life the science of biology 7th ed - bill purves, david sadava

Monster frogs—what a great topic for an undergraduate research project! That’s what Stanford University sophomore Pieter John- son thought when he was shown a jar of Pacific tree frogs with ex- tra legs growing out of their bodies. The frogs were collected from a pond on a farm close to the old Almaden mercury mines south of San Jose, California. Scientists from all over the world were reporting alarming de- clines in populations of many different kinds of frogs, so perhaps these “monster” frogs would hold a clue to why frogs all over the world are in trouble. Possible causes of the deformities could have been agricultural chemicals or heavy metals leaching out of the old mines. Library research, however, suggested other possibilities to Pieter. Pieter studied 35 ponds in the region where the deformed frogs had been found. He counted frogs in the ponds and measured chemicals in the water. Thirteen of the ponds had Pacific tree frogs, but deformed frogs were found in only four ponds. To Pieter’s surprise, analysis of the water samples failed to reveal higher amounts of pesticides, industrial chemicals, or heavy metals in the ponds with deformed frogs. Also surprisingly, when he collected eggs from those ponds and hatched them in the laboratory, he always got normal frogs. The only difference he observed among the ponds he studied was that the ponds with the deformed frogs also contained fresh- water snails. Freshwater snails are hosts for many parasites. Many parasites go through complex life cycles with several stages, each of which requires a specific host animal. Pieter focused on the possibil- ity that some parasite that used fresh- water snails as intermediate hosts was infecting the frogs and causing their de- formities. Pieter found a candidate with this type of life cycle: a small flatworm called Ribeiroia, which was present in the ponds where the deformed frogs were found. Pieter then did an experiment. He collected frog eggs from regions where there were no records of deformed frogs or of Ribeiroia. He hatched the eggs in the laboratory in containers with and without the parasite. When the parasite was present in the contain- An Evolutionary Framework for Biology A Monster Phenomenon As a college sophomore,Pieter Johnson studied ponds that were home to Pacific tree frogs (Hyla regilla), trying to discover a reason for the presence of so many deformed frogs. What appears in the inset to be a tail is an extra leg. 1 ers, 85 percent of the frogs developed deformities. Further experiments showed why not all the frogs were deformed: The infection had to occur before a tadpole started to grow legs. When tadpoles with already developing legs were in- fected, they did not become deformed. Pieter’s project started with a question based on an ob- servation in nature. He formulated several possible answers, made observations to narrow down the list of answers, and then did experiments to test what he thought was the most likely answer. His experiments enabled him to reach a con- clusion: that these deformities were caused by Ribeiroia. Pieter’s project is a good example of the application of scien- tific methods in biology. Biology is the scientific study of living things. Biologists study processes from the level of molecules to the level of en- tire ecosystems. They study events that happen in millionths of seconds and events that occur over millions of years. Biol- ogists ask many different kinds of questions and use a wide range of tools, but they all use the same scientific methods. Their goals are to understand how organisms (and assem- blages of organisms) function, and to use that knowledge to help solve problems. In this chapter, we will take a closer look at what biologists do. First, we will describe the characteristics of living things, the major evolutionary events that have occurred during the history of life on Earth, and the evolutionary tree of life. Then we will discuss the methods biologists use to investigate how life functions. At the end of the chapter, we will discuss how scientific knowledge is used to shape public policy. What Is Life? Before we probe more deeply into the study of life, we need to agree on what life is. Although we all know a living thing when we see one, it is difficult to define life unambiguously. One concise definition of life is: an organized genetic unit ca- pable of metabolism, reproduction, and evolution. Much of this book is devoted to describing these characteristics of life and how they work together to enable organisms to survive and reproduce (Figure 1.1). The following brief overview will guide your study of these characteristics. Metabolism involves conversions of matter and energy Metabolism, the total chemical activity of a living organism, consists of thousands of individual chemical reactions. Chemical reactions result in the capture of matter and energy and its conversion to different forms, as we will see in Part One of this book. For an organism to function, these reac- tions, many of which are occurring simultaneously, must be coordinated. Genes provide that control. The nature of the genetic material that controls these lifelong events has been understood only within the last 100 years. Much of Part Two is devoted to the story of its discovery. The external environment can change rapidly and unpre- dictably in ways that are beyond an organism’s control. An organism can remain healthy only if its