ro y PRE Ce ae Pr RCe etn Rais era) < 130f1478 > Pha @ Levels of Biology Learning Outcome: 4. Explain how life can be viewed at different levels'of biologicalicomplexity. Let’s begin our journey through the wonderful world of biology by considering how life is organized. The term organism can be applied to all forms of life. Organisms maintain an internal order that is separated from the environment. The complexity of living organisms can be analyzed at different levels, starting with the smallest level of organization and progressing to levels that are physically much larger and more complex. @ Figure 1.3 depicts a biologist’s view of the levels of biological organization. @: W- Figure 13. The levels of biological organization. GIs akeeLs At which level of biological organization would you place a herd of br -arnar seen Taal saclaaasdeaRTAAEEAA aR RTcet x + Rca nat Rute aecuy < 130f1478 > Phas Cirexeisg At which level of biological organization would you place a herd of buffalo? Answer : 1. Atoms. An atom is the smallest unit of an element that has the chemical properties of the element. All matter is composed of atoms. 2. Molecules and macromolecules. As discussed in @ Unit 1, atoms bond with each other to form moleentes, A polymer such as a polypeptide is formed of many molecules bonded together and alled ids (DNA and RNA) are important macromolecules found in living organisms. olecul ror Carbohydrates, proteifis, and nuclei 3. Cells, The simplest unit of life is the cell, which we will examine in © Unit 11, A cell is surrounded by a membrane and contains a variety of molecules and macromolecules. Unicellulat organisms are composed of one cell, whereas multicellular organisms, such as plants and animals, contain many cells 4, Tissues. In multicellular organisms, many cells of the same type associate with each other to form tissues. An example is muscle tissue. 5. Organs. In complex multicellular organisms, an organ is composed of two or more types of tissue. For example, the heart is composed of several types of tissues, including muscle, nervous, and connective tissue. Page 3 6. Organism. All living things can be called organisms. Biologists classify organisms as belonging to a particular species, which is a related group of organisms that share a distinetive form and set of attributes in nature. The members of the same species are closely related genetically. In Units VI and (@ VII, we will examine plants and animals at the levels of cells, tissues, organs, and complete organisms. 7. Population. A group of organisms of the same species that occupy the same environment is called a population 8. Community. A biological community is an assemblage of populations of different species. The types of species found in a community are determined by the environiieut and by the interactions of the species with each other. 9. Feoxystem, Researchers may extend their work beyond living organisms and also study the physical environment. Ecologists analyze ecosystems, which are formed by the interactions of a. community of organisms with their physical environment. organization from populations to ecosystems. Unit VIII considers biological 10. Biosphere. The biosphere includes all of the places on the Earth where living organisms exist. Life is found in the air, in bodies of water, on the land, and in the soil.See aa Rca nat Rute aecuy < 14ofta7a > Oe Aa o © | Page 4 1.2 | 4y Core Concepts of Biology Learning Outcome: 4. Describe the core concepts of biology as advocated by Vision and Change. In 2007, the American Association for the Advancement of Science initiated a series of regional conversations with more than 200 biology faculty to discuss how to improve undergraduate biology education. In 2009, using the findings of these regional conversations, the organization held a conference called Vision and Change in Undergraduate Biology Education. More than 500 biology faculty, college and university administrators, representatives of professional societies, and students and postdoctoral scholars from around the country attended the conference. The proceedings led to various recommendations that can be found at http://visionandchange.org. A key outcome of Vision and Change was the identification of five core concepts of biology (@ Figure 1.4) 1. Evolution: The diversity of life evolved over time by processes of mutation, natural selection, and genetic exchange. 2. Structure and function: Basic units of structure define the function of all living things. 3. Information flow, exchange, and storage: The growth and behayior of organisms are activated through the expression of genetic information. 4, Pathways and transformations of encigy sii siaiier: Biological systems grow and change via processes that are based on chemical transformation pathways and are governed by the laws of thermodynamics. 5. Systems: Living systems are interconnected and interacting. The interactions of living systems result in emergent properties, which are properties that manifest themselves as the result of various system components working together, not as a property of any individual component. (a) Evolution: Biological evolution, or simply tePM Sat 9 Sep Peon cme ae Rec te aes ee CR ene Rue ee < 140f1478 > On vAatee es” RR ) (a) Evolution: Biological evolution, or simply evolution, refers to a heritable change in a population of ry organisms from generation to generation. As a result of evolution, populations become better adapted to the environment in which they live. For example, the long snout of an anteater is an adaptation that enhances its ability to obtain food, namely ants, from hard-to-reach places. Over the course of many generations, the fossil record indicates that the long snout occurred via biological evolution in which modern anteaters evolved from populations of organisms with shorter snouts. (b) Structure and function: Biologists often say “structure determines function.” This core concept pertains to very tiny biological molecules and to very large biological structures. The feet of different birds provide a striking example. Aquatic birds have webbed feet that function as paddles for swimming. By comparison, the feet of nonaquatic birds are not webbed and are better adapted for grasping food, perching on branches, and running along the ground. The structure ofrE Ca) < 14ofta7a > fe) £5) ae along the ground. The structure of a bird's feet, webbed versus nonwebbed, is a critical feature that affects their function. (c) Information: Genetic material composed of DNA (deoxyribonucleic acid) provides a blueprint for the organization, development, and function of living things. During reproduction, a copy of this blueprint is transmitted from parents to offspring. DNA is heritable, which means that offspring inherit DNA from their parents. A key feature of reproduction is that offspring tend to have characteristics that greatly resemble those of their parent(s). As seen here, this mother dolphin and her offspring have strikingly similar features. (d) Energy and matter: Allliving organisms acquire