The Scientific Method

For centuries, people based their beliefs on their interpretations of what they saw going on in the world around them without testing their ideas to determine the validity of these theories — in other words, they didn’t use the scientific method to arrive at answers to their questions. Rather, their conclusions were based on untested observations.

Among these ideas, since at least the time of Aristotle (4th Century BC), people (including scientists) believed that simple living organisms could come into being by spontaneous generation. This was the idea that non-living objects can give rise to living organisms. It was common “knowledge” that simple organisms like worms, beetles, frogs, amd salamanders could come from dust, mud, etc., and food left out, quickly “swarmed” with life. For example:

Observation: Every year in the spring, the Nile River flooded areas of Egypt along the river, leaving behind nutrient-rich mud that enabled the people to grow that year’s crop of food. However, along with the muddy soil, large numbers of frogs appeared that weren’t around in drier times.
“Conclusion”: It was perfectly obvious to people back then that muddy soil gave rise to the frogs.

Observation: In many parts of Europe, medieval farmers stored grain in barns with thatched roofs (like Shakespeare’s house). As a roof aged, it was not uncommon for it to start leaking. This could lead to spoiled or moldy grain, and of course there were lots of mice around.
“Conclusion”: It was obvious to them that the mice came from the moldy grain.

Observation: In the cities, there were no sewers nor garbage trucks. Sewage flowed in the gutters along the streets, and the sidewalks were raised above the streets to give people a place to walk. In the intersections, raised stepping stones were strategically placed to allow pedestrians to cross the intersection, yet were spaced such that carriage wheels could pass between them. In the morning, the contents of the chamber pots were tossed out the nearest window. When people were done eating a meal, the bones were tossed out the window, too. A chivalrous gentleman always walked closest to the street when escorting a woman, so if a horse and carriage came by and splashed up this filth, it would land on him, and not the lady’s expensive silk gown. Most of these cities also had major rat problems which contributed to the spread of Bubonic Plague (Black Death) — hence the story of the Pied Piper of Hamelin, Germany.
“Conclusion”: Obviously, all the sewage and garbage turned into the rats.

Observation: Since there were no refrigerators, the mandatory, daily trip to the butcher shop, especially in summer, meant battling the flies around the carcasses. Typically, carcasses were “hung by their heels,” and customers selected which chunk the butcher would carve off for them.
“Conclusion”: Obviously, the rotting meat that had been hanging in the sun all day was the source of the flies.

From this came a number of interesting recipes, such as:
Recipe for bees: Kill a young bull, and bury it in an upright position so that its horns protrude from the ground. After a month, a swarm of bees will fly out of the corpse.

Jan Baptista van Helmont’s recipe for mice: Place a dirty shirt or some rags in an open pot or barrel containing a few grains of wheat or some wheat bran, and in 21 days, mice will appear. There will be adult males and females present, and they will be capable of mating and reproducing more mice.

With the development and refinement of the microscope in the 1600s, people began seeing all sorts of new life forms such as yeast and other fungi, bacteria, and various protists. No one knew from where these organisms came, but people figured out they were associated with things like spoiled broth. This seemed to add new evidence to the idea of spontaneous generation — it seemed perfectly logical that these minute organisms should arise spontaneously. When Jean Baptiste Lamarck proposed his theory of evolution, to reconcile his ideas with Aristotle’s Scala naturae, he proposed that as creatures strive for greater perfection, thus move up the “ladder,” new organisms arise by spontaneous generation to fill the vacated places on the lower rungs.

