Chapter 1: Introduction to Biology PDF

CHAPTER 1 Introduction to Biology FIGURE 1.1 This NASA image is a composite of several satellite-based views of Earth. To make the whole-Earth image, NASA scientists combine observations of different parts of the planet. (credit: modification of work by NASA) CHAPTER OUTLINE 1.1 Themes and Concept...

CHAPTER 1 Introduction to Biology FIGURE 1.1 This NASA image is a composite of several satellite-based views of Earth. To make the whole-Earth image, NASA scientists combine observations of different parts of the planet. (credit: modification of work by NASA) CHAPTER OUTLINE 1.1 Themes and Concepts of Biology 1.2 The Process of Science INTRODUCTION Viewed from space, Earth (Figure 1.1) offers few clues about the diversity of life forms that reside there. The first forms of life on Earth are thought to have been microorganisms that existed for billions of years before plants and animals appeared. The mammals, birds, and flowers so familiar to us are all relatively recent, originating 130 to 200 million years ago. Humans have inhabited this planet for only the last 2.5 million years, and only in the last 300,000 years have humans started looking like we do today. 1.1 Themes and Concepts of Biology LEARNING OBJECTIVES By the end of this section, you will be able to: Identify and describe the properties of life Describe the levels of organization among living things List examples of different sub disciplines in biology Biology is the science that studies life. What exactly is life? This may sound like a silly question with an obvious answer, but it is not easy to define life. For example, a branch of biology called virology studies viruses, which exhibit some of the characteristics of living entities but lack others. It turns out that although viruses can attack living organisms, cause diseases, and even reproduce, 6 1 Introduction to Biology they do not meet the criteria that biologists use to define life. From its earliest beginnings, biology has wrestled with four questions: What are the shared properties that make something “alive”? How do those various living things function? When faced with the remarkable diversity of life, how do we organize the different kinds of organisms so that we can better understand them? And, finally—what biologists ultimately seek to understand—how did this diversity arise and how is it continuing? As new organisms are discovered every day, biologists continue to seek answers to these and other questions. Properties of Life All groups of living organisms share several key characteristics or functions: order, sensitivity or response to stimuli, reproduction, adaptation, growth and development, regulation/homeostasis, energy processing, and evolution. When viewed together, these eight characteristics serve to define life. Order Organisms are highly organized structures that consist of one or more cells. Even very simple, single-celled organisms are remarkably complex. Inside each cell, atoms make up molecules. These in turn make up cell components or organelles. Multicellular organisms, which may consist of millions of individual cells, have an advantage over single-celled organisms in that their cells can be specialized to perform specific functions, and even sacrificed in certain situations for the good of the organism as a whole. How these specialized cells come together to form organs such as the heart, lung, or skin in organisms like the toad shown in Figure 1.2 will be discussed later. FIGURE 1.2 A toad represents a highly organized structure consisting of cells, tissues, organs, and organ systems. (credit: "Ivengo(RUS)"/Wikimedia Commons) Sensitivity or Response to Stimuli Organisms respond to diverse stimuli. For example, plants can bend toward a source of light or respond to touch (Figure 1.3). Even tiny bacteria can move toward or away from chemicals (a process called chemotaxis) or light (phototaxis). Movement toward a stimulus is considered a positive response, while movement away from a stimulus is considered a negative response. Access for free at openstax.org  1.1 Themes and Concepts of Biology 7 FIGURE 1.3 The leaves of this sensitive plant (Mimosa pudica) will instantly droop and fold when touched. After a few minutes, the plant returns to its normal state. (credit: Alex Lomas) LINK TO LEARNING Watch this video (http://openstax.org/l/thigmonasty) to see how the sensitive plant responds to a touch stimulus. Reproduction Single-celled organisms reproduce by first duplicating their DNA, which is the genetic material, and then dividing it equally as the cell prepares to divide to form two new cells. Many multicellular organisms (those made up of more than one cell) produce specialized reproductive cells that will form new individuals. When reproduction occurs, DNA containing genes is passed along to an organism’s offspring. These genes are the reason that the offspring will belong to the same species and will have characteristics similar to the parent, such as fur color and blood type. Adaptation All living organisms exhibit a “fit” to their environment. Biologists refer to this fit as adaptation and it is a consequence of evolution by natural selection, which operates in every lineage of reproducing organisms. Examples of adaptations are diverse and unique, from heat-resistant Archaea that live in boiling hot springs to the tongue length of a nectar-feeding moth that matches the size of the flower from which it feeds. Adaptations enhance the reproductive potential of the individual exhibiting them, including their ability to survive to reproduce. Adaptations are not constant. As an environment changes, natural selection causes the characteristics of the individuals in a population to track those changes. Growth and Development Organisms grow and develop according to specific instructions coded for by their genes. These genes provide instructions that will direct cellular growth and development, ensuring that a species’ young (Figure 1.4) will grow up to exhibit many of the same characteristics as its parents. 