energy and maiter from the environment and use them to synthesize essential molecules and maintain the organization of their cells and bodies. These sunflower plants carry out photosynthesis, in which they capture light energy and acquire carbon dioxide and water, thereby allowing them to make carbohydrates. This process provides energy and organic molecules, allowing the plants to grow and produce beautiful flowers. a ee |ee M Sign In | Connect | McC pete tec ae ie PR et Rue eRe < 140f1478 > Gay bodies: These suntiower plants carry out photosynthesis, in which they capture light energy and acquire carbon dioxide and water, thereby allowing them to make carbohydrates. This process provides energy and organic molecules, allowing the plants to grow and produce beautiful flowers. (e) Systems: When the parts of an organism interact with each other or with the external environment to create novel structures and functions, the resulting characteristics are called \_"S) vemergentipropertis. Forexample) the humanveye is composed of many differenttypés of cellsithat are orgahizéd to sense incoming light and transmit signals to the brain, Our ability to see is an emergent property of this complex arrangement of different cell types. Biologists use the term systems biology to describe the study of how new properties of life emerge due to complex interactions of its individual parts. sy Figure 1.4 Core concepts of biology, as advocated by Vision and Change. These core concepts will Be emphasized throughout this textbook. 2: Lucas Leuzinger/Shutterstock: b: GK. & Vikki HartiGetty Images: c: mage Source/Getty Images; ¢: Photo by Bruce Fritz/USDA Maria Telleiro/Getty Images Page See Co) y Seen a Rca nat Rute aecuy < 160f1478 > ) £5) a Z Classification of Living Things Learning Outcome: 1. Outline how organisms are classified. As biologists study species and discover new species, they try to place them into groups based on their evolutionary history. This is a difficult task because researchers estimate that the Earth has between 5 and 50 million different species! The rationale for classification is based on vertical descent. Species with a recent common ancestor are grouped together, whereas species whose common ancestor was in the very distant past are placed into different groups. The field of biology that is concerned with the grouping and classification of species is termed taxonomy. Why is taxonomy useful? First, taxonomy allows us to appreciate the amazing diversity of life on Earth. Also, because taxonomy is based on evolution, it provides a view of the evolutionary relationships among living species and the relationships between living and extinct species. The Classification of Living Organisms Allows 2 Biologists to Appreciate the Unity and Diversity of Life Let's first consider taxonomy on a broad scale. You may have noticed that a Figure 1.8 showed three main groups of organisms. From an evolutionary perspective, all forms of life can be placed into those three large categories, or domains, called Bacteria, Archaea, and Eukarya (@ Figure 1.11). Bacteria and archa otic because their cell structure is relatively simple. At the molecular level, bacterial and archaeal cells show significant differences in their compositions. By comparison, organisms in the domain Eukarya are eukaryotic and have cells with internal compartments that serve various functions. A defining distinction between prokaryotic and eukaryotic cells is that eukaryotic cells have a col Lnucleus in which the genetic material is surrounded by a membrane. are microorganisms that are also termed prok: Page ILnin |Connect|McGr X | fi 1.4 Classification of Livin X ++ G@ Sener ian ec icy < 16 0f1478 > (o) Domain Sector: Mestyunletlr prokaryotes that inhabit (@) Domain Achaea: Unicel prokaryotes that often Ive mn extreme Plants Mute orpensms hat can cary cat Photooynnes. Fungl Uncelor and mutes organs hathave 8 et ‘Animal: Mulcelior organs that uly have 8 neue (0 Doman Eutarya:Uncetsa and mulceu organisms heving ces wth tel compares that serve vous functors Figure 11 The three domains of life. Two of these domains, (a) Bacteria and (b) Archaea, consist of species with prokaryotic cells. The third domain, (<) Eukarya, comprises species that are eukaryotes. 2 BSIPlagetotostock;b: Eye of Science/Science Source; (protist}: Jan Hinseh/Getty Images; plants: Kent Foster/Science Source; c (ungl: Carl Schmidt-Luchs/Science Source; c (animals Ingram Publishinglage fotostockoes M Sign In | Connect | Mc 1.4 Classification of Livin X ++ Rca nat Rute aecuy < 160f1478 > Oe Aa (© Doman Eukarya: Unketar and mutes organisms having cel with Interna compartment that seve varius funcons. Figure 111 The three domains of life. Two of these domains, (a) Bacteria and (b) Archaea, consist of species with prokaryotic cells, The third domain, (c) Eukarya, comprises species that are eukaryotes 2a: BSIP/agefotostock: b: Eye of Scionce/Scionce Source: c(protsts: Jan HinschiGetty Images: ¢ (plants: Kent Foster/Science ‘Source; ¢ fungi) Carl Schmiet-Luchs/Science Source; ¢ (animals: Ingram Publishinglage fotostock Core Skill: Connections Look ahead to Figure 251. Are fungi more closely related to plants or animals?Answer & Click the arrowheads to expand. v Y Figure 254 Donan: (Eo r 7 Exkoyote supergiouns Type pots: A Large eukaryote ‘engaons: 5 a6 x Figure 25. A classification system for living and extinct organisms. All organisms are grouped into three domains: Bacteria, Archaea, and Eukarya. Eukaryotes are divided into seven supergroups. These seven ‘Supergroups encompass most eukaryotes. However, several small eukaryotic lineages are classified outside of the seven supergroups. v Y Additional eBook Question In the phylogenetic tree, which is shown in Figure 25.1, species with more recent ancestors are grouped more closely together. Fungi and animals had a common ancestor that was a type of protist in the supergroup named Opisthokonta. 2/7 —— FZ | ot POYMEoes M Sign in| Connect | Me Peer ae Pence mim te Mure eRooy @ < 160f1478 > Oe Aa aa the seven supergroups. = ee v Y Additional eBook Question In the phylogenetic tree, which is shown in Figure 25.1, species with more recent ancestors are grouped more closely together. Fungi and animals had a common ancestor that was a type of protist, in the supergroup named Opisthokonta. 