The scientific method

BIO 001L Summer 2018 - LAB 1: The scientific method*

In this class, we’ll be talking about the scientific method, and the components that go into it.

Laboratory Objectives

After completing this lab topic, you should be able to

  1. Identify and understand what plagiarism is and why it is important to avoid doing it.
  2. Identify and characterize questions that can be answered through scientific investigation.
  3. Define hypothesis and explain what characterizes a good scientific hypothesis.
  4. Identify and describe the components of a scientific experiment.
  5. Discuss results and critique experiments.
  6. Design a scientific experiment.
  7. Interpret and communicate results.

First let’s talk about something that needs to be emphasized from the outset of every science course and which you need to always keep in mind when pursuing any scientific work: the issue of plagiarism.

Plagiarism is the uncredited word-for-word copying of material – whether from an online source, a book, a classmate, or even yourself (for example, if you have taken this course before). Often, students commit plagiarism when they are sincerely trying not to, most notably when they copy parts of sentences whole but try to break them up so that they are not exactly like in the source. This can still be plagiarism when whole chunks of sentences are copied word-for-word. Be very mindful of this. Plagiarism is strictly prohibited and can result in severe penalties, up to and including expulsion from the course. If you think you might be plagiarizing, you probably are, and you should seek advice from your TA or lab coordinator before proceeding. There is NO EXCUSE for plagiarism. It does not matter whether you are trying to take a shortcut due to emotional stress or family difficulties, or that you feel pressured by the workload of other course requirements, or that you “didn’t know”. This discussion is your first and final warning. Your TA will go through some examples of plagiarism, so take special note of them and ensure that you are not doing these yourself.

Some students think that plagiarism is worth the risk and that it will sneak under the radar. It is not worth the risk and it will not sneak under the radar. Software for checking plagiarism has become incredibly powerful and efficient, and no effort whatsoever is required on the TA’s part for detecting plagiarism. Take a look at a screenshot of the software called Turnitin that the TA uses to check for it (and that you’ll be submitting assignments through):

*Adapted from Investigating Biology Laboratory Manual, Sixth Edition, Judith G. Morgan and M. Eloise Brown Carter.

The software does a search from a variety of possible sources and color-codes the results based on how closely they match the sources. This particular student got a 0 for her report because she had entire paragraphs copied word-for-word from another student. That student, too, got a 0; no distinction will be made between someone who copies the work of another student and the student who allowed their work to be copied, even if they “thought” that it wouldn’t be. If you get a 0, there will be no chance of resubmission for that report. If you fail the course because of a report in which you were given a 0, that’s all there is to it.

Now, onto the main topics of this lab.

Biology is the study of the phenomena of life, and biological scientists - researches, teachers and students - observe living systems and organisms, ask questions, and propose explanations for those observations. Scientific investigation is a way of testing those explanations. Science assumes that biological systems are understandable and can be explained by fundamental rules or laws. Scientific investigations share some common elements and procedures, which are referred to as the scientific method. Not all scientists follow these procedures in a strict fashion, but each of the elements is usually present. Science is a creative human endeavor that involves asking questions, making observations, developing explanatory hypotheses, and testing those hypotheses. Scientists closely scrutinize investigations in their field, and each scientist must present his or her work at scientific meetings or in professional publications, providing evidence from observations and experiments that supports the scientist’s explanations of biological phenomena.

Questions and Hypotheses

This exercise explores the nature of scientific questions and hypotheses. Before going to lab, read the explanatory paragraphs and then be prepared to present your ideas in the class discussion.

                 

Lab Study A. Asking Questions

Scientists are characteristically curious and creative individuals whose curiosity is directed toward understanding the natural world. They use their study of previous research or personal observations of natural phenomena as a basis for asking questions about the underlying causes or reasons for these phenomena. For a question to be pursued by scientists, the phenomenon must be well defined and testable. The elements must be measurable and controllable.