8 1 Introduction to Biology FIGURE 1.4 Although no two look alike, these kittens have inherited genes from both parents and share many of the same characteristics. (credit: Pieter & Renée Lanser) Regulation/Homeostasis Even the smallest organisms are complex and require multiple regulatory mechanisms to coordinate internal functions, such as the transport of nutrients, response to stimuli, and coping with environmental stresses. Homeostasis (literally, “steady state”) refers to the relatively stable internal environment required to maintain life. For example, organ systems such as the digestive or circulatory systems perform specific functions like carrying oxygen throughout the body, removing wastes, delivering nutrients to every cell, and cooling the body. To function properly, cells require appropriate conditions such as proper temperature, pH, and concentrations of diverse chemicals. These conditions may, however, change from one moment to the next. Organisms are able to maintain homeostatic internal conditions within a narrow range almost constantly, despite environmental changes, by activation of regulatory mechanisms. For example, many organisms regulate their body temperature in a process known as thermoregulation. Organisms that live in cold climates, such as the polar bear (Figure 1.5), have body structures that help them withstand low temperatures and conserve body heat. In hot climates, organisms have methods (such as perspiration in humans or panting in dogs) that help them to shed excess body heat. FIGURE 1.5 Polar bears and other mammals living in ice-covered regions maintain their body temperature by generating heat and reducing heat loss through thick fur and a dense layer of fat under their skin. (credit: "longhorndave"/Flickr) Energy Processing All organisms (such as the California condor shown in Figure 1.6) use a source of energy for their metabolic activities. Some organisms capture energy from the Sun and convert it into chemical energy in food; others use chemical energy from molecules they take in. Access for free at openstax.org  1.1 Themes and Concepts of Biology 9 FIGURE 1.6 A lot of energy is required for a California condor to fly. Chemical energy derived from food is used to power flight. California condors are an endangered species; scientists have strived to place a wing tag on each bird to help them identify and locate each individual bird. (credit: Pacific Southwest Region U.S. Fish and Wildlife) Evolution The diversity of life on Earth is a result of mutations, or random changes in hereditary material over time. These mutations allow the possibility for organisms to adapt to a changing environment. An organism that evolves characteristics fit for the environment will have greater reproductive success, subject to the forces of natural selection. Levels of Organization of Living Things Living things are highly organized and structured, following a hierarchy on a scale from small to large. The atom is the smallest and most fundamental unit of matter that retains the properties of an element. It consists of a nucleus surrounded by electrons. Atoms form molecules. A molecule is a chemical structure consisting of at least two atoms held together by a chemical bond. Many molecules that are biologically important are macromolecules, large molecules that are typically formed by combining smaller units called monomers. An example of a macromolecule is deoxyribonucleic acid (DNA) (Figure 1.7), which contains the instructions for the functioning of the organism that contains it. 10 1 Introduction to Biology FIGURE 1.7 A molecule, like this large DNA molecule, is composed of atoms. (credit: "Brian0918"/Wikimedia Commons) LINK TO LEARNING To see an animation of this DNA molecule, click here (http://openstax.org/l/rotating_DNA2). Some cells contain aggregates of macromolecules surrounded by membranes; these are called organelles. Organelles are small structures that exist within cells and perform specialized functions. All living things are made of cells; the cell itself is the smallest fundamental unit of structure and function in living organisms. (This requirement is why viruses are not considered living: they are not made of cells. To make new viruses, they have to invade and hijack a living cell; only then can they obtain the materials they need to reproduce.) Some organisms consist of a single cell and others are multicellular. Cells are classified as prokaryotic or eukaryotic. Prokaryotes are single- celled organisms that lack organelles surrounded by a membrane and do not have nuclei surrounded by nuclear membranes; in contrast, the cells of eukaryotes do have membrane-bound organelles and nuclei. In most multicellular organisms, cells combine to make tissues, which are groups of similar cells carrying out the same function. Organs are collections of tissues grouped together based on a common function. Organs are present not only in animals but also in plants. An organ system is a higher level of organization that consists of functionally related organs. For example vertebrate animals have many organ systems, such as the circulatory system that transports blood throughout the body and to and from the lungs; it includes organs such as the heart and blood vessels. Organisms are individual living entities. For example, each tree in a forest is an organism. Single-celled prokaryotes and single-celled eukaryotes are also considered organisms and are typically referred to as microorganisms. Access for free at openstax.org  1.1 Themes and Concepts of Biology 11 VISUAL CONNECTION FIGURE 1.8 From an atom to the entire Earth, biology examines all aspects of life. (credit "molecule": modification of work by Jane Whitney; credit "organelles": modification of work by Louisa Howard; credit "cells": modification of work by Bruce Wetzel, Harry Schaefer, National Cancer Institute; credit "tissue": modification of work by "Kilbad"/Wikimedia Commons; credit "organs": modification of work by Mariana Ruiz Villareal, Joaquim Alves Gaspar; credit "organisms": modification of work by Peter Dutton; credit "ecosystem": modification of work by "gigi4791"/Flickr; credit "biosphere": modification of work by NASA) Which of the following statements is false? a. Tissues exist within organs which exist within organ systems. 