32 ose ae oy 2 ¢ 2 ee Panes ey goede re tea a this phylogeny, the mammals would been extension below the Arata Kingdom ea thet there an evolutionary path from Mammalia to Animalia to Opisthokonta to Eukarya. Of these groups, which would you expect to contain the largest number of species? oO Opisthokonta b Animalia O° Oc mammatia oO d Eukarya The organisms in domain Eukaspewereoreesabeereiecsiresteeeniaior categories. orSey M Sign In | Connect | Mc 1.4 Classification of Livin X + Rca nat Rute aecuy < 160f1478 > Oe Aa The organisms in domain Fukarya were once subdivided into four major categories, or kingdoms, called Protista (protists), Plantae (plants), Fungi, and Animalia (animals). However, |“) as discussed in @ Chapter 25 and gathered new information regarding the evolutionary relationships of these organisms. We now know that the protisis do not form a single kingdom but instead are divided into several broad categories called supergroups. Unit V, this traditional view became invalid as biologists Each Species Is Placed into a Taxonomic Hierarchy Taxonomy involves multiple levels in which particular species are placed into progressively smaller and smaller groups whose members are more closely related to each other evolutionarily. Such an approach emphasizes the unity and diversity of different species. As an example, let’s consider the clownfish, a popular saltwater aquarium fish (@ Figure 1.12). Several species of clownfish fiave been identified Tmonomle The ocelors Approximatetime Approximate Examples group clownfléh when the common numberof Istoundin —ancestorforthia "modem specles sroup arose, inthis group Domain Ewan 2.0000 5000000 G Ce Le @ 4 Revere] [Oretetereta (aoe > t000000 aD G Cw ‘fo @ 4 monn nme cm ote DIL ae ee | asc ms Atoptn—20.mn 20000 YD G eG we eri [receretil focee 7000 QD G G Family Pomacentidae - 40 mya 380 YD gg onus Amptron - mya 2 QDoes M Sign In | Connect | Mc 1.4 Classification of Livin X ++ Rca nat Rute aecuy < 160f1478 > Oe Aa Genus Amphivion = 9mya Fy & D weecee cowlos <3 1 @ Figure 142 Taxonomic classification of the ocellaris clownfish. CARS Why is i useful to place organism Answer groupings? One species of clownfish, which is orange with white stripes, has several common names, including ocellaris clownfish. The broadest grouping for this clownfish is the domain, namely, Eukarya, followed by progressively smaller divisions, from supergroup (Opisthokonta), to kingdom (Animalia), and eventually to species. In the animal kingdom, clownfish are part of a phylum, Chordata, the chordates, which is subdivided into classes. Clownfish are in a class called Actinopterygii, which includes all ray-finned fishes. The common ancestor that gave rise to ray-finned fishes arose about 420 million years ago (mya). Actinopterygii is subdivided into several smaller orders. The clownfish are in the order Perciformes (bony fish). The order is, in turn, divided into families; the clownfish belong to the family of marine fish called Pomacentridae, which are often brightly colored. Families are divided into genera (singular, genus). The genus Amphiprion is composed of 28 different species; these are various types of clownfish. Therefore, the genus contains species that are very similar to each other in form and have evolved from a common (extinct) ancestor that lived relatively recently on an evolutionary time scale. Biologists use a two-part description, called binomial nomenclature, to provide each species with a unique scientific name. The scientific name of the ocellaris clownfish is Amphiprion ocellaris. The first word is the genus, and the second word is the specific epithet, or species descriptor. By convention, the genus name is capitalized, whereas the specific epithet is not. Both names are italicized, Scientific names are usually Latinized, which means they are made similar in appearance to Latin words. The origins of scientific names are typically Latin or Greek, but they can come from a variety of sources, including a person's name.oes r In| Connect | Me 1.5 Biology asa Scientifi X + Rca nat Rute aecuy < 17o0f1478 > Pp i BiolSby as a Scientific Discipline Learning Outcomes: 4. Explain how researchers study biology at different levels, ranging from molecules to ecosystems. 2. CoreSKILL » Distinguish between discovery-based science and hypothesis testing, and describe the steps of the scientific method. ‘What is science? Surprisingly, the definition of science is not easy to state. Most people have an idea of what science is, but actually articulating that idea proves difficult. In biology, we can define science as the observation, identification, experimental investigation, and theoretical explanation of natural phenomena. Science is conducted in different ways and at different levels. Some biologists study the molecules that compose life, and others try to understand how organisms survive in their natural nments. Experimentally, researchers often focus their efforts on mode! org organisms studied by many different researchers so they can compare their results and determine scientific principles that apply more broadly to other species. Examples of model organisms include Escherichia coli (a bacterium), Saccharomyces cerevisiae (a yeast), Drosophila melanogaster (fruit fly); Caenorhabditis elegans.(a-nematode worm), Mus musculus (mouse), and Arabidopsis thaliana (a flowering plant). Model organisms offer experimental advantages over other species. For example, £. colt is a very simple organism that can be easily grown in the laboratory. By limiting their work to a few model organisms, researchers can gain a deeper understanding of these species, and their results may apply more broadly to other species, including humans. Page 13 In this section, we will examine how biologists follow a standard approach, called the scientific m ethod, to test their ideas. We will explore how scientific knowledge makes predictions that can be experimentally tested. However, not all discoveries are the result of researchers following the scientific method. Some discoveries are made simply by gathering new information. As illustrated earlier, in @ Figure 1.1 the characterization of many living organisms has led to the development of important medicines. In this section, we will also consider how researchers often set out on fa finding missions aimed at uncovering new information that may eventually lead to important discoveries in biology.Sey M Sign In | Connect | Mc eee eee ae Rca nat Rute aecuy < 1701478 > Oe Aa Biologists Investigate Life at Different Levels of ® Organization In © Figure 1.3, we examined the various levels of biological organization. The study of these different levels depends not only on the scientific interests of biologists but also on the tools available to them, + The study of organisms in their natural environments is a branch of biology called ecology, which considers populations, communities, and ecosystems ((@) Figure 1.13a), + Some researchers examine the structures and functions of plants and animals; these subjects form the disciplines called anatomy and phy + With the advent of microscopy, cell biology, which is the study of cells and their interactions, became an important branch of biology in the early 1900s and remains so today (@ Figure 1.13¢). + In the 1970s, genetic tools became available for studying single genes and the proteins they encode. This genetic technology enabled researchers to study individual molecules, such as proteins, in living cells and thereby gave rise to the field of molecular biology. Together with biochemists and biophysicists, molecular biologists focus their efforts on the structure and function of the molecules of life (@ Figure 1.134). Such researchers want to understand how biology works at the molecular and even atomic