In 2015, Azim Premji University developed a new Bacherlor’s programme in Biology with the goal of helping students become independent thinkers with an integrated view of biology. Interactions with the students made us realize that they have diverse motivations for studying biology at the undergraduate level: for their passion for the subject, to pursue higher education and research, for gainful employment, and out of sheer confusion. The Bachelor’s programme would have to acknowledge these motivations and help students develop academically. However, the teaching resources we were using as instructors, such as a textbook widely used in American universities and video clips from iBiology and similar websites fell short in addressing these concerns. Given the socio-economic and geographic diversity of our students, they often seemed lost at the examples given, such as that of otters and killer whales for trophic levels, or the comments made by the scientists in these videos. Students also came away with the view that no science was practised in India and all biological knowledge is being developed elsewhere. We needed teaching resources that could address some of these concerns.

In 2018, a group of us came together with a view of writing an introductory college-level textbook; not a comprehensive one, but rather a supplement for teachers and students who wish to explore alternate ways of studying life sciences. From the beginning we were sure about making it a free online resource. And rather than view it just as a website to access the book, we saw it as an educational platform with which to engage with learners. After many debates and arguments about its essential attributes and doing much of the writing during the first COVID lockdown in 2020, with authors juggling viral infections, online teaching and tight deadlines, we finally inaugurated the textbook in December 2021. Taking inspiration from Darwin’s famous sketch from ‘The Origin of the Species’, which places evolution as the bedrock of all biology, we called the textbook iThink Biology.

Quoting from the About section of the iThink Biology website, “Our goal in developing the iThink Biology textbook was to produce a context specific resource that is self-contained, views biology as an integrated field, and that nurtures essential capacities for the Indian student”. Here is how we went about building these attributes into the textbook.

Context-specific: Science typically is viewed as a context-free endeavour (e.g., the law of gravity operates on you the same way whether you are bacteria, slime mold, tree or mammal). However, teaching scientific concepts as if they were discovered in vacuum, free of all human drives and emotions, does students a disservice and detracts from their understanding. This context-free thinking permeates standard biology textbooks that focus on building content knowledge, often neglecting the importance of history, collaboration, the process of science, and the context of the readers themselves.

When writing iThink Biology we decided to provide context to the student by developing each chapter as a narrative. This allowed us to provide timelines for a particular concept or discovery or give its socio-cultural background. We often highlighted a scientist’s personal story, allowing students to see that the biological fact they read about was developed via a process of doubt and questioning. An extract from the chapter on Malaria is shown below in which Ronald Ross’ discovery that mosquitoes transmit the malaria parasite is described. In this section we also ask the reader to reflect on what they have read and understood from this discovery about the process of science.

Integrated Biology: We tried to view complex biological systems as a whole, rather than through the lens of separate disciplines such as molecular biology, cell and developmental biology, evolution, and more. This is why the textbook does not have chapters like genetics or biochemistry, but instead is divided into four themes: Land and waterscapes, Human health, Food and agriculture, and Interactions between organisms. Within each theme there are several chapters. For instance, in ‘Interactions between Organisms’, we have a chapter on figs in which we explore different aspects of this organism. These include ecology, species interactions, research design, and science communication. Figure 3 shows a mind map of the chapter and the topics explored within it. The student, upon reading this chapter, will understand the multiple levels at which figs can be understood – species, ecosystem and societal – and also learn some solid biology along the way.

Capacity development: Based on our teaching experience we saw that if students develop basic capacities or skills at the undergraduate level, they are equipped and trained to choose almost any career path. Content knowledge is of course important and relevant, however, we felt that students can absorb content more easily when they have these basic capacities. We identified five basic capacities, and each section of the textbook attempts to develop those competencies. This approach ensures that learners are equipped with the means to critically think about any real-world problem, not specific to studies in biology. Another objective that is met with this type of content is that the reader is allowed to approach questions and biological systems independently.

In addition to being context specific, having an integrative view of biology and emphasizing capacities over content, iThink Biology has other features, such as:

• Case-study-based chapters: Each chapter is based on one or more case studies that belong to one of the four themes mentioned above.
• India-specific content: All case studies use examples from India, highlighting the variety of scientific work done within the country. The Research Highlights section provides annotated scientific articles if students and teachers wish to explore a topic in-depth.
• Writing style: The content is explained in a language that is easy to follow. The tone is conversational and includes many pauses to encourage the reader to think critically about what they have just read. Knowledge of biological concepts is not assumed and terms are often explained in-text, or attached to a pop-up glossary. A motivated student should be able to engage with the content even in the absence of a teacher.
• Digital and dynamic: iThink Biology is an electronic book that can be accessed through a computer, mobile or tablet. A handful of digital features make this resource dynamic and interactive. Web links to external resources on the world wide web, demonstration videos and interview recordings within chapters, and quizzes are some such features. (e.g., the video of Prof. Gagandeep Kang explaining different types of viruses in the Rotavirus chapter).
• Production quality: We wanted to make sure that the production quality of the book matched that of other such resources from around the world. The text, illustrations and colours are meant to make it a pleasing experience to engage with the textbook. A unique feature of the textbook is that the students of Azim Premji University's Biology programme have done all the chapter-opening illustrations.

The features and objectives detailed above try to help teachers and students examine not just what we teach, but why we teach it. We are currently developing teaching guides for each chapter in the textbook. The teaching guide will map the topics in that chapter to current university curricula allowing teachers to see where they could make use of it for their particular course. The teaching guide will also contain suggested activities and worksheets for teaching a particular concept and these will be made available to teachers upon request. We also have new chapters planned with more videos or other learning materials.

Our challenge now is to make teachers across the country see its relevance and encourage its use in their classrooms. To that end, we are conducting seminars and workshops for teachers to demonstrate how the textbook could be used (invite us to your institution). We also use social media handles on Twitter and Instagram to engage with the teaching community.

iThink Biology is a small step on the long path to transforming educational resources in India to make them relevant, accessible, and encouraging of a learner’s curiosities and capabilities. Looking back, it is fulfilling to realize that we have produced a learning resource of quality that can prove useful to generations of learners. We are hoping this textbook to be the start of what could turn into a lifelong journey of learning.

This interview was first published in i wonder..., Issue 8 (June 2022).

Q1. Mala, could you tell us a little more about what you do at present?

Mala: As a computational biophysical chemist, my students and I like to say that we play the role of 'matchmakers' for molecules—we use models based on physics to predict how strongly molecules will interact with each other. These predictions can be used to analyse and design drug molecules or other molecules of biological importance. I’m also working with my research team to develop molecular modelling activities to engage high-school students in interdisciplinary science. I teach a wide array of courses, from introductory chemistry to physical and computational chemistry. I also teach a seminar that engages students with models across disciplines—looking at what models are from philosophical, psychological, and scientific perspectives. This course highlights the power of connecting the humanities, social sciences, and natural sciences to understand the world and our connection to it. My science-related poetry is also rooted in my interest in combining creativity and science. Currently, I’m also interested in collaborative projects to engage science students in writing poetry to reflect on their scientific journeys.