12 1 Introduction to Biology b. Communities exist within populations which exist within ecosystems. c. Organelles exist within cells which exist within tissues. d. Communities exist within ecosystems which exist in the biosphere. All the individuals of a species living within a specific area are collectively called a population. For example, a forest may include many white pine trees. All of these pine trees represent the population of white pine trees in this forest. Different populations may live in the same specific area. For example, the forest with the pine trees includes populations of flowering plants and also insects and microbial populations. A community is the set of populations inhabiting a particular area. For instance, all of the trees, flowers, insects, and other populations in a forest form the forest’s community. The forest itself is an ecosystem. An ecosystem consists of all the living things in a particular area together with the abiotic, or non-living, parts of that environment such as nitrogen in the soil or rainwater. At the highest level of organization (Figure 1.8), the biosphere is the collection of all ecosystems, and it represents the zones of life on Earth. It includes land, water, and portions of the atmosphere. The Diversity of Life The science of biology is very broad in scope because there is a tremendous diversity of life on Earth. The source of this diversity is evolution, the process of gradual change during which new species arise from older species. Evolutionary biologists study the evolution of living things in everything from the microscopic world to ecosystems. In the 18th century, a scientist named Carl Linnaeus first proposed organizing the known species of organisms into a hierarchical taxonomy. In this system, species that are most similar to each other are put together within a grouping known as a genus. Furthermore, similar genera (the plural of genus) are put together within a family. This grouping continues until all organisms are collected together into groups at the highest level. The current taxonomic system now has eight levels in its hierarchy, from lowest to highest, they are: species, genus, family, order, class, phylum, kingdom, domain. Thus species are grouped within genera, genera are grouped within families, families are grouped within orders, and so on (Figure 1.9). FIGURE 1.9 This diagram shows the levels of taxonomic hierarchy for a dog, from the broadest category—domain—to the most specific—species. The highest level, domain, is a relatively new addition to the system since the 1970s. Scientists now recognize three domains of life, the Eukarya, the Archaea, and the Bacteria. The domain Eukarya contains organisms that have cells with nuclei. It includes the kingdoms of fungi, plants, animals, and several kingdoms of protists. The Archaea, are single-celled organisms without nuclei and include many extremophiles that live in harsh environments like hot springs. The Bacteria are another quite different group of single-celled organisms without nuclei (Figure 1.10). Both the Archaea and the Bacteria are prokaryotes, an informal name for cells without nuclei. The recognition in the 1970s that certain “bacteria,” now known as the Archaea, were as different genetically and biochemically from other bacterial cells as they were from eukaryotes, motivated the recommendation to divide life into three domains. This dramatic change in our knowledge of the tree of life demonstrates that classifications are not permanent and will change when new information becomes available. Access for free at openstax.org  1.1 Themes and Concepts of Biology 13 In addition to the hierarchical taxonomic system, Linnaeus was the first to name organisms using two unique names, now called the binomial naming system. Before Linnaeus, the use of common names to refer to organisms caused confusion because there were regional differences in these common names. Binomial names consist of the genus name (which is capitalized) and the species name (all lower-case). Both names are set in italics when they are printed. Every species is given a unique binomial which is recognized the world over, so that a scientist in any location can know which organism is being referred to. For example, the North American blue jay is known uniquely as Cyanocitta cristata. Our own species is Homo sapiens. FIGURE 1.10 These images represent different domains. The scanning electron micrograph shows (a) bacterial cells belong to the domain Bacteria, while the (b) extremophiles, seen all together as colored mats in this hot spring, belong to domain Archaea. Both the (c) sunflower and (d) lion are part of domain Eukarya. (credit a: modification of work by Rocky Mountain Laboratories, NIAID, NIH; credit b: modification of work by Steve Jurvetson; credit c: modification of work by Michael Arrighi; credit d: modification of work by Frank Vassen) EVOLUTION CONNECTION Carl Woese and the Phylogenetic Tree The evolutionary relationships of various life forms on Earth can be summarized in a phylogenetic tree. A phylogenetic tree is a diagram showing the evolutionary relationships among biological species based on similarities and differences in genetic or physical traits or both. A phylogenetic tree is composed of branch points, or nodes, and branches. The internal nodes represent ancestors and are points in evolution when, based on scientific evidence, an ancestor is thought to have diverged to form two new species. The length of each branch can be considered as estimates of relative time. In the past, biologists grouped living organisms into five kingdoms: animals, plants, fungi, protists, and bacteria. The pioneering work of American microbiologist Carl Woese in the early 1970s has shown, however, that life on Earth has evolved along three lineages, now called domains—Bacteria, Archaea, and Eukarya. Woese proposed the domain as a new taxonomic level and Archaea as a new domain, to reflect the new phylogenetic tree (Figure 1.11). Many organisms belonging to the Archaea domain live under extreme conditions and are called extremophiles. To construct his tree, Woese used genetic relationships rather than similarities based on morphology (shape). Various genes were used in phylogenetic studies. Woese’s tree was constructed from comparative sequencing of the genes that are universally distributed, found in some slightly altered form in every organism, conserved (meaning that these genes have remained only slightly changed throughout evolution), and of an appropriate length. 