Biological scientists use a process of inquiry that has developed over centuries and involves the collaboration of a global community.

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1 Principles of Biology contents 3 Practicing Biology Biological scientists use a process of inquiry that has developed over centuries and involves the collaboration of a global community. Biologists study the natural world in a variety of ways. Biologists conduct scientific research both in the lab and in the field. (left) Scott Bauer/Courtesy of U.S. Department of Agriculture. (right) Courtesy of Neal Snyder/U.S. Army Environmental Command. Topics Covered in this Module The Scientific Method Scientific Communication Major Objectives of this Module Describe the scientific method. Describe how data are analyzed. Describe different types of experimental setups. page 14 of pages left in this module

2 Principles of Biology contents 3 Practicing Biology Charles Darwin visited the Galápagos Islands in 1835 and collected finch specimens. He observed that the size and shape of the finches' beaks varied widely among species, depending on diet: seed eaters tended to have wide, strong beaks, while insect eaters tended to have narrow long beaks. Yet similarities existed among the birds as well. From these observations, Darwin concluded that at one time only one species of finch existed on the islands. Darwin speculated that individuals with a competitive advantage for a given ecological niche were better able to survive and reproduce than other members of a population, and over many generations, the population evolved into different species. He called this mechanism of evolution natural selection. More recently, scientists have compared the DNA sequence of various finch species from the Galápagos Islands and found similarities indicating that the birds do have a common ancestor. Both Darwin and these modern scientists are biologists, or scientists who study life. Biologists, like all scientists, use a process called the scientific method to advance their understanding of the natural world. The Scientific Method Science is a way of learning about the universe through a formal process of observation and experimentation called the scientific method. Although humans have made informal observations and experimentations since antiquity, the scientific method developed gradually. The process of observation was formalized by the Greek philosopher Aristotle ( BCE; Figure 1). Aristotle framed questions based on observations and answered these questions to learn "truths" about the universe. This type of analysis, in which general conclusions are drawn from specific observations, is called inductive reasoning. Inductive reasoning is an important part of the scientific method, but Aristotle believed that only observation, not experimentation, could be used to learn the truth. Three Arabic scientists are primarily credited with the development of experimental science: Jābir ibn Hayyān ( ), Abū Rayḥān al-bīrūnī ( ), and ibn Sīnā (also known as Avicenna, ). Experimental science involves a different type of reasoning, called deductive reasoning. In deductive reasoning, specific results are predicted from a general premise.

3 Figure 1: Aristotle, painted centuries after his death by Francesco Hayez. The Greek philosopher Aristotle is credited with the development of formal inductive reasoning. Francesco Haez, Aristotle, In modern practice, an observation may involve simply watching (for example, a scientist may watch a bird feeding its young), or it may involve careful measurements (the scientists may weigh the chicks). Measurements and visual observations that are recorded are called data (singular, datum). From observations, scientists form a hypothesis, a tentative answer to a well-framed question. A hypothesis must be framed so that it is falsifiable, meaning that it can be proven wrong through experimentation. For example, a scientist might observe that some chicks are more brightly colored than others. This may lead the scientists to wonder, "What competitive advantage does the bright color confer?" A tentative answer to this question may be "The parents preferentially feed brightly colored chicks." It is important to emphasize that this is a tentative answer, or hypothesis. To test this hypothesis, the scientist would need to conduct a carefully controlled test called an experiment. Notice that in this example, inductive reasoning (bright color must confer some competitive advantage) leads to deductive reasoning (the parents preferentially feed brightly colored chicks). Cycles of inductive and deductive reasoning are central to the scientific method. Figure 2: Scientific reasoning. Two types of reasoning occur in science: inductive reasoning and deductive reasoning.

4 2014 Nature Education All rights reserved. The example experiment discussed here is one that has in fact taken place. A species of bird called coots has brightly colored chicks, and scientists hypothesized that parents might preferentially feed chicks with brighter plumage. To test their hypothesis, they measured three parameters: feeding rate, growth rate (assessed by measuring the length of chicks), and survival rate. From their hypothesis that the parents preferentially feed the brightly colored chicks, the scientists predicted that the feeding rate, growth rate, and survival rate would all be higher for brightly colored chicks. To conduct the experiment, scientists clipped the bright feathers from half of the chicks in a brood and left the bright feathers of the other half untouched. Feeding, growth, and survival rates were all higher for the brightly colored chicks. These results support the hypothesis that parents preferentially feed brightly colored offspring. However, a hypothesis can never be proven because there always might be an alternative explanation for positive results. For example, it is possible that the parents were able to discern that the dull chicks had been handled, and this handling, rather than feather color, resulted in differential treatment. For this reason, many experiments and observations are needed to advance scientific knowledge. Many students believe that a good hypothesis is one that is correct, but in reality, any hypothesis that is testable is a good hypothesis, even if it is ultimately proven wrong. In fact, many of the greatest advances in science occur when a hypothesis is proven wrong: when this happens, scientists are forced to question their reasoning and may come to a completely different, better understanding of natural phenomena. Analyzing data. In the hypothetical experiment shown in Figure 3, reaction time of eight test subjects is measured when they are talking on a cell phone and when they are not. This experiment generates two groups of data: an experimental group that receives treatment (or in this case uses cell phones) and a control group that does not. Notice that the terms experimental and control refer to the data points, not the individuals being tested. In this particular experiment, each test subject appears in both groups, although this is not always the case. An experiment in which one group receives treatment and the other does not is called a controlled experiment.

