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Experiences in using the scientific method as a structure to teach Biology

Swati Patankar

Scientific Method
Scientific Method   (Photo: Swati Patankar)

When I first started teaching biology at IIT Bombay almost fourteen years ago, I quickly realised that if I taught facts my students and I would have an awful time in class. This was because my students had learned these facts very recently, were much better at memorizing information than me; and in terms of being a repository of facts, my real competition was the internet, which I did not have a hope of beating.

Interestingly, and very intuitively, my strategy to handle this was to use the scientific method to teach biology. Let us quickly remind ourselves what the scientific method involves (see the figure above for a visual representation). 

The crux of the scientific method involves making observations and asking questions. To answer these questions, scientists come up with many hypotheses and then systematically test each hypothesis with experimental approaches. Some hypotheses do not stand the test of rigorous experimental validation and are therefore discarded. The valid hypotheses are further tested by more experiments and finally the one hypothesis that still stands is now used to make predictions. Yet more experiments based on these predictions will tell us whether the hypothesis is valid, needs to be modified or possibly discarded. When the hypothesis has not been falsified for a long time, it becomes a theory. This structure of doing science has been used for centuries.

So now let us get into how one might use the scientific method as a structure for teaching biology and its benefits.

1) Classroom teaching

I have been teaching Molecular Biology for over a decade now and structure many topics along the lines of the scientific method. For example, when we study the discovery of Okazaki fragments, the class is first introduced to the observations that led to the classic Okazaki experiments. These observations include the knowledge that DNA replication is semiconservative , starts at a bi-directional replication fork and occurs only from 5ʹ to 3ʹ. These observations lead to a conceptual problem which is that both of the two strands of DNA cannot be replicated in the same direction as the movement of the replication fork. Indeed, one strand will have a direction of replication that is opposite to the direction of the replication fork (see the figure for a visual representation). The mugged up answer to this problem is One strand (the lagging strand) is synthesized as short fragments called Okazaki fragments while the other (the leading strand) is synthesized as a continuous, long polymer”.pQLF3vE5OBjcZ6z29j_vAdMRk9KgdkAwKwNhw1R3

I next ask the students to come up with at least 3 other mechanisms by which the problem can be solved. This forces them to think of new hypotheses beyond their mugged up facts. Then we look at the experiments and data from the Okazaki experiments and eliminate any of their hypotheses that do not fit the data. While looking at data, the students realise that the early results actually showed short fragments on both strands, not just the lagging strand! This is quite a shock to the students who have mugged up that DNA replication is semi-discontinuous. We further explore the data and the students go off and search the internet for why the data is not consistent with their expectations. I also show them a figure from a biochemistry textbook (Lehninger) from the 70s and 80s showing short fragments on both strands of the replicating DNA, illustrating that even textbooks evolve as more and more experiments are performed. By the way, if anyone is interested in the mystery behind the early observations that both strands appear discontinuous, do a Google search for discontinuous DNA replication and uracil-excision repair and have a look at papers from the 70s and 80s.

When taught through the scientific method, students realise that textbook information is based on data that can change with the next experiment. They are forced to question facts and so leave the class appreciating that biology is more than cramming facts’. This method can be applied to any professional setting: look at the data and decide for yourself” is a good learning even at McKinsey consulting or a bank.

2) Setting exams

The scientific method works well for setting exams. For the first year B. Tech class (~450 students who just cracked the Joint Entrance Exam for IITs and dropped biology years ago), I set an exam paper based on a real case of food poisoning at the hostel mess that had been covered by InsIghT, the student magazine at IIT Bombay. The first question went like this:

You are now an expert in Biology and are called upon as one of the members of the committee that is examining the case. You find that the Chinese dinner contains bacteria called Salmonella that is known to cause food poisoning. You do some further tests on the bacteria.The first test you perform is Gram staining of these Salmonella bacteria. You find it is a rod shaped, Gram-negative bacteria. Draw a schematic of the plasma membrane and cell wall of Gram-positive and Gram-negative bacteria. (2 marks)

This way of framing the question gets the students to think about structure of the bacterial cell wall in the context of a scientific problem. 

