The Scientific Method

2D says, “First, how good is your power of observation? Do you see any animals in the picture, below? (if so, click on them) If not, then what do you think is going on, here?”

who's here?

If you were really in that place and trying to figure out what you were seeing,
you could use the scientific method to study the “problem.” Think about what
you might do, what steps you might follow, to test your idea to see if it’s right.
(There is a link to an explanation of the photograph near the bottom of this page.)

Hey, what's that? There's another one! That banana sure looks spoiled. Did this get dropped here? Yup, it's blue. Is someone under there? They sure are green.

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:

Frog 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.

Mouse 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.

Fly 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:
Bee 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.

Bacteria 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.

Will eating a vegetarian diet make us unhealthy?
Eating a vegetarian diet is healthy (or as health as or more healthy than a rich-food diet).
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.
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.
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.
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.

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: For Pasteur:
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: For Pasteur:
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: For Pasteur: There are several important things to remember about the hypothesis:
Next, the experimenter uses deductive reasoning to test the hypothesis.
For Redi: For Pasteur: There are several important things to remember about the prediction:
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: For Pasteur:

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.

Plant and Window Observation: Have you ever noticed if you place a plant near a window, that after a while, the plant grows or leans toward the window?

Question: Have you ever wondered why the plant grows toward the window?

Hypothesis: What reasons or factors can you list that might cause a plant to lean or grow toward a window? For example, do you think that
plants like Microsoft products
plants catch a virus from the window, and that makes them lean toward the window
plants respond to the glass from which they absorb some needed nutrient
plants respond to the light which they need to make their food
plants respond to fresh air leaking in the window
plants are attracted to the plants outside the window

Prediction: If it is true that and I
grow a plant in front of my computer
grow a plant in front of a PC and one in front of a Mac
grow three plants in front of a PC and three in front of a Mac
grow a plant under a light
grow three plants under a light
grow a plant under a regular light and one under a red light
grow one plant with no added fertilizer and another with 1 T of fertilizer added
grow a plant in the dark
grow a plant in a glass cube in the dark
grow three plants under a light and three plants in the dark
grow three plants with a light to the left of them and three plants with a light to the right of them
grow three plants with a light to the left of them and a piece of glass to the right
grow three plants with light to the left and glass to the right and three more with light to the right and glass to the left
grow three plants with glass on the left and a fan on the right
grow three plants with a light to the left and glass to the right and three plants in the dark with glass on the right
grow three plants with a light to the left and a fan on the right
grow three plants with light to the left and glass to the right and three more with a fan to the left and other plants to the right
grow three plants with other plants on the left and glass on the right and three others with plants on the right and glass on the left
grow three plants outdoors in fresh air and three plants indoors
grow three plants with glass on the left and three with glass on the right
grow 100 plants in 20° C air and 100 plants in 37° C air, and 50 of each have light to the left while the other 50 of each have glass to the left
grow three plants in glass cubes in the light and three plants in glass cubes in the dark
grow three plants on motorized turntables with a light to one side and three plants that are stationary with a light to one side
grow three plants on motorized turntables with glass on one side and three plants that are stationary with glass on one side
grow ten plants in one greenhouse and ten more plants, each in an individual greenhouse

then I should see a difference or change in the

soil nutrients
leaf color
number of leaves
length of the stem
number of blossoms
direction the plant is growing/leaning

Do the Experiment

Review the steps in the Scientific Method

Scientific Method Review 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.


Alcamo, I. Edward. 1997. Fundamentals of Microbiology, 5th 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, 5th 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, 3rd 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!

Copyright © 1996 by J. Stein Carter. All rights reserved.
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