This is a new edition of the winner of the 1999 award of excellence from the Text and Academic Authors Association in the college life sciences category. ASKING ABOUT LIFE, Second Edition promotes student understanding of the experimental origins of biological knowledge through a truly inquiry-based approach. This emphasis helps students learn biology by emphasizing questions, experimentation, and principles of biology. The text presents biology as a dynamic human activity, stressing the importance of questions rather than answers. Through engaging stories, clear illustrations, and verbal and visual metaphors, the authors make biology accessible and friendly, while still conveying the excitement of contemporary research. This edition was developed using the extensive research done with users and non-users of previous editions by the Market Intelligence Group.
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Allan Tobin's undergraduate degree from MIT is in literature and biology and his doctoral degree is in biophysics with an emphasis on physical biochemistry. For more than 35 years he has taught introductory courses in general biology, cell biology, molecular biology, developmental biology, and neuroscience. He is the recipient of the U.C. Los Angeles Faculty Teaching and Service Award and is regarded as an excellent and highly interactive teacher.
Jennie Dusheck has an undergraduate degree in zoology from U.C. Berkeley and her master's degree is also in zoology. She also holds a certificate in science writing from U.C. Santa Cruz. Dusheck has written for "Science News," "Science Magazine," and other publications. From 1985 to1993 she was the Principal Editor at U.C. Santa Cruz and has received several national awards including the Gold Medal for Best-in-Category from the National Council for the Advancement and Support of Education. As a biologist she has studied the effects of light intensity on bird song, social behavior in field mice, food preferences of deer, cattle and skipper butterflies as well as axis formation in Xenopus laevis.
CHAPTER 1 THE UNITY AND DIVERSITY OF LIFE Bacteria: enough to give you an ulcer In 1984, an obscure Australian physician named Barry Marshall secretly performed a dangerous experiment that would ultimately deprive some of the world's largest corporations of billions of dollars (Figure 1-1). Marshall's radical idea was born in 1979 when his colleague and friend J. Robin Warren, a pathologist at Royal Perth Hospital, in Australia, noticed that tissues from patients with ulcers and other stomach problems were often infected with bacteria. To find even one bacterial infection in the stomach would have been strange; to find dozens of stomach infections was bizarre. The human stomach secretes acid so concentrated that few organisms can survive it for more than a few minutes, let alone live and reproduce in it. Yet Warren found bacteria flourishing there. Warren's discovery suggested an alternative to doctors' longstanding belief that ulcers are caused by excess stomach acid. Ulcers, every medical textbook reported, were caused by the oversecretion of stomach acid in people with overanxious, frustrated personalities. Such personality problems were thought to be aggravated by the stressful pace of modern life. But if a bacterium could infect the stomach, Marshall and Warren realized, maybe it could cause ulcers. Intrigued by this idea, Marshall began ordering biopsies for all his patients with stomach problems. He found that nearly every patient with ulcers was infected with the same bacterium. The most common kind of ulcer is a peptic ulcer, an open wound located where the stomach joins the small intestine, at the bottom of the stomach. The word peptic comes from the Greek word peptein, to digest. Nearly one in ten adults has a peptic ulcer. Some people with ulcers feel no discomfort, but most experience at least mild pain, and many suffer excruciating pain for weeks at a time throughout their adult lives. In rare cases, blood may pour from the wound so freely that the victim bleeds to death. The standard treatment for ulcers had always been a high-fat, bland diet, tranquilizers, psychotherapy, and, in severe cases, surgery. But mainly doctors prescribed antacids-lots of antacids. Antacids are the biggest-selling prescription drugs in the world. In 1992, Americans bought $4.4 billion worth of the drugs. Prescription antacids are remarkably effective at controlling the secretion of stomach acid, but remarkably ineffective at controlling ulcers. Ninety-five percent of ulcer patients have a new ulcer within two years of treatment. That means people with ulcers