internal environment remains within a given range of physical and chemical con- ditions. Organisms maintain relatively constant internal en- 2 CHAPTER ONE 1.1 The Many Faces of a Life The caterpillar,pupa, and adult are all stages in the life cycle of a monarch butterfly (Danaeus plexippus). The caterpillar harvests the matter and energy needed to metabolize the millions of chemical reactions that will result in its growth and transformation,first into a pupa and finally into an adult butterfly specialized for reproduction and dispersal.The transition from one stage to another is triggered by internal chemical signals. vironments by making metabolic adjustments to conditions such as changes in temperature, the presence or absence of sunlight, or the presence of foreign agents inside their bodies. Maintenance of a relatively stable internal condition, such as a human’s constant body temperature, is called homeostasis. The adjustments that organisms make to maintain home- ostasis are usually not obvious, because nothing appears to change. However, at some time during their lives, many or- ganisms respond to changing conditions not by maintaining their status, but by undergoing a major reorganization. An early form of such reorganization was the evolution of rest- ing spores, a well protected, inactive form in which organisms survived stressful environments. A striking example that evolved much later is seen in many insects, such as butterflies. In response to internal chemical signals, a caterpillar changes into a pupa and then into an adult butterfly (see Figure 1.1). Reproduction continues life and provides the basis for evolution Reproduction with variation is a major characteristic of life. Without reproduction, life would quickly come to an end. The earliest single-celled organisms reproduced by duplicat- ing their genetic material and then dividing in two. The two resulting daughter cells were identical to each other and to the parent cell, except for mutations that occurred during the process of gene duplication. Such errors, although rare, pro- vided the raw material for biological evolution. The combi- nation of reproduction and errors in the duplication of ge- netic material results in biological evolution, a change in the genetic composition of a population of organisms over time. The diversification of life has been driven in part by vari- ation in the physical environment. There are cold places and warm places, as well as places that are cold during some parts of the year and warm during other parts. Some places (oceans, lakes, rivers) are wet; others (deserts) are usually very dry. No single kind of living thing can perform well in all these environments. In addition, living things generate their own diversity. Once plants evolved, they became a source of food for other living things. Eaters of plants were, in turn, potential food for other organisms. And when living things die, they become food for still other organisms. The differences among living things that enable them to live in different kinds of environments and adopt different lifestyles are called adaptations. The great diversity of living things contributes to making biology a fascinating science and Earth a rich and rewarding place to live. For a long period of time, there was no life on Earth. Then there was an extended period of only unicellular life, fol- lowed by a proliferation of multicellular life. In other words, the nature and diversity of life has changed over time. Iden- tification of the processes that result in biological evolution was one of the great scientific advances of the nineteenth century. These processes will be discussed in detail in Part Four of this book. Here we will briefly describe how they were discovered. Biological Evolution: Changes over Billions of Years Long before the mechanisms of biological evolution were un- derstood, some people realized that organisms had changed over time and that living organisms had evolved from or- ganisms that were no longer alive on Earth. In the 1760s, the French naturalist Count George-Louis Leclerc de Buffon (1707–1788) wrote his Natural History of Animals, which con- tained a clear statement of the possibility of evolution. Buffon observed that the limb bones of all mammals were remark- ably similar in many details (Figure 1.2). He also noticed that the legs of certain mammals, such as pigs, have toes that never touch the ground and appear to be of no use. He found it difficult to explain the presence of these seemingly useless small toes by the commonly held belief that Earth and all its creatures had been divinely created in their current forms rel- atively recently. To explain these observations, Buffon sug- gested that the limb bones of mammals might all have been inherited from a common ancestor, and that pigs might have functionless toes because they inherited them from ancestors that had fully formed and functional toes. AN EVOLUTIONARY FRAMEWORK FOR BIOLOGY 3 Bones of the same type are shown in the same color. Human arm Dog foreleg Seal flipper 1.2 All Mammals Have Similar Limbs Mammalian forelimbs have different purposes:Humans use theirs for manipulating objects, dogs use theirs for walking,and seals use theirs for swimming.But the numbers and types of their bones are similar, indicating that they have been modified over time from the forelimbs of a common ancestor. Buffon did not attempt to explain how such changes took place, but his student Jean-Baptiste de Lamarck (1744–1829) proposed a mechanism for such changes. Lamarck suggested that a lineage of organisms could change gradually over many generations as offspring inherited structures that had become larger and more highly developed as a result of continued use or, conversely, had become smaller and less developed as a result of lack of use. Today scientists do not believe that evolutionary changes are produced by this mech- anism. But Lamarck had made an important effort to explain how living things change over time. Darwin provided a mechanistic explanation of biological evolution By 1858, the climate of opinion (among many biologists, at least) was receptive to a new theory of evolutionary processes proposed independently by Charles Darwin and Alfred Russel Wallace. By that time, geologists had accumu- lated evidence that Earth had existed and changed over mil- lions of years, not merely a few thousand years, as most peo- ple had previously believed. You will learn more about Darwin’s theory of evolution by natural selection in Chapter 23, but its essential features are simple. You will need to be familiar with these ideas to understand the rest of this book. Darwin’s theory rests on three observations and one conclusion he drew from them. The three observations are:  The reproductive rates of all organisms, even slowly reproducing ones, are sufficiently high that populations would quickly become enormous if death rates were not equally high.  Within each type of organism, there are differences among individuals.  Offspring are similar to their parents because they inher- it their parents’ features. Based on these observations (evidence), Darwin drew the following conclusion:  The differences among individuals influence how well those individuals survive and reproduce. Any traits that increase the probability that their bearers will survive and reproduce are passed on to their offspring and to their offspring’s offspring. Darwin called the differential survival and reproductive suc- cess of individuals natural selection. He called the resulting pattern “descent with modification.” Biologists began a major conceptual shift a little more than a century ago with the acceptance of long-term evolutionary change and the gradual recognition that natural selection is the process that adapts organisms to their environments. The shift has taken a long time because it required abandoning many components of an earlier worldview. The pre-Darwin- ian view held that the world was young, and that organisms had been divinely created in their current forms. In the Dar- winian view, the world is ancient, and both Earth and its in- habitants have changed over time. Ancestral forms were very different from the organisms that exist today. Living organ- isms evolved their particular features because ancestors with those features survived and reproduced more successfully than did ancestors with different features. Major Events in the History of Life on Earth The history of life on Earth, depicted on the scale of a 30-day calendar, is outlined in Figure 1.3. The profound changes that have occurred over the 4 billion years of this history are the result of natural processes that can be identified and studied using scientific methods. In this section, we will set the stage for the rest of this book by describing some of the most important of these changes. These six major evolutionary events will provide us with a framework for discussing both life’s characteristics and how those characteristics evolved. By recognizing them, you will be able to better appreciate both the unity and diversity of life. Life arose from nonlife via chemical evolution The first life must have come from nonlife. All matter, living and nonliving, is made up of chemicals. The smallest chemi- cal units are atoms, which bond together into molecules (the properties of these units are the subject of Chapter 2). The processes of chemical evolution that led to the appearance of life began nearly 4 billion years ago, when random inorganic chemical interactions produced molecules that had the re- markable property of acting as templates to form similar mol- ecules. Some of the chemicals involved may have come to Earth from space, but chemical evolution continued on Earth. The information stored in these simple molecules enabled the synthesis of larger molecules with complex but relatively stable shapes. Because they were both complex and stable, these molecules could participate in increasing numbers and kinds of chemical reactions. Certain types of large molecules are found in all living systems; the properties and functions of these complex molecules are the subject of Chapter 3. Biological evolution began when cells formed About 3.8 billion years ago, interacting systems of molecules came to be enclosed in compartments. Within those units— cells—control was exerted over the entrance, retention, and exit of molecules, as well as over the chemical reactions tak- ing place. The origin of cells marked the beginning of bio- 4 CHAPTER ONE logical evolution. Cells and the membranes that enclose them are the subjects of Chapters 4 and 5. Cells are so effective at capturing energy and replicating themselves—two fundamental characteristics of life—that since they evolved, cells have been the unit on which all life is built. Experiments by the French chemist and microbiologist Louis Pasteur and other scientists during the nineteenth cen- tury (described in Chapter 3) convinced most scientists that, under