AP Bio Ch. 1-5 (1) PDF

1 of vertical rock walls, where little soil is present to hold rain- water (Figure 1.2). The plant’s water-conserving characteristics...

1 of vertical rock walls, where little soil is present to hold rain- water (Figure 1.2). The plant’s water-conserving characteristics help it survive and thrive in these nooks and crannies. Sim- ilar features are found in many plants that live in dry envi- ronments, allowing them to eke out a living where rain is unpredictable. Introduction: An organism’s adaptations to its environment, such as adaptations for conserving water, are the result of evolution, Themes in the the process of change that has transformed life on Earth from its earliest beginnings to the diversity of organisms living today. Evolution is the fundamental organizing principle of bi- Study of Life ology and the core theme of this book. Although biologists know a great deal about life on Earth, many mysteries remain. For instance, what exactly led to the origin of flowering among plants such as the one pictured here? Posing questions about the living world and seeking science-based answers—scientific inquiry—are the central ac- tivities of biology, the scientific study of life. Biologists’ ques- tions can be ambitious. They may ask how a single tiny cell becomes a tree or a dog, how the human mind works, or how the different forms of life in a forest interact. Most people won- der about the organisms living around them, and many interest- ing questions probably occur to you when you are out-of-doors, surrounded by the natural world. When they do, you are al- ready thinking like a biologist. More than anything else, biology is a quest, an ongoing inquiry about the nature of life. What is life? Even a small child realizes that a dog or a plant is alive, while a rock or a lawn mower is not. Yet the phenome- non we call life defies a simple, one-sentence definition. We recognize life by what living things do. Figure 1.3, on the next page, highlights some of the properties and processes we asso- ciate with life.  Figure 1.1 How is the mother-of-pearl While limited to a handful of images, Figure 1.3 reminds us plant adapted to its environment? that the living world is wondrously varied. How do biologists KEY CONCEPTS 1.1 The themes of this book make connections across different areas of biology 1.2 The Core Theme: Evolution accounts for the unity and diversity of life 1.3 In studying nature, scientists make observations and then form and test hypotheses 1.4 Science benefits from a cooperative approach and diverse viewpoints OVERVIEW Inquiring About Life The mother-of-pearl plant, or ghost plant (Figure 1.1 and cover), is native to a single mountain in northeastern Mex- ico. Its fleshy, succulent leaves and other features allow this  Figure 1.2 The mother-of-pearl plant (Graptopetalum plant to store and conserve water. Even when rain falls, the paraguayense). This plant’s thick leaves hold water, enabling it to live plant’s access to water is limited because it grows in crevices where soil is scarce. The leaves vary in color, as seen here. CHAPTER 1 Introduction: Themes in the Study of Life 1   Order. This close-up of a sunflower illustrates the highly ordered structure that characterizes life.  Response to the environment. This Venus flytrap closed its trap rapidly in response to the environ- mental stimulus of a damselfly landing on the open trap.  Evolutionary adaptation. The appearance of this pygmy sea horse camouflages the animal in its environment. Such adaptations evolve over many generations by the reproductive success of those individuals with heritable traits that are best suited to their environments.  Reproduction. Organisms (living things) reproduce their own kind. Here, a baby giraffe stands close to its mother.  Regulation. The regulation of blood flow through the blood vessels of this jackrabbit’s ears helps maintain a constant body temperature by  Energy processing. This adjusting heat hummingbird obtains fuel exchange with the in the form of nectar from surrounding air. flowers. The hummingbird  Growth and development. will use chemical energy Inherited information carried stored in its food to power by genes controls the pattern flight and other work. of growth and development of organisms, such as this  Figure 1.3 Some properties of life. Nile crocodile. make sense of this diversity and complexity? This opening chapter sets up a framework for answering this question. The CONCEPT 1.1 first part of the chapter provides a panoramic view of the bio- The themes of this book make logical “landscape,” organized around some unifying themes. connections across different We then focus on biology’s core theme, evolution, with an in- troduction to the reasoning that led Charles Darwin to his ex- areas of biology planatory theory. Next, we look at scientific inquiry—how Biology is a subject of enormous scope, and news reports re- scientists raise and attempt to answer questions about the nat- veal exciting new biological discoveries being made every day. ural world. Finally, we address the culture of science and its ef- Simply memorizing the factual details of this huge subject is fects on society. most likely not the best way to develop a coherent view of 2 CHAPTER 1 Introduction: Themes in the Study of Life life. A better approach is to take a more active role by connect- The Power and Limitations of Reductionism ing the many things you learn to a set of themes that pervade Because the properties of life emerge from complex organiza- all of biology. Focusing on a few big ideas—ways of thinking tion, scientists seeking to understand biological systems con- about life that will still hold true decades from now—will help front a dilemma. On the one hand, we cannot fully explain a you organize and make sense of all the information you’ll en- higher level of order by breaking it down into its parts. A dis- counter as you study biology. To help you, we have selected sected animal no longer functions; a cell reduced to its chem- eight unifying themes to serve as touchstones as you proceed ical ingredients is no longer a cell. Disrupting a living system through this book. interferes with its functioning. On the other hand, some- thing as complex as an organism or a cell cannot be analyzed Theme: New Properties Emerge at Each Level without taking it apart. in the Biological Hierarchy Reductionism—the approach of reducing complex systems The study of life extends from the microscopic scale of the to simpler components that are more manageable to study— molecules and cells that make up organisms to the global is a powerful strategy in biology. For example, by studying the scale of the entire living planet. We can divide this enormous molecular structure of DNA that had been extracted from range into different levels of biological organization. cells, James Watson and Francis Crick inferred, in 1953, how Imagine zooming in from space to take a closer and closer this molecule could serve as the chemical basis of inheritance. look at life on Earth. It is spring in Ontario, Canada, and