take the $100-a-month antacids almost continuously. In a lifetime, an ulcer-sufferer can spend tens of thousands of dollars on antacids. Yet, if ulcers were caused by a bacterium, a two-week course of antibiotics might permanently cure millions of people of what would otherwise be a lifetime of suffering. If Marshall's hunch was right, he had very good news, although not for the companies that were selling antacids. Marshall, however, had insignificant credentials as a doctor and none as a researcher. In 1980, he seemed to have no more chance of selling his idea to the biomedical community than his bacteria had of flourishing in the corrosive environment of the stomach. Nevertheless, in 1983, Marshall presented his hypothesis at a scientific conference in Brussels. His presentation was a disaster. He was unknown, he was young, inexperienced, and overexcited, and he had a seemingly screwball idea. "He didn't have the demeanor of a scientist," later recalled Martin Blaser, professor of medicine at Vanderbilt University. "He was strutting around the stage. I thought, this guy is nuts." When it was over, his audience of eminent medical researchers shifted uneasily in their seats, embarrassed. A few laughed. They couldn't believe he was serious. Most bacteria can barely survive a brief passage through the stomach. How could they flourish there for months or years? Besides, Marshall had no scientific evidence to back up his claim. Maybe, his audience told him, the bacteria had contaminated the stomach samples after the stomach tissues had been removed. Or maybe the bacteria were harmless and unrelated to the ulcers. Or maybe the bacteria were able to colonize the stomach as a result of the ulcer. Marshall realized that the only way to settle these questions was to study the bacterium in an experimental animal. He needed to find an animal whose stomach could be infected with the bacterium. After returning to Australia, he began feeding the bacteria to rats. The bacteria died in the rats' stomachs without having any effect. He fed the bacteria to pigs, with the same result. Now he began to wonder, could the bacteria really infect a stomach? Maybe the researchers in Brussels had been right to laugh at him. Desperate to prove that he was no nut, Marshall did something highly unusual and not very scientific. First, he had a stomach exam and biopsy to make sure his stomach was healthy. Then he made an "ulcer bug" cocktail, containing at least a billion bacteria, and, in a few swift gulps, drank it down. The cocktail was enough, he hoped, to infect his stomach. He told no one ahead of time-not the medical ethics board at the hospital, not his wife. They wouldn't have approved, he knew. At first, nothing happened. Then, eight days later, nausea woke him early and he vomited. For another week he was tired, irritable, and hoarse. He had headaches and foul breath. A second stomach exam and biopsy showed that his stomach was inflamed and swarming with bacteria. By the third week, Marshall was lucky enough to have recovered completely. He had not proved that the bacterium could cause ulcers, or even that it could infect the stomach for years at a time. But he had done something that strongly suggested that the bacterium, still unnamed at the time, could at least infect a healthy human stomach-one that didn't already have an ulcer. In time, other, more-established researchers began to take an interest. Mainly they were interested in proving Marshall wrong. But by the end of the 1980s, the evidence that the bacterium could infect the stomach was unassailable. In 1989, the bacterium was named Helicobacter pylori because of the bacterium's helical shape and because it was known to colonize the pylorus, near the stomach's exit (Figure 1-2). By 1993, definitive studies by other researchers had shown that some 80 percent of ulcers were caused by H. pylori, and were treatable with antibiotics. Drug companies, initially somewhat negative about Marshall's idea, began to see a silver lining in the cloud the Australian had created. It was true that people treated with only $20 worth of antibiotics had a relapse rate of only about five to ten percent-which meant an ulcer sufferer would spend thousands of dollars less on drugs. On the other hand, infection by H. pylori turned out to be one of the most common bacterial infections in humans in the world-infecting up to half of all people worldwide. And mounting evidence suggested that chronic infection by H. pylori not only caused ulcers but also increased the risk of developing stomach cancer. Here was a market for antibiotics consisting of billions of people. Marshall's