1.1 The Science of Biology

The Process 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 that covers general truths or the operation of general laws, especially when acquired and tested by the scientific method. It becomes clear from this definition that the application of the scientific method plays a major role in science. 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 by means of repeatable experiments. A hypothesis is a suggested explanation for an event, which can be tested. Although using the scientific method is inherent to science, it is inadequate in determining what science is. This is because it is relatively easy to apply the scientific method to disciplines such as physics and chemistry, but when it comes to disciplines like archaeology, psychology, and geology, the scientific method becomes less applicable as it becomes more difficult to repeat experiments.

These areas of study are still sciences, however. Consider archeology—even though one cannot perform repeatable experiments, hypotheses may still be supported. For instance, an archeologist can hypothesize that an ancient culture existed based on finding a piece of pottery. Further hypotheses could be made about various characteristics of this culture, and these hypotheses may be found to be correct or false through continued support or contradictions from other findings. A hypothesis may become a verified theory. A theory is a tested and confirmed explanation for observations or phenomena. Science may be better defined as fields of study that attempt to comprehend the nature of the universe.

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 1.4). 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 1.4 The diversity of scientific fields includes astronomy, biology, computer science, geology, logic, physics, chemistry, mathematics, and many other fields. (credit: “Image Editor”/Flickr)

There is no complete agreement when it comes to defining what the natural sciences include, however. 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, geology, physics, and chemistry. Some disciplines such as biophysics and biochemistry build on both life and physical sciences and are interdisciplinary. Natural sciences are sometimes referred to as “hard science” because they rely on the use of quantitative data; social sciences that study society and human behavior are more likely to use qualitative assessments to drive investigations and findings.

Not surprisingly, the natural science of biology has many branches or subdisciplines. Cell biologists study cell structure and function, while biologists who study anatomy investigate the structure of an entire organism. Those biologists studying physiology, however, focus on the internal functioning of an organism. Some areas of biology focus on only particular types of living things. For example, botanists explore plants, while zoologists specialize in animals.

The Scientific Method

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 1.5), who set up inductive methods for scientific inquiry. The scientific method is not exclusively used by biologists but can be applied to almost all fields of study as a logical, rational problem-solving method.

Figure 1.5 Sir Francis Bacon (1561–1626) is credited with being the first to define the scientific method. (credit: Paul van Somer)

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?”

Testing a Hypothesis

A valid hypothesis must be testable. It should also be falsifiable, meaning that it can be disproven by experimental results. Importantly, science does not claim to “prove” anything because scientific understandings are always subject to modification with further information. This step—openness to disproving ideas—is what distinguishes sciences from non-sciences. The presence of the supernatural, for instance, is neither testable nor falsifiable. To test a hypothesis, a researcher will conduct one or more experiments designed to eliminate one or more of the hypotheses. 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. The control group contains every feature of the experimental group except it is not given the manipulation that is hypothesized about. Therefore, if the results of the experimental group differ from the control group, the difference must be due to the hypothesized manipulation, rather than some outside factor. Look for the variables and controls in the examples that follow. To test the first hypothesis, the student would find out if the air conditioning is on. If the air conditioning is turned on but does not work, there should be another reason, and this hypothesis should be rejected. To test the second hypothesis, the student could check if the lights in the classroom are functional. If so, there is no power failure and this hypothesis should be rejected. Each hypothesis should be tested by carrying out appropriate experiments. 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 1.6). Using the scientific method, the hypotheses that are inconsistent with experimental data are rejected.

While this “warm classroom” example is based on observational results, other hypotheses and experiments might have clearer controls. For instance, a student might attend class on Monday and realize she had difficulty concentrating on the lecture. One observation to explain this occurrence might be, “When I eat breakfast before class, I am better able to pay attention.” The student could then design an experiment with a control to test this hypothesis.

In hypothesis-based science, specific results are predicted from a general premise. This type of reasoning is called deductive reasoning: deduction proceeds from the general to the particular. But the reverse of the process is also possible: sometimes, scientists reach a general conclusion from a number of specific observations. This type of reasoning is called inductive reasoning, and it proceeds from the particular to the general. Inductive and deductive reasoning are often used in tandem to advance scientific knowledge (Figure 1.7). 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.

Visual Connection

Art Connection

Figure 1.6 The scientific method consists of a series of well-defined steps. If a hypothesis is not supported by experimental data, a new hypothesis can be proposed.

In the example below, the scientific method is used to solve an everyday problem. Order the scientific method steps (numbered items) with the process of solving the everyday problem (lettered items). Based on the results of the experiment, is the hypothesis correct? If it is incorrect, propose some alternative hypotheses.

1. Observation
2. Question
3. Hypothesis (answer)
4. Prediction
5. Experiment
6. Result

1. There is something wrong with the electrical outlet.
2. If something is wrong with the outlet, my coffeemaker also won’t work when plugged into it.
3. My toaster doesn’t toast my bread.
4. I plug my coffee maker into the outlet.
5. My coffeemaker works.
6. Why doesn’t my toaster work?