There are limits to the ability of science to answer questions. Science is only one of many ways of knowing about the world in which we live. Consider, for example, this question: Do excessively high temperatures cause people to behave immorally? Can a scientist investigate this question? Temperature is certainly a well-defined, measurable, and controllable factor, bur morality of behavior is not scientifically measurable. We probably could nor even reach a consensus on the definition. Thus, there is no experiment that can be performed to test the question. Which of the following questions do you think can be answered scientifically?

  1. Does watching television before the age of one contribute to the development of autism in children?

Yes 

  1. Did the use of the herbal supplement ephedra cause the death of the 18-year old soccer player?

Yes 

  1. Does global warming cause an increase in frequency and intensity of forest fires?

Yes 

  1. Do cactus spines reduce herbivory?

Yes 

  1. Should human embryonic stem cells be used to treat Parkinson's disease? No because no observation can be made and compared.

How did you decide which questions can be answered scientifically?

You would decide if the hypothesis can be proven false. 

Lab Study B. Developing Hypotheses

As questions are asked, scientists attempt to answer them by proposing possible explanations. Those proposed explanations are called hypotheses. A hypothesis tentatively explains something observed. It proposes an answer to a question. Consider question 4, preceding. One hypothesis based on this question might be "spines on cacti reduce herbivory". The hypothesis has suggested a possible explanation for the observed spines. A scientifically useful hypothesis must be testable and falsifiable (able to be proved false). To satisfy the requirement that a hypothesis be falsifiable, it must be possible that the test results do not support the explanation. In our example, if spines are removed from test cacti and the plants are not eaten by animals, then the hypothesis has been falsified. Even though the hypothesis can be falsified, it can never be proved true. The evidence from an investigation can only provide support for the hypothesis. In our example, if cacti without spines were eaten, the hypothesis has not been proved, but has been supported by the evidence. Other explanations still must be excluded, and new evidence from additional experiments and observations might falsify this hypothesis at a later date. In science, seldom does a single test provide results that clearly support or definitely falsify a hypothesis. In most cases, the evidence serves to modify the hypothesis or the conditions of the experiment.

Science is a way of knowing about the natural world (Moore, 1993) that involves testing hypotheses or explanations. The scientific method can be applied to the unusual and the commonplace. You use the scientific method when you investigate why your once-white socks are now blue. Your hypothesis might be that your blue jeans and socks were washed together, an assertion that can be tested through observations and experiments. Students often think that controlled experiments are the only way to test a hypothesis. The test of a hypothesis may include experimentation, additional observations, or the synthesis of information from a variety of sources. Many scientific advances have relied on other procedures and information to test hypotheses. For example, James Watson and Francis Crick developed a model that was their hypothesis for the structure of DNA. Their model could only be supported if the accumulated data from a number of other scientists were consistent with the model. Actually, their first model (hypothesis) was falsified by the work of Rosalind Franklin. Their final model was tested and supported not only by the ongoing work of Franklin and Maurice Wilkins but also by research previously published by Erwin Chargaff and others. Watson and Crick won the Nobel Prize for their scientific work. They did not perform a controlled experiment in the laboratory but tested their powerful hypothesis through the use of existing evidence from other research. Methods other than experimentation are acceptable in testing hypotheses. Think about other areas of science that require comparative observations and the accumulation of data from a variety of sources, all of which must be consistent with and support hypotheses or else be inconsistent and falsify hypotheses.

The information in your biology textbook is often thought of as a collection of facts, well understood and correct. It is true that much of the knowledge of biology has been derived through scientific investigations, has been thoroughly tested, and is supported by strong evidence. However, scientific knowledge is always subject to novel experiments and new technology, any aspect of which may result in modification of our ideas and a better understanding of biological phenomena. The structure of the cell membrane is an example of the self-correcting nature of science. Each model of the membrane has been modified as new results have negated one explanation and provided support for an alternative explanation.

