1 The Science of Biology

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1The Science of Biology

Concept Outline

1.1 Biology is the science of life.

Properties of Life. Biology is the science that studiesliving organisms and how they interact with one another andtheir environment.

1.2 Scientists form generalizations from observations.

The Nature of Science. Science employs both deductivereasoning and inductive reasoning.How Science Is Done. Scientists construct hypothesesfrom systematically collected objective data. They thenperform experiments designed to disprove the hypotheses.

1.3 Darwins theory of evolution illustrates how scienceworks.

Darwins Theory of Evolution. On a round-the-worldvoyage Darwin made observations that eventually led him toformulate the hypothesis of evolution by natural selection.Darwins Evidence. The fossil and geographic patterns oflife he observed convinced Darwin that a process of evolutionhad occurred.Inventing the Theory of Natural Selection. TheMalthus idea that populations cannot grow unchecked ledDarwin, and another naturalist named Wallace, to proposethe hypothesis of natural selection.Evolution After Darwin: More Evidence. In the centurysince Darwin, a mass of experimental evidence has supportedhis theory of evolution, now accepted by practically all prac-ticing biologists.

1.4 This book is organized to help you learn biology.

Core Principles of Biology. The first half of this text isdevoted to general principles that apply to all organisms, thesecond half to an examination of particular organisms.

You are about to embark on a journeya journey ofdiscovery about the nature of life. Nearly 180 yearsago, a young English naturalist named Charles Darwin setsail on a similar journey on board H.M.S. Beagle (figure1.1 shows a replica of the Beagle). What Darwin learned onhis five-year voyage led directly to his development of thetheory of evolution by natural selection, a theory that hasbecome the core of the science of biology. Darwins voyageseems a fitting place to begin our exploration of biology,the scientific study of living organisms and how they haveevolved. Before we begin, however, lets take a moment tothink about what biology is and why its important.

FIGURE 1.1A replica of the Beagle, off the southern coast of SouthAmerica. The famous English naturalist, Charles Darwin,set forth on H.M.S. Beagle in 1831, at the age of 22.

4 Part I The Origin of Living Things

Properties of LifeIn its broadest sense, biology is the study of living thingsthescience of life. Living things come in an astounding variety ofshapes and forms, and biologists study life in many differ-ent ways. They live with gorillas, collect fossils, and listento whales. They isolate viruses, grow mushrooms, and ex-amine the structure of fruit flies. They read the messagesencoded in the long molecules of heredity and count howmany times a hummingbirds wings beat each second.

What makes something alive? Anyone could deducethat a galloping horse is alive and a car is not, but why? Wecannot say, If it moves, its alive, because a car can move,and gelatin can wiggle in a bowl. They certainly are notalive. What characteristics do define life? All living organ-isms share five basic characteristics:

1. Order. All organisms consist of one or more cellswith highly ordered structures: atoms make up mole-cules, which construct cellular organelles, which arecontained within cells. This hierarchical organizationcontinues at higher levels in multicellular organismsand among organisms (figure 1.2).

2. Sensitivity. All organisms respond to stimuli. Plantsgrow toward a source of light, and your pupils dilatewhen you walk into a dark room.

3. Growth, development, and reproduction. All or-ganisms are capable of growing and reproducing, andthey all possess hereditary molecules that are passed totheir offspring, ensuring that the offspring are of thesame species. Although crystals also grow, theirgrowth does not involve hereditary molecules.

4. Regulation. All organisms have regulatory mecha-nisms that coordinate the organisms internal func-tions. These functions include supplying cells with nu-trients, transporting substances through the organism,and many others.

5. Homeostasis. All organisms maintain relativelyconstant internal conditions, different from their envi-ronment, a process called homeostasis.

All living things share certain key characteristics: order,sensitivity, growth, development and reproduction,regulation, and homeostasis.


FIGURE 1.2Hierarchical organization of living things. Life is highly orga-nizedfrom small and simple to large and complex, within cells,within multicellular organisms, and among organisms.

Organelle

Macromolecule

Molecule

Cell

WITHIN CELLS

Chapter 1 The Science of Biology 5

AMONG ORGANISMS

Ecosystem

Community

Species

Population

WITHIN MULTICELLULAR ORGANISMS

Tissue

Organ

Organ system

Organism


The Nature of ScienceBiology is a fascinating and important subject, because itdramatically affects our daily lives and our futures. Manybiologists are working on problems that critically affect ourlives, such as the worlds rapidly expanding population anddiseases like cancer and AIDS. The knowledge these biolo-gists gain will be fundamental to our ability to manage theworlds resources in a suitable manner, to prevent or curediseases, and to improve the quality of our lives and thoseof our children and grandchildren.

Biology is one of the most successful of the natural sci-ences, explaining what our world is like. To understandbiology, you must first understand the nature of science.The basic tool a scientist uses is thought. To understandthe nature of science, it is useful to focus for a moment onhow scientists think. They reason in two ways: deductivelyand inductively.

Deductive Reasoning

Deductive reasoning applies general principles to predictspecific results. Over 2200 years ago, the Greek Era-tosthenes used deductive reasoning to accurately estimatethe circumference of the earth. At high noon on the longestday of the year, when the suns rays hit the bottom of adeep well in the city of Syene, Egypt, Eratosthenes mea-sured the length of the shadow cast by a tall obelisk in Al-exandria, about 800 kilometers to the north. Because heknew the distance between the two cities and the height ofthe obelisk, he was able to employ the principles of Euclid-ean geometry to correctly deduce the circumference of theearth (figure 1.3). This sort of analysis of specific cases us-ing general principles is an example of deductive reasoning.It is the reasoning of mathematics and philosophy and isused to test the validity of general ideas in all branches ofknowledge. General principles are constructed and thenused as the basis for examining specific cases.

Inductive Reasoning

Inductive reasoning uses specific observations to constructgeneral scientific principles. Websters Dictionary defines sci-ence as systematized knowledge derived from observationand experiment carried on to determine the principles un-derlying what is being studied. In other words, a scientistdetermines principles from observations, discovering gen-eral principles by careful examination of specific cases. In-ductive reasoning first became important to science in the1600s in Europe, when Francis Bacon, Isaac Newton, andothers began to use the results of particular experiments toinfer general principles about how the world operates. If

you release an apple from your hand, what happens? Theapple falls to the ground. From a host of simple, specificobservations like this, Newton inferred a general principle:all objects fall toward the center of the earth. What New-ton did was construct a mental model of how the worldworks, a family of general principles consistent with whathe could see and learn. Scientists do the same today. Theyuse specific observations to build general models, and thentest the models to see how well they work.

Science is a way of viewing the world that focuses onobjective information, putting that information to workto build understanding.


FIGURE 1.3Deductive reasoning: How Eratosthenes estimated the cir-cumference of the earth using deductive reasoning. 1. On aday when sunlight shone straight down a deep well at Syene inEgypt, Eratosthenes measured the length of the shadow cast by atall obelisk in the city of Alexandria, about 800 kilometers away.2. The shadows length and the obelisks height formed two sidesof a triangle. Using the recently developed principles of Euclideangeometry, he calculated the angle, a, to be 7 and 12, exactly 150 ofa circle (360). 3. If angle a = 150 of a circle, then the distancebetween the obelisk (in Alexandria) and the well (in Syene) mustequal 150 of the circumference of the earth. 4. Eratosthenes hadheard that it was a 50-day camel trip from Alexandria to Syene.Assuming that a camel travels about 18.5 kilometers per day, heestimated the distance between obelisk and well as 925 kilometers(using different units ofmeasure, of course). 5. Eratosthenes thus de-duced the circumferenceof the earth to be 50 925 46,250kilometers. Modernmeasurements put thedistance from the well tothe obelisk at just over800 kilometers. Employ-ing a distance of 800kilometers, Era-tostheness value wouldhave been 50 800 40,000 kilometers. Theactual circumference is40,075 kilometers.

Sunlightat midday

Distance betweencities = 800 kmWell

Light raysparallel

Height ofobelisk

Length ofshadow

a

a

How Science Is DoneHow do scientists establish which general principles aretrue from among the many that might be true? They dothis by systematically testing alternative proposals. If theseproposals prove inconsistent with experimental observa-tions, they are rejected as untrue. After making careful ob-servations concerning a particular area of science, scien-tists construct a hypothesis, which is a suggestedexplanation that accounts for those observations. A hy-pothesis is a proposition that might be true. Those hy-potheses that have not yet been disproved are retained.They are useful because they fit the known facts, but theyare always subject to future rejection if, in the light of newinformation, they are found to be incorrect.

Testing Hypotheses

We call the test of a hypothesis an experiment (figure1.4). Suppose that a room appears dark to you. To under-stand why it appears dark, you propose several hypotheses.The first might be, There is no light in the room because

the light switch is turned off. An alternative hypothesismight be, There is no light in the room because the light-bulb is burned out. And yet another alternative hypothe-sis might be, I am going blind. To evaluate these hy-potheses, you would conduct an experiment designed toeliminate one or more of the hypotheses. For example, youmight test your hypotheses by reversing the position of thelight switch. If you do so and the light does not come on,you have disproved the first hypothesis. Something otherthan the setting of the light switch must be the reason forthe darkness. Note that a test such as this does not provethat any of the other hypotheses are true; it merely dem-onstrates that one of them is not. A successful experimentis one in which one or more of the alternative hypothesesis demonstrated to be inconsistent with the results and isthus rejected.