In contrast to just guessing based on simple observations, what may well be the first recorded use of the scientific method to conduct an experiment occurred in about 587 bce. To give a bit of background and put this in historical perspective, in that year, the Babylonians under Nebuchadnezzar won a victory over the kingdom of Judah, and the people of Judah were incorporated into the Babylonian empire — or at least that was the Babylonian plan. One of the reasons the Babylonians were such a successful world power is that it was their policy that whenever they conquored another nation, they did away with those people’s cultural identity by assimilating/absorbing those people into their own culture. Some of the newly-conquored people were forced to migrate to other areas of the Babylonian empire, including Babylon itself, while people from other areas of the Babylonian empire were sent to live and mingle with those of the newly-conquored people who were left behind. Young male relatives of the conquored ruling family were often taken to King Nebuchadnezzar’s palace in Babylon, where they were taught Babylonian history, culture, language, and astrology/science, and in general, assimilated into the lower ranks of Babylonian royalty, serving in various roles within the palace. As part of this assimilation process, these young men were also fed the rich food that was the typical diet in Nebuchadnezzar’s palace.

However, in the case of the newly-conquored Judeans, unlike the other cultures which Babylon had conquored, the plan did not work, and the Judeans found ways to maintain their own cultural heritage despite the attempted assimilation. The story is told of four young Judean noblemen whose Hebrew names were Daniel, Hananiah, Mishael, and Azariah, who were given new, Babylonian names of Belteshazzar, Shadrach, Meshach, and Abednego, respectively, and who were brought into Nebuchadnezzar’s palace. Determined to not eat anything that was not in accord with the dietary rules of Judean religious culture, they requested that they be given a vegetarian diet. However, the palace official in charge of them was skeptical of their request, knowing that if they began to look less robust and healthy than the young men from other cultures who were also in training, he would be killed for not taking good care of them. Daniel suggested that they try an experiment. He asked that for ten days, the four of them be fed a vegetarian diet, and at the end of that time, be compared with the other young men to see who looked healthier.

Question:

Will eating a vegetarian diet make us unhealthy?

Hypothesis:

Eating a vegetarian diet is healthy (or as health as or more healthy than a rich-food diet).

Prediction:

After eating a vegetarian diet for ten days, we will look at least as healthy by visual examination, if not healthier, than those who consume a diet of rich foods.

Testing:

For ten days, we will eat a vegetarian diet, while the other young men eat their normal rich-food diet. They are, thus, the control group, and the four of us are the experimental group. Because there are four of us, that both makes us a true group and makes sure there is adequate replication in this experiment.

Data:

Here, by our modern standards, the experiment is a bit weak. All that is specified, data-wise is a general physical inspection at the end of the ten days to see who, subjectively, looks the most robust. Now, we would expect some concrete, numerical data to be gathered, perhaps weight, blood pressure, pulse, etc., and averages calculated for each group. However, in 587 bce, sphygmomanometers and stethoscopes hadn’t been invented, yet, so they did the best they could with the tools they had available. Based on the physical inspection at the end of the ten days, the “data” were that the four Judean young men appeared “healthier and better nourished” (Dan. 1:15) than those who had consumed the rich-food diet.

Conclusion:

Based on the data (the observed differences in appearance), it was concluded that not only was the vegetarian diet not harmful to their health, but that, in fact, it made them healthier than those in the control group, and thus it was not only safe but advantageous to continue feeding them the vegetarian diet they had requested.

The following steps make up the Scientific Method.

These steps make up a method which may be used to logically solve problems in many other areas of life. For example, Françesco Redi and Louis Pasteur used the scientific method to disprove the idea of spontaneous generation.

Observation:

A good scientist is observant and notices thing in the world around him/herself. (S)he sees, hears, or in some other way notices what’s going on in the world and becomes curious about what’s happening. This can and does include reading and studying what others have done in the past because scientific knowledge is cumulative. In physics, when Newton came up with his Theory of Motion, he based his hypothesis on the work of Copernicus, Kepler, and Galileo as well as his own, newer observations. Darwin not only observed and took notes during his voyage, but he also studied the practice of artificial selection and read the works of other naturalists to form his Theory of Evolution. For example:
For Redi:

• Observation: As mentioned above, flies were observed around the carcasses at the butcher shops.