You treat the 16 hospitalized students with Penicillin (an antibiotic whose target is the peptidoglycan cell wall) and find to your surprise that they do not recover from the food poisoning because the Gram negative Salmonella bacteria are not killed efficiently by Penicillin. Based on your answer in Qs 1a, propose an explanation for why Penicillin is not effective for Gram negative bacteria. (2 marks)

Now, the students have to connect the diagrams of the bacterial cell wall from the previous answer with new information and interpret the new data. 

You next treat the students with Erythromycin and they all recover except two. Unfortunately, one of these students seems to have a drug resistant Salmonella infection. Upon further study, the bacteria are seen to have acquired foreign DNA. As a Biology expert, you know drug resistance can be explained by evolution driven via natural selection. One of the 4 concepts in natural selection is variation. Give two ways by which the drug resistant bacteria can acquire genetic variation. (2 marks)

Now, the students are given a completely different topic (evolution) in the context of the same question. In fact, the food poisoning question had 7 sub-questions that covered the topics of bacterial cell structure, antibiotics, drug resistance, evolution, viruses, genome structure and they were all connected by the basic story of the hostel food poisoning. 

3) Lab courses

Rather than simply learning techniques, the students try to answer a problem using the techniques that they learn. I have done this in two ways. First, for a lab course on Genetic Engineering, we were supposed to cover plasmid DNA isolation, PCR, cloning and bacterial transformation. In order to tie these techniques into a cohesive story, I made up a scenario where I told the students that we had isolated a bacterial strain from Powai lake that glows when we shine UV light on it. This strain seems to have a gene similar to Green Fluorescent Protein (GFP) and if we can clone the gene, we could start a biotech company and make lots of money! Now the same experiments had a purpose. 

The second strategy was used during a Microbiology lab course where the students were asked to bring in samples from anywhere and these are typically water from the department purifier, their mess food (this is a recurring theme!), Powai lake, etc. I gave my colleague who was running the lab a suggestion that I would like to collect samples with a hypothesis in mind. For example, I would be interested to know whether the water supply in Mumbai gets more polluted as one moves away from the source (Vihar, Tansi and Vaitarna lakes). The way to answer the question would be to collect samples from the train stations starting closer to the lakes and moving further away. This strategy gave the students a hypothesis-driven lab course to isolate microorganisms as well as a small field trip on the local train. In the future, I would ask students to come up with their own hypotheses. This strategy has been used brilliantly by my classmate Carol Bascom-Slack and her colleagues at Yale (check out their paper).

Most importantly, when lab courses are taught using the scientific method, failure is also a learning experience. Often the experiments did not work, especially in the Genetic Engineering lab. Rather than wanting to just get results, we did a lot of troubleshooting to figure out why the experiment did not work. This gave the students the experience of learning from failure. The lab books were written as the work proceeded, similar to a scientific project (not after the lab was over, at the last minute before submission). Finally, the objectives of the class were to learn techniques, answer the main scientific question, learn time management, learn how to plan your experiments, etc. 

I have tried to illustrate the advantages of teaching science (especially the muggu” aspects of biology) through the scientific method. Nevertheless, I am acutely aware that being at IIT Bombay allows me a lot of freedom in my teaching, which other teachers may not have. I teach B.Tech., M.Sc. and Ph.D. students; I set my own exams and grade them so that I can reinforce the concepts I am trying to get across. Teachers who read this piece might feel that I am in a privileged position while they have many challenges. I urge them to consider my challenge, which was to teach biology to IIT B.Techs — bright students who thought that the subject was utterly boring. We all have constraints, but as I am a scientist, I am always trying new strategies to do overcome them. I think this can be done by anyone.

Acknowledgement: This piece is based on a talk I gave during the 26th Biennial conference of the Asian Association for Biology Education (AABE) at Goa from September 20 – 23, 2016. Thank you to Dr. Narendra Deshmukh and the organizers for inviting me and giving me a chance to organize my thoughts on the strategies I have used for teaching biology.

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