As you proceed through this text, you will encountermany hypotheses that have withstood the test of experiment.Many will continue to do so; others will be revised as newobservations are made by biologists. Biology, like all science,is in a constant state of change, with new ideas appearingand replacing old ones.


FIGURE 1.4How science is done. This diagram il-lustrates the way in which scientific in-vestigations proceed. First, scientistsmake observations that raise aparticular question. They develop anumber of potential explanations(hypotheses) to answer the question.Next, they carry out experiments in anattempt to eliminate one or more ofthese hypotheses. Then, predictions aremade based on the remaininghypotheses, and further experimentsare carried out to test these predictions.As a result of this process, the leastunlikely hypothesis is selected.

Observation

Question

Experiment

Hypothesis 1Hypothesis 2Hypothesis 3Hypothesis 4Hypothesis 5

Potentialhypotheses

Remainingpossiblehypotheses

Last remainingpossible hypothesis

Rejecthypotheses1 and 4

Rejecthypotheses2 and 3

Experiment

Experiment 1

Hypothesis 2Hypothesis 3Hypothesis 5

Hypothesis 5

Predictions

Predictionsconfirmed

Experiment 1 Experiment 2 Experiment 3 Experiment 4

Establishing Controls

Often we are interested in learning about processes that areinfluenced by many factors, or variables. To evaluate alter-native hypotheses about one variable, all other variablesmust be kept constant. This is done by carrying out two ex-periments in parallel: in the first experiment, one variable isaltered in a specific way to test a particular hypothesis; in thesecond experiment, called the control experiment, thatvariable is left unaltered. In all other respects the two exper-iments are identical, so any difference in the outcomes ofthe two experiments must result from the influence of thevariable that was changed. Much of the challenge of experi-mental science lies in designing control experiments thatisolate a particular variable from other factors that might in-fluence a process.

Using Predictions

A successful scientific hypothesis needs to be not only validbut usefulit needs to tell you something you want toknow. A hypothesis is most useful when it makes predic-tions, because those predictions provide a way to test the va-lidity of the hypothesis. If an experiment produces resultsinconsistent with the predictions, the hypothesis must be re-jected. On the other hand, if the predictions are supportedby experimental testing, the hypothesis is supported. Themore experimentally supported predictions a hypothesismakes, the more valid the hypothesis is. For example, Ein-steins hypothesis of relativity was at first provisionally ac-cepted because no one could devise an experiment that in-validated it. The hypothesis made a clear prediction: thatthe sun would bend the path of light passing by it. Whenthis prediction was tested in a total eclipse, the light frombackground stars was indeed bent. Because this result wasunknown when the hypothesis was being formulated, it pro-vided strong support for the hypothesis, which was then ac-cepted with more confidence.

Developing Theories

Scientists use the word theory in two main ways. A theo-ry is a proposed explanation for some natural phenome-non, often based on some general principle. Thus onespeaks of the principle first proposed by Newton as thetheory of gravity. Such theories often bring togetherconcepts that were previously thought to be unrelated,and offer unified explanations of different phenomena.Newtons theory of gravity provided a single explanationfor objects falling to the ground and the orbits of planetsaround the sun. Theory is also used to mean the bodyof interconnected concepts, supported by scientific rea-soning and experimental evidence, that explains the factsin some area of study. Such a theory provides an indis-pensable framework for organizing a body of knowledge.For example, quantum theory in physics brings together a

set of ideas about the nature of the universe, explains ex-perimental facts, and serves as a guide to further questionsand experiments.

To a scientist, such theories are the solid ground of sci-ence, that of which we are most certain. In contrast, to thegeneral public, theory implies just the oppositea lack ofknowledge, or a guess. Not surprisingly, this differenceoften results in confusion. In this text, theory will always beused in its scientific sense, in reference to an accepted gen-eral principle or body of knowledge.

To suggest, as many critics outside of science do, thatevolution is just a theory is misleading. The hypothesisthat evolution has occurred is an accepted scientific fact; it issupported by overwhelming evidence. Modern evolutionarytheory is a complex body of ideas whose importance spreadsfar beyond explaining evolution; its ramifications permeateall areas of biology, and it provides the conceptual frame-work that unifies biology as a science.

Research and the Scientific Method

It used to be fashionable to speak of the scientific meth-od as consisting of an orderly sequence of logical ei-ther/or steps. Each step would reject one of two mutuallyincompatible alternatives, as if trial-and-error testingwould inevitably lead one through the maze of uncertain-ty that always impedes scientific progress. If this were in-deed so, a computer would make a good scientist. But sci-ence is not done this way. As British philosopher KarlPopper has pointed out, successful scientists without ex-ception design their experiments with a pretty fair idea ofhow the results are going to come out. They have whatPopper calls an imaginative preconception of what thetruth might be. A hypothesis that a successful scientisttests is not just any hypothesis; rather, it is an educatedguess or a hunch, in which the scientist integrates all thathe or she knows and allows his or her imagination fullplay, in an attempt to get a sense of what might be true(see Box: How Biologists Do Their Work). It is becauseinsight and imagination play such a large role in scientificprogress that some scientists are so much better at sciencethan others, just as Beethoven and Mozart stand outamong most other composers.

Some scientists perform what is called basic research,which is intended to extend the boundaries of what weknow. These individuals typically work at universities, andtheir research is usually financially supported by their in-stitutions and by external sources, such as the government,industry, and private foundations. Basic research is as di-verse as its name implies. Some basic scientists attempt tofind out how certain cells take up specific chemicals, whileothers count the number of dents in tiger teeth. The infor-mation generated by basic research contributes to thegrowing body of scientific knowledge, and it provides thescientific foundation utilized by applied research. Scien-tists who conduct applied research are often employed in


some kind of industry. Their work may involve the manu-facturing of food additives, creating of new drugs, or test-ing the quality of the environment.

After developing a hypothesis and performing a series ofexperiments, a scientist writes a paper carefully describingthe experiment and its results. He or she then submits thepaper for publication in a scientific journal, but before it ispublished, it must be reviewed and accepted by other scien-tists who are familiar with that particular field of research.This process of careful evaluation, called peer review, lies atthe heart of modern science, fostering careful work, precisedescription, and thoughtful analysis. When an importantdiscovery is announced in a paper, other scientists attemptto reproduce the result, providing a check on accuracy andhonesty. Nonreproducible results are not taken seriouslyfor long.

The explosive growth in scientific research during thesecond half of the twentieth century is reflected in theenormous number of scientific journals now in existence.Although some, such as Science and Nature, are devoted toa wide range of scientific disciplines, most are extremelyspecialized: Cell Motility and the Cytoskeleton, Glycoconju-gate Journal, Mutation Research, and Synapse are just a fewexamples.

The scientific process involves the rejection of hypotheses that are inconsistent with experimental results or observations. Hypotheses that are consistentwith available data are conditionally accepted. The formulation of the hypothesis often involves creativeinsight.


How Biologists DoTheir Work

learn why the ginkgo trees drop all theirleaves simultaneously, a scientist wouldfirst formulate several possible answers,called hypotheses:

Hypothesis 1: Ginkgo trees possess an inter-nal clock that times the release of leaves tomatch the season. On the day Nemerov de-scribes, this clock sends a drop signal(perhaps a chemical) to all the leaves at thesame time.

Hypothesis 2: The individual leaves of ginkgotrees are each able to sense day length, and

when the days get short enough in the fall,each leaf responds independently by falling.

Hypothesis 3: A strong wind arose the nightbefore Nemerov made his observation,blowing all the leaves off the ginkgo trees.

Next, the scientist attempts to eliminateone or more of the hypotheses by conduct-ing an experiment. In this case, one mightcover some of the leaves so that they can-not use light to sense day length. If hypoth-esis 2 is true, then the covered leavesshould not fall when the others do, becausethey are not receiving the same informa-tion. Suppose, however, that despite thecovering of some of the leaves, all theleaves still fall together. This result wouldeliminate hypothesis 2 as a possibility. Ei-ther of the other hypotheses, and manyothers, remain possibilities.

This simple experiment with ginkgoespoints out the essence of scientificprogress: science does not prove that cer-tain explanations are true; rather, it provesthat others are not. Hypotheses that areinconsistent with experimental results arerejected, while hypotheses that are notproven false by an experiment are provi-sionally accepted. However, hypothesesmay be rejected in the future when moreinformation becomes available, if they areinconsistent with the new information. Justas finding the correct path through a mazeby trying and eliminating false paths, sci-entists work to find the correct explana-tions of natural phenomena by eliminatingfalse possibilities.

The Consent

Late in November, on a single nightNot even near to freezing, the ginkgo treesThat stand along the walk drop all their leavesIn one consent, and neither to rain nor to windBut as though to time alone: the golden andgreenLeaves litter the lawn today, that yesterdayHad spread aloft their fluttering fans of light.What signal from the stars? What senses took itin?What in those wooden motives so decidedTo strike their leaves, to down their leaves,Rebellion or surrender? And if thisCan happen thus, what race shall be exempt?What use to learn the lessons taught by time,If a star at any time may tell us: Now.