14 1 Introduction to Biology FIGURE 1.11 This phylogenetic tree was constructed by microbiologist Carl Woese using genetic relationships. The tree shows the separation of living organisms into three domains: Bacteria, Archaea, and Eukarya. Bacteria and Archaea are organisms without a nucleus or other organelles surrounded by a membrane and, therefore, are prokaryotes. (credit: modification of work by Eric Gaba) Branches of Biological Study The scope of biology is broad and therefore contains many branches and sub disciplines. Biologists may pursue one of those sub disciplines and work in a more focused field. For instance, molecular biology studies biological processes at the molecular level, including interactions among molecules such as DNA, RNA, and proteins, as well as the way they are regulated. Microbiology is the study of the structure and function of microorganisms. It is quite a broad branch itself, and depending on the subject of study, there are also microbial physiologists, ecologists, and geneticists, among others. Another field of biological study, neurobiology, studies the biology of the nervous system, and although it is considered a branch of biology, it is also recognized as an interdisciplinary field of study known as neuroscience. Because of its interdisciplinary nature, this sub discipline studies different functions of the nervous system using molecular, cellular, developmental, medical, and computational approaches. FIGURE 1.12 Researchers work on excavating dinosaur fossils at a site in Castellón, Spain. (credit: Mario Modesto) Access for free at openstax.org  1.1 Themes and Concepts of Biology 15 Paleontology, another branch of biology, uses fossils to study life’s history (Figure 1.12). Zoology and botany are the study of animals and plants, respectively. Biologists can also specialize as biotechnologists, ecologists, or physiologists, to name just a few areas. Biotechnologists apply the knowledge of biology to create useful products. Ecologists study the interactions of organisms in their environments. Physiologists study the workings of cells, tissues and organs. This is just a small sample of the many fields that biologists can pursue. From our own bodies to the world we live in, discoveries in biology can affect us in very direct and important ways. We depend on these discoveries for our health, our food sources, and the benefits provided by our ecosystem. Because of this, knowledge of biology can benefit us in making decisions in our day-to-day lives. The development of technology in the twentieth century that continues today, particularly the technology to describe and manipulate the genetic material, DNA, has transformed biology. This transformation will allow biologists to continue to understand the history of life in greater detail, how the human body works, our human origins, and how humans can survive as a species on this planet despite the stresses caused by our increasing numbers. Biologists continue to decipher huge mysteries about life suggesting that we have only begun to understand life on the planet, its history, and our relationship to it. For this and other reasons, the knowledge of biology gained through this textbook and other printed and electronic media should be a benefit in whichever field you enter. CAREER CONNECTION Forensic Scientist Forensic science is the application of science to answer questions related to the law. Biologists as well as chemists and biochemists can be forensic scientists. Forensic scientists provide scientific evidence for use in courts, and their job involves examining trace material associated with crimes. Interest in forensic science has increased in the last few years, possibly because of popular television shows that feature forensic scientists on the job. Also, the development of molecular techniques and the establishment of DNA databases have updated the types of work that forensic scientists can do. Their job activities are primarily related to crimes against people such as murder, rape, and assault. Their work involves analyzing samples such as hair, blood, and other body fluids and also processing DNA (Figure 1.13) found in many different environments and materials. Forensic scientists also analyze other biological evidence left at crime scenes, such as insect parts or pollen grains. Students who want to pursue careers in forensic science will most likely be required to take chemistry and biology courses as well as some intensive math courses. FIGURE 1.13 This forensic scientist works in a DNA extraction room at the U.S. Army Criminal Investigation Laboratory. (credit: U.S. Army 16 1 Introduction to Biology CID Command Public Affairs) Scientific Ethics Scientists must ensure that their efforts do not cause undue damage to humans, animals, or the environment. They also must ensure that their research and communications are free of bias and that they properly balance financial, legal, safety, replicability, and other considerations. Bioethics is an important and continually evolving field, in which researchers collaborate with other thinkers and organizations. They work to define guidelines for current practice, and also continually