Q2. When and how did your interest in chemistry begin?

Mala: My high school chemistry teacher was one of the most enthusiastic teachers I have had. It was so clear that he was excited about the discipline and wanted us to see how exciting it can be. I think it is important to embrace and honestly own your passion for whatever it is that you like, and he taught me that it is okay to do so (in addition to teaching me a lot of chemistry)!

Q3. What inspired you to write poems, particularly ones on chemistry?

Mala: My journey started from the world of spoken-word poetry. My inspiration came from attending poetry open mics and poetry slams where I listened to what others wrote about and performed. Before this, I had known 'in theory' that poetry could be written about 'anything', but I had never explicitly appreciated the diversity of topics that one could engage with via poetry. The first time I read a poem I had written at an open mic, it was not about chemistry. The inspiration to write poems about chemistry came from some amazing students I had taught at a high school in California, U.S. I would often talk about chemistry as a soap opera on the molecular level (atoms come together, break up, etc.). When the students painted a mural that narrated the story of ions within such a soap opera, it inspired me to think about other creative ways to communicate chemistry. So I wrote a poem that narrated a molecular-level soap opera and read it at a poetry venue’s open mic. The (non-chemistry) audience loved it! So I wrote another, and another, and I kept coming back each week. The audience would always react (pun?) favourably and would sometimes comment on how they learned a little bit about chemistry through the poems. I realized that such poems could have educational value, so I started to write with an eye toward communicating specific chemical concepts while still keeping the storylines compelling and entertaining. Eventually, I started doing poetry features and was even part of a spoken-word poetry troupe. It was an amazing experience and I found the other poets very inspiring.

Q4. For readers who may want to try their hand at poetry, could you tell us something about the process you use to compose poems?

Mala: The answer to this question really varies. If I have a good storyline for a poem, it sometimes almost writes itself. The poems that require more effort are the ones written for a particular purpose (like to teach a specific concept) because the storyline has to be created around this goal as opposed to just arising “organically”. For example, in some poems, I try to focus on developing one skill, like rhythm. Or I think up a good rhyme and craft a poem all around that. For example, a poem in my book 'Atomic Romances, Molecular Dances' was inspired by an effort to rhyme as many things as possible with the word 'anonymous'. In my opinion, rhyming verses can help reinforce concepts, and make the content feel more 'approachable'. This is because we associate rhyming verses with songs and stories from our youth. Longer poems can take anywhere from just a couple of hours to days to draft, but I always go back, edit, and reword them multiple times. In contrast, couplets (two-line poems) are often rather spontaneous. Part of the point with couplets is to show that anyone can be a poet. In fact, I moved to mainly writing short couplets in part because my life has been so busy recently that I rarely have time to sit down and write a longer poem. This is my way of still engaging that side of my brain with whatever time I have.

Q5. Could you tell us a little bit about your two poetry collections?

Mala: The two collections (each dedicated to one of my children, incidentally), complement each other. The first one (Atomic Romances, Molecular Dances) is more pedagogical in the sense that I specifically crafted many of the poems to teach particular concepts in chemistry (the common ion effect, the second law of thermodynamics, etc.). It consists of narrative poems that use personification to describe chemical concepts and processes from the perspective of the atoms and molecules experiencing them first-hand. In other words, it uses everyday language to describe chemistry. In contrast, the second collection (Thinking, Periodically) is meant to be more whimsical, representing 'spontaneous' thoughts I had in my daily life (as a working mother of young children) that were articulated through chemical language. In other words, it uses the language of chemistry to describe everyday life. This collection consists of individual rhyming couplets that can make great 'exclamation points' at the end of a class period, and are also valuable resources for teachers. In this way, both books bridge the everyday world with the chemical world, but they do this by moving in opposite directions.

Q6. That you humanize chemicals and give them personalities makes your poems both relatable and interesting. Does this approach present any challenges or limitations?

Mala: Personification can help people relate the 'unfamiliar' molecular world to their own familiar, everyday lives. It also can remove the barrier of unfamiliar lingo. One challenge is that I obviously take some poetic license— clearly, molecules don’t 'talk' or have the emotions the poems ascribe to them. But one can think of a narrative poem as yet another type of model. Just like a Lewis structure or a balanced chemical equation, it has limitations in how and what it can represent. It is, therefore, important to discuss the limitations of models, analogies, and other constructions used to convey information. But these different representations complement each other, and when used in conjunction can help a student get a better, more holistic understanding of chemistry. Another challenge is that whenever one uses personification, pop culture, or other human-oriented strategies to communicate, it will not work for everyone and can even make some people feel uncomfortable. For example, in my first collection, there are some poems that touch on themes that may be more appropriate for older audiences (as indicated in the Table of Contents). There are others that make references to, for example, a television show that people at only one point in time or in one part of the world may be familiar with. It can be difficult to find analogies and narratives that can appeal to and be pedagogically effective for a broad audience. Realizing that, I think it is important to continue evolving one’s poetry keeping inclusivity and the audience in mind.

Q7. How do you see the intersection of art and science? For example, do facts, wonder, passion, beauty, and metaphor take on different meanings in science and poetry?

Mala: I think the arts and sciences are more similar than people recognize. Both use ideas that have been generated by people to help us understand the world and our connection to it. Such constructions are called models in science, but in the philosophical sense, they are not all that different from, say, realistic fiction (or even science fiction). Both are meant to make us think differently about, say, how humans respond to a mass epidemic. Obviously, there are differences in approach. In the arts, more focus is put on the process, the intention of the artist, and the artist’s connection to the work. Science, sadly, has become dehumanized to the point where publications are often written in passive voice and the process is distilled to only the 'minimum necessary path' to get from the hypothesis to the results. The 'reproducible' path, results, and end products are obviously important in both the arts and science. But, I think, focusing more on subjective processes and interpretations can help us remember, for example, that it is possible that you and I could look at the same data and still arrive at different conclusions. And these conclusions could both be reasonable in different contexts. There is a lot more subjectivity in science than people recognize. Seeing it as just facts and a reproducible process rather than an ongoing dialogue and an evolving, subjective process can make it less exciting—and less impactful—for people who want to make a difference and contribute creatively. And science needs creative people to maximize impact! For example, wonder, passion, beauty, and metaphor are just as much a part of science as they are in any other discipline, but they do not appear to be celebrated as much in science. This is one of the reasons why many people view science as dull.

Q8. Are there some considerations that the scientist-poet needs to keep in mind to balance the rigour of science with the creativity of poetry?

Mala: It depends on one’s goals. For poems aimed to teach chemical concepts in the classroom, I think it is very important to be as accurate as possible within the constraints of poetic license (like atoms and molecules talking, etc.). But if one’s goal is to be thought-provoking in other ways, or to convey emotions (as it sometimes is), then I might just use imagery in ways that might not be 100% accurate but still generates the intended effect. I think different poets fall on different parts of the continuum, and I don’t think that creativity and accuracy are mutually exclusive. On the contrary, sometimes you need to be creative to accurately convey something (quantum mechanics, for example).