levels. Overall, the 20th century saw a progressive increase in the number of biologists who used an approach to understanding biology called reduetionism—reducing complex systems to simpler components as a way to understand how the system works. In biology, reductionists study the parts of a cell or organism as individual units. + In the 1990s, the pendulum began to swing in the other direction. Scientists have invented new tools that allow them to study groups of genes (genomic techniques) and groups of proteins (proteomic techniques). Biologists now use the term systems biology to describe research aimed at understanding how emergent properties arise. This term is often applied to the study of cells. In this context, systems biology may involve the investigation of groups of genes that encode proteins with a common purpose (( Figure 1.13e). For example, a systems biologist may conduct experiments that try to characterize an entire cellular process, which is driven by dozens of different proteins. Page 14 + However, systems biology is not new. Animal and plant physiologists have been studying the functions of complex organ systems for centuries. Likewise, ecologists have been characterizing ecosystems for a very long time. The excitement surrounding systems biology inoes Cenc me eae Lee a G@ Pee Bcc re mUIR ces eer onc) < 1701478 > POE Age i Pree 14 [=] + However, systems biology is not new. Animal and plant physiologists have been studying the functions of complex organ systems for centuries. Likewise, ecologists have been characterizing ecosystems for a very long time. The excitement surrounding systems biology in logists to study recent years has been the result of new experimental tools that allow complex interactions at the molecular level sss sy species in Anatomists and pasos ‘reanams ae ried o hr (2) Ecoloay— population’ (©) Anstomy and physiology — communityeconytors {sssveorganvorganim levels fevele al bts ten we Moles bok and calls nation reels te (e)eaoonycetularievels _&)Melecl bony tomicimolecatovela \coe Cee cme eae Lee a @ Eyer Rc cre CRRA reer oR) < 0f1478 > P ba (0) Systems biology loves, shown here a the molecular level Figure 143. Biological investigation at different levels of organization. «a: Purestock/SuperStock; b: Diane NeIson;c: Erk IsaksorvBlend Images; d: Dmytro Zinkewych/Alamy Stock Photo; e: Andrew Brookes/Corbis/Getty Images: ¢ (ise): Alfred Pasioka/Science Source A Hypothesis Is a Proposed Idea, Whereas a Theory Is a Broad Explanation Backed by Extensive Evidence Let's now consider the process of science. In biology, a liothesis is a proposed explanation for a.natutal fphgnofiends) It is a proposition based on previous observations or experimental studies. For example, with knowledge of seasonal changes, you might hypothesize that maple trees drop their leaves in the autumn because of the shortened amount of daylight. An alternative hypothesis might be that the trees drop their leaves because of lower temperatures. In biology, a hypothesis requires more work by researchers to evaluate its validity. A useful hypothesis must make predictions~expected outcomes that can be shown to be correct or incorrect. In other words, a useful hypothesis is testable, which means that the hypothesis can be shown to be consistent or inconsistent with data that are obtained via experimentation. If a hypothesis is incorrect, it should be falsifiable—it can be shown to be incorrect by additional observations or experimentation. Alternatively, a hypothesis may be correct, so further work will not disprove it, In such es, We say that the researchers have failed to reject the hypothesis, Even so, in science, a hypothesis is never really proven but rather always remains provisional, Researchers accept the possibility that perhaps they have not yet conceived of the correct hypothesis. After many experiments, biologists may conclude that a hypothesis is consistent with known data, but they should never say the hypothesis is provencoe Cee cme eae Lee a @ Eyer Rc cre CRRA reer oR) < 0f1478 > P hao hypothesis, After igéy experiments, biologists may conclude that a hypothesis is consistent wit known data, but they should never say the hypothesis is proven. ®) By comparison, a theory, as the term is used in biology, is a broad explanation of some aspect of the natural world that is substantiated by a large body of evidence. Biological theories incorporate observations, hypothesis testing, and the laws of other disciplines such as chemistry and physics. Theories are powerful because they allow us to make many predictions about the properties of living organisms. ‘As an example, let's consider the theory that DNA is the genetic material and that it is organized into units called genes. An overwhelming body of evidence has substantiated this theory. Thousands of living species have been analyzed at the molecular level. All of them have been found to use DNA as their genetic material and to express genes that produce the proteins that lead to their characteristics. This theory makes many valid predictions. For example, certain types of mutations in genes are expected to affect the tra of organisms. This prediction has been confirmed experimentally. Similarly, this theory predicts that genetic material is copied and transmitted from parents to offspring. Through comparisons of the DNA of parents and offspring, this prediction has also been confirmed. Furthermore, the theory explains the observation that offspring resemble their parents. Overall, two key attributes of a scientific theory are (1) consistency with a vast amount of known data and (2) the ability to make many correct predictions, The meaning of the term theory is sometimes muddled, because the word is used in different situations. In everyday language, a theory is often viewed as little more than a guess. For example, a person might say, “My theory is that Professor Simpson did not come to class because he went to the beach.” However, in biology, a theory is much more than a gue: theory is an established set of ideas that explains a vast amount of data and offers valid predictions that can be tested. Like a hypothesis, a theory can never be proven to be true. Scientists acknowledge that they do not know everything. Even so, biologists would say that theories are extremely likely to be true, based on all known information. In this regard, theories are viewed as knowledge, which is the awareness and understanding of information. ‘oday A Discovery-Based Science and Hypothesis Testing Are Scientific Approaches That Help Us Understand Biology The path that leads to an important discovery is rarely a straight line, Rather, scientists ask questions, make observations, ask modified questions, and may eventually conduet experiments to test their hypotheses. The first attempts at experimentation may fail, and new experimentalcoe Cee cme eae Lee a @ Eyer Rc cre CRRA reer oR) < 1701478 > Oe Aa Discovery-Based Science and Hypothesis Testing | _~ Are Scientific Approaches That Help Us Understand Biology The path that leads to