘‘An elephant, your majesty, is just like a winnowing basket.’’ The blind men who touched its tusk declared, ‘‘An elephant, your majesty, is just like a plowshare.’’ The ones who touched the trunk replied, ‘‘An elephant, your majesty, is just like a plow pole.’’ The blind men who touched the body replied, ‘‘An elephant, your majesty, is just like a storeroom.’’ The blind men who touched the foot replied, ‘‘An elephant, your majesty, is just like a post.’’ The blind men who touched the hindquarters replied, ‘‘An elephant, your majesty, is just like a mortar.’’ The blind men who touched the tail replied, ‘‘An elephant, your majesty, is just like a pestle.’’ And the blind men who touched the tuft at the end of the tail replied, ‘‘An elephant, your majesty, is just like a broom.’’ The blind men fell into a fistfight, shouting, ‘‘An elephant is like this, an elephant is not like that! An elephant is not like this, an elephant is like that!’’ [1] I am a science writer, and my chief passion is biology. I spend time with biologists of all stripes—computational biologists, paleontologists, biochemists, ecologists, and all the rest. It is a marvelous privilege. But there are times, I must confess, when I feel like I am watching a blind fistfight. One of the first bouts I witnessed took place in the late 1990s, when I was researching the origin of whales. Whales descend from terrestrial mammals, and made the transition to water between about 50 million and 40 million years ago. In the 1990s paleontologists began unearthing a series of spectacular fossils documenting that transition, including whales with full-blown legs. Functional morphologists joined forces to investigate the transition, studying swimming otters to understand how proto-whales might have moved through the water. I spent a lot of time with scientists such as these. They are naturalists. They have to know a lot of natural history. They have to memorize the details of many species, to understand how the physiology, behavior, morphology, and ecology of each animal add up into an integrated whole. Yet these naturalists also know that they only have a slippery grasp on all of that embodied complexity. I put what I learned from those naturalists into my first book, At the Water’s Edge [2]. As I was finishing up my manuscript, I began coming across papers in which scientists were taking a radically different approach to the question of whale origins: they were comparing the DNA of whales to that of other mammals. At the time, molecular phylogenies were still a novelty. The computational methods for calculating them were relatively new, and scientists could only use them to compare a few gene sequences of whales and other mammals. But the conclusions from these few studies were the same: the closest living cousins of whales are hippos. This may not seem like a big deal. It certainly didn’t seem to bother the scientists who carried out the studies. They were just analyzing digital code, abstracted from the animals that carried it. The results spoke for themselves. Nevertheless, they gave paleontologists and mammalian systematists conniptions. Here’s why. Hippos are artiodactyls (also known as eventoed ungulates). Other artiodactyls include cows, camels, and pigs, and goats. Zoologists have long recognized a number of anatomical features that unite artiodactyls in their own group, distinct from other hoofed mammals such as horses and rhinos. One of the most obvious hallmarks was a bone in the ankle, the astragalus. The artiodactyl astragalus has a unique double-pulley shape that allows the artiodactyl hoof to swing back and forth in a distinctive way. In the 1990s paleontologists found a number of spectacular early whale fossils, but they had yet to find bones from the whale ankle. The bones and teeth they did find suggested that the closest relatives of whales were an extinct group of mammals called mesonychids. Mesonychids were hoofed mammals, but they did not have a double-pulley astragalus. Therefore, paleontologists concluded, they were probably not artiodactyls. And if mesonychids were not artiodactyls, then whales could not be either. And that meant that the whale– hippo link had to be wrong. As far as I could tell, this line of reasoning caused no distress among the scientists who found the hippo–whale link in their genetic data. Frankly, I’m not sure they knew what an astragalus was. How many computational biologists are trained in anatomy? The shape of the mesonychid astragulus was irrelevant to them, really. To them, DNA was an overwhelmingly superior source of information. It could be analyzed precisely. It was strings of code, rather than a maddening blur of phenotype. I decided that this potential whale–hippo link was important enough to mention in my book, but did so only briefly because the results were so preliminary. Still, I left the matter open, and I’m glad I did. Subsequent studies on mammal DNA continued to support the whale–hippo link. And meanwhile paleontologists discovered more fossils of ancient walking whales. In 2001 Phil Gingerich and his colleagues from the University of Michigan and from Pakistan