For Pasteur:

• Observation: It was known that soup that was exposed to the air spoiled — bacteria grew in it. Some people claimed that there was a “life force” present in the molecules of all inorganic matter, including air and the oxygen in it, that could cause spontaneous generation to occur, thus accounting for the presence of bacteria in spoiled soups. Even when briefly-boiled soup was poured into “clean” flasks with cork lids, microorganisms still grew there. Containers of soup that had been boiled for one hour, and then were sealed, remained sterile. Boiling for only a few minutes was not enough to sterilize the soup.

Question:

The scientist then raises a question about what (s)he sees going on. The question raised must have a “simple,” concrete answer that can be obtained by performing an experiment. For example, “How many students came to school today?” could be answered by counting the students present on campus, but “Why did you come to school today?” couldn’t really be answered by doing an experiment. For example:
For Redi:

• Question: Where do the flies at the butcher shop really come from? Does rotting meat turn into or produce the flies?

For Pasteur:

• Question: Is there indeed a “life force” present in air (or oxygen) that can cause bacteria to develop by spontaneous generation? Is there a means of allowing air to enter a container, thus any life force, if such does exist, but not the bacteria that are present in that air?

Hypothesis:

This is a tentative answer to the question: a testable explanation for what was observed. The scientist tries to explain what caused what was observed. For example:
For Redi:

• Hypothesis: Rotten meat does not turn into flies. Only flies can make more flies.

For Pasteur:

• Hypothesis: There is no such life force in air, and a container of sterilized broth will remain sterile, even if exposed to the air, as long as bacteria cannot enter the flask.

There are several important things to remember about the hypothesis:

• In a cause and effect relationship, what you observe is the effect, and hypotheses are possible causes. A generalization based on inductive reasoning is not a hypothesis. An hypothesis is not an observation, rather, a tentative explanation for the observation. For example, I might observe the effect that my throat is sore. Then I might form hypotheses as to the cause of that sore throat, including a bacterial infection, a viral infection, or screaming too much at a ball game.
• Hypotheses reflect past experience with similar questions (“educated propositions” about cause) and the work of others. Hypotheses are based on previous knowledge, facts, and general principles. Your answer to the question of what caused the observed effect will be based on your previous knowledge of what causes similar effects in similar situations. For example, I know that colds are contagious, I don’t know anyone with a cold, I was at the ball game yesterday, and I was doing a lot of yelling while I was there, so I think that caused my sore throat.
• Multiple hypotheses should be proposed whenever possible. One should think of alternative causes that could explain the observation. (the correct one may not even be one that was thought of!) For example, maybe somebody sitting near me at the ball game had a sore throat and passed it on to me.
• Hypotheses should be testable by experimentation and deductive reasoning. For example, throat culture and other tests yielded no signs of a bacterial or viral infection, I have no fever or other signs/symptoms, and the doctor says my vocal cords are “swollen” in a way that would indicate overuse.
• Hypotheses can be proven wrong/incorrect, but can never be proven or confirmed with absolute certainty. It is impossible to test all given conditions, and someone with more knowledge, sometime in the future, may find a condition under which the hypothesis does not hold true.

Prediction:

Next, the experimenter uses deductive reasoning to test the hypothesis.
For Redi:

• Prediction: If meat cannot turn into flies, rotting meat in a sealed (fly-proof) container should not produce flies or maggots.

For Pasteur:

• Prediction: If there is no life force, broth in swan-neck flasks should remain sterile, even if exposed to air, because any bacteria in the air will settle on the walls of the initial portion of the neck. Broth in flasks plugged with cotton should remain sterile because the cotton is able to filter bacteria out of the air.