present conditions on Earth, cells do not arise from non- cellular material, but come only from other cells. For 2 billion years after cells originated, all organisms were unicellular (had only one cell). They were confined to the oceans, where they were shielded from lethal ultraviolet light. These simple cells, called prokaryotic cells, had no in- ternal membrane-enclosed compartments. Photosynthesis changed the course of evolution A major event that took place about 2.5 billion years ago was the evolution of photosynthesis: the ability to use the energy of sunlight to power metabolism. All cells must obtain raw materials and energy to fuel their metabolism. Photosynthetic cells take up raw materials from their environment, but the en- ergy they use to metabolize those chemicals comes directly from the sun. Early photosynthetic cells were probably simi- lar to present-day prokaryotes called cyanobacteria (Figure 1.4). The energy-capturing process they used, which we will de- scribe in Chapter 8, is the basis of nearly all life on Earth today. Oxygen gas (O 2 ) is a by-product of photosynthesis. Once photosynthesis evolved, photosynthetic prokaryotes became so abundant that they released vast quantities of O 2 into the atmosphere. The O 2 we breathe today would not exist with- out photosynthesis. When it first appeared in the atmos- phere, however, O 2 was poisonous to most organisms then living on Earth. Those prokaryotes that evolved a tolerance to O 2 were able to successfully colonize en- vironments emptied of other organisms and proliferate in great abundance. For those prokaryotes, the presence of oxygen opened up new avenues of evolution. Metabolic re- actions that use O 2 , called aerobic metabolism, are more efficient than the anaerobic (non- oxygen-using) metabolism that earlier prokaryotes had used. Aerobic metabolism allowed cells to grow larger, and it came to be used by most organisms on Earth. Over a much longer time frame, the vast quantities of oxygen released by photosyn- thesis had another effect. Formed from O 2 , ozone (O 3 ) began to accumulate in the up- per atmosphere. The ozone slowly formed a dense layer that acted as a shield, inter- AN EVOLUTIONARY FRAMEWORK FOR BIOLOGY 5 27 First life? 12 6 39 27 28 29 30 Each “day” represents about 150 million years. Life appeared some time during “days” 3–4, or about 4 billion years ago. Homo sapiens (modern humans) appeared in the last 10 minutes of day 30. Recorded history fills the last 5 seconds of day 30. 1.3 Life’s Calendar If the history of life on Earth is “drawn”as a 30-day calendar,recorded human history takes up only the last 5 seconds. 1.4 Oxygen Produced by Prokaryotes Changed Earth’s Atmosphere This modern cyanobacterium may be very similar to early photosynthetic prokaryotes. cepting much of the sun’s deadly ultraviolet radiation. Even- tually (although only within the last 800 million years of evo- lution), the presence of this shield allowed organisms to leave the protection of the ocean and establish new lifestyles on Earth’s land surfaces. Cells with complex internal compartments arose As the ages passed, some prokaryotic cells became large enough to attack, engulf, and digest smaller prokaryotes, be- coming the first predators. Usually the smaller cells were de- stroyed within the predators’ cells, but some of these smaller cells survived and became permanently integrated into the operation of their host cells. In this manner, cells with com- plex internal compartments, called eukaryotic cells, arose. The hereditary material of eukaryotic cells is contained within a membrane-enclosed nucleus and is organized into discrete units. Other compartments are specialized for other purposes, such as photosynthesis (Figure 1.5). Multicellularity arose and cells became specialized Until slightly more than 1 billion years ago, only unicellular organisms (both prokaryotic and eukaryotic) existed. Two key developments made the evolution of multicellular organ- isms—organisms consisting of more than one cell—possible. One was the ability of a cell to change its structure and func- tioning to meet the challenges of a changing environment. This was accomplished when prokaryotes evolved the abil- ity to transform themselves from rapidly growing cells into resting spores that could survive harsh environmental con- ditions. The second development allowed cells to stick to- gether after they divided and to act together in a coordinated manner. Once organisms began to be composed of many cells, it became possible for the cells to specialize. Certain cells, for example, could be specialized to perform photosynthesis. Other cells might become specialized to transport raw mate- rials, such as water and nitrogen, from one part of an organ- ism to another. Sex increased the rate of evolution The earliest unicellular organisms reproduced by dividing, and the resulting daughter cells were identical to the parent cell. But sexual recombination—the combining of genes from two different cells in one cell—appeared early during the evolution of life. Early prokaryotes engaged in sex (ex- changes of genetic material) and reproduction (cell division) at different times. Even today in many unicellular organisms, sex and reproduction are separated in time. Simple nuclear division—mitosis—was sufficient for the reproductive needs of most unicellular organisms, and gene exchange (a separate event) could occur at any time. Once or- ganisms came to be composed of many cells, however, cer- tain