Visual Connection

Art Connection

Figure 1.7 Scientists use two types of reasoning, inductive and deductive reasoning, to advance scientific knowledge. As is the case in this example, the conclusion from inductive reasoning can often become the premise for inductive reasoning.

Decide if each of the following is an example of inductive or deductive reasoning.

1. All flying birds and insects have wings. Birds and insects flap their wings as they move through the air. Therefore, wings enable flight.
2. Insects generally survive mild winters better than harsh ones. Therefore, insect pests will become more problematic if global temperatures increase.
3. Chromosomes, the carriers of DNA, separate into daughter cells during cell division. Therefore, DNA is the genetic material.
4. Animals as diverse as humans, insects, and wolves all exhibit social behavior. Therefore, social behavior must have an evolutionary advantage.

The scientific method may seem too rigid and structured. It is important to keep in mind that, although scientists often follow this sequence, there is flexibility. 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. Notice, too, that the scientific method can be applied to solving problems that aren’t necessarily scientific in nature.

Two Types of Science: Basic Science 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 if we can apply it to solving a specific problem or to 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 a practical 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 (Figure 1.8). In applied science, the problem is usually defined for the researcher.

Figure 1.8 After Hurricane Ike struck the Gulf Coast in 2008, the U.S. Fish and Wildlife Service rescued this brown pelican. Thanks to applied science, scientists knew how to rehabilitate the bird. (credit: FEMA)

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 wide knowledge foundation 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, DNA makes new copies of itself, shortly before a cell divides. 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 would 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; an individual’s complete collection of genes is his or her genome.) Other less complex organisms have also been studied as part of this project in order to gain a better understanding of human chromosomes. The Human Genome Project (Figure 1.9) relied on basic research carried out with simple organisms and, later, with the human genome. An important end goal eventually became using the data for applied research, seeking cures and early diagnoses for genetically related diseases.

Figure 1.9 The Human Genome Project was a 13-year collaborative effort among researchers working in several different fields of science. The project, which sequenced the entire human genome, was completed in 2003. (credit: the U.S. Department of Energy Genome Programs (http://genomics.energy.gov))

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. Penicillin was discovered when biologist Alexander Fleming accidentally left a petri dish of Staphylococcus bacteria open. An unwanted mold grew on the dish, killing the bacteria. The mold turned out to be Penicillium, and a new antibiotic was discovered. Even in the highly organized world of science, luck—when combined with an observant, curious mind—can lead to unexpected breakthroughs.

Reporting Scientific Work

Whether scientific research is basic science or applied science, scientists must share their findings in order for other researchers to expand and build upon their discoveries. Collaboration with other scientists—when planning, conducting, and analyzing results—are all important for scientific research. For this reason, important aspects of a scientist’s work are communicating with peers and disseminating results to peers. Scientists can share results by presenting them at a scientific meeting or conference, but this approach can reach only the select few who are present. Instead, most scientists present their results in peer-reviewed manuscripts that are published in scientific journals. Peer-reviewed manuscripts are scientific papers that are reviewed 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. The experimental results must be consistent with the findings of other scientists.

A scientific paper is very different from creative writing. Although creativity is required to design experiments, there are fixed guidelines when it comes to presenting scientific results. First, scientific writing must be brief, concise, and accurate. A scientific paper needs to be succinct but detailed enough to allow peers to reproduce the experiments.

The scientific paper consists of several specific sections—introduction, materials and methods, results, and discussion. This structure is sometimes called the “IMRaD” format. There are usually acknowledgment and reference sections as well as an abstract (a concise summary) at the beginning of the paper. There might be additional sections depending on the type of paper and the journal where it will be published; for example, some review papers require an outline.

The introduction starts with brief, but broad, background information about what is known in the field. A good introduction also gives the rationale of the work; it justifies the work carried out and also briefly mentions the end of the paper, where the hypothesis or research question driving the research will be presented. The introduction refers to the published scientific work of others and therefore requires citations following the style of the journal. Using the work or ideas of others without proper citation is considered plagiarism.

The materials and methods section includes a complete and accurate description of the substances used, and the method and techniques used by the researchers to gather data. The description should be thorough enough to allow another researcher to repeat the experiment and obtain similar results, but it does not have to be verbose. This section will also include information on how measurements were made and what types of calculations and statistical analyses were used to examine raw data. Although the materials and methods section gives an accurate description of the experiments, it does not discuss them.

Some journals require a results section followed by a discussion section, but it is more common to combine both. If the journal does not allow the combination of both sections, the results section simply narrates the findings without any further interpretation. The results are presented by means of tables or graphs, but no duplicate information should be presented. In the discussion section, the researcher will interpret the results, describe how variables may be related, and attempt to explain the observations. It is indispensable to conduct an extensive literature search to put the results in the context of previously published scientific research. Therefore, proper citations are included in this section as well.

Finally, the conclusion section summarizes the importance of the experimental findings. While the scientific paper almost certainly answered one or more scientific questions that were stated, any good research should lead to more questions. Therefore, a well-done scientific paper leaves doors open for the researcher and others to continue and expand on the findings.

Review articles do not follow the IMRAD format because they do not present original scientific findings, or primary literature; instead, they summarize and comment on findings that were published as primary literature and typically include extensive reference sections.