There are several important things to remember about the prediction:

• Inductive reasoning goes from a set of specific observations to general conclusions: I observed cells in x, y, and z organisms, therefore all animals have cells.
• Deductive reasoning flows from general to specific. From general premises, a scientist would extrapolate to specific results: if all organisms have cells and humans are organisms, then humans should have cells. This is a prediction about a specific case based on the general premises.
• Generally, in the scientific method, if a particular hypothesis/premise is true and “X” experiment is done, then one should expect (prediction) a certain result. This involves the use of “if-then” logic. For example, if my hypothesis that my throat is sore because I did too much screaming at the ball game is true and if a doctor examines my vocal cords, then (s)he should be able to observe that they are inflamed, and as the inflammation heals, the sore throat should go away.
• A prediction is the expected results if the hypothesis and other underlying assumptions and principles are true and an experiment is done to test that hypothesis. For example, in physics if Newton’s Theory of Motion is true and certain “unexplained” measurements and calculations pointing to the possibility of another planet are correct, then if I point my telescope to the specific position that I can calculate mathematically, I should be able to discover/observe that new planet. Indeed, that is the way in which Neptune was discovered in 1846.

Testing:

Then, the scientist performs the experiment to see if the predicted results are obtained. If the expected results are obtained, that supports (but does not prove) the hypothesis.
For Redi:

• 
  Redi’s Fly Experiment Testing: Wide-mouth jars each containing a piece of meat were subjected to several variations of “openness” while all other variables were kept the same.
  control group — These jars of meat were set out without lids so the meat would be exposed to whatever it might be in the butcher shop.
  experimental group(s) — One group of jars were sealed with lids, and another group of jars had gauze placed over them.
  replication — Several jars were included in each group.
• Data: Presence or absence of flies and maggots seen in each jar was recorded. In the control group of jars, flies were seen entering the jars. Later, maggots, then more flies were seen on the meat. In the gauze-covered jars, no flies were seen in the jars, but were observed around and on the gauze, and later a few maggots were seen on the meat. In the sealed jars, no maggots or flies were ever seen on the meat.
• Conclusion(s): Only flies can make more flies. In the uncovered jars, flies entered and laid eggs on the meat. Maggots hatched from these eggs and grew into more adult flies. Adult flies laid eggs on the gauze on the gauze-covered jars. These eggs or the maggots from them dropped through the gauze onto the meat. In the sealed jars, no flies, maggots, nor eggs could enter, thus none were seen in those jars. Maggots arose only where flies were able to lay eggs. This experiment disproved the idea of spontaneous generation for larger organisms.

For Pasteur:

• 
  Pasteur’s Broth Experiment Testing: Broth was boiled in various-shaped flasks to sterilize it. As the broth and air in the containers cooled, fresh room air was drawn into the containers. None of the flasks were sealed — all were exposed to the outside air in one way or another.
  control group — Some flasks opened straight up, so not only air, but any bacteria present in that air, could get into them.
  experimental group(s) — Some flasks had long, S-shaped necks (swan-neck flasks) and others were “closed” with cotton plugs. This allowed air to enter these flasks, but the long, swan neck or the cotton balls filtered out any bacteria present in that air. The long necks were subsequently broken off some of the swan-neck flasks.
  replication — Several flasks were used in each of the groups.
• Data: Broth in flasks with necks opening straight up spoiled (as evidenced by a bad odor, cloudiness in previously clear broth, and microscopic examination of the broth confirming the presence of bacteria), while broth in swan-neck flasks did not, even though fresh air could get it. Broth in flasks with cotton plugs did not spoil, even though air could get through the cotton. If the neck of a swan-neck flask was broken off short, allowing bacteria to enter, then the broth became contaminated.
• Conclusion(s): There is no such life force in air, and organisms do not arise by spontaneous generation in this manner. To quote Louis Pasteur, “Life is a germ, and a germ is Life. Never will the doctrine of spontaneous generation recover from the mortal blow of this simple experiment.”

In science when testing, when doing the experiment, it must be a controlled experiment. The scientist must contrast an “experimental group” with a “control group”. The two groups are treated EXACTLY alike except for the ONE variable being tested. Sometimes several experimental groups may be used (but only that one thing may vary among the groups). For example, in an experiment to test the effects of day length on plant flowering, one could compare normal, natural day length supplied by an artificial light source (the control group) to several variations in length of exposure to the same type of artificial light source (the experimental groups).