cloud definitely had a silver lining. By 1993, drug companies were hastily developing new diagnostic tests for H. pylori and new antibiotics to treat the infection. Biotechnology companies were trying to develop a vaccine, to be given in childhood, that would protect against H. pylori, ulcers, and maybe even stomach cancer, a leading cause of death in Asia. In early 1994, experts at the National Institutes of Health declared antibiotics the official treatment for ulcers. For the first time, doctors began treating their patients with antibiotics that would offer a permanent cure. Change came slowly. By 1996, only one-third of doctors were prescribing antibiotics for ulcer patients. The rest continued to prescribe antacids only. Marshall ultimately won acceptance as a scientist, earning a position on the faculty at the University of Virginia Medical School. He succeeded in part because he possessed many of the attributes of a good scientist. He had curiosity, intelligence, vision, and the dogged determination to pursue an idea-even when his stubbornness made him appear foolish. Perhaps most important, Marshall displayed an unusual independence of thought that allowed him to pursue an idea unimaginable to more dogmatic thinkers. In this book we will meet many scientists who are as curious, independent, and stubborn as Marshall. Some are occasionally impulsive, like Marshall. Others are careful thinkers, who take years to reach their conclusions. Most work long hours for years on end. A very few seem merely to play at science, reaping brilliant discoveries from a few hours work. We'll see some of them risk their reputations to defend the ideas they believe in. A few even lose their lives. Right or wrong, all are fascinated by questions about what makes living things tick. Good biologists, like other scientists, are people who are intensely engaged with life. In this first chapter of Asking About Life, we will examine two important aspects of biology, the science of life. We will see how biologists try to answer questions about life, and we will try to define life itself. What makes life what it is? How do biologists study it? TABLE OF CONTENTS: Chapter 1. The Unity and Diversity of Life Part I: Chemistry and Cell Biology Chapter 2. The Chemical Foundations of Life Chapter 3. Biological Molecules Small and Large Chapter 4. Why Are All Organisms Made of Cells? Chapter 5. Directions and Rates of Biochemical Processes Chapter 6. How Do Organisms Supply Themselves with Energy? Chapter 7. Photosynthesis: How Do Organisms Get Energy from the Sun? Part II: Genetics: The Continuity of Life
Cell Reproduction Chapter 9.
From Meiosis to Mendel Chapter 10. The Structure, Replication and Repair of DNA Chapter 11. How Are Genes Expressed? Chapter 12. Jumping Genes and Other Unconventional Genetic Systems Chapter 13. Genetic Engineering and Recombinant DNA Chapter 14. Human Genetics Part III: Evolution Chapter 15. What Is the Evidence for Evolution? Chapter 16. Microevolution: How Does a Population Evolve? Chapter 17. Macroevolution: How Do Species Evolve? Chapter 18. How Did the First Organisms Evolve? Part IV: Diversity Chapter 19. Classification: What's in a Name? Chapter 20. Prokaryotes: How Does the Other Half Live? Chapter 21. Classifying the Protists and Multicellular Fungi Chapter 22. How Did Plants Adapt to Dry Land? Chapter 23. Protostome Animals: Most Animals Form Mouth First Chapter 24. Deuterostome Animals: Echinoderms and Chordates Part V: Ecology Chapter 25. Ecosystems Chapter 26. Communities: How Do Species Interact? Chapter 27. Biomes and Aquatic Communities Chapter 28. Populations and the Human Place in the Biosphere Chapter 29. The Ecology of Animal Behavior Part VI: Structural and Physiological Adaptations of Flowering Plants Chapter 30. Structural and Chemical Adaptations of Plants Chapter 31. What Drives Water Up and Sugars Down? Chapter 32. Growth and Development of Flowering Plants Chapter 33. How do Plant Hormones Regulate Growth and Development? Part VII: Structural and Physiological Adaptations of Animals Chapter 34. Form and Function in Animals Chapter 35. How Do Animals Obtain Nourishment from Food? Chapter 36. How Do Animals Coordinate Cells and Organs? Chapter 37: Blood, Circulation, and the Heart Chapter 38. How Do Animals Obtain and Distribute Oxygen? Chapter 39. How Do Animals Manage Water, Salts, and Wastes? Chapter 40. Defense: Inflammation and Immunity Chapter 41. The Cells of The Nervous System Chapter 42. The Nervous System and the Sense Organs Chapter 43. Sexual Reproduction Chapter 44. How Do Organisms Become Complex?
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