cells began to be specialized for sex. Only these special- ized sex cells, called gametes, could exchange genes, and the sex lives of multicellular organisms became more compli- cated. A whole new method of nuclear division—meiosis— evolved. An intricate and complex process, meiosis opened up a multitude of possibilities for genetic recombination be- tween gametes. Mitosis and meiosis are explained and com- pared in Chapter 9. Sex increased the rate of evolution because an organism that exchanges genetic information with another individual produces offspring that are more genetically variable than the offspring of an organism that reproduces by mitotic di- vision of its own cells. Some of these varied offspring are likely to survive and reproduce better than others in a vari- able and changing environment. It is this genetic variation that natural selection acts on. Levels of Organization of Life Biology can be visualized as a hierarchy of units, ordered from the smallest to the largest. These units are molecules, cells, tissues, organs, organisms, populations, communities, and the biosphere (Figure 1.6). The organism is the central unit of study in biology; Parts Six and Seven of this book discuss organismic biology in de- tail. But to understand organisms, biologists study life at all its levels of organization. They study molecules, chemical re- actions, and cells to understand the functioning of tissues and organs. They study organs and organ systems to determine how organisms maintain homeostasis. At higher levels in the hierarchy, biologists study how organisms interact with one 6 CHAPTER ONE Nucleus Eukaryotic cells contain many membrane-enclosed compartments, known as organelles. 1.5 Multiple Compartments Characterize Eukaryotic Cells The nucleus and other specialized compartments of eukaryotic cells evolved from small prokaryotes that were ingested by larger pro- karyotic cells. another to form social systems, populations, and ecological communities, which are the subjects of Part Eight of this book. The Evolutionary Tree of Life All organisms on Earth today are the descendants of a single kind of unicellular organism that lived almost 4 billion years ago. But if that were the whole story, only one kind of or- ganism might exist on Earth today. Instead, Earth is popu- lated by many millions of different kinds of organisms that do not interbreed with one another. We call these genetically independent kinds species. Why are there so many species? As long as individuals within a population mate at random and reproduce, struc- tural and functional changes may evolve within that popu- lation, but only one species will exist. However, if a popula- tion becomes separated and isolated into two or more groups, individuals within each group will mate only with one another. When this happens, structural and functional differences between the groups may accumu- late over time, and the groups may evolve into different species. The splitting of groups of organisms into separate species has re- sulted in the great diversity of life found on Earth today. The ways in which species form are explained in Chapter 24. Sometimes humans refer to a species as “primitive” or “advanced.” These and similar terms, such as “lower” and “higher,” are best avoided in biology because they imply that some organisms function better than others. In fact, all living organisms are successfully adapted to their environments. The shape and strength of a bird’s beak, or the form and dis- persal mechanisms of a plant’s seeds are ex- amples of the rich array of adaptations found among living organisms (Figure 1.7). The abundance and success of prokaryotes—all of which are relatively simple organisms—read- ily demonstrates that they are highly func- tional. In this book, we use the terms simple and complex to refer to the level of complexity of a particular organism. We use the terms an- cestral and derived to distinguish characteris- tics that appeared earlier from those that ap- peared later in evolution. As many as 30 million species of organ- isms may live on Earth today. Many times that number lived in the past, but are now ex- AN EVOLUTIONARY FRAMEWORK FOR BIOLOGY 7 Molecules are made up of atoms, and in turn can be organized into cells. A tissue is a group of many cells with similar and coordinated functions. Atoms Molecule Cell (neuron) Tissue (ganglion) Organ (brain) Organism (fish) Population (school of fish) An organism is a recognizable, self- contained individual made up of organs and organ systems. Communities consist of populations of many different species. Biosphere A population is a group of many organisms of the same species. Community (coral reef) Biological communities exchange energy with one another, combining to create the biosphere of Earth. Cells of many types are the working components of living organisms. Organs combine several tissues that function together. Organs form systems, such as the nervous system. 