Howard Nemerov

What is bothering the poet Howard Nem-erov is that life is influenced by forces hecannot control or even identify. It is the jobof biologists to solve puzzles such as the onehe poses, to identify and try to understandthose things that influence life.

Nemerov asks why ginkgo trees (figure1.A) drop all their leaves at once. To findan answer to questions such as this, biolo-gists and other scientists pose possible an-swers and then try to determine which an-swers are false. Tests of alternativepossibilities are called experiments. To

FIGURE 1.AA ginkgo tree.


Darwins Theory of EvolutionDarwins theory of evolution explainsand describes how organisms on earthhave changed over time and acquired adiversity of new forms. This famoustheory provides a good example of howa scientist develops a hypothesis andhow a scientific theory grows and winsacceptance.

Charles Robert Darwin (18091882;figure 1.5) was an English naturalistwho, after 30 years of study and obser-vation, wrote one of the most famousand influential books of all time. Thisbook, On the Origin of Species by Meansof Natural Selection, or The Preservationof Favoured Races in the Struggle for Life,created a sensation when it was pub-lished, and the ideas Darwin expressedin it have played a central role in thedevelopment of human thought eversince.

In Darwins time, most people be-lieved that the various kinds of organ-isms and their individual structures re-sulted from direct actions of the Creator(and to this day many people still believethis to be true). Species were thought tobe specially created and unchangeable,or immutable, over the course of time.In contrast to these views, a number ofearlier philosophers had presented theview that living things must havechanged during the history of life onearth. Darwin proposed a concept hecalled natural selection as a coherent,logical explanation for this process, andhe brought his ideas to wide public at-tention. His book, as its title indicates,presented a conclusion that differedsharply from conventional wisdom. Al-though his theory did not challenge theexistence of a Divine Creator, Darwinargued that this Creator did not simplycreate things and then leave them forev-er unchanged. Instead, Darwins Godexpressed Himself through the operation of natural lawsthat produced change over time, or evolution. Theseviews put Darwin at odds with most people of his time,who believed in a literal interpretation of the Bible and ac-cepted the idea of a fixed and constant world. His revolu-

tionary theory deeply troubled not only many of his con-temporaries but Darwin himself.

The story of Darwin and his theory begins in 1831, whenhe was 22 years old. On the recommendation of one of hisprofessors at Cambridge University, he was selected to serve

1.3 Darwins theory of evolution illustrates how science works.

FIGURE 1.5Charles Darwin. This newly rediscovered photograph taken in 1881, the year beforeDarwin died, appears to be the last ever taken of the great biologist.

as naturalist on a five-year navigational mapping expeditionaround the coasts of South America (figure 1.6), aboardH.M.S. Beagle (figure 1.7). During this long voyage, Darwinhad the chance to study a wide variety of plants and animalson continents and islands and in distant seas. He was able toexplore the biological richness of the tropical forests, exam-ine the extraordinary fossils of huge extinct mammals inPatagonia at the southern tip of South America, and observethe remarkable series of related but distinct forms of life onthe Galpagos Islands, off the west coast of South America.Such an opportunity clearly played an important role in thedevelopment of his thoughts about the nature of life onearth.

When Darwin returned from the voyage at the age of 27,he began a long period of study and contemplation. Duringthe next 10 years, he published important books on several

different subjects, including the formation of oceanic islandsfrom coral reefs and the geology of South America. He alsodevoted eight years of study to barnacles, a group of smallmarine animals with shells that inhabit rocks and pilings,eventually writing a four-volume work on their classificationand natural history. In 1842, Darwin and his family movedout of London to a country home at Down, in the county ofKent. In these pleasant surroundings, Darwin lived, studied,and wrote for the next 40 years.

Darwin was the first to propose natural selection as anexplanation for the mechanism of evolution that produced the diversity of life on earth. His hypothesisgrew from his observations on a five-year voyage aroundthe world.


British Isles

WesternIsles

Europe

Africa

IndianOcean

Madagascar

MauritiusBourbon Island

Cape ofGood Hope

King GeorgesSound

Hobart

Sydney

Australia

NewZealand

FriendlyIslands

PhillippineIslands

Equator

North PacificOcean

Asia

North AtlanticOcean

Cape Verde

Marquesas

GalpagosIslands

ValparaisoSocietyIslands

Straits of Magellan

Tierra del FuegoCape Horn

FalklandIslands

Port DesireSouth AtlanticOcean

Montevideo

Buenos Aires

Rio de JaneiroSt. Helena

Ascension

North America

CanaryIslands

KeelingIslands

SouthAmerica

Bahia

FIGURE 1.6The five-year voyage of H.M.S. Beagle. Most of the time was spent exploring the coasts and coastal islands of South America,such as the Galpagos Islands. Darwins studies of the animals of the Galpagos Islands played a key role in his eventualdevelopment of the theory of evolution by means of natural selection.

FIGURE 1.7Cross section of theBeagle. A 10-gun brig of242 tons, only 90 feet inlength, the Beagle had acrew of 74 people! After hefirst saw the ship, Darwinwrote to his collegeprofessor Henslow: Theabsolute want of room is anevil that nothing cansurmount.


Darwins EvidenceOne of the obstacles that had blocked the acceptance ofany theory of evolution in Darwins day was the incorrectnotion, widely believed at that time, that the earth wasonly a few thousand years old. Evidence discovered duringDarwins time made this assertion seem less and less likely.The great geologist Charles Lyell (17971875), whosePrinciples of Geology (1830) Darwin read eagerly as hesailed on the Beagle, outlined for the first time the story ofan ancient world of plants and animals in flux. In thisworld, species were constantly becoming extinct while oth-ers were emerging. It was this world that Darwin sought toexplain.

What Darwin Saw

When the Beagle set sail, Darwin was fully convinced thatspecies were immutable. Indeed, it was not until two orthree years after his return that he began to consider seri-ously the possibility that they could change. Nevertheless,during his five years on the ship, Darwin observed a numberof phenomena that were of central importance to him inreaching his ultimate conclusion (table 1.1). For example, inthe rich fossil beds of southern South America, he observedfossils of extinct armadillos similar to the armadillos thatstill lived in the same area (figure 1.8). Why would similarliving and fossil organisms be in the same area unless theearlier form had given rise to the other?

Repeatedly, Darwin saw that the characteristics of simi-lar species varied somewhat from place to place. Thesegeographical patterns suggested to him that organismal lin-eages change gradually as species migrate from one area toanother. On the Galpagos Islands, off the coast of Ecua-dor, Darwin encountered giant land tortoises. Surprisingly,these tortoises were not all identical. In fact, local residentsand the sailors who captured the tortoises for food couldtell which island a particular tortoise had come from just bylooking at its shell. This distribution of physical variationsuggested that all of the tortoises were related, but thatthey had changed slightly in appearance after becomingisolated on different islands.

In a more general sense, Darwin was struck by the factthat the plants and animals on these relatively young vol-canic islands resembled those on the nearby coast ofSouth America. If each one of these plants and animalshad been created independently and simply placed on theGalpagos Islands, why didnt they resemble the plantsand animals of islands with similar climates, such as thoseoff the coast of Africa, for example? Why did they resem-ble those of the adjacent South American coast instead?

The fossils and patterns of life that Darwin observed onthe voyage of the Beagle eventually convinced him thatevolution had taken place.

Table 1.1 Darwins Evidence that Evolution Occurs

FOSSILS1. Extinct species, such as the fossil armadillo in figure 1.8,

most closely resemble living ones in the same area,suggesting that one had given rise to the other.

2. In rock strata (layers), progressive changes in characteristicscan be seen in fossils from earlier and earlier layers.

GEOGRAPHICAL DISTRIBUTION3. Lands with similar climates, such as Australia, South Africa,

California, and Chile, have unrelated plants and animals,indicating that diversity is not entirely influenced by climateand environment.

4. The plants and animals of each continent are distinctive; all South American rodents belong to a single group,structurally similar to the guinea pigs, for example, whilemost of the rodents found elsewhere belong to other groups.

OCEANIC ISLANDS5. Although oceanic islands have few species, those they do

have are often unique (endemic) and show relatedness toone another, such as the Galpagos tortoises. This suggeststhat the tortoises and other groups of endemic speciesdeveloped after their mainland ancestors reached the islandsand are, therefore, more closely related to one another.

6. Species on oceanic islands show strong affinities to those onthe nearest mainland. Thus, the finches of the GalpagosIslands closely resemble a finch seen on the western coast ofSouth America. The Galpagos finches do not resemble thebirds on the Cape Verde Islands, islands in the AtlanticOcean off the coast of Africa that are similar to theGalpagos. Darwin visited the Cape Verde Islands andmany other island groups personally and was able to makesuch comparisons on the basis of his own observations.

FIGURE 1.8Fossil evidence of evolution. The now-extinct glyptodont (a)was a 2000-kilogram South American armadillo, much larger thanthe modern armadillo (b), which weighs an average of about 4.5kilograms. (Drawings are not to scale.)