Q9. In one of your writings, you share: “I ask that all scientists take time to write poetically about their personal scientific stories and share widely with each other, so we are regularly reminded that science is a human endeavour”. Could you elaborate on this?

Mala: Poetry is special because it is inherently personal. If asked to write a poem about how a chemical reaction progresses, for example, your poem will not look like mine, whereas our prose descriptions will likely be much more similar. Poetry gives each person a way to connect to science in a way that they feel comfortable with, that draws from their own experiences in a nonjudgmental way, because there is no one 'right' poem about something. It can give each person a unique voice and complement the standardized scientific writing that we’re all familiar with.

Q10. Would you have any suggestions for chemistry teachers who might want to use your poems in their classrooms?

Mala: There are many ways to incorporate poems and to use them as a catalyst for students to create their own. I use my poetry in nearly all my classes, and students almost universally find them helpful as another way to engage with concepts. When I assign creative assignments, students often write impressive poems. Similarly, I know of teachers who either simply read a poem, have students illustrate or create a poster depicting the story in a poem, or have students work through a numerical or conceptual problem based on a poem. My suggestion to teachers would be to encourage their students to write poems about a chemical concept or process. They are likely to be amazed at what their students can come up with. Students' poems may provide interesting windows into their understanding, while also being a fun way for them to engage with science. Sometimes, they may also help teachers get insights into student misunderstandings that may not have been apparent in traditional assessments.

Q11. Any thoughts that you’d like to leave our readers with?

Mala: We often think about science as a bunch of 'facts' that live outside of us. But the models that shape how we think about the world were developed by people and would probably be different if different people had participated. What this means is that YOUR perspective will make you a unique contributor to science. So be creative as a scientist. And in addition to the more 'traditional' ways of communicating science, find ways that work for you—in doing so, you might inspire others to understand the world in a new way!

It was the Diwali vacation of 2005. With great difficulty, I convinced the lordly security guards at the gate that I was indeed a student of the very college they were guarding ­– D. G. Ruparel College, Mumbai – and that all I wanted to do by entering the premises during vacation time was to check out the Zoology Department notice board.

It was almost evening when I finally entered the eerily silent Science Wing of the college. The shuttered classrooms made the corridors look longer. As I approached the Zoology Department, I saw that the entrance door to the laboratory was ajar and the lights were on. I peered inside and saw the Department Head sitting on one of the long ancient wooden tables with one of her PhD students. The chief lab techie, Yashwant kaka, was jostling around the lab carrying jars of preserved zoological specimens. The place reeked of formaldehyde. The specimen jars were out on the lab desks instead of the cabinets lining the walls. Wooden boxes of microscopy slides were stacked on the tables too, and the once dusty, stuffed taxidermic specimens of an anteater, barasingha and a juvenile Indian mugger glistened on the floor.

All three (live) occupants of the room were busy with their work and, I presumed, had not noticed me walk to the notice board hung outside the lab. I was only there to check which practical we would be doing on the first day of college reopening so I could come prepared. But I forgot all about the notice board as I peered inside. The sight of our Department Head made my palms sweat and increased my heart rate. She did that to people. I was just about to slip out of sight when she called out to me. She had noticed me, after all.

Women are known to have a higher pitched voice than men, but Dr. Madhavi Indap’s voice is a notch above the average woman’s. Nothing about her is average, for that matter; from her physique to her style of work. When broad-shouldered, 5-foot-8-inch Dr. Indap, wrapped in a rare expensive saree that is never even a centimetre out of place, walked the corridor, we undergrads shivered and walked out of her way; so did most of the postgrads and many of the staff too.

I walked in.

Her eyes bore into mine and said, “Diwali is a time we clean our house. Then why shouldn’t we clean our workplace too?” That explained the sight of the lab. Indap ma’am had sat there all day changing the age-old formalin that preserved the zoological specimens, meticulously re-labelling each jar with a fresh label, while the lab techie cleaned and dusted, and her student helped in arranging the jars back in place. In that one day spent away from her family during a time of festivity, she breathed new life in those lifeless specimens. Visit the lab today and pick up a random jar and read its label. Chances are, you read Indap madam's handwriting, as perfect and structured as if it’s in print.

She pointed at the stacked boxes of slides and said, “Some of these slides are about 80 years old. They have been imported from the US when the college was established. You will not get such good quality slides even if you pay a fortune today”. I heard the sheer passion in her voice as she spoke about the artefacts of the lab. Later, I was to see that passion reflected in all that she did.

The year I witnessed the Diwali lab cleaning was the year Dr. Indap became the Head of the Zoology Department. Within six months we saw the lab transform from an average uninspiring place to a space of innovation and inspiration. Nothing escaped her eye. She did not fail to notice Rohini Tai, one of the lab techies, drawing intricately on blackboards in her free time one day. Instead of berating her and assigning her more work, she encouraged Rohini to draw more. This while preparing for a massive marine biotech conference with delegates arriving from the world over.

She expected all her students, faculty, and non-teaching staff to do more with their time in the department than their basic duties. If you gave her the moon, she wanted the sun, stars and the rest of the planets too. And she led by example.

Not content with teaching alone, Dr. Indap almost single-handedly erected an animal cell culture facility in the college to conduct research. Research not being a focus area for a Mumbai undergraduate college in the 1990s, all that the institution could spare for her endeavour was the tiniest room on campus located adjacent to a ladies’ toilet – not an ideal location for a facility that requires sterilized conditions to function, where a single germ could impede months, even years of hard work. Undaunted, she endeavoured, and maintained several cell cultures on which she and her research students studied the effects of bioactive compounds from marine extracts. Today she heads the Central Research Laboratory of the college, where she is Prof. Emeritus, and continues to work in the realm of marine biotech, anti-cancer drug discovery, immunomodulation, and chemical communication in insects.

She made us develop our own research projects in our final year of BSc, which was over and beyond what was expected of us to clear our exams. What’s more, she made us submit the project reports before the exams. All our efforts to convince her to let us write the project reports after the exams were turned down. We wrote the reports somehow, keeping our exam syllabus aside, and then resumed studying for the exams. One of us entered the university’s toppers list that year. Dr. Indap had showed us that if we pushed ourselves hard enough, we could achieve anything. Also, though I didn’t know it then, I had just learnt the importance of completing a job on time. Many of us conduct our research but don’t write about it on time, and crucial publications never see the light of day.

Her modus operandi was simple. Find an unfathomable part of the sea, throw us in the deep end and show no mercy. Eventually, we found a way to swim back. But once we did swim back to shore, her affection knew no bounds. From paying the fees of a deserving student who could not afford them to purchasing the best quality lab equipment from her pocket, she did everything within her capacity for her students.