consider new developments and emerging technologies in order to form answers for the years and decades to come. Unfortunately, the emergence of bioethics as a field came after a number of clearly unethical practices, where biologists did not treat research subjects with dignity and in some cases did them harm. In the 1932 Tuskegee syphilis study, 399 African American men were diagnosed with syphilis but were never informed that they had the disease, leaving them to live with and pass on the illness to others. Doctors even withheld proven medications because the goal of the study was to understand the impact of untreated syphilis on Black men. While the decisions made in the Tuskegee study are unjustifiable, some decisions are genuinely difficult to make. For example, bioethicists may examine the implications of gene editing technologies, including the ability to create organisms that may displace others in the environment, as well as the ability to “design” human beings. In that effort, ethicists will likely seek to balance the positive outcomes -- such as improved therapies or prevention of certain illnesses -- with negative outcomes. Bioethics are not simple, and often leave scientists balancing benefits with harm. In this text and course, you will discuss medical discoveries that, at their core, have what many consider an ethical lapse. In 1951, Henrietta Lacks, a 30-year-old African American woman, was diagnosed with cervical cancer at Johns Hopkins Hospital. Unique characteristics of her illnesses gave her cells the ability to divide continuously, essentially making them “immortal.” Without her knowledge or permission, researchers took samples of her cells and with them created the immortal HeLa cell line. These cells have contributed to major medical discoveries, including the polio vaccine and work related to cancer, AIDS, cell aging, and even very recently in COVID-19 research. For the most part, Lacks has not been credited for her role in those discoveries, and her family has not benefited from the billions of dollars in pharmaceutical profits obtained partly through the use of her cells. Today, harvesting tissue or organs from a dying patient without consent is not only considered unethical but also illegal, regardless of whether such an act could save other patients’ lives. Part of the role of ethics in scientific research is to examine similar issues before, during, and after research or practice takes place, as well as to adhere to established professional principles and consider the dignity and safety of all organisms involved or affected by the work. 1.2 The Process of Science LEARNING OBJECTIVES By the end of this section, you will be able to: Identify the shared characteristics of the natural sciences Understand the process of scientific inquiry Compare inductive reasoning with deductive reasoning Describe the goals of basic science and applied science Access for free at openstax.org  1.2 The Process of Science 17 FIGURE 1.14 Formerly called blue-green algae, the (a) cyanobacteria seen through a light microscope are some of Earth’s oldest life forms. These (b) stromatolites along the shores of Lake Thetis in Western Australia are ancient structures formed by the layering of cyanobacteria in shallow waters. (credit a: modification of work by NASA; scale-bar data from Matt Russell; credit b: modification of work by Ruth Ellison) Like geology, physics, and chemistry, biology is a science that gathers knowledge about the natural world. Specifically, biology is the study of life. The discoveries of biology are made by a community of researchers who work individually and together using agreed-on methods. In this sense, biology, like all sciences is a social enterprise like politics or the arts. The methods of science include careful observation, record keeping, logical and mathematical reasoning, experimentation, and submitting conclusions to the scrutiny of others. Science also requires considerable imagination and creativity; a well-designed experiment is commonly described as elegant, or beautiful. Like politics, science has considerable practical implications and some science is dedicated to practical applications, such as the prevention of disease (see Figure 1.15). Other science proceeds largely motivated by curiosity. Whatever its goal, there is no doubt that science, including biology, has transformed human existence and will continue to do so. FIGURE 1.15 Biologists may choose to study Escherichia coli (E. coli), a bacterium that is a normal resident of our digestive tracts but which is also sometimes responsible for disease outbreaks. In this micrograph, the bacterium is visualized using a scanning electron microscope and digital colorization. (credit: Eric Erbe; digital colorization by Christopher Pooley, USDA-ARS) The Nature of Science Biology is a science, but what exactly is science? What does the study of biology share with other scientific disciplines? Science (from the Latin scientia, meaning "knowledge") can be defined as knowledge about the natural world. Science is a very specific way of learning, or knowing, about the world. The history of the past 500 years demonstrates that science is a very powerful way of knowing about the world; it is largely responsible for the 18 1 Introduction to Biology technological revolutions that have taken place during this time. There are however, areas of knowledge and human experience that the methods of science cannot be applied to. These include such things as answering purely moral questions, aesthetic questions, or what can be generally categorized as spiritual questions. Science cannot investigate these areas because they are outside the realm of material phenomena, the phenomena of matter and energy, and cannot be observed and measured. The scientific method is a method of research with defined steps that include experiments and careful observation. The steps of the scientific method will be examined in detail later, but one of the most important aspects of this method is the