Theories

In science, the term ‘theory’ has a special technical definition: it is a body of knowledge connecting a multitude of facts about the world into an explanatory framework that explains an aspect of nature. But theories can be expanded and deepened, modified, rejected, or given support by evidence (gleaned from experiments and observations). We derive predictions and hypotheses from theories and use observations and experiments to test whether these predictions stand up to scrutiny (Figure 1). If an experiment or set of observations contradicts the predictions of a theory, the theory must be modified. If enough experiments or observations contradict the predictions of a theory, the theory must be rejected and replaced with one that can account for these phenomena.

Figure 1. Summary of scientific inquiry.

There is a lot more that can be said about theories, how they are constructed and how they are rejected, and what their role in human knowledge is. Much of this is well beyond the scope of this course, but it is important to keep in mind that theories are not vague guesses or hunches (of the sort that we might make when we state “I have a theory that my friend is backstabbing me”); it is a much more systematic and sophisticated category of understanding the world.

Take a few minutes to write down five scientific theories that you know about:

Application

Before scientific questions can be answered, they must first be converted to hypotheses, which can be tested. For each of the following questions, write an explanatory hypothesis. Recall that the hypothesis is a statement that explains the phenomenon you are interested in investigating.

  1. Does cell phone usage reduce auditory function?

Cell phone usage reduces auditory functions.

  1. Do offspring of mothers who jog each day have a mental advantage over offspring of sedentary mothers?

The off springs of mothers who jog each day have a mental advantage over off springs of sedentary

mothers.

Scientists often propose and reject a variety of hypotheses before they design a single test. Discuss with your class which of the following statements would be useful as scientific hypotheses and could be investigated using scientific procedures. Give the reason for each answer by stating whether it could possibly be falsified and what factors are measurable and controllable.

  1. The death of unborn horses on Kentucky farms is due to toxic fungi growing on grass eaten by the mares.

This could be falsified because there could be other reasons as to why unborn horses die. The control

group is the toxic fungi and the measurable aspects are how many horses die.

  1. Crime rates increase during the full moon.

This could be falsified because there could be other reasons why crime rates increase There is no direct

correlation. The control group is full moon and the aspect that can be measured are the amount of

crimes committed.

  1. Positive emotions prolong life.

This is not falsified because there is no way of seeing what someone is feeling, much less control the

emotions, however, you would be able to measure the length of someone’s life.

  1. Exposure to low levels of pesticides increases the risk of developing Parkinson's disease.

This could be falsified because there could be no correlation between the two. The control group would

be the amount of pesticides the subject is exposed to and the aspect that can be measured is the

amount of subjects who develop Parkinson’s disease.

  1. Modern birds are closely related to dinosaurs.

This could be falsified because you could prove they are in no way related. The control group could be the ancestor that links both, while the measureable aspect is the amount of traits shared between them. 

Exercise 2 - Designing experiments to test hypotheses

The most creative aspect of science is designing a test of your hypothesis that will provide unambiguous evidence to falsify or support a particular explanation. Scientists often design, critique, and modify a variety of experiments and other tests before they commit the time and resources to perform a single experiment. ln this exercise, you will follow the procedure for experimentally testing hypotheses, but it is important to remember that other methods, including observation and the synthesis of other sources of data, are acceptable in scientific investigations. An experiment involves defining variables, outlining a procedure, and determining controls to be used as the experiment is performed. Once the experiment is defined, the investigator predicts the outcome of the experiment based on the hypothesis. Read the following description of a scientific investigation on the effects of sulfur dioxide on soybean reproduction. Then in Lab Study A you will determine the types of variables involved, and in Lab Study B, the experimental procedure for this experiment and for others.