One day, in my second year of BSc, I mustered the courage to tell her about my interest in studying evolutionary biology and behavioural ecology. Many students chose a subject like Zoology at that time simply to get the stamp of graduation on their resumes. Many jumped to an MBA course or joined banking soon after. Evolutionary biology was a bit more elitist, not a piece to be chewed on by an undergrad student. Indap ma'am dispelled this myth and encouraged me to study the subjects that I loved. After my post-graduation, I toyed with the idea of working on the behavioural ecology of rock lizards through a project at the National Centre for Biological Sciences, Bengaluru. Dr. Indap was the first to tell me to pack my bags and head to Bengaluru. If it hadn’t been for her, I probably would not have chased those rock lizards, or studied tigers in India’s north, surveyed birds in the west, flirted with butterflies for my doctorate, or even tackled corporate sharks as I worked with businesses as a biodiversity professional for my day job.

When it was time to decide the topic for my PhD, while I played safe with subjects I could juggle with my day job, she gave me the courage to work on what I truly loved. PhDs can’t be done on something you don’t enjoy doing, she said. If it wasn’t for that advice, I would not have worked on sexual communication in butterflies for my doctorate and discovered presumptive pheromones in a butterfly species, the first for the Indian subcontinent. During my PhD, tired of having to juggle research and a job, one day I decided to quit my job. “You will do your PhD along with your job”, she declared when I told her of my decision. She mobilised the entire lab to come to my aid and made sure every instrument, every lab member, and every lab chore was bent to fit my schedule so I could manage my job and research. She even made sure the college security guards knew of me and let me inside the campus on weekends, public holidays, after-hours and vacations. She would lay down the red carpet for you, all you had to do, was perform.

Once during my undergrad years, we did not see Indap ma’am for about a week. Later we learnt that she was on a short break as her family from abroad was visiting, including her two granddaughters. Then one day, our ears finally caught that all too familiar voice from the corridor and the whole department milled into the largest lab for a meeting. Instead of the office chair, ma’am was casually plopped on the desk. Two little girls played around her. One snatched her saree’s pallu playfully while the other climbed on top of the desk to hug her grandma from behind. This sight of Indap madam, my Indap madam, resolving the lab’s problems while her grandchildren tugged at her clothes in the background, has been her defining image in my head. Like a tigress with her cubs, her stern and fierce side were in complete harmony with her gentle, kind and loving self. Under her guidance, we produced quality research projects, developed a butterfly garden in the college, organised a marine biotech conference, countless symposia and workshops, earned our doctorate degrees, and most importantly, began our journey towards the best version of ourselves. We were all, indeed, cubs of that tigress.

While teaching biology and their applications to my undergraduate students, I often make use of analogies that bring home the concepts in a simple yet effective manner. I find analogies very useful, especially during online teaching sessions, in helping students visualize the concepts being discussed.

For example, the concept of prokaryotic and eukaryotic cells. In prokaryotic cells, all metabolic activities happen within a single cell membrane without any compartments whereas in eukaryotes, each organelle has its own membrane and a different function. This concept can be explained by comparing a prokaryotic cell to a studio apartment where everything is accommodated within a single room, whereas a eukaryotic cell can be compared to a 4 or 5 BHK apartment with dedicated rooms for specific work such as kitchen, bedroom, study, drawing room etc. This comparison gives the students a start towards a clear and complete understanding of the features of these two types of cells.

Analogies can be used to bring home various concepts in immunology, bioprocess technology, or molecular biology, such as self and non-self recognition, innate and acquired immunity, replication, transcription, translation, etc. Following are the examples of analogies that I have found useful in my classroom.

1. The innate immunity can be compared with the police force in a city, which is always present and looks after the law and order in the city. The police van keeps going around in all the lanes and by-lanes of the city to counter any untoward incident that may happen during their rounds. Similarly, the phagocytic cells of our body also circulate throughout the body and any non-self substances or foreign organisms encountered are phagocytosed and eliminated.

2. Just as the police use a photograph of the culprit to search an area, the immune cells such as macrophages and neutrophils can recognize specific epitopes on the pathogen cell surface with the help of TOLL-like receptors. The antigenic determinants can be compared to the fingerprints of an individual that are unique and can be used for identifying and eliminating the pathogens.

The police use hand-cuffs to prevent the thief from running away. This can be compared to the antibodies that opsonize the antigen and help to anchor the pathogen on the phagocytic cell surface with the Fc receptors and facilitate phagocytosis.

3. Just like a security guard can catch hold of a thief before he can break into a house, when a pathogen tries to enter the body through any of the mucosal linings of respiratory tract, digestive tract or urogenital tract then the IgA antibodies and the mucosal macrophages catch hold and engulf these pathogens and eliminate them.

4. If a gang of terrorists or foreign enemy (highly virulent pathogens) enters the country in huge numbers, with advance arms and ammunitions (capsule or toxin secretion), then the normal police cannot overpower them. In such cases, special forces, such as the NSG or the Military (Acquired Immunity) need to be called, strictly under orders from the Chief of Army or the President of the country.. Similarly, cells of the acquired immune system such as the T helper and T cytotoxic cells can only be activated when presented with the antigen by the Antigen Presenting Cells (Macrophages, Dendritic cells, Neutrophils etc.)

5. When terrorists are hidden in a deserted house (intracellular pathogens) and a local informer helps to identify that house (Antibodies), then the military may decide to destroy the entire house by bombing it instead of ambushing the terrorists individually. Similarly, the T cytotoxic cell also recognizes the infected self-cell and destroys it completely along with the pathogens.

6. Compared to a new and unknown enemy, the military can elimiate a known enemy faster and with enhanced capacity, as it is already aware of its strengths and weaknesses. Similarly, when the same pathogen infects the second time the immunological memory of the acquired immunity elicits a secondary response which is enhanced and faster than the primary response.

7. During gene expression, the processes of transcription and translation can be compared to an interior designing company, in which the chief designer (DNA) makes the designs and hands over the responsibility of executing designs of individual rooms to assistant managers (mRNA). These managers then instruct the artisans and carpenters (ribosomes and tRNA), to build different furniture pieces such as chairs, tables, cupboards (proteins), using pieces of wood (amino acids).

8. Plasmid vectors in bacterial cells can be explained by using the analogy of a person staying in our house as a guest. An unknown person is not allowed to enter or stay, similarly only when the plasmid has an origin of replication recognizable to the enzymes of the host cell, it can replicate in the host. If the guest is a paying guest, he/ she will be allowed to stay for a longer period of time, likewise, only if the plasmid is providing any survival advantage to the host cell (Antibiotic resistance marker) will it be retained in the host.

9. In Bioprocess technology, the process of primary and secondary screening of organisms for production of biological products, such as antibiotics, growth factors, organic acids, etc., can be compared to the audition and elimination rounds of reality talent hunt shows, such as Indian Idol, Dance India Dance, etc. Here the candidates (wild type organisms) are screened and the most talented ones (potential strains) are selected for the final round. Before the final round, the candidates are groomed (strain improvement by mutagenesis) before the winner (Industrial strain) is selected.