(a) Glyptodont(b) Armadillo

Inventing the Theory of Natural SelectionIt is one thing to observe the results of evolution, butquite another to understand how it happens. Darwinsgreat achievement lies in his formulation of the hypothe-sis that evolution occurs because of natural selection.

Darwin and Malthus

Of key importance to the development of Darwins in-sight was his study of Thomas Malthuss Essay on thePrinciple of Population (1798). In his book, Malthuspointed out that populations of plants and animals (in-cluding human beings) tend to increase geometrically,while the ability of humans to increase their food supplyincreases only arithmetically. A geometric progression isone in which the elements increase by a constant factor;for example, in the progression 2, 6, 18, 54, . . . , eachnumber is three times the preceding one. An arithmeticprogression, in contrast, is one in which the elements in-crease by a constant difference; in the progression 2, 6, 10,14, . . . , each number is four greater than the preced-ing one (figure 1.9).

Because populations increase geometrically, virtuallyany kind of animal or plant, if it could reproduce un-checked, would cover the entire surface of the worldwithin a surprisingly short time. Instead, populations ofspecies remain fairly constant year after year, becausedeath limits population numbers. Malthuss conclusionprovided the key ingredient that was necessary for Dar-win to develop the hypothesis that evolution occurs bynatural selection.

Sparked by Malthuss ideas, Darwin saw that althoughevery organism has the potential to produce more off-spring than can survive, only a limited number actuallydo survive and produce further offspring. Combiningthis observation with what he had seen on the voyage ofthe Beagle, as well as with his own experiences in breed-ing domestic animals, Darwin made an important associ-ation (figure 1.10): Those individuals that possess supe-rior physical, behavioral, or other attributes are morelikely to survive than those that are not so well endowed.By surviving, they gain the opportunity to pass on theirfavorable characteristics to their offspring. As the fre-quency of these characteristics increases in the popula-tion, the nature of the population as a whole will gradu-ally change. Darwin called this process selection. Thedriving force he identified has often been referred to assurvival of the fittest.


Geometric progression

Arithmetic progression

2

6

18

54

46

8

FIGURE 1.9Geometric and arithmetic progressions. A geometric progressionincreases by a constant factor (e.g., 2 or 3 or 4), while anarithmetic progression increases by a constant difference (e.g.,units of 1 or 2 or 3) . Malthus contended that the human growthcurve was geometric, but the human food production curve wasonly arithmetic. Can you see the problems this difference wouldcause?

FIGURE 1.10An excerpt from Charles Darwins On the Origin of Species.

Natural Selection

Darwin was thoroughly familiar withvariation in domesticated animals andbegan On the Origin of Species with adetailed discussion of pigeon breeding.He knew that breeders selected certainvarieties of pigeons and other animals,such as dogs, to produce certain char-acteristics, a process Darwin called ar-tificial selection. Once this had beendone, the animals would breed true forthe characteristics that had been select-ed. Darwin had also observed that thedifferences purposely developed be-tween domesticated races or breedswere often greater than those that sep-arated wild species. Domestic pigeonbreeds, for example, show muchgreater variety than all of the hundredsof wild species of pigeons foundthroughout the world. Such relation-ships suggested to Darwin that evolu-tionary change could occur in naturetoo. Surely if pigeon breeders couldfoster such variation by artificial selec-tion, nature could do the same, play-ing the breeders role in selecting thenext generationa process Darwincalled natural selection.

Darwins theory thus incorporatesthe hypothesis of evolution, the pro-cess of natural selection, and the mass of new evidencefor both evolution and natural selection that Darwincompiled. Thus, Darwins theory provides a simple anddirect explanation of biological diversity, or why animalsare different in different places: because habitats differ intheir requirements and opportunities, the organisms withcharacteristics favored locally by natural selection willtend to vary in different places.

Darwin Drafts His Argument

Darwin drafted the overall argument for evolution by natu-ral selection in a preliminary manuscript in 1842. Aftershowing the manuscript to a few of his closest scientificfriends, however, Darwin put it in a drawer, and for 16 years turned to other research. No one knows for surewhy Darwin did not publish his initial manuscriptit isvery thorough and outlines his ideas in detail. Some histo-rians have suggested that Darwin was shy of igniting publiccriticism of his evolutionary ideasthere could have beenlittle doubt in his mind that his theory of evolution by nat-ural selection would spark controversy. Others have pro-

posed that Darwin was simply refininghis theory all those years, althoughthere is little evidence he altered hisinitial manuscript in all that time.

Wallace Has the Same Idea

The stimulus that finally brought Dar-wins theory into print was an essay hereceived in 1858. A young English nat-uralist named Alfred Russel Wallace(18231913) sent the essay to Darwinfrom Malaysia; it concisely set forththe theory of evolution by means ofnatural selection, a theory Wallace haddeveloped independently of Darwin.Like Darwin, Wallace had beengreatly influenced by Malthuss 1798essay. Colleagues of Wallace, knowingof Darwins work, encouraged him tocommunicate with Darwin. After re-ceiving Wallaces essay, Darwin ar-ranged for a joint presentation of theirideas at a seminar in London. Darwinthen completed his own book, expand-ing the 1842 manuscript which he hadwritten so long ago, and submitted itfor publication.

Publication of Darwins Theory

Darwins book appeared in November 1859 and caused animmediate sensation. Many people were deeply disturbed bythe suggestion that human beings were descended from thesame ancestor as apes (figure 1.11). Darwin did not actuallydiscuss this idea in his book, but it followed directly from theprinciples he outlined. In a subsequent book, The Descent ofMan, Darwin presented the argument directly, building apowerful case that humans and living apes have common an-cestors. Although people had long accepted that humansclosely resembled apes in many characteristics, the possibilitythat there might be a direct evolutionary relationship was un-acceptable to many. Darwins arguments for the theory ofevolution by natural selection were so compelling, however,that his views were almost completely accepted within the in-tellectual community of Great Britain after the 1860s.

The fact that populations do not really expandgeometrically implies that nature acts to limitpopulation numbers. The traits of organisms thatsurvive to produce more offspring will be morecommon in future generationsa process Darwincalled natural selection.


FIGURE 1.11Darwin greets his monkey ancestor. Inhis time, Darwin was often portrayedunsympathetically, as in this drawing froman 1874 publication.

Evolution After Darwin: More EvidenceMore than a century has elapsed since Darwins death in1882. During this period, the evidence supporting his the-ory has grown progressively stronger. There have alsobeen many significant advances in our understanding ofhow evolution works. Although these advances have notaltered the basic structure of Darwins theory, they havetaught us a great deal more about the mechanisms bywhich evolution occurs. We will briefly explore some ofthis evidence here; in chapter 21 we will return to the the-ory of evolution and examine the evidence in more detail.

The Fossil Record

Darwin predicted that the fossil record would yield inter-mediate links between the great groups of organisms, forexample, between fishes and the amphibians thought tohave arisen from them, and between reptiles and birds. Wenow know the fossil record to a degree that was unthink-able in the nineteenth century. Recent discoveries of mi-croscopic fossils have extended the known history of life onearth back to about 3.5 billion years ago. The discovery ofother fossils has supported Darwins predictions and hasshed light on how organisms have, over this enormous timespan, evolved from the simple to the complex. For verte-brate animals especially, the fossil record is rich and exhib-its a graded series of changes in form, with the evolutionaryparade visible for all to see (see Box: Why Study Fossils?).

The Age of the Earth

In Darwins day, some physicists argued that the earth wasonly a few thousand years old. This bothered Darwin, be-cause the evolution of all living things from some single

original ancestor would have required a great deal moretime. Using evidence obtained by studying the rates of ra-dioactive decay, we now know that the physicists of Dar-wins time were wrong, very wrong: the earth was formedabout 4.5 billion years ago.

The Mechanism of Heredity

Darwin received some of his sharpest criticism in the area ofheredity. At that time, no one had any concept of genes orof how heredity works, so it was not possible for Darwin toexplain completely how evolution occurs. Theories of he-redity in Darwins day seemed to rule out the possibility ofgenetic variation in nature, a critical requirement of Dar-wins theory. Genetics was established as a science only atthe start of the twentieth century, 40 years after the publica-tion of Darwins On the Origin of Species. When scientistsbegan to understand the laws of inheritance (discussed inchapter 13), the heredity problem with Darwins theoryvanished. Genetics accounts in a neat and orderly way forthe production of new variations in organisms.

Comparative Anatomy

Comparative studies of animals have provided strong evi-dence for Darwins theory. In many different types of verte-brates, for example, the same bones are present, indicatingtheir evolutionary past. Thus, the forelimbs shown in figure1.12 are all constructed from the same basic array of bones,modified in one way in the wing of a bat, in another way inthe fin of a porpoise, and in yet another way in the leg of ahorse. The bones are said to be homologous in the differ-ent vertebrates; that is, they have the same evolutionary ori-gin, but they now differ in structure and function. This con-trasts with analogous structures, such as the wings of birdsand butterflies, which have similar structure and functionbut different evolutionary origins.


Human Cat Bat Porpoise Horse

FIGURE 1.12Homology among vertebratelimbs. The forelimbs of thesefive vertebrates show the waysin which the relativeproportions of the forelimbbones have changed in relationto the particular way of life ofeach organism.