1.6 From Molecules to the Biosphere:The Hierarchy of Life tinct. This diversity is the result of millions of splits in popu- lations, known as speciation events. The unfolding of these events can be expressed as an evolutionary “tree” showing the order in which populations split and eventually evolved into new species (see Figure 1.8). An evolutionary tree, with its “trunk” and its increasingly finer “branches,” traces the descendants coming from ancestors that lived at different times in the past. That is, a tree shows the evolutionary rela- tionships among species and groups of species. The organ- isms on any one branch share a common ancestor at the base of that branch. The most closely related groups are together on the same branch. More distantly related organisms are on different branches. In this book, we adopt the convention that time flows from left to right, so the tree in Figure 1.8 (and other trees in this book) lies on its side, with its root—the an- cestor of all life—at the left. The U.S. National Science Foundation is sponsoring a ma- jor initiative, called Assembling the Tree of Life (ATOL). Its goal is to determine the evolutionary relationships among all species on Earth. Achieving this goal is possible today be- cause, for the first time, biologists have the technology to as- semble the complete tree of life, from microbes to mammals. Data for ATOL come from a variety of sources. Fossils—the preserved remains of organisms that lived in the past—tell us where and when ancestral organisms lived and what they may have looked like. With modern molecular genetic tech- niques such as DNA sequencing, we can determine how many genes different species share, and information tech- 8 CHAPTER ONE (a) (b) The strong, curved beak of the bald eagle is able to tear the flesh from large fish and other sizeable prey. The curlew uses its long, curved, pointed beak to extract small crustaceans from the surface of mud, sand, and soil. The roseate spoonbill moves its bill through the water, from which it filters food items. The coconut seed is covered by a thick husk that protects it as it drifts across thousands of miles of ocean. Mammals and birds eat blackberries, then disseminate the seeds when they defecate. The seeds of milkweeds are surrounded by “kites” of fibers that carry them on wind currents. 1.7 Adaptations to the Environment (a) Bird beaks are adapted to specific types of food items.(b) Plants cannot move, but their seeds have adaptations that allow them to travel varying distances from the parent plant. nology enables us to synthesize masses of genetic data. The ATOL initiative, one of the grandest projects of modern biol- ogy, is projected to take at least two decades and to involve hundreds of scientists working in a diverse array of fields. The reason it will take so long to complete is that most of Earth’ species have not yet been described. The Tree of Life will be an information framework for bi- ology in much the same way that the periodic table of ele- ments is an information framework for chemistry and physics. Evolution has conducted several billion years of free research and development. Every living thing carries a ge- netic “package” that has been tested by natural selection. Sci- entists can now unwrap and study these packages, learning much about the processes that produced them. Although much remains to be accomplished, biologists know enough to have assembled a provisional tree of life, the broad outlines of which are shown in Figure 1.8. The branch- ing patterns of this tree are based on a rich array of evidence, but no fossils are available to help us determine the earliest divisions in the lineages of life because those simple organ- isms had no parts that could be preserved as fossils. There- fore, molecular evidence has been used to separate all living organisms into three major domains. Organisms belonging to a particular domain have been evolving separately from organisms in the other domains for more than a billion years. Organisms in the domains Archaea and Bacteria are prokaryotes. Archaea and Bacteria differ so fundamentally from one another in their metabolic processes that they are be- lieved to have separated into distinct evolutionary lineages very early dur- ing the evolution of life. These two do- mains are described in Chapter 27. Members of the other domain— Eukarya—have eukaryotic cells. The Eukarya are divided into four groups: Protista, Plantae, Fungi, and Animalia. The Protista (protists), the subject of Chapter 28, contains mostly single- celled organisms. The other three groups, referred to as kingdoms, are be- lieved to have arisen from ancestral protists. All of their members are mul- ticellular. Some bacteria, some protists, and most members of the kingdom Plantae (plants) convert light energy to chem- ical energy by photosynthesis. These organisms are called autotrophs (“self-feeders”). The biological molecules they produce are the primary food for nearly all other living organisms. The kingdom Plantae is covered in Chapters 29 and 30. The kingdom Fungi, the subject of Chapter 31, includes molds, mushrooms, yeasts, and other similar organisms, all of which are heterotrophs (“other-feeders”)—that is, they re- quire a source of energy-rich molecules synthesized by other organisms. Fungi break down food molecules in their envi- ronment and then absorb the breakdown products into their cells. They are important as decomposers of the dead mate- rials of other organisms. Members of the kingdom Animalia (animals) are het- erotrophs that ingest their food source, digest the food out- side their cells, and then absorb the breakdown products. An- imals eat other forms of life to obtain their raw materials and energy. This kingdom is covered in Chapters 32, 33, and 34. We will discuss the principal levels used in today’s clas- sification scheme for living organisms in Chapter 25. But to understand some of the terms we will use in the interven- ing chapters, you need to know that each species