our The central role of DNA in cells and organisms became better destination is a local forest, where we will eventually explore understood, however, when scientists were able to study the a maple leaf right down to the molecular level. Figure 1.4, on interactions of DNA with other molecules. Biologists must the next two pages, narrates this journey into life, with the balance the reductionist strategy with the larger-scale, holistic numbers leading you through the levels of biological organi- objective of understanding emergent properties—how the zation illustrated by the photographs. parts of cells, organisms, and higher levels of order, such as ecosystems, work together. This is the goal of an approach de- Emergent Properties veloped over the last 50 years called systems biology. If we now zoom back out from the molecular level in Figure 1.4, we can see that novel properties emerge at each step, prop- Systems Biology erties that are not present at the preceding level. These A system is simply a combination of components that func- emergent properties are due to the arrangement and in- tion together. A biologist can study a system at any level of or- teractions of parts as complexity increases. For example, al- ganization. A single leaf cell can be considered a system, as though photosynthesis occurs in an intact chloroplast, it can a frog, an ant colony, or a desert ecosytem. To understand will not take place in a disorganized test-tube mixture of how such systems work, it is not enough to have a “parts list,” chlorophyll and other chloroplast molecules. Photosynthe- even a complete one. Realizing this, many researchers are sis requires a specific organization of these molecules in the now complementing the reductionist approach with new chloroplast. To take another example, if a blow to the head strategies for studying whole systems. This change in perspec- disrupts the intricate architecture of a human brain, the tive is analogous to moving from ground level on a street cor- mind may cease to function properly even though all of the ner, where you can observe local traffic, to a helicopter high brain tissues are still present. Our thoughts and memories above a city, from which you can see how variables such as are emergent properties of a complex network of nerve cells. time of day, construction projects, accidents, and traffic-signal At a much higher level of biological organization—at the malfunctions affect traffic throughout the city. ecosystem level—the recycling of chemical elements essen- Systems biology is an approach that attempts to model tial to life, such as carbon, depends on a network of diverse the dynamic behavior of whole biological systems based on a organisms interacting with each other and with the soil, study of the interactions among the system’s parts. Successful water, and air. models enable biologists to predict how a change in one or Emergent properties are not unique to life. A box of bicycle more variables will affect other components and the whole sys- parts won’t take you anywhere, but if they are arranged in a cer- tem. Thus, the systems approach enables us to pose new kinds tain way, you can pedal to your chosen destination. And while of questions. How might a drug that lowers blood pressure af- the graphite in a pencil “lead” and the diamond in a wedding fect the functioning of organs throughout the human body? ring are both pure carbon, they have very different appearances How might increasing a crop’s water supply affect processes in and properties due to the different arrangements of their car- the plants, such as the storage of molecules essential for human bon atoms. Both of these examples point out the importance of nutrition? How might a gradual increase in atmospheric car- arrangement. Compared to such nonliving examples, however, bon dioxide alter ecosystems and the entire biosphere? The ul- the unrivaled complexity of biological systems makes the emer- timate aim of systems biology is to answer large-scale questions gent properties of life especially challenging to study. like the last one. CHAPTER 1 Introduction: Themes in the Study of Life 3  Figure 1.4 Exploring Levels of Biological Organization 1 The Biosphere As soon as we are near enough to Earth to make out its continents and oceans, we begin to see signs of life—in the green mosaic of the planet’s forests, for example. This is our first view of the biosphere, which consists of all life on Earth and all the places where life exists—most regions of land, most bodies of water, the atmosphere to an altitude of several kilometers, and even sediments far below the ocean floor and rocks many kilometers below Earth’s surface. 2 Ecosystems As we approach Earth’s surface for an imag- inary landing in Ontario, we can begin to make out a forest with an abundance of trees that lose their leaves in one season and grow new ones in another (deciduous trees). Such a deciduous forest is an exam- ple of an ecosystem. Grasslands, deserts, and the ocean’s coral reefs are other types of ecosystems. An ecosystem consists of all the living things in a particular area, along with all the nonliving components of the environment with which life interacts, such as soil, water, atmospheric gases, and light. All of Earth’s ecosystems combined 3 Communities make up the biosphere. The entire array of organ- isms inhabiting a particular ecosystem is called a biological community. The community in our forest ecosystem includes many kinds of trees and other plants, a diversity of ani- mals, various mushrooms and other fungi, and enor- mous numbers of diverse microorganisms, which are living forms, such as bacte- ria, that are too small to see without a microscope. Each of these forms of life is called a species. 4 Populations A population consists of all the individuals of a species living within the bounds of a specified area. For example, our Ontario 5 Organisms forest includes a population of Individual living things are called organ- sugar maple trees and a popula- isms. Each of the maple trees and other tion of white-tailed deer. We plants in the forest is an organism, and can now refine our definition so is each forest animal—whether deer, of a community as the set of squirrel, frog, or beetle. The soil teems with populations that inhabit a par- microorganisms such as bacteria. ticular area. 4 CHAPTER 1 Introduction: Themes in the Study of Life 6 Organs and Organ Systems The structural hierarchy of life continues to unfold as we explore the architecture of the 50 μm more complex organisms. A maple leaf is an example of an organ, a body part that carries 7 Tissues out a particular function in the body. Stems and roots are the other major organs of plants. Our next scale change—to see the Examples of human organs are the brain, heart, tissues of a leaf—requires a micro- and kidney. The organs of humans, other com- scope. Each tissue is made up of a plex animals, and plants are organized into group of cells that work together, organ systems, each a team of organs that performing a specialized function. cooperate in a larger function. For example, The leaf shown here has been cut the human digestive system includes such on an angle. The honeycombed organs as the tissue in the interior of the leaf tongue, stomach, (left portion of photo) is the main and intestines. location of photosynthesis, the Organs consist of process that converts light energy multiple tissues. to the chemical energy of sugar and other food. We are viewing the sliced leaf from a perspective that also enables us to see the jig- saw puzzle–like “skin” on the sur- face of the leaf, a tissue called epi- Cell 10 μm dermis (right part of photo). The pores through the epidermis al- low the gas carbon dioxide, a raw material for sugar production, to reach the photosynthetic tissue inside the leaf. At this scale, we can also see that each tissue has a distinct cellular structure. 