an important discovery is rarely a straight line, Rather, scientists ask questions, make observations, ask modified questions, and may eventually conduct experiments to test their hypotheses. The first attempts at experimentation may fail, and new experimental approaches may be needed. To suggest that scientists follow a rigid scientific method is an oversimplification of the process of science. Scientific advances often occur as scientists dig deeper and deeper into a topic that interests them. Curiosity is the key phenomenon that sparks scientific inquiry. How is biology actually conducted? As discussed next, researchers typically follow two general types of approaches: discovery-based science and hypothesis testing. Discovery-Based Science 0 The collection and analysis of data without the need for a preconceived hypothesis is called e, or simply discovery science. Why is discovery-based science carried out? The information gained from discovery-based science may lead to the formation of new hypotheses and, in the long run, may have practical applications that benefit people. Researchers, for example, have identified and begun to investigate previously unknown genes within the human genome without already knowing the function of those genes. The goal is to gather additional clues that may eventually allow them to propose a hypothesis that explains a gene’s function Discovery-based science often leads to hypothesis testing. Hypothesis Testing In biological science, the scientific method, also known as hypothesis testing, is usually followed to formulate and test the validity of a hypothesis. This strategy may be described as a five-step method: 1. Observations are made regarding natural phenomena. 2. These observations lead to a hypothesis that tries to explain the phenomena. A useful hypothesis is one that is testable because it makes specific predictions. . Experimentation is conducted to determine if the predictions are correct. 4. The data from the experiment are analyzed. 5. The hypothesis is considered to be consistent with the data, or it is rejected Page 15Doe uee ae Reet cr Malice el iaecuy < 170f1478 > Phas m Pages The scientific method is intended to be an objective way to gather knowledge. As an exampl let's return to the question of why maple trees drop their leaves in autumn. By observing the length of daylight throughout the year and comparing that data with the time of the year when leaves fall, one hypothesis might be that leaves fall in response to shorter periods of daylight (@ Figure 1.14). This hypothesis makes a prediction—exposure of maple trees to shorter periods of daylight will cause their leaves to fall. To test this prediction, researchers would design and conduct an experiment, |. OBSERVATIONS The leaves on maple trees fall in autumn when the days get colder and shorter. Pe HYPOTHESIS The shorter amount of daylight causes the leaves to fall. 3. EXPERIMENTATION Small maple trees are grown in 2 greenhouses where the only variable is the length of daily light. ms Control group: Amount of daily light remains constant for 180 days. Experimental group: Amount of daily light becomes progressively shorter for 180 days. 4. THE DATA : A statistical analysis can 33 determine if the control and the experimental data are significantly different. In thisDoe uee ae @ prod.reader-ui.prod.mheducation.com < 1701478 > ean & a |. OBSERVATIONS The leaves on maple trees fall in autumn when the days get colder’ and shorter. 2. HYPOTHESIS The shorter amount of daylight causes the leaves to fall. }. EXPERIMENTATION Small maple trees are grown in 2 greenhouses where the only variable is the length of daily light. Control group: Amount of daily light remains constant for 180 days. Experimental group: Amount of daily light becomes progressively shorter for 180 days. |. THE DATA 8 A statistical analysis can determine if the control and the experimental data are significantly different. In this Control Experimental case, they are, con up leaves dronpes 100 i 5 5. CONCLUSION The hypothesis cannot be rejected. 4 Figure 144 The steps of the scientific method, also known as hypothesis testing. Core Skill: Process of Science In this example, the goal is to test the hypothesis that maple trees, drop their leaves in the autumn due to the shorter amount of daylight.1.5 Biology asa Scientifi X + Rca nat Rute aecuy < 0f1478 > Answer (vo How is hypothesis testing conducted? Although hypothesis testing may follow many paths, certain experimental features are common to this approach. First, data are often collected in two parallel ways. One set of experiments is done on the control grou whereas another set is conducted on the group. In an ideal experiment, the control and experimental groups differ by only one factor. For example, an experiment could be conducted in which two groups of trees are observed, and the only difference between their environments is the length of light each day. To conduct such an experiment, researchers would grow small trees in a greenhouse where they could keep other factors such as temperature, water, and nutrients the same between the control and experimental groups, while providing the two groups with different amounts of light via artificial lighting, In the control group, the number of hours of light provided would be kept constant each day, whereas in the experimental group, the amount of light provided each day becomes progressively shorter to mimic seasonal light changes. The researchers would then record the number of leaves dropped by the two groups of trees over a certain period of time. Another key feature of hypothesis testing is data analysis. The result of experimentation is a set of data from which a biologist tries to draw conclusions. Biology is a quantitative science. When experimentation involves control and experimental groups, a common form of analysis is to determine if the data collected from the two groups are truly different. Biologists apply statistical analyses to their data to determin: the outcomes from the control and experimental groups are likely to differ because of the single variable that is different between the two groups. When differences between the control and experimental data are statistically significant, they are not likely to have occurred as a matter of random chance. In our example in © Figure 1.14, the trees in the control group dropped far fewer leaves than did those in the experimental group. A statistical analysis could determine if the data collected from the two greenhouses are significantly different from each other. If the two sets of data are found not to be significantly different, the hypothesis will be rejected. Alternatively, if the differences between the two sets of data are significant, as shown in © Figure 1.14, biologists can conclude that the hypothesis is consistent with the data, though it is not proven. A hallmark of science is that valid experiments are repeatable, which means that similar results are obtained when an experiment is conducted on multiple occasions. For our example in