Investigation of the effect of sulfur dioxide on soybean reproduction

Agricultural scientists were concerned about the effect of air pollution, sulfur dioxide in particular, on soybean production in fields adjacent to coal powered power plants. Based on initial investigations, they proposed that sulfur dioxide in high concentrations would reduce reproduction in soybeans. They designed an experiment to test this hypothesis (Figure 2). In this experiment, 48 soybean plants, just beginning to produce flowers, were divided into two groups, treatment and no treatment. The 24 treated plants were divided into four groups of 6. One group of 6 treated plants was placed in a fumigation chamber and exposed to 0.6 ppm (parts per million) of sulfur dioxide for 4 hours to simulate sulfur dioxide emissions from a power plant. 

Figure 2. Experimental design for soybean experiment. The experiment was repeated four times. Soybeans were fumigated for 4 hours.

The experiment was repeated on the remaining three treated groups. The no-treatment plants were divided similarly into four groups of 6. Each group in turn was placed in a second fumigation chamber and exposed to filtered air for 4 hours. Following the experiment, all plants were returned to the greenhouse. When the beans matured, the number of bean pods, the number of seeds per pod, and the weight of the pods were determined for each plant.

Lab Study A. Determining the Variables

Read the description of each category of variable, then identify the variable described in the preceding investigation. The variables in an experiment must be clearly defined and measurable. The investigator will identify and define dependent, independent, and controlled variables for a particular experiment.

The Dependent Variable

The amount of soybeans produced. 

Within the experiment, one variable will be measured or counted or observed in response to the experimental conditions. This variable is the dependent variable. For the soybeans, several dependent variables are measured, all of which provide information about reproduction. What are they?

The Independent Variable

The scientist will choose one variable, or experimental condition, to manipulate. This variable is considered the most important variable by which to test the investigators hypothesis and is called the independent variable. What was the independent variable in the investigation of the effect of sulfur dioxide on soybean reproduction?

The level of SO2 they are exposed to. 

Can you suggest other variables that the investigator might have changed that would have had an effect on the dependent variables?

Other variables that the investigator might have changed would be light and water exposure. 

Although other factors, such as light, temperature, time, and fertilizer, might affect the dependent variables, only one independent variable is usually chosen.

Why might it be useful to have more than one dependent variable?

It would be useful because you would be able to test one variable at once, rather than getting results from numerous things getting tested. 

The Controlled (or Standardized) Variable

Consider the variables that you identified as alternative independent variables. Although they are not part of the hypothesis being tested in this investigation, they would have significant effects on the outcome of this experiment. These variables must, therefore, be kept constant during the course of the experiment. They are known as the controlled variables. The underlying assumption in experimental design is that the selected independent variable is the one affecting the dependent variable. This is only true if all other variables are controlled. What are the controlled variables in this experiment? What variables other than those you may have already listed can you now suggest?

Control variables would be light exposure, number of plants, water exposure, and temperature.  Lab Study B. Choosing or Designing the Procedure

The procedure is the stepwise method, or sequence of steps, to be performed for the experiment. It should be recorded in a laboratory notebook before initiating the experiment, and any exceptions or modifications should be noted during the experiment. The procedures may be designed from research published in scientific journals, through collaboration with colleagues in the lab or other institutions, or by means of one's own novel and creative ideas. The process outlining the procedure includes determining control treatment(s), levels of treatments, and numbers of replications.

Level of Treatment

The value set for the independent variable is called the level of treatment. For this experiment, the value was determined based on previous research and preliminary measurements of sulfur dioxide emissions. The scientists may select a range of concentrations from no sulfur dioxide to an extremely high concentration. The levels should be based on knowledge of the system and the biological significance of the treatment. In some experiments, however, independent variables represent categories that do not have a level of treatment (for example, gender). What was the level of treatment in the soybean experiment?

The amount of concentrations when going from low or no levels of sulfur dioxide to high levels of

concentration.