Teachers in the field of biological sciences can use these as well as other such analogies in their teaching pedagogies and improve the attention and understanding of their students. However, it should be kept in mind that the analogies should not confuse students or infuse misconceptions about the topic. Teachers have to choose the analogy that is closest to the concept being explained. The analogies are not a substitute for the explanation, hence the concepts have to be introduced first and theoretically explained, and only then the analogy should be given.

Govinda-style dance and the social media rants

It was the beginning of November 2019, almost towards the end of the semester, when I had to take an online quiz for the undergrads taking my Ecology course. I hate taking assignments such as quizzes, but I have to say, given the size of the class (usually upwards of 105 students), it is an easy way out. Online platforms such as Google forms make life easier for the instructor since the assignment results are obtained immediately. There was one issue, though. The students, at that time, were in their homes, unsurveilanced, and as a result, some of them would choose to find answers using unfair means. Here’s a sample question from the quiz:

The honeybee Apis mellifera communicates with other members of its hive to provide the location of food source. Based on experimental studies, which of the following best describes a food source found in close proximity?

1. Round dance
2. Waggle dance
3. Disco dance
4. Govinda-style dance
5. Kathakali

For questions (and options) like these, it is easy for the student to discard the last three options and remember from the class lectures whether it is the “round dance” or the “waggle dance”. For someone who does not recall the correct answer from the class lectures, an easy way out is to 'search' on the internet using strings like “honeybee”, “dance”, “close”, and “proximity”. That would give them the answer they are looking for. I thought that the only way to ensure that the students do not use unfair means to get to the answers is by assigning a time-constrained quiz. I thought that by reducing time, the students would not have the leeway to search for answers on the internet. So I gave them 15 minutes to answer 30 questions that were short, direct, and easy to read, such as the question above.

To my surprise, I found some students choosing “Govinda-style dance” as the answer! Perhaps 15 minutes was too short to answer 30 questions for many students, which is why some chose options randomly. I enquired with the students on the Google Classroom platform, asking why they would choose options such as “Govinda-style dance” or “Kathakali” in response to the question. Some of the students mailed me directly, confirming that they panicked because of the time constraint.

I later found out that some students posted screenshots of my Google Classroom message on Instagram with captions such as “30 questions, 15 minutes, cannot blame them” and “15 mins, 30 questions, you decide whom to pick..whom to throw”. I was not very happy about students taking to social media with their rants, and therefore I asked them to refrain from putting them up. A few of the students mailed me to apologize for putting up the stories, but almost all of them said that they, as students, tend to have the habit of making memes out of situations to make them humorous.

Memes, huh?

I knew the evolutionary definition of the word meme, as was coined by the British evolutionary biologist Prof. Richard Dawkins. A meme refers to a pattern of behaviour or idea that spreads within a culture via imitation. I was woefully unaware of the use of the “other” meme (internet memes), which are images or videos that may be copied with slight variations and used in a humorous way to explain a trending situation. The humorous nature of internet memes strikes a chord with young students, and that is when I realized that memes have the potential to be used as a teaching tool!

The assignment

I decided to assign meme-making as one of my undergrad-level evolutionary biology course assignments. Towards the end of the course, when I had almost finished teaching the syllabus contents, I announced this assignment so that people can use the concepts taught in class to make internet memes. I asked each student to submit one meme that is based on a concept that was taught in class. It could even be related to an example that I may have mentioned in the classroom. I saw their faces light up in excitement when I announced this in the classroom. I knew that the students would enjoy this assignment, but little did I expect that some would even submit 5-6 additional memes just because they were having so much fun making them!

In my experience of teaching undergraduates, students tend to procrastinate; they either submit minutes before the deadline or well past it. In the case of the meme assignment, I faced the unprecedented situation of the entire batch of registered students (107) submitting their assignments a day before the deadline! This shows that novel and more relatable approaches are required to keep up the interest level of the students; else, it becomes mundane for the students.

A ‘serious’ jury

Being unaware of the circulating internet memes, one of the issues I faced was grading the assignments. Thankfully, some of the members of my lab (about five members) understood memes very well and helped out in the grading. All these students had taken my course earlier and were well aware of the concepts and examples that were taught in class. I learned from them that every illustration in the ‘meme-pool’ should be used in a specific manner. (The meme makers take themselves very seriously!) Keeping this in mind, the ‘meme-judging committee’ and I sat together and went through the main entries made by each student. The submission was displayed through a projector so that all the jury members could see it at once and discuss it. Thereafter, we assigned a score to each meme ranging from 1-10, with 10 being par excellence. It was GREAT fun going through each of the entries, and at times all of us would be cackling raucously.

The prize

Besides the grading, I provided further incentive to the students by announcing that the top five memes would be printed, framed, and presented to the maker in front of the class. After going through all the entries, we realized that many of the memes were brilliantly designed and deserved appreciation. Therefore, I went ahead and printed the top five memes as T-shirts and presented them to the meme makers. The top 6-10 meme makers were presented with framed prints that could sit at a desk. This could serve as a souvenir while giving them a sense of achievement.

As course instructors moulding young impressionable minds, it is also up to us to keep up with the changing times and devise new ways to reach out to the students. Access to information is much easier now than a decade or two earlier. However, at times, students get bombarded with too much information and much of this is not retained or leaves an impression. Novel methods of teaching, such as meme-making or similarly engaging assignments that the students of that age can relate to, make a massive impression down the line.

This article was first published by Editage Insights, Cactus Communications.

A hypothesis is an idea that can be tested by using scientific methods, such as by performing experiments or statistical analysis or both. A well-framed research hypothesis helps identify the most appropriate experimental design to adopt and the exact nature of data to collect so that it can be tested effectively. It helps make the research objective as clear as possible and is an informed guess about how the experimental results may answer a research question.

In this post, I discuss how to frame a good research hypothesis.

Find a research theme or question

The big question students often ask me is how to find ideas that can be tested. The answer is simple —start with a why. Ask yourself why something piqued your curiosity and why you want to study it.

The next step is to figure out how you would answer the research question. Try to inculcate two important practices that may help you frame an apt research hypothesis:

1. Honing your observation and critical-thinking skills

The power of observation is the ability to spot detail in things that others might overlook. Scientists have discovered many fundamental truths by critically analyzing certain observations. For example, observing the fall of an apple and thinking critically about the same helped Newton develop a hypothesis about the force of gravity. He eventually explained the fundamental reason behind why things fall by performing experiments and mathematical calculations.

Thus, keenly observing events and reflecting deeply on what caught your attention is an important way to practice the scientific method, and framing a good hypothesis is the first step to mastering it.

2. Developing the habit of reading scientific literature

A hypothesis emerges out of existing theories and available knowledge. So, spend time learning more about topics of your interest. A simple way to do this is to develop a habit of reading popular science articles, science magazines, scientific review articles, and research papers.