5 Figure 3: Setup and results for a hypothetical scientific experiment. (1) Researchers observe that more accidents occur when a driver is using a cell phone; using inductive reasoning, the researchers hypothesize that cell phone use increases reaction time. (2) To measure reaction time experimentally, subjects are asked to loosely grasp a ruler at the zero mark and to grab it when the experimenter drops it. Reaction time is measured when test subjects are using a cell phone (experimental group) and when they are not (control group). (3) The researchers conducting the experiment record the number at which the ruler is grabbed and calculate the mean and standard deviation. (4) Reaction time is slower when a cell phone is being used. The data support the hypothesis that cell phone use increases reaction time Nature Education All rights reserved. In a controlled experiment, the variable that differs between the experimental and control groups, or the one that is controlled by the scientist, is called the independent variable. Data collected in an experiment are called dependent variables because they depend on the independent variable. In the cell phone experiment, reaction time (the dependent variable) depends on cell phone usage (the independent variable). Look carefully at data points in Figure 3, panel 3: they vary widely, and although reaction time is usually faster for the control group, in one case it is not. Because variability occurs in scientific measurements, measurements must be repeated, and a mathematical analysis must be used to determine whether data is statistically significant. Statistical significance refers to the probability that a given result is not due to random chance. The mean, or average, is a common statistical test that is calculated by adding all the values in a data set and dividing by the number of data points (N). The symbol Σ means "the sum of," so mean can be calculated using the following equation: Mean = Σ/N The mean reaction time for the experimental group (4.4) is slower than the mean reaction time for the control group (2.3). Another statistical value that

6 is commonly calculated is the variance. Variance, a measure of how much spread there is in the data, is calculated using the following equation: 2014 Nature Education All rights reserved. From the variance, the standard deviation can be calculated. The standard deviation is a measure of dispersion from the mean. The lower the standard deviation, the less the dispersion. Standard deviation is the square root of the variance: 2014 Nature Education All rights reserved. Standard deviation is often written in the following format: mean ± standard deviation. Thus, the data for the experimental group is written as follows: 4.4 ± 1.5; and the data for the control group is written as follows: 2.3 ± 1.0. Experimental setups. Unintentional bias of both scientists and human test subjects can potentially skew results. For example, an experimental subject receiving an investigational drug may feel better simply because he thinks the drug is effective. Likewise, the researcher conducting the drug trial may rate improvement of experimental subjects as better than control subjects. For this reason, most clinical studies are double blind, meaning that neither the researcher nor the test subjects know who is in the experimental group and who is in the control group. In clinical drug trials, subjects in the control group are given a placebo (a drug that looks the same as the real drug but contains no active ingredients) and otherwise treated exactly the same as the test subjects to ensure that the results are not skewed by unintentional bias or differences in treatment. Although controlled experiments are the ones that students are generally most familiar with, researchers devise other types of experiments when it is impossible, impractical, or unethical to set up a controlled experiment. Examples of other experimental setup include natural experiments, regression analysis, and active controlled experiments. In a natural experiment, two existing natural populations, such as smokers and non-smokers, are compared. In a regression analysis experiment, varying levels of treatment are applied to test subjects. For example, varying levels of an experimental drug may be given to different patients to optimize dosage and minimize side effects. In an active controlled experiment, the experimental group is given a new treatment, and the control group is given an existing treatment. Active controlled experiments are used to test new antibiotics: in such experiments, all patients receive an antibiotic to treat an infection, but some receive a new one, while others receive a standard treatment. Regardless of what experimental setup is used, the population of the experimental and control groups should be similar in regard to age, sex, health, and other variables. Scientific laws and theories. A scientific law is a general statement based on repeated observations that can be used to predict future observations. In biology, the statement that "the cell is the basic unit for all forms of life" is a scientific law based on many years of research by many scientists. Because the concept that all life is cell-based is scientific law, scientists can predict that organisms found in the future will be cell-based. A scientific theory attempts to explain a broad