Molecular Biology

Biochemical tools are now of major importance in efforts toreach a better understanding of how evolution occurs.Within the last few years, for example, evolutionary biolo-gists have begun to read genes, much as you are readingthis page. They have learned to recognize the order of theletters of the long DNA molecules, which are present inevery living cell and which provide the genetic informationfor that organism. By comparing the sequences of lettersin the DNA of different groups of animals or plants, we canspecify the degree of relationship among the groups moreprecisely than by any other means. In many cases, detailedfamily trees can then be constructed. The consistent patternemerging from a growing mountain of data is one of pro-gressive change over time, with more distantly relatedspecies showing more differences in their DNA than closelyrelated ones, just as Darwins theory predicts. By measuringthe degree of difference in the genetic coding, and by inter-preting the information available from the fossil record, we

can even estimate the rates at which evolution is occurringin different groups of organisms.

Development

Twentieth-century knowledge about growth and develop-ment further supports Darwins theory of evolution. Strik-ing similarities are seen in the developmental stages ofmany organisms of different species. Human embryos, forexample, go through a stage in which they possess thesame structures that give rise to the gills in fish, a tail, andeven a stage when the embryo has fur! Thus, the develop-ment of an organism (its ontogeny) often yields informa-tion about the evolutionary history of the species as awhole (its phylogeny).

Since Darwins time, new discoveries of the fossilrecord, genetics, anatomy, and development all supportDarwins theory.


by studying modern organisms. But historyis complex and unpredictableand princi-ples of evolution (like natural selection)cannot specify the pathway that lifes histo-ry has actually followed. Paleontology holdsthe archives of the pathwaythe fossilrecord of past life, with its fascinating histo-ry of mass extinctions, periods of rapidchange, long episodes of stability, and con-stantly changing patterns of dominance anddiversity. Humans represent just one tiny,largely fortuitous, and late-arising twig onthe enormously arborescent bush of life.Paleontology is the study of this grandest ofall bushes.

geological time, occur by a natural processof evolutionary transformationdescentwith modification, in Darwins words. Iwas thrilled to learn that humans had arisenfrom apelike ancestors, who had themselvesevolved from the tiny mouselike mammalsthat had lived in the time of dinosaurs andseemed then so inconspicuous, so unsuc-cessful, and so unpromising.

Now, at mid-career (I was born in 1941)I remain convinced that I made the rightchoice, and committed to learn and convey,as much as I can as long as I can, about evo-lution and the history of life. We can learna great deal about the process of evolution

I grew up on the streets of New York City,in a family of modest means and little for-mal education, but with a deep love oflearning. Like many urban kids who be-come naturalists, my inspiration camefrom a great museumin particular, fromthe magnificent dinosaurs on display at theAmerican Museum of Natural History. Aswe all know from Jurassic Park and othersources, dinomania in young children (Iwas five when I saw my first dinosaur) isnot rarebut nearly all children lose thepassion, and the desire to become a pale-ontologist becomes a transient momentbetween policeman and fireman in a chro-nology of intended professions. But I per-sisted and became a professional paleontol-ogist, a student of lifes history as revealedby the evidence of fossils (though I endedup working on snails rather than dino-saurs!). Why?

I remained committed to paleontologybecause I discovered, still as a child, thewonder of one of the greatest transformingideas ever discovered by science: evolution.I learned that those dinosaurs, and all crea-tures that have ever lived, are bound to-gether in a grand family tree of physical re-lationships, and that the rich and fascinatingchanges of life, through billions of years in

Why Study Fossils? Flight has evolvedthree separatetimes among ver-tebrates. Birds andbats are still withus, but pterosaurs,such as the onepictured, becameextinct with the di-nosaurs about 65million years ago.

Stephen Jay GouldHarvard University


Core Principles of BiologyFrom centuries of biological observation and inquiry, oneorganizing principle has emerged: biological diversity re-flects history, a record of success, failure, and change ex-tending back to a period soon after the formation of theearth. The explanation for this diversity, the theory of evo-lution by natural selection, will form the backbone of yourstudy of biological science, just as the theory of the covalentbond is the backbone of chemistry, or the theory of quan-tum mechanics is that of physics. Evolution by natural selec-tion is a thread that runs through everything you will learnin this book.

Basic Principles

The first half of this book is devoted to a description of thebasic principles of biology, introduced through a levels-of-organization framework (see figure 1.2). At the molecular,organellar, and cellular levels of organization, you will be in-troduced to cell biology. You will learn how cells are con-structed and how they grow, divide, and communicate. Atthe organismal level, you will learn the principles of genetics,which deal with the way that individual traits are transmit-ted from one generation to the next. At the population level,

you will examine evolution, the gradual change in popula-tions from one generation to the next, which has ledthrough natural selection to the biological diversity we seearound us. Finally, at the community and ecosystem levels,you will study ecology, which deals with how organisms in-teract with their environments and with one another to pro-duce the complex communities characteristic of life onearth.

Organisms

The second half of the book is devoted to an examination oforganisms, the products of evolution. It is estimated that atleast 5 million different kinds of plants, animals, and micro-organisms exist, and their diversity is incredible (figure 1.13).Later in the book, we will take a particularly detailed look atthe vertebrates, the group of animals of which we are mem-bers. We will consider the vertebrate body and how it func-tions, as this information is of greatest interest and impor-tance to most students.

As you proceed through this book, what you learn at onestage will give you the tools to understand the next. Thecore principle of biology is that biological diversity is theresult of a long evolutionary journey.


Plantae

AnimaliaFungi

Eubacteria

Archaebacteria

Protista

FIGURE 1.13The diversity of life. Biologists categorizeall living things into six major groupscalled kingdoms: archaebacteria,eubacteria, protists, fungi, plants, andanimals.

Chapter 1Summary Questions Media Resources



Living things are highly organized, whether as singlecells or as multicellular organisms, with several hier-archical levels.

1. What are the characteristicsof living things?


Science is the determination of general principlesfrom observation and experimentation.

Scientists select the best hypotheses by usingcontrolled experiments to eliminate alternativehypotheses that are inconsistent with observations.

A group of related hypotheses supported by a largebody of evidence is called a theory. In science, atheory represents what we are most sure about.However, there are no absolute truths in science, andeven theories are accepted only conditionally.

Scientists conduct basic research, designed to gaininformation about natural phenomena in order tocontribute to our overall body of knowledge, andapplied research, devoted to solving specific problemswith practical applications.

2. What is the difference be-tween deductive and inductivereasoning? What is a hypothesis?3. What are variables? How arecontrol experiments used in test-ing hypotheses?4. How does a hypothesisbecome a theory? At what pointdoes a theory become acceptedas an absolute truth, no longersubject to any uncertainty?5. What is the differencebetween basic and appliedresearch?

6. Describe the evidence that ledDarwin to propose that evolu-tion occurs by means of naturalselection. What evidencegathered since the publication ofDarwins theory has lent furthersupport to the theory?7. What is the difference be-tween homologous and analo-gous structures? Give anexample of each.

8. Can you think of any alterna-tives to levels-of-organization asways of organizing the mass ofinformation in biology?

One of the central theories of biology is Darwinstheory that evolution occurs by natural selection. Itstates that certain individuals have heritable traits thatallow them to produce more offspring in a given kindof environment than other individuals lacking thosetraits. Consequently, those traits will increase infrequency through time.

Because environments differ in their requirementsand opportunities, the traits favored by naturalselection will vary in different environments.

This theory is supported by a wealth of evidence ac-quired over more than a century of testing andquestioning.

Biological diversity is the result of a long history ofevolutionary change. For this reason evolution is thecore of the science of biology.

Considered in terms of levels-of-organization, thescience of biology can be said to consist of subdisci-plines focusing on particular levels. Thus one speaksof molecular biology, cell biology, organismal biolo-gy, population biology, and community biology.

1.3 Darwins theory of evolution illustrates how science works.


Art Activity: Biologicalorganization

Scientists on Science:Why Paleonthology?

Experiments:Probability andHypothesis Testing inBiology

Introduction toEvolution

Before Darwin Voyage of the Beagle Natural Selection The Process of Natural

Selection Evidence for Evolution

Student Research: TheSearch for MedicinalPlants on ScienceArticles

140 Years WithoutDarwin Are Enough

Bird-Killing Cats:Natures Way ofMaking Better Bids

http://www.mhhe.com/raven6e http://www.biocourse.com

19

2The Nature of Molecules

Concept Outline

2.1 Atoms are natures building material.

Atoms. All substances are composed of tiny particles calledatoms, each a positively charged nucleus around which orbitnegative electrons.Electrons Determine the Chemical Behavior of Atoms.Electrons orbit the nucleus of an atom; the closer anelectrons orbit to the nucleus, the lower its energy level.

2.2 The atoms of living things are among the smallest.

Kinds of Atoms. Of the 92 naturally occurring elements,only 11 occur in organisms in significant amounts.

2.3 Chemical bonds hold molecules together.

Ionic Bonds Form Crystals. Atoms are linked togetherinto molecules, joined by chemical bonds that result fromforces like the attraction of opposite charges or the sharing ofelectrons.Covalent Bonds Build Stable Molecules. Chemicalbonds formed by the sharing of electrons can be very strong,and require much energy to break.