Reading scientific literature may draw your attention toward new emerging areas in research and deepens your understanding of the subject matter. This will enable you to ask original questions that open a fresh line of investigation. Once you have a question, you can read more literature and convert your question into a specific, focused, and testable hypothesis.

Understand variables

A hypothesis is centered around variables. Consider the hypothesis “manuring helps plants grow tall faster.” You can test it by conducting an experiment wherein manure is added to one set of plants and not added to another. Next, you collect data by measuring the heights of plants in both the sets and comparing them to see if they differ. Thus, your hypothesis keeps you focused on the specific trait that you intend to study (plant height) and how a variable (manure) influences it.

Hypothesis framing and testing happens around collecting data for objects, features, events, and patterns referred to as “variables” and the relationship between them. Variables are of two types.

The first type is an independent variable: that which you can control while performing an experiment. In the above example, manuring is an independent variable. You can use different types of manure, add different amounts, or even use combinations of several kinds of manure. Thus, you can modify the independent variable in many ways. The second type is a dependent variable: that which you measure in your experiment to collect data. In the above example, plant height is the dependent variable and thus cannot be changed or altered.

If you change the dependent variable, your research question also changes. For example, if you replace plant height with flowering, your research hypothesis changes to “manuring helps plants to flower faster.” Now, you will measure the rate of flowering rather than plant height and thus answer a new research question.

If you change the independent variable manuring with watering, the hypothesis may be rewritten as “Regular watering helps plants grow tall faster.” To test this hypothesis, you will still measure the plant height – the dependent variable – which is fixed.

Thus, a clear understanding of variables and their relationships is important to coming up with a workable hypothesis and to staying focused on your original research query.

Learn to use the if/then format

Commonly, hypothesis statements are framed using the if/then format. This suggests an underlying cause-effect relationship, meaning that one variable influences the other, for example, “If you eat vegetables and fruits daily, then you will develop strong immunity.”

Fine-tune your hypothesis

Now consider this statement: “Exposure to pollution has detrimental effects on skin.” Such a hypothesis is ineffective because it does not indicate what specifically to consider and study as a detrimental effect. This lack of clarity may lead to ambiguity in data collection. For example, one may consider a gamut of features to describe the harmful effects of pollution on skin, such as dryness, pigmentation, allergy etc. Hence, the research hypothesis is too broad and needs to be narrowed down.

Now consider this: “Exposure to pollution leads to acne and related skin conditions.” This hypothesis clearly indicates that the experimental design should involve a comparative study of acne in people who are exposed to pollution and those who are not. This fine-tuning of a research hypothesis is key to developing a robust methodology.

Know different types of hypotheses

1. Simple hypothesis: This describes the relationship between two variables – one independent and the other dependent.

Example:

Drinking tea may reduce iron absorption in the body.

2. Complex hypothesis: This involves more than two variables. The combination may go from two independent variables and one dependent variable or vice versa.

Examples:

Tea consumption and vitamin C deficiency can both individually reduce iron absorption in the body.

Tea consumption and vitamin C deficiency can both individually reduce iron absorption in the body, but differently in men and women.

3. Empirical hypothesis: This is a hypothesis that is tested based on an assumption. Whether the assumption is true or not is decided based on the interpretation of the collected data.

Example:

Masks can protect against all coronavirus variants equally.

4. Null (H0) and alternate (H1) hypotheses: A null hypothesis describes an absence of relationship between variables. It is called a null hypothesis because researchers collect evidence to nullify it.

Example:

The use of hair oil or hair growth serum does not influence the rate of hair loss in men.

A null hypothesis cannot be proved; it can only be rejected. Hence, it is mostly supplemented by alternative hypotheses. An alternative hypothesis states the opposite of the null hypothesis. For the above example, an alternate hypothesis may be written as follows:

The rate of hair loss is lower in men using hair growth serum than in those using hair oil.

Considering null and alternate hypotheses while designing your experiments is a way to minimize flaws and get precise/reliable results. Proving an alternate hypothesis without disproving the null hypothesis is acknowledged as an unethical research practice. This is because experimental results are never absolute but rather the closest approximation. Hence, researchers cannot prove an alternative hypothesis with 100% confidence. Thus, it is imperative to collect evidence to reject the null hypothesis before one proves an alternate one.

Let us understand this using the above example. You first need to provide evidence that hair oil/growth serum affects the rate of hair loss in men. Such evidence would refute the null hypothesis. The next step would be to collect data to compare the efficacy of hair growth serum vs hair oil for promoting hair growth in men (collecting evidence to support your alternate hypothesis).

5. Statistical hypothesis: This is statistically tested on a fraction or subset of the population to generate statistical evidence and the findings are extrapolated to the remaining population. Such a hypothesis holds true if verified statistically even if it does not fall within the reigns of logic.

Example:

Seventy-five percent of the Indian population is deficient in vitamin D.

6. Logical Hypothesis: This hypothesis uses logic to explain an observation or suggest a relationship between variables, but for which, extensive evidence may be lacking. In most cases, it might not be possible to gather evidence, yet a logical hypothesis is often not rejected.

Example:

A fixed sleep-wake pattern improves focus and increases productivity in students.

Finally, use the following guidelines to frame a good research hypothesis.

• Always adhere to ethics. Consider the ethical demarcation between what you should test vs what you can test. Your hypothesis must respect scientific responsibility and laws that protect socio-cultural and scientific norms.
• Define variables clearly. Readers are able to visualize the experimental design if the relationship between variables is clearly described.
• Frame the hypothesis such that it is clear whether a cause-effect relationship is being explored.
• Account for testability. A hypothesis is an idea that can be tested, meaning it can be proved or disproved. If an idea, thought or observation cannot be tested within the confines of the scientific method, then it forms a weak or forced hypothesis. Thus, a hypothesis must allow the researcher to experimentally manipulate or control an independent variable.
• Use simple, clear, and concise language to write a hypothesis. It must be free of complex jargon.
• Make sure your hypothesis can answer a question in a way that adds value to the existing knowledge.

Life science students gain skills and experience by working in labs. The Covid-19 pandemic placed limitations on experimental work for not only PhD students and researchers but students of undergraduate and postgraduate courses as well. Some of the challenges included, uncertainty over when students could resume or complete lab experiments, difficulties associated with maintaining cell culture and lab animals, inability to process and analyse data, unpredictable access to labs because of restricted logistics, and delays in procuring reagents and materials due to supply chain issues.

Owing to the forced transition into remote learning, educators were strapped with the unprecedented job of having to cater classes that were equivalent to the wet lab. Some educators opted to incorporate literature reviews, whilst others offered bioinformatics-based project work and virtual simulations as a substitute. For instance, a study carried out at Stockton University describes a virtual lab exercise that involved teaching students about PCR and gel electrophoresis using a SARS-CoV2 theme. It was found to be useful in enabling students to understand basic molecular biology as well as bioinformatics concepts. A few also began to include massive open online courses (MOOCs), which are typically popular among engineering students, in the life sciences classroom.

