bio formal lab
1 Laboratory Formal Experiment THE SCIENTIFIC METHOD AND EXPERIMENTAL DESIGN and the ATTACK OF THE KILLER FUNGUS EXPERIMENT (Experiment created by Brian K. Sato, Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 found in the JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION, December 2013, p. 230-237 DOI: http://dx.doi.org/10.1128/jmbe.v14i2.612) 1.1 The Scientific Method (from BLG143 lab manual) The scientific approach is a powerful method for understanding the natural world because it is based on observations about how the world works. The observations must be systematic and objective to be useful. The procedure for making these observations is very rigorous and is broken down into several steps and is referred to the Scientific Method, which we will be studying today. The Scientific Method consists of five interrelated operations, in this order: Observation, Question, Hypothesis, Experiment, Conclusions Scientific method is a way in which a hypothesis, (a tentative explanation) is formulated, and provides a step-by-step method to gather information in order to prove or disprove this hypothesis. However, most scientists do not strictly follow the scientific method but rather use deductive or inductive reasoning with experiments then being done in order to test the hypothesis. When using deductive reasoning, the scientist develops a hypothesis first and then attempts to test the validity of their hypothesis. Based on the “hypothesis” the scientist expects certain specific events to occur in the experimentation. In this type of reasoning, if something is true of a class in general, it is also true for all members of that class. For example, “All men are mortal. John is a man. Therefore, John is mortal”. For deductive reasoning to be sound, the hypothesis must be correct. With inductive reasoning, the scientist makes a number of observations and then attempts to formulate a hypothesis that will support their observations. Inductive reasoning makes broad generalizations from specific observations. Even if all the premises are true in the statement, inductive reason allows for the conclusion to be false. For example, “John is a grandfather. John is bald. Therefore, all grandfathers are bald”. This final statement is not true. Inductive reasoning has its place in the Scientific Method. It allows scientists to form hypotheses while deductive reasoning allows scientists to apply these hypotheses to a specific situation. The following example is from a study conducted by Francesco Redi during the 1600’s, which led to the Scientific Method upon which modern science is based. At the time, spontaneous generation (production of living things from non-living matter) was a very popular belief. This example will be used to illustrate the five steps of the Scientific Method shown below: 2 Observation→→Question→→Hypothesis→→Experiment→→Conclusion 1. Observation: We use our senses constantly to gather information about the world we live in. To question a process or phenomenon, one must first recognize or observe its existence. i.e. Flies swarm around spoiled meat; maggots later appear on meat. 2. Observations of phenomena lead to questions. Clearly define the problem/question to be solved/answered. i.e. Why do maggots appear on spoiled meat? 3. The question(s) lead to a tentative explanation or educated guess, called a hypothesis. Prior knowledge or even intuition can contribute to the formulation of a hypothesis. A good scientific hypothesis must be relevant, and should be testable. i.e. Flies produce maggots. Science as a body of knowledge does not progress by "proving" hypotheses, but rather by disproving or falsifying hypotheses. We can never prove that a hypothesis is true, since it’s truth might be conditional. However, we can usually pretty quickly prove if it is NOT true. 4a. Design experiments to test your hypothesis. i) Clearly define the experiment's independent variable. This is the factor or experimental condition that CAUSES an observation. The independent variable is usually the variable we control and manipulate in our experiment. i.e. remove the flies OR change the type of meat OR move the meat to another location, etc. ii) Clearly define the experiment's dependent variable. This is the factor that results from or is affected by the independent variable. This is usually the variable that we OBSERVE, the variable that shows some response to the manipulations of the independent variable. This is what you measure, count, or record during your experiment. i.e. the appearance (if any) of maggots iii) Clearly define the experiment’s controlled variable(s). These are factors that remain the same throughout all experiments. This is important in order to ensure that any changes observed in the dependant variable are correctly attributed to the independent variable. i.e. temperature, jar size, access to air, or lighting conditions etc. remain constant, 3 iv) Additionally, a proper experiment must have the following components: a. Replication – Suppose you run an experiment in which you have two jars, one that will be accessible to flies and one that will exclude flies. Suppose the meat in the jar that is accessible becomes covered with maggots and the other does not. Will this really demonstrate that flies result in maggots? What if the meat that was covered failed to produce maggots by chance? We should have more than one jar exposed to each treatment (i.e. covered or not covered) to reduce the likelihood of chance events leading us to a wrong conclusion. b. Reference(s) – A reference (or control) is not the same as a controlled variable. A reference or control group is a set of replicates that are treated exactly the same as the experimental group, but which excludes the effect of the independent variable. In the case of Redi’s experiment, the reference is the group of jars (replicates) that are covered excluding access by flies. The experimental group is the group of jars that are uncovered providing access by flies (our independent variable). v) Select materials and identify experimental methods, methods of data collection and analysis, and plan the experimental design. i.e. Since Redi felt the factor producing maggots was presence of flies (stated in his hypothesis) and not kind of meat, etc., he chose to remove access of flies to the meat. Redi took several identical, clean jars and placed identical pieces of rotting meat in them. He covered half of the jars with gauze; the other half were uncovered where flies could gain access. His null hypothesis would be: Covered jars have the same results as uncovered jars in terms of the presence of maggots His alternate hypothesis would be: The uncovered jars will have a different result than the covered jars in terms of the presence of maggots 4b. Conduct experiments, i) Record the observations as objectively as possible. i.e. After several days, he noted that meat swarming with flies had maggots. Meat covered with gauze did not have maggots. ii) Analyze the results from the experiments that tested the original hypothesis. Use statistics when necessary to interpret these results. 4 As mentioned above, scientists generate concise statements, called hypotheses. The null hypothesis states that the independent variable has no effect on the dependent variable (or that there is no difference between the control group and the experimental group). For example, a Null Hypothesis could be: Ho: Group A is the same as Group B, or Ho: Accessibility of meat to flies DOES NOT affect presence of maggots. While the alternate hypothesis, your working hypothesis, is that the independent variable DOES have an effect on the dependent variable. In other words, the control group is different that the experimental group. In this experiment, the Alternate Hypothesis could be: Ha: Group A is not the same as Group B, or: Ha: Accessibility of meat to flies DOES affect presence of maggots Again, we cannot prove Ha, since the access of meat to flies may affect presence of maggots, but not under all circumstances. However, we can disprove Ho by showing that, in at least some circumstances, access of meat to flies does affect presence of maggots. 5. Make a conclusion drawing on the analysis of the results, determine whether the hypothesis should be supported or rejected. Again, consider your pair of null hypotheses. If you data fail to support your Null Hypothesis, then we conclude the Alternate Hypothesis is a better explanation of how the Independent variable relates to the Dependent Variable. i.e. Redi’s hypothesis was correct. Flies produce maggots. He rejected his null hypothesis. Additionally, state any further testing that may need to be carried out due to new questions that arose from your results. 5 References Aracena, J. (2011). Using Foraging Behavior of Fruit Flies to Introduce Undergraduates to Research. Pages 304-309, in Tested Studies for Laboratory Teaching, Volume 32 (K. McMahon, Editor). Proceedings of the 32nd Conference of the Association for Biology Laboratory Education (ABLE), 445 pages. http://www.ableweb.org/volumes/vol-32/v32reprint.php?ch=23 Aracena, J. (1996). Feeding and foraging behavior of the fruit fly Drosophila melanogaster. Ph.D. Thesis, University of Kansas, 106 pages. Bell, W. J. 1991. Searching Behaviour: The behavioural ecology of finding resources. Chapman and Hall, NY, 358 pages. Perieira