testing of hypotheses. A hypothesis is a suggested explanation for an event, which can be tested. Hypotheses, or tentative explanations, are generally produced within the context of a scientific theory. A generally accepted scientific theory is thoroughly tested and confirmed explanation for a set of observations or phenomena. Scientific theory is the foundation of scientific knowledge. In addition, in many scientific disciplines (less so in biology) there are scientific laws, often expressed in mathematical formulas, which describe how elements of nature will behave under certain specific conditions. There is not an evolution of hypotheses through theories to laws as if they represented some increase in certainty about the world. Hypotheses are the day-to-day material that scientists work with and they are developed within the context of theories. Laws are concise descriptions of parts of the world that are amenable to formulaic or mathematical description. Natural Sciences What would you expect to see in a museum of natural sciences? Frogs? Plants? Dinosaur skeletons? Exhibits about how the brain functions? A planetarium? Gems and minerals? Or maybe all of the above? Science includes such diverse fields as astronomy, biology, computer sciences, geology, logic, physics, chemistry, and mathematics (Figure 1.16). However, those fields of science related to the physical world and its phenomena and processes are considered natural sciences. Thus, a museum of natural sciences might contain any of the items listed above. FIGURE 1.16 Some fields of science include astronomy, biology, computer science, geology, logic, physics, chemistry, and mathematics. (credit: "Image Editor"/Flickr) There is no complete agreement when it comes to defining what the natural sciences include. For some experts, the natural sciences are astronomy, biology, chemistry, earth science, and physics. Other scholars choose to divide natural sciences into life sciences, which study living things and include biology, and physical sciences, which study nonliving matter and include astronomy, physics, and chemistry. Some disciplines such as biophysics and biochemistry build on two sciences and are interdisciplinary. Scientific Inquiry One thing is common to all forms of science: an ultimate goal “to know.” Curiosity and inquiry are the driving forces for the development of science. Scientists seek to understand the world and the way it operates. Two methods of Access for free at openstax.org  1.2 The Process of Science 19 logical thinking are used: inductive reasoning and deductive reasoning. Inductive reasoning is a form of logical thinking that uses related observations to arrive at a general conclusion. This type of reasoning is common in descriptive science. A life scientist such as a biologist makes observations and records them. These data can be qualitative (descriptive) or quantitative (consisting of numbers), and the raw data can be supplemented with drawings, pictures, photos, or videos. From many observations, the scientist can infer conclusions (inductions) based on evidence. Inductive reasoning involves formulating generalizations inferred from careful observation and the analysis of a large amount of data. Brain studies often work this way. Many brains are observed while people are doing a task. The part of the brain that lights up, indicating activity, is then demonstrated to be the part controlling the response to that task. Deductive reasoning or deduction is the type of logic used in hypothesis-based science. In deductive reasoning, the pattern of thinking moves in the opposite direction as compared to inductive reasoning. Deductive reasoning is a form of logical thinking that uses a general principle or law to predict specific results. From those general principles, a scientist can deduce and predict the specific results that would be valid as long as the general principles are valid. For example, a prediction would be that if the climate is becoming warmer in a region, the distribution of plants and animals should change. Comparisons have been made between distributions in the past and the present, and the many changes that have been found are consistent with a warming climate. Finding the change in distribution is evidence that the climate change conclusion is a valid one. Both types of logical thinking are related to the two main pathways of scientific study: descriptive science and hypothesis-based science. Descriptive (or discovery) science aims to observe, explore, and discover, while hypothesis-based science begins with a specific question or problem and a potential answer or solution that can be tested. The boundary between these two forms of study is often blurred, because most scientific endeavors combine both approaches. Observations lead to questions, questions lead to forming a hypothesis as a possible answer to those questions, and then the hypothesis is tested. Thus, descriptive science and hypothesis-based science are in continuous dialogue. Hypothesis Testing Biologists study the living world by posing questions about it and seeking science-based responses. This approach is common to other sciences as well and is often referred to as the scientific method. The scientific method was used even in ancient times, but it was first documented by England’s Sir Francis Bacon (1561–1626) (Figure 1.17), who set up inductive methods for scientific inquiry. The scientific method is not exclusively used by biologists but can be applied to almost anything as a logical problem-solving method. FIGURE 1.17 Sir Francis Bacon is credited with being the first to document the scientific method. 