MOOCs, delivered through various online learning platforms, provide courses taught by experts to almost any part of the globe, offer a great deal of flexibility, a wide range of subjects, and provide students with the option to gain course completion certificates that are recognised by various educational institutes. They are curated with videos, tutorials, discussions, reading material, and assessments.

MOOCs are also suitable for life science students looking for a substitute for wet labs. Some notable examples include,

1. MITx offers courses on molecular biology, where students can learn how to design experiments to test DNA replication and repair hypotheses and learn how to interpret data from such experiments.
2. ‘Biochemistry, Biomolecules, Methods and Mechanisms’ is another course offered by MITx that enables students to understand how protein structure is determined, how to interpret graphs, plot behaviours, and calculate constants related to enzyme function.
3. The ‘Quantitative Workshop on Biology’ is a course that enables students to write Python, MATLAB, and R code, aiding in the analysis of biological data as well as instructing students on how to examine protein structure with PyMol. HarvardX offers a similar course in programming and data analysis with MATLAB, with an emphasis on application to biology and medicine.
4. A course that is relatively popular with students is ‘BioStatistics,’ offered by DoaneX, which upon completion will enable students to design experimental, quasi-experimental, and observational studies, as well as learn how to collect, analyse, and interpret data using appropriate statistical tools.
5. A challenging field is microscopy, where image analysis is a serious concern for students from non-engineering backgrounds. EPFLx offers a course, ‘Image Processing and Analysis for Life Scientists,’ which covers core concepts from image acquisition to image filtering, and segmentation, using open-source solutions, ultimately enabling students to work independently on information-rich images. Johns Hopkins University, through Coursera Inc., offers ‘Fundamental Neuroscience for Neuroimaging,’ which is designed for clinical practice and basic research and pertains to the principles of neuroimaging methods and introduces concepts necessary for a basic understanding of neuroimaging applications.
6. State University of New York offers a course that enables students to master Big Data analytics using real datasets, including Next Generation Sequencing data, in healthcare and biological context.
7. One of the key areas that require systematic honing is academic writing. Stanford University offers its trademark course, ‘Writing in the Sciences,’ which is entirely devoted to equipping students with the necessary skills to write manuscripts, grant proposals, and general science communication.

Taking into consideration the nature of the course content, assessment methods, and financial factors, students may benefit from custom-made online courses. Educators can design their own online courses tailor-made to suit their own students. Educators can even incorporate different academic exercises to provide holistic content.

For instance, videos of lab demonstrations and virtual simulations can be combined with data sets and quizzes to keep students engaged and provide opportunities for discussions with peers. A challenging area for students is data analysis. Online course content that involves analysis of literature, particularly that of the methods and results sections on select topics, can be a great tool to incite critical thinking. This would enable students to closely examine the techniques applied and determine the robustness of experimental data. Exercises such as these would empower students with the know-how of methodically and clinically assessing data that is presented before them, either their own work or that of their peers. Designing courses that involve a combination of these methods would be greatly beneficial to students and would enable them to develop well-rounded research prowess.

In light of the Covid-19 pandemic, MOOCs turned into a saviour, at least to the lucky few who had the right devices and internet speeds to access them. But the growing popularity of MOOCs is a testament to the changing demands in education. Students who are looking to further their education or enhance their skill set have unique requirements and the MOOC platform is able to provide tangible benefits, such as versatility, lower financial burden, as well as a unique learning experience.

Leaving aside the necessity of online learning, which was brought about by the pandemic, and its role as a substitute to wet labs, education right now and in the future is likely to involve blended learning, i.e. a combination of online and face-to-face instructions. MOOCs do not have to be restricted to the pandemic scenario; instead, they can be utilized to introduce innovative teaching methods, provide a platform for students with a more flexible, broadened, multi-dimensional approach to learning, and can offset the burden that future challenges to education may bring about. Additionally, it can act as a balance to a relatively rigid university curriculum.

The main disadvantage posed by MOOCs is the attrition rates, the limited scope for personalised courseware, limited faculty interaction, as well as the digital divide. This can however be substituted through traditional classrooms. MOOCs can therefore form part of existing curricula and still provide well-structured, highly effective courses.

Recent studies indicate that there was an increase in enrolments in MOOCs offered by Coursera Inc. and Udemy Inc., with Coursera enrolling ten times more people in 2020 than in 2019. The majority comprised undergraduate students and professionals seeking to improve their technical skills. In contrast to previous studies, it was observed that there were greater instances of students completing the course and obtaining the necessary credentials to advance their career goals. This suggests that students have begun to embrace the benefits of the internet age, enabling them to learn any subject without spatial and temporal constraints.

There is ample scope for redefining online education, taking inspiration from MOOCs. A revamping will aid in the development of transferrable skills, ultimately enhancing employability in research and development sectors, like health, nutrition, pharmaceuticals, food processing, textiles, biomaterials, and agriculture. Collectively, as we move towards a period of reinvention of the education industry, it must be borne in mind that whilst learning is an active process, the way we channel education to our students also requires dynamism.

Deoxyribonucleic acid (DNA) is the genetic blueprint in all living organisms on earth. It serves as the ‘instruction manual’ to create new life. The information stored within the DNA, in regions termed ‘genes’, is expressed transiently in the form of messenger ribonucleic acids (mRNA), and then as proteins. The change in biological alphabet from that of nucleic acids (in DNA and RNA) to that of amino acids (in proteins), is termed ‘translation’, akin to translating one language into another. While fascinating mechanisms weave together this process of ‘gene expression’^[1], students are often confounded by the intricacies. In this second article around common misconceptions in gene expression, we will deal with two such misconceptions related to mRNA translation and protein synthesis.

Misconception 1:

‘The entire messenger RNA (mRNA) is translated into a protein’.

I realized this problem when I asked students to diagrammatically explain the process of translation starting with an mRNA sequence. Most students depicted the entire mRNA to be protein coding, failing to indicate the untranslated, non-coding regulatory regions.

This misconception arises when students fail to link mRNA structure to its translation – concepts that get covered in separate chapters in most textbooks.

Correct Concept:

During protein synthesis, translation begins at the ‘start’ or ‘initiation’ codon (usually AUG, rarely CUG and GUG) and ends at the ‘stop’ or ‘termination’ codon (either one of the triplets UAG, UAA, UGA).^[1] The region between the initiation and termination codons is termed the ‘coding region’ that codes for the specific sequence of amino acids in a protein. However, the mRNA is much longer than the coding region.