9 Organelles 8 Cells Chloroplasts are examples Chloroplast The cell is life’s fundamental unit of organelles, the various of structure and function. Some functional components organisms, such as amoebas and present in cells. In this most bacteria, are single cells. image, a very powerful Other organisms, including plants tool called an electron and animals, are multicellular. microscope brings a single Instead of a single cell performing chloroplast into sharp all the functions of life, a multi- 1 μm cellular organism has a division of labor among focus. specialized cells. A human body consists of tril- lions of microscopic cells of many different kinds, such as muscle cells and nerve cells, which are organized into the various specialized tissues.  10 Molecules For example, muscle tissue consists of bundles of muscle cells. In the photo at the upper left, we Our last scale change drops us into a chloroplast for a view see a more highly magnified view of some cells of life at the molecular level. A molecule is a chemical in a leaf tissue. One cell is only about 40 micro- Atoms structure consisting of two or more small chemical units meters (μm) across. It would take about 500 of called atoms, which are represented as balls in this com- these cells to reach across a small coin. As tiny puter graphic of a chlorophyll molecule. Chlorophyll is as these cells are, you can see that each contains Chlorophyll numerous green structures called chloroplasts, the pigment molecule that makes a maple leaf green. One molecule which are responsible for photosynthesis. of the most important molecules on Earth, chlorophyll absorbs sunlight during the first step of photosynthesis. Within each chloroplast, millions of chlorophyll mol- ecules, together with accessory molecules, are organized into the equipment that converts light energy to the chemical energy of food. CHAPTER 1 Introduction: Themes in the Study of Life 5  Systems biology is relevant to the study of life at all levels. A tree also interacts with other organisms, such as soil During the early years of the 20th century, biologists studying microorganisms associated with its roots, insects that live in how animal bodies function (animal physiology) began inte- the tree, and animals that eat its leaves and fruit. Interactions grating data on how multiple organs coordinate processes between organisms ultimately result in the cycling of nutrients such as the regulation of sugar concentration in the blood. in ecosystems. For example, minerals acquired by a tree will And in the 1960s, scientists investigating ecosystems pio- eventually be returned to the soil by other organisms that de- neered a more mathematically sophisticated systems ap- compose leaf litter, dead roots, and other organic debris. The proach with elaborate models diagramming the network of minerals are then available to be taken up by plants again. interactions between organisms and nonliving components Like all organisms, we humans interact with our environ- of ecosystems, such as salt marshes. More recently, with the ment. Unfortunately, our interactions sometimes have drastic sequencing of DNA from many species, systems biology has consequences. For example, since the Industrial Revolution in taken hold at the cellular and molecular levels, as we’ll de- the 1800s, the burning of fossil fuels (coal, oil, and gas) has scribe later when we discuss DNA. been increasing at an ever-accelerating pace. This practice re- leases gaseous compounds into the atmosphere, including prodigious amounts of carbon dioxide (CO2). About half the Theme: Organisms Interact with Other human-generated CO2 stays in the atmosphere, acting like a Organisms and the Physical Environment layer of glass around the planet that admits radiation that Turn back again to Figure 1.4, this time focusing on the for- warms the Earth but prevents heat from radiating into outer est. In an ecosystem, each organism interacts continuously space. Scientists estimate that the average temperature of the with its environment, which includes both other organisms planet has risen 1°C since 1900 due to this “greenhouse ef- and physical factors. The leaves of a tree, for example, ab- fect,” and they project an additional rise in average global sorb light from the sun, take in carbon dioxide from the air, temperature of at least 3°C over the course of the 21st century. and release oxygen to the air (Figure 1.5). Both the organ- This global warming, a major aspect of global climate ism and the environment are affected by the interactions change, has already had dire effects on life-forms and their between them. For example, a plant takes up water and habitats all over planet Earth. Polar bears have lost a signifi- minerals from the soil through its roots, and its roots help cant portion of the ice platform from which they hunt, and form soil by breaking up rocks. On a global scale, plants and there are examples of small rodents and plant species that other photosynthetic organisms have generated all the oxy- have shifted their ranges to higher altitudes, as well as bird gen in the air. populations that have altered their migration schedules. Only time will reveal the consequences of Sunlight these changes. Scientists predict that even if we stopped burning fossil fuels Leaves absorb light today, it would take several centuries to energy from the sun. Leaves take in CO2 carbon dioxide return to preindustrial CO2 levels. That from the air and scenario is highly improbable, so it is im- release oxygen. perative that we learn all we can about O2 the effects of global climate change on Earth and its populations. Acting as the stewards of our planet, we must strive to find ways to address this problem. Cycling of Theme: Life Requires Energy chemical nutrients Transfer and Transformation As you saw in Figure 1.5, a tree’s leaves Leaves fall to the Water and Animals eat absorb sunlight. The input of energy ground and are minerals in the leaves and fruit from the tree. from the sun makes life possible: A fun- decomposed by soil are taken organisms that up by the damental characteristic of living organ- return minerals tree through isms is their use of energy to carry out to the soil. its roots. life’s