igure 1.14, the data would be valid only if the experiment was repeatable. Page 16 As described next, discovery-based science and hypothesis testing are often used together to learn more about a particular sesestifiedopionbetemetasaplepietiedook at how both approachesee Cee cme eae Lee a @ Eyer Rc cre CRRA reer oR) < 1701478 > Oe Aa sage te As described next, discovery-based science and hypothesis testing are often used together to 2) Iearn more about a particular scientific topic. As an example, let’s look at how both approaches led to successes in the study of the disease called cystic fibrosis. The Study of Cystic Fibrosis Provides Examples of Discovery-Based Science and Hypothesis Testing Let's consider how biologists made discoveries related to the disease cystic fibrosis (CF), which affects about | in every 3,500 Americans. Persons with CF produce abnormally thick and sticky mucus that obstructs the lungs and leads to life-threatening lung infections. The thick mucus also blocks ducts in the pancreas, which prevents the digestive enzymes this organ produces from reaching the intestine, Without these enzymes, the intestine cannot fully absorb amino acids and fats, which can cause malnutrition. Persons with this disease may also experience liver damage because the thick mucus can obstruct the liver. On average, people with CF in the United States, currently live into their late 30s. Fortunately, as more advances have been made in treatment, this number has steadily increased. Because of its medical significance, many scientists are interested in CF and are conducting studies aimed at gaining greater information regarding its underlying cause. The hope is that knowing more about the disease may lead to improved treatment options, and perhaps even a cure. As described next, discovery-based science and hypothesis testing have been critical to gaining a better understanding of this The CFTR Gene and Discovery-Based Science In 1935, American physician Dorothy Andersen determined that cystic fibrosis is a genetic disorder. Persons with CF have inherited two faulty CFTR genes, one from each parent. (We now know this gene encodes a protein named the cystic fibrosis transmembrane regulator, abbreviated CFTR.) In the 1980s, researchers used discovery-based science to identify this gene. Their search for the CFTR gene did not require any preconceived hypothesis regarding the function of the gene. Rather, they used genetic strategies similar to those deseribed in Chapter 21. Research groups headed by Lap-Chee Tsui, Francis Collins, and John Riordan identified the CFTR gene in 1989. The discovery of the CFTR gene made it possible to devise diagnostic testing methods to determine if a person carries a faulty version of that gene. In addition, the characterization of the CFTR gene provided important clues about its function. Researchers observed striking similarities between the CFTR gene and other genes that were already known to encode proteinsee Cee cme eae Lee a @ Eyer Rc cre CRRA reer oR) < 0f1478 > P ba The CFTR Gene and Discovery-Based Science In 1935, American physician Dorothy Andersen determined that cystic fibrosis is a genetic disorder. Persons with CF have inherited two faulty CFTR genes, one from each parent. (We now know this gene encodes a protein named the cystic fibrosis transmembrane regulator, abbreviated CFTR.) In the 1980s, researchers used discovery-based science to identify this gene. Their search for the CFTR gene did not require any preconceived hypothesis regarding the function of the gene. Rather, they used genetic strategies similar to those described in Chapter 21. Research groups headed by Lap-Chee Tsui, Francis Collins, and John Riordan identified the CFTR gene in 1989. The discovery of the CFTR gene made it possible to devise diagnostic testing methods to determin ation of a person carries a faulty version of that gene. In addition, the charact the CFTR gene provided important clues about its function. Researchers observed striking similarities between the CFTR gene and other genes that were already known to encode proteins that function in the transport of substances across membranes, Based on this observation, as well as other kinds of data, the scientists hypothesized that the function of the normal CFTR gene is to encode a transport protein. In this way, the identification of the CFTR gene led them to conduct experiments aimed at testing a hypothesis about its function. The CFTR Gene and Hypothesis Testing Researchers interested in the CFTR gene also considered studies showing that patients with CF have an abnormal regulation of salt balance across their plasma membranes. They hypothesized that the normal CFTR gene encodes a protein that functions in the transport of chloride ions (CI) across the membranes of cells ((@ Figure 1.15). This hypothesis led to experimentation that tested normal cells and cells from CF patients for their ability to transport CI”. The CF cells were found to be defective in chloride transport. In 1990, scientists successfully transferred the normal CFTR gene into cells from CF patients in the laboratory. The introduction of the normal gene corrected the cells’ defect in chloride transport. Overall, the results showed that the CFTR gene encodes a protein that transports CI- across the plasma membrane. A mutation in this gene causes it to encode a defective protein, leading to a salt imbalance that affects water levels outside the cell, which explains the thick and sticky mucus in CF patients. In this example, hypothesis testing provided a way to evaluate a hypothesis about how a disease is caused by a genetic change.Doe uee ae Reet cr Malice el iaecuy < 1701478 > fe) £5) 7 costar P][) svertumecendeminess | [*| lung eet pomal CFTR gene Lung cell wehauly OFT gene Figure 115 A hypothesis suggesting an ‘explanation for the defective function of a gene in patients with cystic fibrosis. The normal CFTR gene, which does not carry a mutation, encodes a protein that transports chioride ions (CI’) across the plasma membrane to the outside of the cell. In persons with CF, this protein is defective due to a mutation in the CFTR gene. GAAKeMas xplain how discovery-based science helped researchers to hypothesize that the CFTR gene encodes a transport protein. Answer Biology Is a Social Discipline Finally, it is worthwhile to point out that biology is a social as well as a scientific discipline Several laboratories often collaborate on scientific projects. After performing observations and experiments, biologists communicate their results in various ways. Most importantly, papers are submitted to scientific journals. Following submission, a paper usually undergoes a peer-review pr ‘cess in which other scientists, who are experts in the area, evaluate the paper and make comments regarding its quality. As a result of peer review, a paper is accepted for publication or rejected, or the authors of the paper may be given suggestions for how to revise the work or conduct additional experiments to make it acceptable for publication. Page 17 