7 group of laws and observations. The concept that natural selection results in evolution is a theory that attempts to explain how differences arose among various organisms that appear to have a common ancestor. Test Yourself How does a hypothesis differ from a scientific law? Submit IN THIS MODULE The Scientific Method Scientific Communication Summary Test Your Knowledge WHY DOES THIS TOPIC MATTER? A Sea of Microbes Drives Global Change Do floating microbes in the ocean s surface waters play an outsize role in global climate? Stem Cells Stem cells are powerful tools in biology and medicine. What can scientists do with these cells and their incredible potential? Cancer: What's Old Is New Again Is cancer ancient, or is it largely a product of modern times? Can cutting-edge research lead to prevention and treatment strategies that could make cancer obsolete? The Climate Connection How is life on Earth reacting to climate change? PRIMARY LITERATURE Brain preplay anticipates the future Preplay of future place cell sequences by hippocampal cellular assemblies. Classic paper: The discovery of the neutron (1932) Possible existence of a neutron. Aneuploids may not be so abnormal Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast. A new technique for detecting autoimmune diseases Autoantigen discovery with a synthetic human peptidome. page 15 of pages left in this module

8 Principles of Biology contents 3 Practicing Biology Scientific Communication The seventeenth-century physicist Sir Isaac Newton said, "If I have seen further, it is by standing on the shoulders of giants," meaning that an understanding of the works of his predecessors was critical to his success. Today, as in Newton's time, scientific advancement requires a broad scientific knowledge. The best source for quality scientific research is peer-reviewed journals. All the research published in these journals must pass a peer-review process, in which anonymous scientists decide whether the research merits publication and whether further experiments are necessary. Other important sources of information include review articles written by well-established scientists and databases containing collections of scientific data from various sources. Although the format of different journals varies considerably, a peer-reviewed scientific paper will generally include the following sections: (1) Abstract. The abstract is a short, one- or two-paragraph summary of the hypothesis being tested, the methods, results, and conclusion. (2) Introduction. The introduction provides the context for the work being done. It usually begins with a broad overview and then focuses on the specific research being conducted. (3) Materials and Methods. The materials and methods section provides a summary of reagents and equipment used as well as a specific explanation of how the experiments were conducted. Usually the Materials and Methods section follows the introduction, but sometimes it is placed at the end. (4) Results. The results section includes all of the data collected. Often, tables and graphs are included to show the data visually. (5) Discussion. The discussion states whether or not the results support the hypothesis. The discussion may also describe concerns with the current study and give suggestions for future studies. (6) References. This final section of the paper lists the research articles and other sources of information cited in the paper. IN THIS MODULE The Scientific Method Scientific Communication Summary Test Your Knowledge WHY DOES THIS TOPIC MATTER? A Sea of Microbes Drives Global Change Do floating microbes in the ocean s surface waters play an outsize role in global climate? Stem Cells Stem cells are powerful tools in biology and medicine. What can scientists do with these cells and their incredible potential? Cancer: What's Old Is New Again Is cancer ancient, or is it largely a product of modern times? Can cutting-edge research lead to prevention and treatment strategies that could make cancer obsolete? How is life on Earth reacting to climate

9 The Climate Connection change? PRIMARY LITERATURE Brain preplay anticipates the future Preplay of future place cell sequences by hippocampal cellular assemblies. Classic paper: The discovery of the neutron (1932) Possible existence of a neutron. Aneuploids may not be so abnormal Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast. A new technique for detecting autoimmune diseases Autoantigen discovery with a synthetic human peptidome. page 16 of pages left in this module

10 Principles of Biology contents 3 Practicing Biology Summary OBJECTIVE Describe the scientific method. The scientific method is a process of learning about the world through observation and experimentation. Two types of reasoning are used in the course of scientific research: inductive reasoning and deductive reasoning. In inductive reasoning, a general conclusion is drawn from specific observations. In deductive reasoning, specific results are predicted from a general premise. A hypothesis is formed through inductive reasoning and is a tentative answer to a well-framed question. A scientific law is a general statement summarizing many observations. Laws are based on many experiments that all support the same hypothesis. A scientific theory is an explanation for laws and hypotheses. OBJECTIVE Describe how data are analyzed. In a controlled experiment, an experimental group, which receives treatment, is compared to a control group, which does not receive treatment. The variable that differs between the experimental and control groups is called the independent variable, and the data collected in an experiment are called dependent variables. In any experiment, data must be mathematically analyzed to determine whether it is statistically significant. OBJECTIVE Describe different types of experimental setups. In a controlled experiment, the experimental group receives the treatment and the control group does not. In a natural experiment, two different natural populations are compared. In a regression analysis experiment, varying levels of treatment are compared. In an active controlled experiment, a new treatment is compared to an old one. Key Terms active controlled experiment Experiment in which one group is given a new treatment, and another group is given an existing treatment. control group A group that does not receive treatment in an experiment. controlled experiment An experiment in which one group receives treatment and the other does not. data (singular datum) Recorded observations or measurements. deductive reasoning Predicting a specific result from general principles. dependent variable Measured results of an experiment; dependent on the independent variable. double blind Experiment in which neither researcher nor subject knows who is in the treatment group or the control group until after the data have been collected. experiment A carefully controlled observation. experimental group A group that receives treatment in an experiment.