of organ- ism is identified by two Latinized names (a binomial). The first name identifies the genus—a group of species that share a recent common ancestor—of which the species is a member. The second name is the species name. To avoid confusion, no combination of two names is assigned to more than one species. For example, the scientific name of the hu- man species is Homo sapiens: Homo is our genus and sapiens is our species. The Pacific tree frogs Pieter Johnson studied are called, in scientific nomenclature, Hyla regilla. Biology is the study of all of Earth’s organisms, both those living today and those that lived in the past, so even extinct species are given binomials. These unique and exact names AN EVOLUTIONARY FRAMEWORK FOR BIOLOGY 9 PresentAncient Time Archaea and Eukarya share a common ancestor not shared by bacteria. There are multiple protist lineages. Plants, fungi, and animals are descended from different protist ancestors. Protists Animalia Fungi Plantae Protists Protists Archaea Bacteria Common ancestor of all organisms BACTERIA ARCHAEA EUKARYA 1.8 A Provisional Tree of Life The classification system used in this book divides Earth’s organisms into three domains; Bacteria, Archaea, and Eukarya. Protists are descen- dants of multiple ancestors. illuminate the tremendous diversity of life, and are im- portant tools for biologists because, as in all the sciences, precise and unambiguous communication of research infor- mation is critical. Biology Is a Science To study the rich variety of living things, biologists employ many different methods. Direct observations by unaided senses are central to many scientific investigations, but sci- entists also use many tools that augment the human senses. For example, to study objects that are too small to be seen with the unaided eye, scientists use microscopes. To observe and magnify remote objects, scientists use telescopes. To study events that happened thousands to millions of years ago, scientists “read” radioactive isotopes of chemical ele- ments that decay at specific rates. Conceptual tools guide scientific research In addition to such technical tools, scientists use a variety of conceptual tools to help them answer questions about nature. The method that underlies most scientific research is the hypothesis-prediction (H–P) approach. The H–P approach allows scientists to modify their conclusions as new infor- mation becomes available. The method has five steps: 1. Making observations 2. Asking questions 3. Forming hypotheses, which are tentative answers to the questions 4. Making predictions based on the hypotheses 5. Testing the predictions by making additional observa- tions or conducting experiments If the results of the testing support the hypothesis, it is sub- jected to additional predictions and tests. If they continue to support it, confidence in its correctness increases, and the hy- pothesis comes to be considered a theory. If the results do not support the hypothesis, it is abandoned or modified in ac- cordance with the new information. Then new predictions are made, and more tests are conducted. Hypotheses are tested in two major ways Tests of hypotheses are varied, but most are of two types: controlled experiments and the comparative method. When possible, scientists use controlled experiments to test pre- dictions from hypotheses. That is what Pieter Johnson was doing when he hatched frog eggs in the laboratory. He pre- dicted that if his hypothesis—that the parasite Ribeiroia caused deformities in frogs—was correct, then frogs raised with the parasite would develop deformities and frogs raised in the absence of the parasite would not. The advantage of controlled experiments is that all factors other than the one hy- pothesized to be causing the effect can be kept constant; that is, any other factors that might influence the outcome (such as wa- ter temperature and pH in Pieter’s experiment) are con- trolled. The most powerful experiments are those that have the ability to demonstrate that the hypothesis or the predic- tions made from it are wrong. But many hypotheses cannot be tested with controlled ex- periments. Such hypotheses are tested by making predic- tions about patterns that should exist in nature if the hy- pothesis is correct. Data are then gathered to determine whether those patterns in fact do exist. This approach is called the comparative method. It is the primary approach of scientists in some fields, such as astronomy, in which ex- periments are rarely possible. Biologists regularly use the comparative method. A single piece of supporting evidence rarely leads to wide- spread acceptance of a hypothesis. Similarly, a single contrary result rarely leads to abandonment of a hypothesis. Results that do not support the hypothesis can be obtained for many reasons, only one of which is that the hypothesis is wrong. For example, incorrect predictions can be made from a cor- rect hypothesis. Poor experimental design, or the use of an inappropriate organism, can also lead to erroneous results. We will now show how the H–P method was used by other researchers to investigate the larger question that con- cerned Pieter Johnson: Why are amphibian populations de- clining dramatically in many places on Earth? STEP 1: MAKING OBSERVATIONS. Amphibian populations, like populations of most organisms, fluctuate over time. Before we decide that the current declines are different from “normal” population fluctuations, we first need to establish that they are unusual. To assess whether the cur- rent declines are unusual, an international group of scien- tists has been gathering worldwide data on amphibian populations. The group’s data show that amphibian popu- lations are declining seriously in some parts of the world, especially western North America, Central America, and northeastern Australia, but not others, such as the Amazon Basin. Their data also show that population declines are greater in mountains than in adjacent lowlands. These sci- entists also discovered that no data on population trends in amphibians are available from Africa or Asia. STEP 2: ASKING QUESTIONS. Two questions were suggested by these observations: Why are amphibian declines greater at high elevations? Why are amphibians declining in some regions, but not in others? 