Another social aspect of research is that biologists often attend meetings where they report their most recent work to the scientific community ((@ Figure 1.16). They comment on each other's ideas and results, eventually putting together the information that builds into scientific theories cower many veare Ac von devel ASSERTS SMPTE onic it ic helnful to diccuec.Doe uee ae @ prod.reader-ui.prod.mheducation.com < 1701478 > ean Finally, it is wort to point out that biology is a social as well as a scientific discipline. [=| Several laboratories often collaborate on scientific projects. After performing observations and experiments, biologists communicate their results in various ways. Most importantly, papers are submitted to scientific journals. Following submission, a paper usually undergoes a peer-review pr ocess in which other scientists, who are experts in the area, evaluate the paper and make comments regarding its quality. As a result of peer review, a paper is accepted for publication or rejected, or the authors of the paper may be given suggestions for how to revise the work or conduct additional experiments to make it acceptable for publication. Page 17 Another social aspect of research is that biologists often attend meetings where they report their most recent work to the scientific community ((@ Figure 1.16). They comment on each other's ideas and results, eventually putting together the information that builds into scientific theories over many years. As you develop your skills at scrutinizing experiments, it is helpful to discuss your ideas with other people, including fellow students and faculty members. Importantly, you do not need to know all the answers before you enter into a scientific discussion. Instead, a more realistic way to view science is as an ongoing and neverending series of questions Figure 146 One of the social aspects of science. Dita Alangkara/AP Photo Core Skill: Communication and Collaboration At scientific meetings, researchers from various disciplines gather together to discuss new data and discoveries. Research that is conducted by professors, students, lab technicians, and industrial participants is sometimes hotly debated.STS Cie ae Rca nat Rute aecuy < 190f1478 > P Ba TTT ola CN Aerts) eet + Biology is the study of life. Discoveries in biology help us understand how life exists, and they also have many practical applications, such as the development of drugs to treat human diseases ((@! Figures 1.1, @ 1.2, 1.1 Levels of Biology + Living organisms can be viewed at different levels of biological organization: atoms, molecules and macromolecules, cells, tissues, organs, organisms, populations, communities, ecosystems, and the biosphere (( Figure 1.3). 1.2 Core Concepts of Biology + Vision and Change has identified five core concepts in biology ((@ Figure 1.4). These are evolution; structure and function; information flow, exchange, and storage; pathways and transformations of energy and matter; and systems. 3 Biological Evolution + Changes in species often occur as a result of modification of pre-existing structures (G' Figure 1.5). + During vertical evolution, mutations in a lineage alter the characteristics of species from one generation to the next. Individuals with greater reproductive success are more likely to contribute their characteristics to future generations, a process known as natural selection. Over the long run, this process alters species and may produce new species ((@ Figure 1.6). + Horizontal gene transfer is the transfer of genetic material from one organism to another organism that is not its offspring. Along with vertical descent with mutation, it is an important process in biological evolution, producing a web of life (@ Figures 1.7, 8). + An analysis of genomes and proteomes helps us to understand how information at the molecular level relates to the characteristics of individuals and how they survive in their native environments ((@ Figure 1.9). + Artificial selection can change the characteristics of a population from generation to generation, such as promoting tame behavior in red foxes ((@! Figure 1.10). 1.4 Classification of Living Thingscee M Sign In | Connect | Mc on ae Rca nat Rute aecuy < 190f1478 > Oe Aa generation, {as promoting tame behavior in red foxes ((@ Figure 1.10). 1.4 Classification of Living Things + Taxonomy is the grouping of species according to their evolutionary relatedness to other species. Going from broad to narrow groups, each species is placed into a domain, a supergroup, a kingdom, a phylum, a class, an order, a family, and a genus (@ Figures 1.11, 1.12). + Biologists use a two-part description, called binomial nomenclature, to provide each species with a unique scientific name. 1.5 Biology as a Scientific Discipline + Biological science is the observation, identifics theoretical explanation of natural phenomena. ion, experimental investigation, and + Biologists study life at different levels, ranging from ecosystems to the molecular components in cells (@ Figure 1.13). + A hypothesis is a proposal to explain a natural phenomenon, A usefull hypothesis makes a testable prediction. A biological theory is a broad explanation that is substantiated by a large body of evidence. + Discovery-based science is an approach in which researchers conduct experiments and analyze data without a preconceived hypothesis. + The scientific method, also called hypothesis testing, is a series of steps to formulate and test the validity of a hypothesis. The experimentation often involves a comparison between control and experimental groups ((2! Figure 1.14). + The study of cystic fibrosis provides an example in which both discovery-based science and hypothesis testing led to key insights regarding the nature of the disease ((@ Figure 1.15). + Biology is a social discipline in which scientists often work in teams. To be published, a scientific paper is usually subjected to a peer-review process in which other scientists evaluate the paper and make suggestions regarding its quality. Advances in science often occur when scientists gather and discuss their data ((@ Figure 1.16) 1.6 Core Skills of Biology + Vision and Change recognized the need to focus on the development of certain skills in students: the ability to apply the process of science; the ability to use quantitative reasoning; the ability to use models and simulation; the ability to tap into the interdisciplinary nature Qbsciepeeetheabiliniecommunicate and collaborate withce Eu y 7 ing Your Knowles X_ + Pn etn cna er icy < 200f1478 > Phas @ Assessing Your Knowledge and Skills Foundational Knowledge Multiple Choice 1. Populations of organisms change over the course of many generations. Many of these changes result in increased survival and reproduction. This phenomenon is a, evolution, b. homeostasis. c. development. d. genetics. e. metabolism. > > Answer . Which of the following is an example of horizontal gene transfer? a, the transmission of an eye color gene from father to daughter b. the transmission of a mutant gene causing cystic fibrosis