2.4 Water is the cradle of life.

Chemistry of Water. Water forms weak chemicalassociations that are responsible for much of the organizationof living chemistry.Water Atoms Act Like Tiny Magnets. Because electronsare shared unequally by the hydrogen and oxygen atoms ofwater, a partial charge separation occurs. Each water atomacquires a positive and negative pole and is said to be polar.Water Clings to Polar Molecules. Because the oppositepartial charges of polar molecules attract one another, watertends to cling to itself and other polar molecules and toexclude nonpolar molecules.Water Ionizes. Because its covalent bonds occasionallybreak, water contains a low concentration of hydrogen (H+)and hydroxide (OH) ions, the fragments of broken watermolecules.

A bout 10 to 20 billion years ago, an enormous explo-sion likely marked the beginning of the universe.With this explosion began the process of evolution, whicheventually led to the origin and diversification of life onearth. When viewed from the perspective of 20 billionyears, life within our solar system is a recent development,but to understand the origin of life, we need to considerevents that took place much earlier. The same processesthat led to the evolution of life were responsible for theevolution of molecules (figure 2.1). Thus, our study of lifeon earth begins with physics and chemistry. As chemicalmachines ourselves, we must understand chemistry tobegin to understand our origins.

FIGURE 2.1Cells are made of molecules. Specific, often simple, combina-tions of atoms yield an astonishing diversity of molecules withinthe cell, each with unique functional characteristics.

weight will be greater on the earth because the earths grav-itational force is greater than the moons. The atomicmass of an atom is equal to the sum of the masses of itsprotons and neutrons. Atoms that occur naturally on earthcontain from 1 to 92 protons and up to 146 neutrons.

The mass of atoms and subatomic particles is measuredin units called daltons. To give you an idea of just how smallthese units are, note that it takes 602 million million billion(6.02 1023) daltons to make 1 gram! A proton weighs ap-proximately 1 dalton (actually 1.009 daltons), as does a neu-tron (1.007 daltons). In contrast, electrons weigh only 11840 ofa dalton, so their contribution to the overall mass of an atomis negligible.


AtomsAny substance in the universe that hasmass (see below) and occupies space isdefined as matter. All matter is com-posed of extremely small particlescalled atoms. Because of their size,atoms are difficult to study. Not untilearly in this century did scientistscarry out the first experiments sug-gesting what an atom is like.

The Structure of Atoms

Objects as small as atoms can beseen only indirectly, by using verycomplex technology such as tunnelingmicrocopy. We now know a greatdeal about the complexities of atomicstructure, but the simple view putforth in 1913 by the Danish physicistNiels Bohr provides a good startingpoint. Bohr proposed that every atompossesses an orbiting cloud of tinysubatomic particles called electronswhizzing around a core like the plan-ets of a miniature solar system. At thecenter of each atom is a small, verydense nucleus formed of two otherkinds of subatomic particles, protonsand neutrons (figure 2.2).

Within the nucleus, the cluster ofprotons and neutrons is held togetherby a force that works only over shortsubatomic distances. Each proton car-ries a positive (+) charge, and eachelectron carries a negative () charge.Typically an atom has one electronfor each proton. The number of protons (the atomsatomic number) determines the chemical character of theatom, because it dictates the number of electrons orbitingthe nucleus which are available for chemical activity. Neu-trons, as their name implies, possess no charge.

Atomic Mass

The terms mass and weight are often used interchangeably,but they have slightly different meanings. Mass refers to theamount of a substance, while weight refers to the forcegravity exerts on a substance. Hence, an object has thesame mass whether it is on the earth or the moon, but its

2.1 Atoms are natures building material.

FIGURE 2.2Basic structure of atoms. All atoms have a nucleus consisting of protons and neutrons,except hydrogen, the smallest atom, which has only one proton and no neutrons in itsnucleus. Oxygen, for example, has eight protons and eight neutrons in its nucleus. Electronsspin around the nucleus a far distance away from the nucleus.

Proton

(Positive charge) (No charge) (Negative charge)

Neutron Electron

Hydrogen1 Proton1 Electron

Oxygen8 Protons8 Neutrons8 Electrons

Isotopes

Atoms with the same atomic number (that is, the same num-ber of protons) have the same chemical properties and aresaid to belong to the same element. Formally speaking, anelement is any substance that cannot be broken down to anyother substance by ordinary chemical means. However, whileall atoms of an element have the same number of protons,they may not all have the same number of neutrons. Atoms ofan element that possess different numbers of neutrons arecalled isotopes of that element. Most elements in nature existas mixtures of different isotopes. Carbon (C), for example,has three isotopes, all containing six protons (figure 2.3).Over 99% of the carbon found in nature exists as an isotopewith six neutrons. Because its total mass is 12 daltons (6 fromprotons plus 6 from neutrons), this isotope is referred to ascarbon-12, and symbolized 12C. Most of the rest of the natu-rally occurring carbon is carbon-13, an isotope with sevenneutrons. The rarest carbon isotope is carbon-14, with eightneutrons. Unlike the other two isotopes, carbon-14 is unsta-ble: its nucleus tends to break up into elements with loweratomic numbers. This nuclear breakup, which emits a signifi-cant amount of energy, is called radioactive decay, and iso-topes that decay in this fashion are radioactive isotopes.

Some radioactive isotopes are more unstable than othersand therefore decay more readily. For any given isotope,however, the rate of decay is constant. This rate is usuallyexpressed as the half-life, the time it takes for one half of theatoms in a sample to decay. Carbon-14, for example, has ahalf-life of about 5600 years. A sample of carbon containing1 gram of carbon-14 today would contain 0.5 gram of car-bon-14 after 5600 years, 0.25 gram 11,200 years from now,0.125 gram 16,800 years from now, and so on. By determin-ing the ratios of the different isotopes of carbon and otherelements in biological samples and in rocks, scientists areable to accurately determine when these materials formed.

While there are many useful applications of radioactivity,there are also harmful side effects that must be considered inany planned use of radioactive substances. Radioactive sub-stances emit energetic subatomic particles that have the po-

tential to severely damage living cells, producing mutations intheir genes, and, at high doses, cell death. Consequently, ex-posure to radiation is now very carefully controlled and regu-lated. Scientists who work with radioactivity (basic re-searchers as well as applied scientists such as X-raytechnologists) wear radiation-sensitive badges to monitor thetotal amount of radioactivity to which they are exposed. Eachmonth the badges are collected and scrutinized. Thus, em-ployees whose work places them in danger of excessive radio-active exposure are equipped with an early warning system.

Electrons

The positive charges in the nucleus of an atom are counter-balanced by negatively charged electrons orbiting at vary-ing distances around the nucleus. Thus, atoms with thesame number of protons and electrons are electrically neu-tral, having no net charge.

Electrons are maintained in their orbits by their attrac-tion to the positively charged nucleus. Sometimes otherforces overcome this attraction and an atom loses one ormore electrons. In other cases, atoms may gain additionalelectrons. Atoms in which the number of electrons doesnot equal the number of protons are known as ions, andthey carry a net electrical charge. An atom that has moreprotons than electrons has a net positive charge and iscalled a cation. For example, an atom of sodium (Na) thathas lost one electron becomes a sodium ion (Na+), with acharge of +1. An atom that has fewer protons than elec-trons carries a net negative charge and is called an anion. Achlorine atom (Cl) that has gained one electron becomes achloride ion (Cl), with a charge of 1.

An atom consists of a nucleus of protons and neutronssurrounded by a cloud of electrons. The number of itselectrons largely determines the chemical properties ofan atom. Atoms that have the same number of protonsbut different numbers of neutrons are called isotopes.Isotopes of an atom differ in atomic mass but havesimilar chemical properties.

Chapter 2 The Nature of Molecules 21

Carbon-126 Protons6 Neutrons6 Electrons



FIGURE 2.3The three most abundantisotopes of carbon. Isotopesof a particular atom havedifferent numbers ofneutrons.

Electrons Determine the ChemicalBehavior of AtomsThe key to the chemical behavior of an atom lies in the ar-rangement of its electrons in their orbits. It is convenient tovisualize individual electrons as following discrete circularorbits around a central nucleus, as in the Bohr model of theatom. However, such a simple picture is not realistic. It isnot possible to precisely locate the position of any individualelectron precisely at any given time. In fact, a particularelectron can be anywhere at a given instant, from close tothe nucleus to infinitely far away from it.

However, a particular electron is more likely to be locat-ed in some positions than in others. The area around a nu-cleus where an electron is most likely to be found is calledthe orbital of that electron (figure 2.4). Some electron or-bitals near the nucleus are spherical (s orbitals), while oth-ers are dumbbell-shaped (p orbitals). Still other orbitals,more distant from the nucleus, may have different shapes.Regardless of its shape, no orbital may contain more thantwo electrons.

Almost all of the volume of an atom is empty space, be-cause the electrons are quite far from the nucleus relativeto its size. If the nucleus of an atom were the size of an ap-ple, the orbit of the nearest electron would be more than1600 meters away. Consequently, the nuclei of two atomsnever come close enough in nature to interact with eachother. It is for this reason that an atoms electrons, not itsprotons or neutrons, determine its chemical behavior. This

also explains why the isotopes of an element, all of whichhave the same arrangement of electrons, behave the sameway chemically.