10 CHAPTER ONE [...]... products The arrow symbolizes the direction of the chemical reaction The numbers preceding the molecular formulas balance the equation and indicate how many molecules are used or are produced In this and all other chemical reactions, matter is neither created nor destroyed The total number of carbons on the left equals the total number of carbons on the right However, there is another product of this... are the most powerful tools that humans have developed to understand how the world works Their strength is founded on the development of hypotheses that can be tested The process is self-correcting because if the evidence fails to support a hypothesis, it is either abandoned or modified and subjected to further tests In addition, because scientists publish detailed descriptions of the methods they... equals the number of protons in an atom c equals the number of protons minus the number of neutrons d equals the number of neutrons plus the number of protons e depends on the isotope 2 The atomic weight (atomic mass) of an element a equals the number of neutrons in an atom b equals the number of protons in an atom c equals the number of electrons in an atom d equals the number of neutrons plus the number... typical, some of them have the water needed for life As biologists contemplate how life could originate from nonliving matter, their attention focuses not just on the presence of water, but on what is dissolved in it A major discovery of biology is that living things are composed of the same types of chemical elements as the vast nonliving portion of the universe This mechanistic view— that life is chemically... Probability of dying 1.9 A Controlled Experiment Tests the Effects of UV-B The results of this experiment suggest that UV-B susceptibility has contributed to the decline of some amphibian populations Experimental populations of both species were subjected to different levels of UV radiation; the filtered-light population (no UV-B exposure) acted as a control EXPERIMENT Hypothesis: Susceptibility to UV-B radiation... individual cells of multicellular organisms became modified to carry out varied functions within the organism The evolution of sex sped up rates of biological evolution Levels of Organization of Life Life is organized hierarchically, from molecules to the biosphere Review Figure 1.6 See Web/CD Activity 1.1 The Evolutionary Tree of Life A major effort called Assembling the Tree of Life (ATOL) is underway... plus the number of protons e depends on the relative abundances of its isotopes 34 CHAPTER T WO 3 Which of the following statements about all the isotopes of an element is not true? a They have the same atomic number b They have the same number of protons c They have the same number of neutrons d They have the same number of electrons e They have identical chemical properties 4 Which of the following... signifera if exposed to UV-B radiation typical of high elevations (Figure 1.9) As predicted, when exposed to UV-B radiation, individuals of C signifera survived well, but all individuals of L verreauxii died within two weeks Among control populations raised in tanks covered by filters that blocked UV transmission, individuals of both species survived well Thus, the results supported the hypothesis 11 STEP... Mars and landed in Antarctica, contains the chemical signatures of life Theories of the Origin of Life Living things are composed of the same elements as the inanimate universe, the 92 elements of the periodic table (see Figure 2.3) But the arrangements of these atoms into molecules in biological 1 cm 36 CHAPTER THREE systems are unique You cannot find DNA in rocks unless it came from a once-living organism... special properties The water molecule, H2O, has unique chemical features As we learned in the preceding sections, water is a polar molecule that can form hydrogen bonds In addition, the shape of water is a tetrahedron The four pairs of electrons in the outer shell of oxygen repel one another, producing a tetrahedral shape The four orbitals are directed toward the corners of a tetrahedron Non-bonding electron . Then there was an extended period of only unicellular life, fol- lowed by a proliferation of multicellular life. In other words, the nature and diversity of life has changed over time. Iden- tification. that they are be- lieved to have separated into distinct evolutionary lineages very early dur- ing the evolution of life. These two do- mains are described in Chapter 27. Members of the other. thousands of miles of ocean. Mammals and birds eat blackberries, then disseminate the seeds when they defecate. The seeds of milkweeds are surrounded by “kites” of fibers that carry them on