The Tangled Tree: A Radical New History of Life. David Quammen

76

       Chapter 77

       Chapter 78

       Chapter 79

       Chapter 80

       Chapter 81

       Chapter 82

       Chapter 83

       Chapter 84

       Notes

       Bibliography

       Illustration Credits

       Index

       Acknowledgments

       About the Book

       About the Author

       Also by David Quammen

       About the Publisher

       THREE SURPRISES

      

       An Introduction

      Life in the universe, as far as we know, and no matter how vividly we may imagine otherwise, is a peculiar phenomenon confined to planet Earth. There’s plenty of speculation and probabilistic noodling, but zero evidence, to the contrary. The mathematical odds and chemical circumstances do seem to suggest that life should exist elsewhere. But the reality of such alternate life, if any, is so far unavailable for inspection. It’s a guess, whereas earthly life is fact. Some astounding discovery of extraterrestrial beings, announced tomorrow, or next year, or long after your time and mine, may disprove this impression of Earth’s uniqueness. For now, though, it’s what we have: life is a story that has unfolded here only, on a relatively small sphere of rock in an inconspicuous corner of one middling galaxy. It’s a story that, to the best of our knowledge, has occurred just once.

      The shape of this story, in its broad outlines as well as its finer details, is therefore a matter of some interest.

      What happened, over the course of roughly four billion years, to bring life from its primordial origins into the fluorescence of diversity and complexity we see now? How did it happen? By what concatenation of accident and determination did it yield creatures so wondrous as humans—and blue whales, and tyrannosaurs, and giant sequoias? We know there have been crucial transitions in evolutionary history, improbable incidents of convergence, dead ends, mass extinctions, big events, and little ones with big consequences—including some fateful contingencies that have left behind evidence of their occurrence embedded subtly throughout the fossil record and the living world. Alter those few contingencies, as a thought experiment, and everything would be different. We wouldn’t exist. Animals and plants wouldn’t exist. Why did it happen as it did, and not some other way? Religions have their responses to such questions, but for science, the answers must be discovered and then supported with empirical evidence, not received in a holy trance.

      This book is about a new method of telling that story, a new method of deducing it, and certain unexpected insights that have flowed from the new method. The method has a name: molecular phylogenetics. Wrinkle your nose at that fancy phrase, if you will, and I’ll wrinkle with you, but, in fact, what it means is fairly simple: reading the deep history of life and the patterns of relatedness from the sequence of constituent units in certain long molecules, as those molecules exist today within living creatures. The molecules mainly in question are DNA, RNA, and a few select proteins. The constituent units are nucleotide bases and amino acids—more definition of those to come. The unexpected insights have fundamentally reshaped what we think we know about life’s history and the functional parts of living beings, including ourselves. In particular, there have come three big surprises about who we are—we multicellular animals, more particularly we humans—and what we are, and how life on our planet has evolved.

      One of those three surprises involves an anomalous form of creature, a whole category of life, previously unsuspected and now known as the archaea. (Their name gets uppercased when used as a formal taxonomic category: Archaea.) Another is a mode of hereditary change that was also unsuspected, now called horizontal gene transfer. The third is a revelation, or anyway a strong likelihood, about our own deepest ancestry. We ourselves—we humans—probably come from creatures that, as recently as forty years ago, were unknown to exist.

      The discovery and identification of the archaea, which had long been mistaken for subgroups of bacteria, revealed that present-day life at the microbial scale is very different from what science had previously depicted, and that the early history of life was very different too. The recognition of horizontal gene transfer (HGT, in the alphabet soup of the experts) as a widespread phenomenon has overturned the traditional certitude that genes flow only vertically, from parents to offspring, and can’t be traded sideways across species boundaries. The latest news on archaea is that all animals, all plants, all fungi, and all other complex creatures composed of cells bearing DNA within nuclei—that list includes us—have descended from these odd, ancient microbes. Maybe. It’s a little like learning, with a jolt, that your great-great-great-grandfather came not from Lithuania but from Mars.

      Taken together, these three surprises raise deep new uncertainties—and carry big implications about human identity, human individuality, human health. We are not precisely who we thought we were. We are composite creatures, and our ancestry seems to arise from a dark zone of the living world, a group of creatures about which science, until recent decades, was ignorant. Evolution is trickier, far more intricate, than we had realized. The tree of life is more tangled. Genes don’t move just vertically. They can also pass laterally across species boundaries, across wider gaps, even between different kingdoms of life, and some have come sideways into our own lineage—the primate lineage—from unsuspected, nonprimate sources. It’s the genetic equivalent of a blood transfusion or (different metaphor, preferred by some scientists) an infection that transforms identity. “Infective heredity.” I’ll say more about that in its place.

      And meanwhile, speaking of infection: another result of this sideways gene movement involves the global medical challenge of antibiotic-resistant bacteria, a quiet crisis destined to become noisier. Dangerous bugs such as MRSA (methicillin-resistant Staphylococcus aureus, which kills more than eleven thousand people annually in the United States and many more thousands around the world) can abruptly acquire whole kits of drug-resistance genes, from entirely different kinds of bacteria, by horizontal gene transfer. That’s why the problem of multiple-drug-resistant superbugs—unkillable bacteria—has spread around the world so quickly. By such revelations, both practical and profound, we’re suddenly challenged to adjust our basic understandings of who we humans are, what has gone into the making of us, and how the living world works.

      This whole radical reset of biological thinking arose from several points of origin in space and time. One among them, maybe the most crucial, deserves mentioning here: the time was autumn 1977; the place was Urbana, Illinois, where a man named Carl Woese sat with his feet on his desk, before a blackboard filled with notes and figures, posed jauntily for a photographer from the New York Times. The accompanying Times story for which the photo was shot, announcing that Woese and his colleagues had discovered “a separate form of life” constituting a “third kingdom” of biological forms in addition to the recognized two, ran on November 3, 1977. It was front page, above the fold, shouldering aside items on the kidnapped heiress Patty Hearst and an arms embargo against the apartheid regime in South Africa. Big news, in other words, whether or not the average Times reader could grasp, from such a lean telling, just what was meant by “a separate form of life.” That article marked the apex