activities. Moving, growing, repro- ducing, and the other activities of life  Figure 1.5 Interactions of an African acacia tree with other organisms and the are work, and work requires energy. In physical environment. the business of living, organisms often 6 CHAPTER 1 Introduction: Themes in the Study of Life  Sunlight Heat When energy is used to do Producers absorb light energy and work, some energy is con- transform it into chemical energy. verted to thermal energy, which is lost as heat. An animal’s muscle cells convert chemical Chemical energy from food to energy kinetic energy, the energy of motion. A plant’s cells use chemical energy to do work such as Chemical energy in food growing new leaves. is transferred from plants to consumers. (a) Energy flow from sunlight to producers (b) Using energy to do work to consumers  Figure 1.6 Energy flow in an ecosystem. This endangered Red Colobus monkey lives in Tanzania. transform one form of energy to another. Chlorophyll mol- Theme: Structure and Function Are Correlated ecules within the tree’s leaves harness the energy of sunlight at All Levels of Biological Organization and use it to drive photosynthesis, converting carbon dioxide and water to sugar and oxygen. The chemical energy in sugar Another theme evident in Figure 1.4 is the idea that form fits is then passed along by plants and other photosynthetic or- function, which you’ll recognize from everyday life. For ex- ganisms (producers) to consumers. Consumers are organ- ample, a screwdriver is suited to tighten or loosen screws, a isms, such as animals, that feed on producers and other hammer to pound nails. How a device works is correlated consumers (Figure 1.6a). with its structure. Applied to biology, this theme is a guide to An animal’s muscle cells use sugar as fuel to power move- the anatomy of life at all its structural levels. An example ments, converting chemical energy to kinetic energy, the en- from Figure 1.4 is seen in the leaf: Its thin, flat shape maxi- ergy of motion (Figure 1.6b). The cells in a leaf use sugar to mizes the amount of sunlight that can be captured by its drive the process of cell proliferation during leaf growth, chloroplasts. Analyzing a biological structure gives us clues transforming stored chemical energy into cellular work. In about what it does and how it works. Conversely, knowing both cases, some of the energy is converted to thermal en- the function of something provides insight into its construc- ergy, which dissipates to the surroundings as heat. In contrast tion. An example from the animal kingdom, the wing of a to chemical nutrients, which recycle within an ecosystem, bird, provides additional instances of the structure-function energy flows through an ecosystem, usually entering as theme (Figure 1.7). In exploring life on its different struc- light and exiting as heat. tural levels, we discover functional beauty at every turn. (a) A bird’s wings have an aerodynamically (b) Wing bones have a honeycombed internal structure that is strong efficient shape. but lightweight.  Figure 1.7 Form fits function in a gull’s wing. (a) The shape How does form fit function of a bird’s wings and (b) the structure of its bones make flight possible. ? in a human hand? CHAPTER 1 Introduction: Themes in the Study of Life 7 Theme: The Cell Is an Organism’s Basic Unit generally smaller than eukaryotic cells, as seen clearly in of Structure and Function Figure 1.8. In a prokaryotic cell, the DNA is not separated from the rest of the cell by enclosure in a membrane-bounded In life’s structural hierarchy, the cell has a special place as the nucleus. Prokaryotic cells also lack the other kinds of lowest level of organization that can perform all activities re- membrane-enclosed organelles that characterize eukaryotic quired for life. Moreover, the activities of organisms are all cells. The properties of all organisms, whether prokaryotic or based on the activities of cells. For instance, the movement of eukaryotic, are based in the structure and function of cells. your eyes as you read this line is based on activities of muscle and nerve cells. Even a global process such as the recycling of Theme: The Continuity of Life Is Based carbon is the cumulative product of cellular activities, includ- on Heritable Information in the Form of DNA ing the photosynthesis that occurs in the chloroplasts of leaf cells. Understanding how cells work is a major focus of bio- The division of cells to form new cells is the foundation for logical research. all reproduction and for the growth and repair of multicellu- All cells share certain characteristics. For example, every lar organisms. Inside the dividing cell in Figure 1.9, you can cell is enclosed by a membrane that regulates the passage of see structures called chromosomes, which are stained with a materials between the cell and its surroundings. And every blue-glowing dye. The chromosomes have almost all of the cell uses DNA as its genetic information. However, we can dis- cell’s genetic material, its DNA (short for deoxyribonucleic tinguish between two main forms of cells: prokaryotic cells acid). DNA is the substance of genes, the units of inheritance and eukaryotic cells. The cells of two groups of microorgan- that transmit information from parents to offspring. Your isms, called bacteria (singular, bacterium) and archaea (singu- blood group (A, B, AB, or O), for example, is the result of cer- lar, archaean), are prokaryotic. All other forms of life, including tain genes that you inherited from your parents. plants and animals, are composed of eukaryotic cells. DNA Structure and Function A eukaryotic cell is subdivided by internal membranes into various membrane-enclosed organelles (Figure 1.8). In Each chromosome contains one very long DNA molecule, most eukaryotic cells, the largest organelle is the nucleus, with hundreds or thousands of genes arranged along its which contains the cell’s DNA. The other organelles are lo- length. The genes encode the information necessary to build cated in the cytoplasm, the entire region between the nucleus other molecules in the cell, most notably proteins. Proteins and outer membrane of the cell. The chloroplast you saw in play structural roles and are also responsible for carrying out Figure 1.4 is an organelle found in eukaryotic cells that carry cellular work. They thus establish a cell’s identity. out photosynthesis. Prokaryotic cells are much simpler and The DNA of chromosomes replicates as a cell prepares to divide, and each of the two cellular offspring inherits a com- plete set of genes, identical to that of the parent cell. Each of Prokaryotic cell us began life as a single cell stocked with DNA inherited from Eukaryotic cell DNA (no nucleus) our parents. Replication of that DNA with each round of cell Membrane division transmitted copies of the DNA to our trillions of Membrane cells. The DNA controls the development and maintenance Cytoplasm of the entire organism and, indirectly, everything the organ- ism does (Figure 1.10). The DNA serves as a central database. 