Energy within the Atom

All atoms possess energy, defined as the ability to do work.Because electrons are attracted to the positively chargednucleus, it takes work to keep them in orbit, just as it takeswork to hold a grapefruit in your hand against the pull ofgravity. The grapefruit is said to possess potential energy,the ability to do work, because of its position; if you wereto release it, the grapefruit would fall and its energy wouldbe reduced. Conversely, if you were to move the grapefruitto the top of a building, you would increase its potentialenergy. Similarly, electrons have potential energy of posi-tion. To oppose the attraction of the nucleus and move theelectron to a more distant orbital requires an input of en-ergy and results in an electron with greater potential ener-gy. This is how chlorophyll captures energy from lightduring photosynthesis (chapter 10)the light excites elec-trons in the chlorophyll. Moving an electron closer to thenucleus has the opposite effect: energy is released, usuallyas heat, and the electron ends up with less potential energy(figure 2.5).

A given atom can possess only certain discrete amountsof energy. Like the potential energy of a grapefruit on a stepof a staircase, the potential energy contributed by the posi-tion of an electron in an atom can have only certain values.


1s Orbital

x x

y

z

Orbital for energy level K:one spherical orbital (1s)

2s Orbital

2p Orbitals

Composite ofall p orbitals

Orbitals for energy level L:one spherical orbital (2s) andthree dumbbell-shaped orbitals (2p)

z

y

FIGURE 2.4Electron orbitals. The lowest energy level or electron shell, which is nearest the nucleus, is level K. It is occupied by a single s orbital,referred to as 1s. The next highest energy level, L, is occupied by four orbitals: one s orbital (referred to as the 2s orbital) and three porbitals (each referred to as a 2p orbital). The four L-level orbitals compactly fill the space around the nucleus, like two pyramids set base-to-base.

Every atom exhibits a ladder of potential energy values,rather than a continuous spectrum of possibilities, a discreteset of orbits at particular distances from the nucleus.

During some chemical reactions, electrons are trans-ferred from one atom to another. In such reactions, the lossof an electron is called oxidation, and the gain of an elec-tron is called reduction (figure 2.6). It is important to real-ize that when an electron is transferred in this way, it keepsits energy of position. In organisms, chemical energy isstored in high-energy electrons that are transferred fromone atom to another in reactions involving oxidation andreduction.

Because the amount of energy an electron possesses isrelated to its distance from the nucleus, electrons that arethe same distance from the nucleus have the same energy,even if they occupy different orbitals. Such electrons aresaid to occupy the same energy level. In a schematic dia-gram of an atom (figure 2.7), the nucleus is represented as asmall circle and the electron energy levels are drawn as con-centric rings, with the energy level increasing with distancefrom the nucleus. Be careful not to confuse energy levels,which are drawn as rings to indicate an electrons energy,with orbitals, which have a variety of three-dimensionalshapes and indicate an electrons most likely location.

Electrons orbit a nucleus in paths called orbitals. Noorbital can contain more than two electrons, but manyorbitals may be the same distance from the nucleus and,thus, contain electrons of the same energy.


Energy released

Energylevel

3

Energylevel

2

Energylevel

1

M L K

Energylevel

1

Ener

gy a

bsor

bed

Energylevel

2

Energylevel

3

+

+ +++

+ +MLK

FIGURE 2.5Atomic energy levels. When an electronabsorbs energy, it moves to higher energylevels farther from the nucleus. When anelectron releases energy, it falls to lowerenergy levels closer to the nucleus.

FIGURE 2.6Oxidation and reduction. Oxidation is the loss of an electron;reduction is the gain of an electron.

Oxidation Reduction

Helium Nitrogen

77n

22n KK L

Nucleus

L

M

N

K

Energy level

FIGURE 2.7Electron energy levels for helium and nitrogen. Gold ballsrepresent the electrons. Each concentric circle represents adifferent distance from the nucleus and, thus, a different electronenergy level.


1

H

1

H

3

Li4

Be

19

K

12

Mg

93

Np94

Pu95

Am96

Cm97

Bk98

Cf99

Es100

Fm101

Md102

No103

Lr

37

Rb38

Sr39

Y42

Mo45

Rh46

Pd47

Ag48

Cd49

In50

Sn51

Sb52

Te53

I54

Xe

21

Sc40

Zr

22

Ti23

V24

Cr25

Mn27

Co28

Ni29

Cu30

Zn36

Kr

5

B6

C6 C

8

O 2He

55

Cs56

Ba72

Hf73

Ta74

W75

Re76

Os77

Ir78

Pt79

Au80

Hg81

Tl82

Pb83

Bi84

Po85

At86

Rn87

Fr88

Ra

57

La89

Ac104 105 106 107 108 109

58

Ce59

Pr60

Nd61

Pm62

Sm63

Eu64

Gd65

Tb66

Dy67

Ho68

Er69

Tm70

Yb71

Lu

90

Th91

Pa92

U

(Lanthanide series)

(Actinide series)

11

Na20

Ca

41

Nb43

Tc44

Ru

26

Fe

13

Al

31

Ga32

Ge

14

Si

7

N15

P

33

As

16

S

35

Br34

Se

9

F

18

Ar

10

Ne17

Cl

110

FIGURE 2.8Periodic table of the elements. In this representation, the frequency of elements that occur in the earths crust is indicated by the heightof the block. Elements found in significant amounts in living organisms are shaded in blue.

Kinds of AtomsThere are 92 naturally occurring elements, each with a dif-ferent number of protons and a different arrangement ofelectrons. When the nineteenth-century Russian chemistDmitri Mendeleev arranged the known elements in a tableaccording to their atomic mass (figure 2.8), he discoveredone of the great generalizations in all of science. Mendeleevfound that the elements in the table exhibited a pattern ofchemical properties that repeated itself in groups of eight el-ements. This periodically repeating pattern lent the table itsname: the periodic table of elements.

The Periodic Table

The eight-element periodicity that Mendeleev found isbased on the interactions of the electrons in the outer en-ergy levels of the different elements. These electrons arecalled valence electrons and their interactions are thebasis for the differing chemical properties of the elements.For most of the atoms important to life, an outer energy

level can contain no more than eight electrons; the chemi-cal behavior of an element reflects how many of the eightpositions are filled. Elements possessing all eight elec-trons in their outer energy level (two for helium) areinert, or nonreactive; they include helium (He), neon(Ne), argon (Ar), krypton (Kr), xenon (Xe), and radon(Rn). In sharp contrast, elements with seven electrons (onefewer than the maximum number of eight) in their outerenergy level, such as fluorine (F), chlorine (Cl), andbromine (Br), are highly reactive. They tend to gain theextra electron needed to fill the energy level. Elementswith only one electron in their outer energy level, such aslithium (Li), sodium (Na), and potassium (K), are alsovery reactive; they tend to lose the single electron in theirouter level.

Mendeleevs periodic table thus leads to a useful generali-zation, the octet rule (Latin octo, eight) or rule of eight:atoms tend to establish completely full outer energy levels.Most chemical behavior can be predicted quite accuratelyfrom this simple rule, combined with the tendency of at-oms to balance positive and negative charges.

2.2 The atoms of living things are among the smallest.

Distribution of the Elements

Of the 92 naturally occurring elements on earth, only 11 arefound in organisms in more than trace amounts (0.01% orhigher). These 11 elements have atomic numbers less than21 and, thus, have low atomic masses. Table 2.1 lists thelevels of various elements in the human body; their levels inother organisms are similar. Inspection of this table suggeststhat the distribution of elements in living systems is by nomeans accidental. The most common elements inside or-ganisms are not the elements that are most abundant in the

earths crust. For example, silicon, aluminum, and iron con-stitute 39.2% of the earths crust, but they exist in traceamounts in the human body. On the other hand, carbon at-oms make up 18.5% of the human body but only 0.03% ofthe earths crust.

Ninety-two elements occur naturally on earth; onlyeleven of them are found in significant amounts in livingorganisms. Four of themoxygen, hydrogen, carbon,nitrogenconstitute 96.3% of the weight of your body.