When doing an experiment, replication is important. Everything should be tried several times on several subjects. For example, in the experiment just mentioned, a student scientist would have at least three plants in the control group and each of the experimental groups, while a “real” researcher would probably have several dozen. If a scientist had only one plant in each group, and one of the plants died, there would be no way of determining if the cause of death was related to the experiment being conducted.

The experimenter gathers actual, quantitative data from the subjects. For example, it’s not enough to say, “I’m going to see how the dog reacts in this situation.” That’s too vague, so rather, in that experiment, the scientist might have a list of certain behaviors, and record how often each of the dogs tested exhibits each of those pre-defined behavior patterns. Data for each of the groups are then averaged and compared statistically. It’s not enough to say that the average for group “X” was one thing and the average for group “Y” was another, so they were different or not. The scientist must also calculate the standard deviation or some other statistical analysis to document that any difference is statistically significant.

Research is cumulative and progressive. Scientists build on the work of previous researchers, and one important part of any good research is to first do a literature review to find out what previous research has already been done in the field. Science is a process — new things are being discovered and old, long-held theories are modified or replaced with better ones as more data/knowledge is accumulated. For example, the idea that the sun is at the center of our solar system replaced the idea that the earth was at the center of the universe, and the idea that ulcers are caused by stress has been replaced by the idea that ulcers are caused by bacterial infection. Scientists are human, too, and so these major changes are often controversial and accompanied by violent debate!

A theory is a generalization based on many observations and experiments; a well-tested, verified hypothesis that fits existing data and explains how processes or events are thought to occur. It is a basis for predicting future events or discoveries. Theories may be modified as new information is gained. This definition of a theory is in sharp contrast to colloquial usage, where people say something is “just a theory,” thereby intending to imply a great deal of uncertainty.

Review the steps in the Scientific Method

Click (double-click in SeaMonkey) on the photo to re-start the animation.

Sometimes, it doesn’t go this way. Sometimes serendipity (Serendib = former name for Ceylon) happens. The Persian fairy-tale The Three Princes of Serendip illustrates the principle known as serendipity. In this story, three princes make discoveries by insight into accidents pertaining to things they were not seeking. Serendipity is not discovery just by accident alone, but includes the idea that the investigator has intuition, or knowledge, which enables him/her to recognize and take advantage of unexpected events unrelated to his/her original quest. The discovery of aspartame is a good example of serendipity, but also an example of very bad lab technique. A chemist at Searle Chemical Company had his coffee cup sitting on the benchtop in the chemistry lab next to his experiment. Somehow in the process of doing his experiment and drinking coffee all at the same time (not a good idea if you value your life), he stuck his fingers in his experiment, then into his mouth. The serendipity comes in when he realized that this sweet-tasting accident could make his company and him rich.

To give you an idea of how the scientific method works, your study group is asked to go through the steps we just discussed as though you were real biologists getting ready to do real research. You will be doing all of the background work and designing the experiment, but not actually doing it since this is not a lab course. However, you are asked to do a write-up of the experiment as though you had done it. For more information on this, refer to the Assignment on Scientific Method.

References:

Alcamo, I. Edward. 1997. Fundamentals of Microbiology, 5^th Ed. Benjamin Cummings Publ. Co., Menlo Park, CA.

Borror, Donald J. 1960. Dictionary of Root Words and Combining Forms. Mayfield Publ. Co.

Campbell, Neil A., Lawrence G. Mitchell, Jane B. Reece. 1999. Biology, 5^th Ed.   Benjamin/Cummings Publ. Co., Inc. Menlo Park, CA. (plus earlier editions)

Campbell, Neil A., Lawrence G. Mitchell, Jane B. Reece. 1999. Biology: Concepts and Connections, 3^rd Ed.   Benjamin/Cummings Publ. Co., Inc. Menlo Park, CA. (plus earlier editions)

Marchuk, William N. 1992. A Life Science Lexicon. Wm. C. Brown Publishers, Dubuque, IA.

Tell me about the picture of the bananas!