25 μm Nucleus (membrane- enclosed) Membrane- DNA (throughout enclosed organelles nucleus) 1 μm  Figure 1.8 Contrasting eukaryotic and prokaryotic cells  Figure 1.9 A lung cell from a newt divides into two in size and complexity. smaller cells that will grow and divide again. 8 CHAPTER 1 Introduction: Themes in the Study of Life  Sperm cell Nuclei containing DNA Fertilized egg with DNA from Embyro’s cells with both parents copies of inherited DNA Egg cell Offspring with traits inherited from  Figure 1.10 Inherited DNA directs development of an organism. both parents The molecular structure of DNA accounts for its ability to store information. Each DNA molecule is made up of two long chains, called strands, arranged in a double helix. Each chain Nucleus is made up of four kinds of chemical building blocks called nu- DNA cleotides, abbreviated A, T, C, and G (Figure 1.11). The way DNA encodes information is analogous to how we arrange the letters of the alphabet into precise sequences with specific Cell meanings. The word rat, for example, evokes a rodent; the A words tar and art, which contain the same letters, mean very different things. We can think of nucleotides as a four-letter al- C phabet of inheritance. Specific sequential arrangements of Nucleotide T these four nucleotide letters encode the information in genes, A which are typically hundreds or thousands of nucleotides long. DNA provides the blueprints for making proteins, and pro- T teins are the main players in building and maintaining the cell A and carrying out its activities. For instance, the information C carried in a bacterial gene may specify a certain protein in a C bacterial cell membrane, while the information in a human gene may denote a protein hormone that stimulates growth. G Other human proteins include proteins in a muscle cell that T drive contraction and the defensive proteins called antibodies. A Enzymes, which catalyze (speed up) specific chemical reac- tions, are mostly proteins and are crucial to all cells. G The DNA of genes controls protein production indirectly, T using a related kind of molecule called RNA as an intermedi- A ary. The sequence of nucleotides along a gene is transcribed into RNA, which is then translated into a specific protein with (a) DNA double helix. This (b) Single strand of DNA. These a unique shape and function. This entire process, by which the model shows each atom geometric shapes and letters are information in a gene directs the production of a cellular prod- in a segment of DNA. Made simple symbols for the nucleo- uct, is called gene expression. In translating genes into pro- up of two long chains of tides in a small section of one building blocks called chain of a DNA molecule. Genetic teins, all forms of life employ essentially the same genetic nucleotides, a DNA molecule information is encoded in specific code. A particular sequence of nucleotides says the same thing takes the three-dimensional sequences of the four types of in one organism as it does in another. Differences between or- form of a double helix. nucleotides. (Their names are abbreviated A, T, C, and G.) ganisms reflect differences between their nucleotide sequences rather than between their genetic codes.  Figure 1.11 DNA: The genetic material. CHAPTER 1 Introduction: Themes in the Study of Life 9  Not all RNA molecules in the cell are translated into pro- was only the beginning of an even bigger research endeavor, tein; some RNAs carry out other important tasks. We have an effort to learn how the activities of the myriad proteins known for decades that some types of RNA are actually com- encoded by the DNA are coordinated in cells and whole or- ponents of the cellular machinery that manufactures pro- ganisms. To make sense of the deluge of data from genome- teins. Recently, scientists have discovered whole new classes sequencing projects and the growing catalog of known of RNA that play other roles in the cell, such as regulating the protein functions, scientists are applying a systems approach functioning of protein-coding genes. All these RNAs are spec- at the cellular and molecular levels. Rather than investigating ified by genes, and the process of their transcription is also re- a single gene at a time, these researchers have shifted to ferred to as gene expression. By carrying the instructions for studying whole sets of genes of a species as well as comparing making proteins and RNAs and by replicating with each cell genomes between species—an approach called genomics. division, DNA ensures faithful inheritance of genetic infor- Three important research developments have made the mation from generation to generation. genomic approach possible. One is “high-throughput” tech- nology, tools that can analyze biological materials very rap- Genomics: Large-Scale Analysis of DNA Sequences idly and produce enormous amounts of data. The automatic The entire “library” of genetic instructions that an organism DNA-sequencing machines that made the sequencing of the inherits is called its genome. A typical human cell has two human genome possible are examples of high-throughput similar sets of chromosomes, and each set has DNA totaling devices (see Figure 1.12). The second major development is about 3 billion nucleotide pairs. If the one-letter abbrevia- bioinformatics, the use of computational tools to store, or- tions for the nucleotides of one strand were written in letters ganize, and analyze the huge volume of data that result from the size of those you are now reading, the genetic text would high-throughput methods. The third key development is the fill about 600 books the size of this one. Within this genomic formation of interdisciplinary research teams—melting pots of library of nucleotide sequences are genes for about 75,000 diverse specialists that may include computer scientists, math- kinds of proteins and an as yet unknown number of RNA ematicians, engineers, chemists, physicists, and, of course, bi- molecules that do not code for proteins. ologists from a variety of fields. Since the early 1990s, the pace at which we can sequence genomes has accelerated at an almost unbelievable rate, en- Theme: Feedback Mechanisms Regulate abled by a revolution in technology. The development of new Biological Systems methods and DNA-sequencing machines, such as those shown Just as a coordinated control of traffic flow is necessary for a in Figure 1.12, have led the charge. The entire sequence of nu- city to function smoothly, regulation of biological processes cleotides in the human genome is now known, along with the is crucial to the operation of living systems. Consider your genome sequences of many other organisms, including bacte- muscles, for instance. When your muscle cells require more ria, archaea, fungi, plants, and other animals. energy during exercise, they increase their consumption of The sequencing of the human genome was heralded as a the sugar molecules that serve as fuel. In contrast, when you scientific and technological achievement comparable to rest, a different set of chemical reactions converts surplus landing the Apollo astronauts on the moon in 1969. But it sugar to storage molecules. Like most of the cell’s chemical processes, those that either decompose or store sugar are accelerated, or catalyzed, by proteins called enzymes. Each type of enzyme catalyzes a spe- cific chemical reaction. In many cases, these reactions are linked into chemical pathways, each step with its own en- zyme. How does the cell coordinate its various chemical pathways? In our example of sugar management, how does the cell match fuel supply to demand, regulating its opposing pathways of sugar consumption and storage? The key is the ability of many biological processes to self-regulate by a mechanism called feedback. In feedback regulation, the output, or product, of a process regulates that very process. The most common form of regula- tion in living systems is negative feedback, in which accu- mulation of an end product of a process slows that process.  