11 hypothesis Tentative answer to a well-framed question. independent variable The variable that is controlled by the scientist. inductive reasoning Inferring general principles from specific observations. law A general statement, based on repeated observations, that can be used to predict future observations. mean The average, calculated by adding together individual values and dividing by the number of values in the set. natural experiment An experiment in which two existing natural populations are compared. natural selection A process through which advantageous traits are passed from one generation to the next because individuals with those traits are better able to survive and reproduce. observation A description or measurement of a natural phenomenon. regression analysis experiment An experiment in which varying levels of treatment are applied to test subjects. science A systematic enterprise that builds and organizes knowledge in the form of testable explanations and predictions about the universe. scientific inquiry Search for information and explanation. scientific method A process of learning through observation and experimentation. standard deviation A measure of deviation from the mean. statistical significance Probability that a given result is not due to random chance. theory An explanation for observations. variance A measure of the spread in data. IN THIS MODULE The Scientific Method Scientific Communication Summary Test Your Knowledge WHY DOES THIS TOPIC MATTER? A Sea of Microbes Drives Global Change Do floating microbes in the ocean s surface waters play an outsize role in global climate? Stem Cells Stem cells are powerful tools in biology and medicine. What can scientists do with these cells and their incredible potential? Cancer: What's Old Is New Again Is cancer ancient, or is it largely a product of modern times? Can cutting-edge research lead to prevention and treatment strategies that could make

12 cancer obsolete? The Climate Connection How is life on Earth reacting to climate change? PRIMARY LITERATURE Brain preplay anticipates the future Preplay of future place cell sequences by hippocampal cellular assemblies. Classic paper: The discovery of the neutron (1932) Possible existence of a neutron. Aneuploids may not be so abnormal Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast. A new technique for detecting autoimmune diseases Autoantigen discovery with a synthetic human peptidome. page 17 of pages left in this module

13 Principles of Biology contents 3 Practicing Biology Test Your Knowledge 1. Which term describes the data that are collected during an experiment? independent variable dependent variable control group hypothesis conclusion 2. Which of these is a characteristic of a good hypothesis? It is based on previous observations or results. It cannot be tested. It cannot be falsified. It is correct. None of these choices is correct. 3. How might a scientific theory be modified? by a change in the experimental methods that leads to the same result by the declaration of a scientific society Theories cannot be changed. They are natural laws. by consensus of the top scientists in the field by the uncovering of new information 4. Students compared their resting heart rate to their heart rate after exercise. They measured their resting heart rate after sitting for five minutes; they then did 50 jumping jacks and afterward measured their heart rate. What was the dependent variable of this study? whether or not the person was resting when the heart rate was measured how many jumping jacks were done heart rate how long the person rested before heart rate was measured There was no dependent variable. 5. Which of the following statements about types of experimental setup is correct? A controlled experiment is one in which the experimental group receives the treatment and the control group does not. A natural experiment is one in which two different natural populations are compared. A regression analysis experiment is one in which varying levels of treatment are compared. An active controlled experiment is one in which a new treatment is compared to an old one. All of the answers are correct. Submit IN THIS MODULE The Scientific Method Scientific Communication

14 Summary Test Your Knowledge WHY DOES THIS TOPIC MATTER? A Sea of Microbes Drives Global Change Do floating microbes in the ocean s surface waters play an outsize role in global climate? Stem Cells Stem cells are powerful tools in biology and medicine. What can scientists do with these cells and their incredible potential? Cancer: What's Old Is New Again Is cancer ancient, or is it largely a product of modern times? Can cutting-edge research lead to prevention and treatment strategies that could make cancer obsolete? The Climate Connection How is life on Earth reacting to climate change? PRIMARY LITERATURE Brain preplay anticipates the future Preplay of future place cell sequences by hippocampal cellular assemblies. Classic paper: The discovery of the neutron (1932) Possible existence of a neutron. Aneuploids may not be so abnormal Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast. A new technique for detecting autoimmune diseases Autoantigen discovery with a synthetic human peptidome. page 18 of 989