from father to daughter ¢. the transmission of a gene conferring pathogenicity (the ability to cause disease) from one bacterial species to another d. the transmission of a gene conferring antibiotic resistance from a mother cell to its two daughter cells e. all of the above > > Answer — Page 22 3. The scientific name for humans is Homo sapiens. The name Homo is the to which humans are classified. a, kingdom b. phylum c. order sala aaacee M Sign In | Connect | Mc Co Rd ce aa Rca nat Rute aecuy Ge 20.of 1075 Oe Aa 3. The scientific name for humans is Homo sapiens. The name Homo is the humans are classified. a, kingdom b. phylum ©. order d. genus €. species > > Answer 4. The underlying factor that explains the unity and diversity of modern species is a, energy. b. evolution. c. information. d. systems biology. e. all of the above. > > Answer 5. In science, a theory should be equated with knowledge. a b. be supported by a substantial body of evidence. ¢. provide the ability to make many correct pre 4d. do all of the above. e. do band ¢ only, > > Answer Short Answer 1, Explain how it is possible for evolution to result in unity among different species yet also produce amazing diversity. > > Answer 2. sy Core Concepts Which core concept of biology is illustrated by the observation that plants can utilize sunlight tqgunthesizecarbobydrates Brisfusxplaincee M Sign In | Connect | Mc Co Rd ce aa Rca nat Rute aecuy < 200f1478 > Phas Short Answer _ 1. Explain how it is possible for evolution to result in unity among different species yet also produce amazing diversity. > > Answer AQY Core Concepts Which core concept of biology is illustrated by the observation that plants can utilize sunlight to synthesize carbohydrates? Briefly explain. > > Answer Critical-Thinking Skills Multiple Choice 1. Refer back to) Figure 1.12 to answer this question. Based on taxonomic classification, which of the following species is most closely related to the clownfish (Amphiprion ocellaris)? cauliflower jellyfish (Cephea cephea); kingdom: Animalia; phylu ve giant carpet anemone (Heteractis crispa); kingdom: Animalia; phylu house mouse (Mus musculus); kingdom: Animalia; phylum: Chordata; class: Mammalia . Escherichia coli (a bacterium); domain: Bacteria e. aor > > Answer 2. Ampicillin is an antibiotic used to treat bacterial infections. A hospital reported the ‘occurrence of a new ampicillin-resistant strain of Escherichia coli in 11 out of 33 patients in an intensive care unit. This new strain was found only in patients who had developed symptoms of pneumonia while in the hospital. This pneumonia was caused by an ampicillin-resistant strain of Streptococcus pneumonia. Which of the following is the most likely explanation for the development of this new antibiotic-resistant strain of E. coli? a, New mutations arose separately in the E. coli strains from each of the 11 patients, leading to the independent evolution of ampicillin resistance in E. coli from each patient. b. A new mutation arose i E, coli from a single patient, conferring ampicillin resistance, and this strain of £, coli was transmitted to the other 10 patients. ©. Streptococcus pneumoniae and E. coli can easily exchange genetic material. Antibiotic resistance was passed from Streptococcus pneumoniae to E. coli by horizontal gene transfer in gach of the eeinfectadeh Ot cree aa Rca nat Rute aecuy < 200f1478 > Phas [SP Answer |@@y [=] 2. Ampicillin is an antibiotic used to treat bacterial infections. A hospital reported the occurrence of a new ampicillin-resistant strain of Escherichia coli in 11 out of 33 patients in an intensive care unit, This new strain was found only in patients who had developed symptoms of pneumonia while in the hospital. This pneumonia was caused by an ampicillin-resistant, strain of Streptococcus pneumonia. Which of the following is the most likely explanation for the development of this new antibioticresistant strain of E. coli? a. New mutations arose separately in the E. coli strains from each of the 11 patients, leading to the independent evolution of ampicillin resistance in E. coli from each patient. b. A new mutation arose in E. coli from a single patient, conferring ampicillin resistance, and this strain of E, coli was transmitted to the other 10 patients. €. Streptococcus pneumoniae and E. coli can easily exchange genetic material. Antibiotic resistance was passed from Streptococcus pneumoniae to E. coli by horizontal gene transfer in each of the co-infected patients. 4d, The 11 patients probably had acquired the ampicillin-resistant £. coli strain prior to coming to the hospital but the symptoms did not appear until after they entered the hospital. e. Both b and d are equally likely. > > Answer 3. An ecologist is studying the species of living organisms in a valley in western Colorado and their interactions with the environment. In particular, she is interested in the relative amounts of water that each species requires. She is studying a. an ecosystem. b. a community. ¢. the biosphere. d. a viable landmass. . a population, > > Answer 4, Some birds migrate from their northern breeding grounds to their southern wintering grounds by flying over very high mountains at elevations where oxygen levels in the air are extremely low. Even so, these birds can produce enough muscle power to complete their incredible journey. A possible research question involving such bird behavior is this: Do the number of mitochondria in muscle cells of such birds increase prior to their southern migration? At which research level is this question?eas Ca) a cen Co a Rca nat Rute aecuy > answer") @ 4, Some birds migrate from their northern breeding grounds to their southern wintering grounds by flying over very high mountains at elevations where oxygen levels in the air are extremely low. Even so, these birds can produce enough muscle power to complete their incredible journey. A possible research question involving such bird behavior is this: Do the number of mitochondria in muscle cells of such birds increase prior to their southern migration? At which research level is this question? a, molecular biology b. cell biology ¢. anatomy and physiology 4. ecology e. systems biology > > Answer 5. A plant biologist spends 2 years observing three different species of desert plants in their native environment. Following this observation period, the researcher proposes that all three species drop their leaves to conserve water. This is an example of a theory. a b. alaw. a prediction. a a hypothesis. e. an experiment. > > Answer Short Answer 1. Rank the following levels of biological organization from the lowest level of complexity to the highest level of complexity: a protein; everything in a mountain valley in Colorado; a school of dolphins; a skin cell; the living species in a small pond; the human heart; muscle tissue; and a carbon atom > > Answer sy Core Skill: Modeling @ Figure 1.12 is a model that describes the taxonomic classification of the ocellaris clownfish. What type of model is it? Explain your choice. > > Answer = SG 010f 147 P ba