20 1 Introduction to Biology The scientific process typically starts with an observation (often a problem to be solved) that leads to a question. Let’s think about a simple problem that starts with an observation and apply the scientific method to solve the problem. One Monday morning, a student arrives at class and quickly discovers that the classroom is too warm. That is an observation that also describes a problem: the classroom is too warm. The student then asks a question: “Why is the classroom so warm?” Recall that a hypothesis is a suggested explanation that can be tested. To solve a problem, several hypotheses may be proposed. For example, one hypothesis might be, “The classroom is warm because no one turned on the air conditioning.” But there could be other responses to the question, and therefore other hypotheses may be proposed. A second hypothesis might be, “The classroom is warm because there is a power failure, and so the air conditioning doesn’t work.” Once a hypothesis has been selected, a prediction may be made. A prediction is similar to a hypothesis but it typically has the format “If... then....” For example, the prediction for the first hypothesis might be, “If the student turns on the air conditioning, then the classroom will no longer be too warm.” A hypothesis must be testable to ensure that it is valid. For example, a hypothesis that depends on what a bear thinks is not testable, because it can never be known what a bear thinks. It should also be falsifiable, meaning that it can be disproven by experimental results. An example of an unfalsifiable hypothesis is “Botticelli’s Birth of Venus is beautiful.” There is no experiment that might show this statement to be false. To test a hypothesis, a researcher will conduct one or more experiments designed to eliminate one or more of the hypotheses. This is important. A hypothesis can be disproven, or eliminated, but it can never be proven. Science does not deal in proofs like mathematics. If an experiment fails to disprove a hypothesis, then we find support for that explanation, but this is not to say that down the road a better explanation will not be found, or a more carefully designed experiment will be found to falsify the hypothesis. Each experiment will have one or more variables and one or more controls. A variable is any part of the experiment that can vary or change during the experiment. A control is a part of the experiment that does not change. Look for the variables and controls in the example that follows. As a simple example, an experiment might be conducted to test the hypothesis that phosphate limits the growth of algae in freshwater ponds. A series of artificial ponds are filled with water and half of them are treated by adding phosphate each week, while the other half are treated by adding a salt that is known not to be used by algae. The variable here is the phosphate (or lack of phosphate), the experimental or treatment cases are the ponds with added phosphate and the control ponds are those with something inert added, such as the salt. Just adding something is also a control against the possibility that adding extra matter to the pond has an effect. If the treated ponds show lesser growth of algae, then we have found support for our hypothesis. If they do not, then we reject our hypothesis. Be aware that rejecting one hypothesis does not determine whether or not the other hypotheses can be accepted; it simply eliminates one hypothesis that is not valid (Figure 1.18). Using the scientific method, the hypotheses that are inconsistent with experimental data are rejected. In recent years a new approach of testing hypotheses has developed as a result of an exponential growth of data deposited in various databases. Using computer algorithms and statistical analyses of data in databases, a new field of so-called "data research" (also referred to as "in silico" research) provides new methods of data analyses and their interpretation. This will increase the demand for specialists in both biology and computer science, a promising career opportunity. Access for free at openstax.org  1.2 The Process of Science 21 VISUAL CONNECTION FIGURE 1.18 The scientific method is a series of defined steps that include experiments and careful observation. If a hypothesis is not supported by data, a new hypothesis can be proposed. In the example below, the scientific method is used to solve an everyday problem. Which part in the example below is the hypothesis? Which is the prediction? Based on the results of the experiment, is the hypothesis supported? If it is not supported, propose some alternative hypotheses. 1. My toaster doesn’t toast my bread. 2. Why doesn’t my toaster work? 3. There is something wrong with the electrical outlet. 4. If something is wrong with the outlet, my coffeemaker also won’t work when plugged into it. 5. I plug my coffeemaker into the outlet. 6. My coffeemaker works. In practice, the scientific method is not as rigid and structured as it might at first appear. Sometimes an experiment leads to conclusions that favor a change in approach; often, an experiment brings entirely new scientific questions to the puzzle. Many times, science does not operate in a linear fashion; instead, scientists continually draw inferences and make generalizations, finding patterns as their research proceeds. Scientific reasoning is more complex than the scientific method alone suggests. Basic and Applied Science The scientific community has been debating for the last few decades about the value of different types of science. Is it valuable to pursue science for the sake of simply gaining knowledge, or does scientific knowledge only have worth 22 1 Introduction to Biology if we can apply it to solving a specific problem or bettering our lives? This question focuses on the differences between two types of science: basic science and applied science. Basic science or “pure” science seeks to expand knowledge regardless of the short-term application of that knowledge. It is not focused on developing a product or a service of immediate public or commercial value. The immediate goal of basic science is knowledge for knowledge’s sake, though this does not mean that in the end it may not result in an application. In contrast, applied science or “technology,” aims to use science to solve real-world problems, making it possible, for example, to improve a crop