Replication

Scientific investigations are not valid if the conclusions drawn from them are based on one experiment with one or two individuals. Generally, the same procedure will be repeated several times (replication), providing consistent results. Notice that scientists do not expect exactly the same results inasmuch as individuals and their responses will vary. Results from replicated experiments are usually averaged and may be further analyzed using statistical tests. Describe replication in the soybean experiment.

They tested the same experiment with same conditions, but constant results. 

Control

The experimental design includes a control in which the independent variable is held at an established level or is omitted. The control or control treatment serves as a benchmark that allows the scientist to decide whether the predicted effect is really due to the independent variable. In the case of the soybean experiment, what was the control treatment?

The control variables would be the number of sprouts exposed and for what length of time. 

What is the difference between the control and the controlled variables discussed previously?

The control variable is the variable that you compare all of the data to, whereas the controlled variable

is altered at the start and is an established to remain constant thereafter.

Lab Study C. Making Predictions

The investigator never begins an experiment without a prediction of its outcome. The prediction is always based on the particular experiment designed to test a specific hypothesis. Predictions are written in the form of if/then statements: "lf the hypothesis is true, then the results of the experiment will be…"; for example, "if cactus spines reduce herbivory, then removal of the spines will result in greater surface area removed by herbivores." Making a prediction provides a critical analysis of the experimental design. If the predictions are not clear, the procedure can be modified before beginning the experiment. For the soybean experiment, the hypothesis was: "Exposure to sulfur dioxide reduces reproduction." What should the prediction be? State your prediction.

The sulfur dioxide reduces reproduction. 

To evaluate the results of the experiment, the investigator always returns to the prediction. If the results match the prediction, then the hypothesis is supported. If the results do not match the prediction, then the hypothesis is falsified. Either way, the scientist has increased knowledge of the process being studied. Many times the falsification of a hypothesis can provide more information than confirmation does, since the ideas and data must be critically evaluated in light of new information. In the soybean experiment, the scientist may learn that the prediction is true (sulfur dioxide does reduce reproduction at the concentration tested). As a next step, the scientist may now wish to identify the particular level at which the effect is first demonstrated. Review your hypotheses for the numbered questions. Consider how you might design an experiment to test the first hypothesis. For example, you might measure auditory function by performing hearing tests or observing changes in structures in the ear. The prediction might be:

IF cell phone usage reduces auditory function (a restatement of the hypothesis), then people who use cell phones will score lower on hearing tests than persons who do not (predicting the results from the experiment).

Now consider an experiment you might design to test the second hypothesis. How will you measure "mental advantage"?

State a prediction for this hypothesis and experiment. Use the if/then format:

If a student studies prior to the exam, then they will have a mental advantage when exam day comes.

The actual test of the prediction is one of the great moments in research. No matter the results, the scientist is not just following a procedure but truly testing a creative explanation derived from an interesting question.

Discussion

  1. From this exercise, list the components of scientific investigations from asking a question to carrying out an experiment.

The list goes as follows: question, hypothesis, assign data, conduct experiment, collect data, analyze data, draw conclusions, and discuss conclusion.

  1. From this exercise, list the variables that must be identified in designing an experiment.

The variables that must be identified in designing an experiment are dependent, independent, and control variables.

  1. What are the components of an experimental procedure?

The components of an experimental procedure are hypothesis, prediction, observation, method, and experiment

Practicing Experimental Design

1.Honeybees provide 80% of the pollination services for crops, including almonds, squash, melons, alfalfa, apples, and pumpkins. Migratory beekeepers transport over 2 million hives to farmland as crops begin to flower. In 2006-2007 beekeepers were alarmed when 50% of the honeybee colonies in 26 states were lost. In fact one of the biggest mysteries was that the bees were not found dead in the hives, but rather were simply gone! Scientists have termed this Colony Collapse Disorder (CCD). They are currently considering three alternative hypotheses: emerging pathogens (viruses, bacteria, and/or fungi), environmental toxins or chemicals; or abduction by humans (or aliens). Using the criteria in Lab Study B, Developing Hypotheses, select the hypothesis you would pursue as a scientist and justify your choice.