Figure 1.12 Biology as an information science. Automatic For example, the cell’s breakdown of sugar generates chemical DNA-sequencing machines and abundant computing power make the sequencing of genomes possible. This facility in Walnut Creek, energy in the form of a substance called ATP. When a cell California, is part of the Joint Genome Institute. makes more ATP than it can use, the excess ATP “feeds back” 10 CHAPTER 1 Introduction: Themes in the Study of Life  Such regulation is an example of the integration that makes A Negative living systems much greater than the sum of their parts. feedback – Enzyme 1 Evolution, the Overarching Theme of Biology Having considered all the other themes that run through this B book, let’s now turn to biology’s core theme—evolution. Evo- D Enzyme 2 lution is the one idea that makes sense of everything we know Excess D about living organisms. Life has been evolving on Earth for blocks a step. D billions of years, resulting in a vast diversity of past and pres- D C ent organisms. But along with the diversity we find many shared features. For example, while the sea horse, jackrabbit, Enzyme 3 hummingbird, crocodile, and giraffes in Figure 1.3 look very different, their skeletons are basically similar. The scientific D explanation for this unity and diversity—and for the suitabil- ity of organisms for their environments—is evolution: the (a) Negative feedback. This three-step chemical pathway converts substance A to substance D. A specific enzyme catalyzes each idea that the organisms living on Earth today are the modi- chemical reaction. Accumulation of the final product (D) inhibits fied descendants of common ancestors. In other words, we the first enzyme in the sequence, thus slowing down production can explain traits shared by two organisms with the idea that of more D. they have descended from a common ancestor, and we can account for differences with the idea that heritable changes W have occurred along the way. Many kinds of evidence support Enzyme 4 the occurrence of evolution and the theory that describes how it takes place. In the next section, we’ll consider the fun- damental concept of evolution in greater detail. X Positive feedback + CONCEPT CHECK 1.1 Enzyme 5 1. For each biological level in Figure 1.4, write a sen- Excess Z Z tence that includes the next “lower” level. Example: Y stimulates a Z “A community consists of populations of the various step. species inhabiting a specific area.” Z Enzyme 6 2. What theme or themes are exemplified by (a) the sharp spines of a porcupine, (b) the cloning of a plant Z from a single cell, and (c) a hummingbird using sugar (b) Positive feedback. In a biochemical pathway regulated by positive to power its flight? feedback, a product stimulates an enzyme in the reaction 3. WHAT IF? For each theme discussed in this section, sequence, increasing the rate of production of the product. give an example not mentioned in the book.  Figure 1.13 Regulation by feedback mechanisms. For suggested answers, see Appendix A. What would happen to the feedback system ? if enzyme 2 were missing? and inhibits an enzyme near the beginning of the pathway CONCEPT 1.2 (Figure 1.13a). The Core Theme: Evolution accounts Though less common than processes regulated by negative for the unity and diversity of life feedback, there are also many biological processes regulated by positive feedback, in which an end product speeds up its EVOLUTION The list of biological themes discussed in own production (Figure 1.13b). The clotting of your blood in Concept 1.1 is not absolute; some people might find a response to injury is an example. When a blood vessel is dam- shorter or longer list more useful. There is consensus among aged, structures in the blood called platelets begin to aggregate biologists, however, as to the core theme of biology: It is evo- at the site. Positive feedback occurs as chemicals released by lution. To quote one of the founders of modern evolutionary the platelets attract more platelets. The platelet pileup then ini- theory, Theodosius Dobzhansky, “Nothing in biology makes tiates a complex process that seals the wound with a clot. sense except in the light of evolution.” Feedback is a regulatory motif common to life at all levels, In addition to encompassing a hierarchy of size scales from the molecular level to ecosystems and the biosphere. from molecules to the biosphere, biology extends across the CHAPTER 1 Introduction: Themes in the Study of Life 11 great diversity of species that have ever lived on Earth. To un- gives biology a very broad scope. Biologists face a major chal- derstand Dobzhansky’s statement, we need to discuss how bi- lenge in attempting to make sense of this variety. ologists think about this vast diversity. Grouping Species: The Basic Idea Classifying the Diversity of Life There is a human tendency to group diverse items according Diversity is a hallmark of life. Biologists have so far identified to their similarities and their relationships to each other. For and named about 1.8 million species. To date, this diversity instance, we may speak of “squirrels” and “butterflies,” though of life is known to include at least 100,000 species of fungi, we recognize that many different species belong to each 290,000 plant species, 52,000 vertebrate species (animals group. We may even sort groups into broader categories, such with backbones), and 1 million insect species (more than half as rodents (which include squirrels) and insects (which include of all known forms of life)—not to mention the myriad types butterflies). Taxonomy, the branch of biology that names and of single-celled organisms. Researchers identify thousands of classifies species, formalizes this ordering of species into additional species each year. Estimates of the total number of groups of increasing breadth, based on the degree to which species range from about 10 million to over 100 million. they share characteristics (Figure 1.14). You will learn more Whatever the actual number, the enormous variety of life about the details of this taxonomic scheme in Chapter 26. For Species Genus Family Order Class Phylum Kingdom Domain Ursus americanus (American black bear) Ursus Ursidae Carnivora Mammalia Chordata Animalia  Figure 1.14 Classifying life. To help make sense of the diversity of life, biologists classify species into groups that are then combined into even broader groups. In the traditional “Linnaean” system, species that are very closely related, such as polar bears and brown bears, are placed in the same genus; genera (plural of genus) are grouped into families; and so on. This example classifies Eukarya the species Ursus americanus, the American black bear. (Alternative classification schemes will be discussed in detail in Chapter 26.) 