Table 2.1 The Most Common Elements on Earth and Their Distribution in the Human Body

Approximate Percent of Percent of Earths Crust Human Body

Element Symbol Atomic Number by Weight by Weight Importance or Function

Oxygen

SiliconAluminumIron

Calcium

Sodium

Potassium

Magnesium

Hydrogen

ManganeseFluorinePhosphorus

CarbonSulfurChlorineVanadiumChromiumCopperNitrogen

BoronCobaltZincSeleniumMolybdenumTinIodine

O

SiAlFe

Ca

Na

K

Mg

H

MnFP

CSClVCrCuN

BCoZnSeMoSnI

8

141326

20

11

19

12

1

259

15

616172324297

5273034425053

46.6

27.76.55.0

3.6

2.8

2.6

2.1

0.14

0.10.070.07

0.030.030.010.010.010.01

Trace

TraceTraceTraceTraceTraceTraceTrace

65.0

TraceTraceTrace

1.5

0.2

0.4

0.1

9.5

TraceTrace1.0

18.50.30.2

TraceTraceTrace3.3

TraceTraceTraceTraceTraceTraceTrace

Required for cellular respiration;component of water

Critical component of hemoglobin inthe bloodComponent of bones and teeth; trig-gers muscle contractionPrincipal positive ion outside cells;important in nerve functionPrincipal positive ion inside cells; im-portant in nerve functionCritical component of many energy-transferring enzymesElectron carrier; component of waterand most organic molecules

Backbone of nucleic acids; importantin energy transferBackbone of organic moleculesComponent of most proteinsPrincipal negative ion outside cells

Key component of many enzymesComponent of all proteins and nucleicacids

Key component of some enzymes

Key component of many enzymes

Component of thyroid hormone


Na

Sodium atom

Sodium ion

Chlorine atom

Chloride ion+

Na+

Cl

Cl

(a)

FIGURE 2.9The formation of ionic bonds by sodium chloride. (a) When a sodium atom donates an electron to a chlorine atom, the sodium atombecomes a positively charged sodium ion, and the chlorine atom becomes a negatively charged chloride ion. (b) Sodium chloride forms ahighly regular lattice of alternating sodium ions and chloride ions.

NaCl crystal

Cl

Cl

ClCl

Cl

NaNa

Na

Na

(b)

Ionic Bonds Form CrystalsA group of atoms held together by energy in a stable associ-ation is called a molecule. When a molecule contains atomsof more than one element, it is called a compound. Theatoms in a molecule are joined by chemical bonds; thesebonds can result when atoms with opposite charges attract(ionic bonds), when two atoms share one or more pairs ofelectrons (covalent bonds), or when atoms interact in otherways. We will start by examining ionic bonds, which formwhen atoms with opposite electrical charges (ions) attract.

A Closer Look at Table Salt

Common table salt, sodium chloride (NaCl), is a lattice ofions in which the atoms are held together by ionic bonds(figure 2.9). Sodium has 11 electrons: 2 in the inner energylevel, 8 in the next level, and 1 in the outer (valence) level.The valence electron is unpaired (free) and has a strong ten-dency to join with another electron. A stable configurationcan be achieved if the valence electron is lost to anotheratom that also has an unpaired electron. The loss of thiselectron results in the formation of a positively chargedsodium ion, Na+.

The chlorine atom has 17 electrons: 2 in the inner energylevel, 8 in the next level, and 7 in the outer level. Hence, oneof the orbitals in the outer energy level has an unpairedelectron. The addition of another electron to the outer levelfills that level and causes a negatively charged chloride ion,Cl, to form.

When placed together, metallic sodium and gaseouschlorine react swiftly and explosively, as the sodium atomsdonate electrons to chlorine, forming Na+ and Cl ions. Be-cause opposite charges attract, the Na+ and Cl remain asso-ciated in an ionic compound, NaCl, which is electricallyneutral. However, the electrical attractive force holdingNaCl together is not directed specifically between particularNa+ and Cl ions, and no discrete sodium chloride mole-cules form. Instead, the force exists between any one ion andall neighboring ions of the opposite charge, and the ions ag-gregate in a crystal matrix with a precise geometry. Such ag-gregations are what we know as salt crystals. If a salt such asNaCl is placed in water, the electrical attraction of the watermolecules, for reasons we will point out later in this chapter,disrupts the forces holding the ions in their crystal matrix,causing the salt to dissolve into a roughly equal mixture offree Na+ and Cl ions.

An ionic bond is an attraction between ions of oppositecharge in an ionic compound. Such bonds are notformed between particular ions in the compound;rather, they exist between an ion and all of theoppositely charged ions in its immediate vicinity.

2.3 Chemical bonds hold molecules together.

Covalent Bonds BuildStable MoleculesCovalent bonds form when two atomsshare one or more pairs of valenceelectrons. Consider hydrogen (H) as anexample. Each hydrogen atom has anunpaired electron and an unfilled outerenergy level; for these reasons the hy-drogen atom is unstable. When twohydrogen atoms are close to eachother, however, each atoms electroncan orbit both nuclei. In effect, the nu-clei are able to share their electrons.The result is a diatomic (two-atom)molecule of hydrogen gas (figure 2.10).

The molecule formed by the two hy-drogen atoms is stable for three reasons:

1. It has no net charge. The di-atomic molecule formed as a resultof this sharing of electrons is notcharged, because it still containstwo protons and two electrons.

2. The octet rule is satisfied.Each of the two hydrogen atomscan be considered to have two or-biting electrons in its outer energylevel. This satisfies the octet rule,because each shared electron orbitsboth nuclei and is included in theouter energy level of both atoms.

3. It has no free electrons. Thebonds between the two atomsalso pair the two free electrons.

Unlike ionic bonds, covalent bondsare formed between two specific atoms, giving rise to true,discrete molecules. While ionic bonds can form regular crys-tals, the more specific associations made possible by covalentbonds allow the formation of complex molecular structures.

Covalent Bonds Can Be Very Strong

The strength of a covalent bond depends on the number ofshared electrons. Thus double bonds, which satisfy the oc-tet rule by allowing two atoms to share two pairs of elec-trons, are stronger than single bonds, in which only oneelectron pair is shared. This means more chemical energy isrequired to break a double bond than a single bond. Thestrongest covalent bonds are triple bonds, such as thosethat link the two nitrogen atoms of nitrogen gas molecules.Covalent bonds are represented in chemical formulations aslines connecting atomic symbols, where each line betweentwo bonded atoms represents the sharing of one pair ofelectrons. The structural formulas of hydrogen gas andoxygen gas are HH and OO, respectively, while theirmolecular formulas are H2 and O2.

Molecules with Several CovalentBonds

Molecules often consist of more thantwo atoms. One reason that larger mole-cules may be formed is that a given atomis able to share electrons with more thanone other atom. An atom that requirestwo, three, or four additional electronsto fill its outer energy level completelymay acquire them by sharing its elec-trons with two or more other atoms.

For example, the carbon atom (C)contains six electrons, four of which arein its outer energy level. To satisfy theoctet rule, a carbon atom must gain ac-cess to four additional electrons; that is,it must form four covalent bonds. Be-cause four covalent bonds may form inmany ways, carbon atoms are found inmany different kinds of molecules.

Chemical Reactions

The formation and breaking of chemi-cal bonds, the essence of chemistry, iscalled a chemical reaction. All chemi-cal reactions involve the shifting of at-oms from one molecule or ionic com-pound to another, without any changein the number or identity of the atoms.For convenience, we refer to the origi-nal molecules before the reaction startsas reactants, and the molecules result-ing from the chemical reaction as prod-ucts. For example:

A B + C D A C + B + Dreactants products

The extent to which chemical reactions occur is influ-enced by several important factors:

1. Temperature. Heating up the reactants increasesthe rate of a reaction (as long as the temperature isntso high as to destroy the molecules).

2. Concentration of reactants and products. Reac-tions proceed more quickly when more reactants areavailable. An accumulation of products typicallyspeeds reactions in the reverse direction.

3. Catalysts. A catalyst is a substance that increases therate of a reaction. It doesnt alter the reactions equi-librium between reactants and products, but it doesshorten the time needed to reach equilibrium, oftendramatically. In organisms, proteins called enzymescatalyze almost every chemical reaction.

A covalent bond is a stable chemical bond formed whentwo atoms share one or more pairs of electrons.


FIGURE 2.10Hydrogen gas. (a) Hydrogen gas is adiatomic molecule composed of twohydrogen atoms, each sharing its electronwith the other. (b) The flash of fire thatconsumed the Hindenburg occurred whenthe hydrogen gas that was used to inflate thedirigible combined explosively with oxygengas in the air to form water.

H2 (hydrogen gas)

Covalent bond

+ +

(a)

(b)

Chemistry of WaterOf all the molecules that are common on earth, only wa-ter exists as a liquid at the relatively low temperatures thatprevail on the earths surface, three-fourths of which iscovered by liquid water (figure 2.11). When life was origi-nating, water provided a medium in which other moleculescould move around and interact without being held inplace by strong covalent or ionic bonds. Life evolved as aresult of these interactions, and it is still inextricably tiedto water. Life began in water and evolved there for 3 bil-lion years before spreading to land. About two-thirds ofany organisms body is composed of water, and no organ-ism can grow or reproduce in any but a water-rich envi-ronment. It is no accident that tropical rain forests arebursting with life, while dry deserts appear almost lifelessexcept when water becomes temporarily plentiful, such asafter a rainstorm.

The Atomic Structure of Water

Water has a simple atomic structure. It consists of an oxy-gen atom bound to two hydrogen atoms by two single cova-lent bonds (figure 2.12a). The resulting molecule is stable: itsatisfies the octet rule, has no unpaired electrons, and carriesno net electrical charge.

The single most outstanding chemical property of wa-ter is its ability to form weak chemical associations withonly 5 to 10% of the strength of covalent bonds. This

property, which derives directly from the structure of wa-ter, is responsible for much of the organization of livingchemistry.

The chemistry of life is water chemistry. The way inwhich life first evolved was determined in large part bythe chemical properties of the liquid water in whichthat evolution occurred.


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1 The Science of Biology