I would use the hypothesis that the bees were abducted by humans. I would monitor this by using a heat

censor around the specific areas, which would monitor when a bee would leave.

  1. "Grains of paradise" plants grow in the swampy region inhabited by the western lowland gorilla, make up 80-90% of their diet, and are even utilized in constructing their nests each night. Captive lowland gorillas in zoos are not fed grains of paradise, but rather have a complex diet of processed vitamin-rich food plus fruits and vegetables available in the marketplace. Recently scientists identified potent antiinflammatory and antimicrobial compounds in grains of paradise that may hold the key to a puzzling question: "Why do western lowland gorillas in zoos have an alarmingly high rate of cardiomyopathy (a type of heart disease)?" Hypothesize about the effect of diet (grains of paradise) on rates of heart disease. Describe a simple preliminary experiment to test your hypothesis, and state a prediction.

Hypothesis: If gorillas eat only grains, high rate of cardiomyopathy.

Experiment: To design the experiment, you would give the gorillas the grain, while the others get the vitamin rich food. 

Prediction: The gorillas will develop cardiomyopathy.

                 

The red-cockaded woodpecker (Picoides borealis), listed as a federally endangered species, lives in old growth longleaf pine forests of southern Georgia and other southeastern states (Figure 3). Populations of these birds are declining because of loss of suitable habitat. Red-cockaded woodpeckers excavate nesting holes primarily in living longleaf pines with red heart disease, a fungus that affects the tree's hard wood. The ideal forest has short, sparse undergrowth, usually maintained by fire. Establishing new populations of these woodpeckers is limited by their preference to colonize sites with existing nesting holes, rarely moving into new territories, perhaps because of the high energy demands of excavating new cavities, which can take from 10 months to several years. Hoping to find management techniques to help increase populations of these birds, four researchers from North Carolina State University questioned if artificially constructed nesting cavities could be used to increase family groups of birds. They hypothesized that artificially constructed cavities in unoccupied habitats or those abandoned because of unsuitable cavities would increase groups of birds (Walters et al., 1992).

To test this hypothesis they identified 20 suitable sites that had not been previously occupied and contained trees suitable for cavities. In 10 of these sites they constructed clusters of new cavities. In the remaining 10 they constructed no cavities. In addition to the new sites, they chose 20 abandoned sites with trees suitable for cavities. In 10 of the sites they constructed new cavities, but in the remaining 10 they constructed no cavities. 

Figure 3. Red-cockaded woodpecker. A federally endangered species that lives in old growth longleaf pine forests of the southeastern U.S.

What prediction might the researchers make based on their hypothesis and experiment?

The researchers might predict that the amount of captives will increase. 

The results of the experiment show of the 20 sites with constructed artificial cavities, 18 were subsequently occupied (Table 1).

Table 1. Family Groups of Red-cockaded Woodpeckers Colonizing Previously Unoccupied or Abandoned Habitats with and Without Artificially Constructed Cavities.

In this experiment, what is the independent variable? The independent variable is the total number of sites.

What is the dependent variable? The dependent variable are the amount of group nests. 

Identify the controls. The controls are the artificial and non-artificial cavities. 

How many replicates were used? There were 20 replications. 

What controlled variables might need to be considered in designing this experiment? The controlled variables that might need to be considered are the cavities. 

Did the results support the hypothesis? Yes, the results supported the hypothesis. 

Based on these results, what would you recommend for conservation of this species? Based on these results, I would recommend more artificial cavities. 

References

Moore, J. Science as a Way of Knowing. Cambridge, MA: Harvard University Press, 1993.

Walters, J. R., C. K. Copeyon, and J. H. Carter. “Test of the Ecological Basis of Cooperative Breeding in Red-cockaded Woodpeckers.” The Auk, 1009(1), 1992, pp. 90-97.

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