12 CHAPTER 1 Introduction: Themes in the Study of Life now, we will focus on the big picture by considering the levels of classification called domains. The three domains are broadest units of classification, kingdoms and domains. named Bacteria, Archaea, and Eukarya (Figure 1.15). The organisms making up two of the three domains— domain Bacteria and domain Archaea—are all prokaryotic. The Three Domains of Life Most prokaryotes are single-celled and microscopic. Previ- Historically, scientists have classified the diversity of life- ously, bacteria and archaea were combined in a single king- forms into kingdoms and finer groupings by careful compar- dom because they shared the prokaryotic form of cell isons of structure, function, and other obvious features. In structure. But much evidence now supports the view that bac- the last few decades, new methods of assessing species rela- teria and archaea represent two very distinct branches of tionships, such as comparisons of DNA sequences, have led prokaryotic life, different in key ways that you’ll learn about in to an ongoing reevaluation of the number and boundaries of Chapter 27. There is also evidence that archaea are at least as kingdoms. Researchers have proposed anywhere from six closely related to eukaryotic organisms as they are to bacteria. kingdoms to dozens of kingdoms. While debate continues at All the eukaryotes (organisms with eukaryotic cells) are now the kingdom level, there is consensus among biologists that grouped in domain Eukarya. This domain includes three the kingdoms of life can be grouped into three even higher kingdoms of multicellular eukaryotes: kingdoms Plantae,  Figure 1.15 The three domains of life. (a) Domain Bacteria (b) Domain Archaea 2 μm 2 μm Bacteria are the most diverse and widespread prokaryotes and are Many of the prokaryotes known as archaea live in Earth’s extreme now classified into multiple kingdoms. Each rod-shaped structure environments, such as salty lakes and boiling hot springs. Domain in this photo is a bacterial cell. Archaea includes multiple kingdoms. Each round structure in this photo is an archaeal cell. (c) Domain Eukarya  Kingdom Animalia consists of multicellular eukaryotes that ingest other organisms. 100 μm  Kingdom Plantae consists of terrestrial multicellular eukaryotes (land plants) that carry out photosynthesis, the  Protists are mostly conversion of light energy to unicellular eukaryotes the chemical energy in food. and some relatively simple multicellular  Kingdom Fungi relatives. Pictured is defined in part here is an assortment by the nutritional of protists inhabiting mode of its members (such as this mushroom), which pond water. Scientists are currently debating how to classify protists absorb nutrients from outside their bodies. in a way that accurately reflects their evolutionary relationships. CHAPTER 1 Introduction: Themes in the Study of Life 13 Fungi, and Animalia. These three kingdoms are distinguished How can we account for life’s dual nature of unity and di- partly by their modes of nutrition. Plants produce their own versity? The process of evolution, explained next, illuminates sugars and other food molecules by photosynthesis. Fungi ab- both the similarities and differences in the world of life and sorb dissolved nutrients from their surroundings; many de- introduces another dimension of biology: historical time. compose dead organisms and organic wastes (such as leaf litter and animal feces) and absorb nutrients from these sources. An- Charles Darwin and the Theory imals obtain food by ingestion, which is the eating and digest- of Natural Selection ing of other organisms. Animalia is, of course, the kingdom to The history of life, as documented by fossils and other evi- which we belong. But neither animals, plants, nor fungi are as dence, is the saga of a changing Earth billions of years old, in- numerous or diverse as the single-celled eukaryotes we call habited by an evolving cast of living forms (Figure 1.17). protists. Although protists were once placed in a single king- This evolutionary view of life came into sharp focus in No- dom, biologists now realize that they do not form a single nat- vember 1859, when Charles Robert Darwin published one of ural group of species. And recent evidence shows that some the most important and influential books ever written. Enti- protist groups are more closely related to multicellular eukary- tled On the Origin of Species by Means of Natural Selection, Dar- otes such as animals and fungi than they are to each other. win’s book was an immediate bestseller and soon made Thus, the recent taxonomic trend has been to split the protists “Darwinism,” as it was dubbed at the time, almost synony- into several groups. mous with the concept of evolution (Figure 1.18). The Origin of Species articulated two main points. The first Unity in the Diversity of Life point was that contemporary species arose from a succession As diverse as life is, it also displays remarkable unity. Earlier we of ancestors, an idea that Darwin supported with a large mentioned both the similar skeletons of different vertebrate amount of evidence. (We will discuss the evidence for evolu- animals and the universal genetic language of DNA (the ge- tion in detail in Chapter 22.) Darwin called this evolutionary netic code). In fact, similarities between organisms are evident history of species “descent with modification.” It was an in- at all levels of the biological hierarchy. For example, unity is sightful phrase, as it captured the duality of life’s unity and obvious in many features of cell structure (Figure 1.16). diversity—unity in the kinship among species that descended 15 μm 5 μm Cilia of Paramecium. The cilia of the single-celled Cilia of windpipe cells. Paramecium propel the The cells that line the organism through pond human windpipe are water. equipped with cilia that help keep the lungs clean by sweeping a film of debris-trapping 0.1 μm mucus upward. Cross section of a cilium, as viewed with an electron microscope  Figure 1.16 An example of unity underlying the diversity of life: the architecture of cilia in eukaryotes. Cilia (singular, cilium) are extensions of cells that function in locomotion. They occur in eukaryotes as diverse as Paramecium and humans. Even organisms so different share a common architecture for their cilia, which have an elaborate system of tubules that is striking in cross-sectional views. 