yield, find a cure for a particular disease, or save animals threatened by a natural disaster. In applied science, the problem is usually defined for the researcher. Some individuals may perceive applied science as “useful” and basic science as “useless.” A question these people might pose to a scientist advocating knowledge acquisition would be, “What for?” A careful look at the history of science, however, reveals that basic knowledge has resulted in many remarkable applications of great value. Many scientists think that a basic understanding of science is necessary before an application is developed; therefore, applied science relies on the results generated through basic science. Other scientists think that it is time to move on from basic science and instead to find solutions to actual problems. Both approaches are valid. It is true that there are problems that demand immediate attention; however, few solutions would be found without the help of the knowledge generated through basic science. One example of how basic and applied science can work together to solve practical problems occurred after the discovery of DNA structure led to an understanding of the molecular mechanisms governing DNA replication. Strands of DNA, unique in every human, are found in our cells, where they provide the instructions necessary for life. During DNA replication, new copies of DNA are made, shortly before a cell divides to form new cells. Understanding the mechanisms of DNA replication enabled scientists to develop laboratory techniques that are now used to identify genetic diseases, pinpoint individuals who were at a crime scene, and determine paternity. Without basic science, it is unlikely that applied science could exist. Another example of the link between basic and applied research is the Human Genome Project, a study in which each human chromosome was analyzed and mapped to determine the precise sequence of DNA subunits and the exact location of each gene. (The gene is the basic unit of heredity represented by a specific DNA segment that codes for a functional molecule.) Other organisms have also been studied as part of this project to gain a better understanding of human chromosomes. The Human Genome Project (Figure 1.19) relied on basic research carried out with non-human organisms and, later, with the human genome. An important end goal eventually became using the data for applied research seeking cures for genetically related diseases. FIGURE 1.19 The Human Genome Project was a 13-year collaborative effort among researchers working in several different fields of science. The project was completed in 2003. (credit: the U.S. Department of Energy Genome Programs) While research efforts in both basic science and applied science are usually carefully planned, it is important to note that some discoveries are made by serendipity, that is, by means of a fortunate accident or a lucky surprise. Access for free at openstax.org  1.2 The Process of Science 23 Penicillin was discovered when biologist Alexander Fleming accidentally left a petri dish of Staphylococcus bacteria open. An unwanted mold grew, killing the bacteria. The mold turned out to be Penicillium, and a new critically important antibiotic was discovered. In a similar manner, Percy Lavon Julian was an established medicinal chemist working on a way to mass produce compounds with which to manufacture important drugs. He was focused on using soybean oil in the production of progesterone (a hormone important in the menstrual cycle and pregnancy), but it wasn't until water accidentally leaked into a large soybean oil storage tank that he found his method. Immediately recognizing the resulting substance as stigmasterol, a primary ingredient in progesterone and similar drugs, he began the process of replicating and industrializing the process in a manner that has helped millions of people. Even in the highly organized world of science, luck—when combined with an observant, curious mind focused on the types of reasoning discussed above—can lead to unexpected breakthroughs. Reporting Scientific Work Whether scientific research is basic science or applied science, scientists must share their findings for other researchers to expand and build upon their discoveries. Communication and collaboration within and between sub disciplines of science are key to the advancement of knowledge in science. For this reason, an important aspect of a scientist’s work is disseminating results and communicating with peers. Scientists can share results by presenting them at a scientific meeting or conference, but this approach can reach only the limited few who are present. Instead, most scientists present their results in peer-reviewed articles that are published in scientific journals. Peer-reviewed articles are scientific papers that are reviewed, usually anonymously by a scientist’s colleagues, or peers. These colleagues are qualified individuals, often experts in the same research area, who judge whether or not the scientist’s work is suitable for publication. The process of peer review helps to ensure that the research described in a scientific paper or grant proposal is original, significant, logical, and thorough. Grant proposals, which are requests for research funding, are also subject to peer review. Scientists publish their work so other scientists can reproduce their experiments under similar or different conditions to expand on the findings. There are many journals and the popular press that do not use a peer-review system. A large number of online open-access journals, journals with articles available without cost, are now available many of which use rigorous peer-review systems, but some of which do not. Results of any studies published in these forums without peer review are not reliable and should not form the basis for other scientific work. In one exception, journals may allow a researcher to cite a personal communication from another researcher about unpublished results with the cited author’s permission.