14 CHAPTER 1 Introduction: Themes in the Study of Life  profound. Others had the pieces of the puzzle, but Darwin saw how they fit to- gether. He started with the following three observations from nature: First, individu- als in a population vary in their traits, many of which seem to be heritable (passed on from parents to off- spring). Second, a popula- tion can produce far more offspring than can survive to produce offspring of their own. With more individuals than the environment is able to support, competition is inevitable. Third, species  Figure 1.18 Charles generally suit their environ- Darwin as a young man. ments—in other words, they are adapted to their environments. For instance, a common adaptation among birds with tough seeds as their major food source is that they have especially strong beaks. Darwin made inferences from these observations to arrive at his theory of evolution. He reasoned that individuals with inherited traits that are best suited to the local environment  Figure 1.17 Digging into the past. Paleontologists carefully are more likely to survive and reproduce than less suited indi- excavate the hind leg of a long-necked dinosaur (Rapetosaurus krausei) from rocks in Madagascar. viduals. Over many generations, a higher and higher propor- tion of individuals in a population will have the advantageous from common ancestors, diversity in the modifications that traits. Evolution occurs as the unequal reproductive success of evolved as species branched from their common ancestors individuals ultimately leads to adaptation to their environ- (Figure 1.19). Darwin’s second main point was a proposed ment, as long as the environment remains the same. mechanism for descent with modification. He called this evo- Darwin called this mechanism of evolutionary adapta- lutionary mechanism “natural selection.” tion natural selection because the natural environment Darwin synthesized his theory of natural selection from “selects” for the propagation of certain traits among natu- observations that by themselves were neither new nor rally occurring variant traits in the population. The example  Figure 1.19 Unity and diversity in the orchid family. These three orchids are variations on a common floral theme. For example, each of these flowers has a liplike petal that helps attract pollinating insects and provides a landing platform for the pollinators. CHAPTER 1 Introduction: Themes in the Study of Life 15 1 Population with varied 2 Elimination of 3 Reproduction of 4 Increasing frequency inherited traits individuals with certain survivors of traits that enhance traits survival and repro- ductive success  Figure 1.20 Natural selection. This imaginary beetle population has colonized a locale where the soil has been blackened by a recent brush fire. Initially, the population varies extensively in the inherited coloration of the individuals, from very light gray to charcoal. For hungry birds that prey on the beetles, it is easiest to spot the beetles that are lightest in color. in Figure 1.20 illustrates the ability of natural selection to concept of descent with modification. In this view, the unity “edit” a population’s heritable variations in color. We see the of mammalian limb anatomy reflects inheritance of that products of natural selection in the exquisite adaptations of structure from a common ancestor—the “prototype” mam- various organisms to the special circumstances of their way mal from which all other mammals descended. The diversity of life and their environment. The wings of the bat shown in of mammalian forelimbs results from modification by natu- Figure 1.21 are an excellent example of adaptation. ral selection operating over millions of generations in differ- ent environmental contexts. Fossils and other evidence The Tree of Life corroborate anatomical unity in supporting this view of mammalian descent from a common ancestor. Take another look at the skeletal architecture of the bat’s Darwin proposed that natural selection, by its cumulative wings in Figure 1.21. These forelimbs, though adapted for effects over long periods of time, could cause an ancestral flight, actually have all the same bones, joints, nerves, and species to give rise to two or more descendant species. This blood vessels found in other limbs as diverse as the human could occur, for example, if one population fragmented into arm, the horse’s foreleg, and the whale’s flipper. Indeed, all several subpopulations isolated in different environments. In mammalian forelimbs are anatomical variations of a com- these separate arenas of natural selection, one species could mon architecture, much as the flowers in Figure 1.19 are vari- gradually radiate into multiple species as the geographically ations on an underlying “orchid” theme. Such examples of isolated populations adapted over many generations to dif- kinship connect life’s unity in diversity to the Darwinian ferent sets of environmental factors. The “family tree” of 14 finches in Figure 1.22 illustrates a fa- mous example of adaptive radiation of new species from a com- mon ancestor. Darwin collected specimens of these birds during his 1835 visit to the remote Galápagos Islands, 900 kilometers (km) off the Pacific coast of South America. These relatively young, volcanic islands are home to many species of plants and animals found nowhere else in the world, though most Galápagos organisms are clearly related to species on the South American mainland. After volcanism built the Galápagos several million years ago, finches probably diversified on the various islands from an ancestral finch species that by chance reached the archipelago from elsewhere. (Once thought to have originated on the mainland of South America like many  Figure 1.21 Evolutionary adaptation. Bats, the only mammals Galápagos organisms, the ancestral finches are now thought to capable of active flight, have wings with webbing between extended “fingers.” In the Darwinian view of life, such adaptations are refined over have come from the West Indies—islands of the Caribbean that time by natural selection. were once much closer to the Galápagos than they are now.) 16 CHAPTER 1 Introduction: Themes in the Study of Life  Warbler finches Insect-eaters Green warbler finch Certhidea olivacea COMMON Gray warbler finch ANCESTOR Certhidea fusca Seed-eater Sharp-beaked ground finch Geospiza difficilis Bud-eater Vegetarian finch Platyspiza crassirostris Mangrove finch Cactospiza heliobates Insect-eaters Tree finches Woodpecker finch Cactospiza pallida Medium tree finch Camarhynchus pauper Each branch point represents Large tree finch the common ancestor of the Camarhynchus psittacula evolutionary lineages originating there and their descendants (to the right in Small tree finch this diagram). Camarhynchus parvulus Cactus-flower- Large cactus ground finch eaters Geospiza conirostris Cactus ground finch Ground finches Geospiza scandens Seed-eaters Small ground finch Geospiza fuliginosa Medium ground finch Geospiza fortis  Figure 1.22 Descent with modification: adaptive radiation of finches on the Galápagos Islands. This “tree” Large ground finch illustrate