A short stretch of untranslated nucleotides is present upstream (immediately preceding) of the start codon. Similarly, a short stretch downstream (immediately succeeding) of the stop codon does not encode amino acids and remains untranslated (Figure 1). These regions, present in both prokaryotes and eukaryotes, are termed the 5’-untranslated region (5’-UTR) or ‘leader’, and the 3’-untranslated region (3’-UTR) or ‘trailer’, respectively. These play a role in mRNA stability by providing sites for addition of the 5-methyl guanosine cap at the 5’ end and the poly-A tail at the 3’ end. The 5'- UTR is also where a ribosome – the site of protein synthesis in the cell – can bind to the mRNA and initiate translation.^[1,2]

Further, in eukaryotes, the coding regions of mRNA (‘exons’) are interrupted by non-coding regions (‘intron’). The introns must be cleaved and removed and all the exons joined together (‘spliced) to give the complete, uninterrupted coding sequence in its entirety. This is achieved by a process termed ‘splicing’.^[2]

While discussing translation, I recapitulate mRNA structure shown in Figure 1 so that students relate to the region being translated and those which are not.

Misconception 2:

Mixing up the orientations of codon-anticodon pairings while writing them in standard convention.

This confusion reveals itself when students are asked to recognize the correct codon-anticodon pairing from several given options (Figure 2a). Students often end up selecting an incorrect pairing as they are confused by the anti-parallel nature of the codon-anticodon interaction, and the necessity of representing all nucleic acid sequences in the 5’-3’ orientation (reading from left to right) as per standard convention.

Correct Concept:

During protein synthesis, the specific interaction between an mRNA codon and a tRNA anticodon specifies the amino acid that will be added to the growing protein chain. The mRNA is ‘read’ in the 5’ to 3’ direction, one codon at a time, by tRNA molecules carrying their cognate amino acids. The first two bases in the codon follow the rules of complementary base pairing with the corresponding bases in the anticodon (Figure 2b). However, more flexibility is accorded to the base in the third position of the codon, where non-complementary base pairing is tolerated. This is termed the ‘Wobble hypothesis’ and the third nucleotide in the mRNA codon, corresponding to the first in the tRNA anticodon, is called the ‘wobble base’.

The wobble base at the 3’ end of the mRNA codon (Figure 2b, red colour) thus pairs with the nucleotide present at the 5’ end of the anticodon, a 3’↔5’ correspondence in the pictorial depiction. However, while writing the anticodon sequence, the usual 5’-3’ convention is followed, creating confusion. For instance, consider the nucleotide sequences shown in Figure 2c. While codon 5’-CUU-3’ pairs with anticodon 3’-GAA-5’, the anticodon sequence is written as 5’-AAG-3’ in the standard convention. Students are perplexed as to whether GAA or AAG pairs with the codon.

Moreover, if the sequence of an anticodon is provided and students are asked to determine the sequence of the corresponding codon and the amino acid it codes for, there is confusion galore! Consider the same example (Figure 2c). If the anticodon is 5’-AAG-3’, the corresponding codon would be 3’-UUC-5’, viz, 5’-CUU-3’ as per the standard convention. A student confusing the 5’-3’ orientation might incorrectly infer from the standard genetic code^[3] the codon to be UUC coding for amino acid phenylalanine, instead of CUU coding for leucine, which is the correct answer.

I usually clear this confusion by pictorially representing the codon-anticodon base pairing on the blackboard, with numbers and actual nucleotide sequences to represent the codon and anticodon, and by highlighting the orientation of the strands (Figure 2b and 2c). Then I invoke the standard convention of writing nucleotide sequences, and turn the anticodon sequence around in the 5’-3’ direction as shown in Figure 2c. I test their understanding with practice problems (Figure 2a) and then by reversing the question itself – by giving them an anticodon sequence (5’-3’) asking for the corresponding codon. Teachers could devise their own problem sets catering to the common and specific problems encountered in their classrooms.

It is immensely satisfying to experience the joy of students correctly grasping a concept – that ‘Aha!’ moment when their eyes brighten with the light of understanding and a happy grin spreads on their face.

Problem-based learning (PBL) is a creative pedagogical approach that aims to promote self-learning by engaging students in contextual exercises. McMaster University, Canada, was the first to introduce PBL in their classrooms, way back in the 1960s, and shortly after, it was established in Europe and Australia. According to an eminent researcher in higher education from Deakin University, the main idea behind PBL is that ‘the starting point for learning should be a problem, a query, or a puzzle that the learner wishes to solve.’

In this approach, students are given authentic problems that are in need of resolution. They are required to understand the situation, use prior knowledge to make connections, find resource material to better understand the concept, and formulate a solution. These exercises can be carried out individually or in small peer groups. Additionally, as it is carried out through discussion and analysis, a tutor facilitates these interactions and steers students along guided inquiry paths. This approach encourages students to think outside the box and realise that there might not be just one correct answer to a given problem.

Examples of PBL

(a) Students are given a DNA sequence; asked to identify the regions that are required for transcription and translation, identify signal and localisation sequences, and functional motifs in the peptide, and determine its function and under what conditions it is expressed.

Students could be further asked to design an experiment that involves cloning the cDNA into a suitable expression system.

This problem requires students to familiarise themselves with bioinformatics and applies molecular biology tools in a digital-lab format.

(b) Jenny is a teenager facing a critical decision. Should she have DNA testing for Huntington's Disease (HD), a genetic disease that took the life of her grandmother? Why does her mother insist that Jenny get tested? Why won't her father get tested when he's started to show symptoms of HD? What are the potential consequences of this decision for Jenny and for her family?

This problem requires students to understand the genetic cause of Huntington’s Disease as well as the process of genetic testing, its risks, limitations, and bioethics.

Advantages of PBL

PBL has been popularly identified with medicine, nursing, and biological sciences, though it can be applied to any discipline. Studies have shown that PBL offers a significant advantage over traditional lecture-based learning environments in undergraduate biology courses. According to the Hun School of Princeton, PBL empowers students to think independently and become drivers of their own learning. It appears to be effective in imparting long-term retentivity and is efficient in developing critical thinking and collaborative skills. PBL encourages students to formulate new ideas based on scientific evidence. It coaches students to understand natural phenomena and find solutions to existing challenges, thereby applying scientific ideas and practices.

Problem-based learning does not dismiss the importance of traditional teaching styles, rather it reinforces material that has already been taught in the classroom by making students understand real-life concepts and apply knowledge. In PBL classrooms, instructors will need to divide the cohort into groups and constantly move around the room and engage with different groups. By roving, instructors will fulfil the role of ‘cognitive coaches,’ where they guide, probe, and support student initiatives, as opposed to lecturing and directing. In addition, the inclusion of novel assessment methods, including, self-reflection and peer assessment enables students to keep a track of their own learning.

Challenges

Implementing a problem-based learning method to a curriculum is challenging and poses certain questions, including, how can PBL be scheduled within the curriculum, will it meet course objectives, how will student learning outcomes be evaluated, and what methods will be included to organise and monitor groups. Higher-education providers could offer training programmes and workshops so that educators can have a defined understanding of the roles and responsibilities of instructors and students, thus equipping instructors with the necessary skills needed to lead PBL-based teaching.

Studies indicate that most of the challenges faced by educators stem from controlling course content, devising unique problems and questions, as well as ensuring that the problems meet academic standards. Despite its challenges, the PBL approach also serves as an avenue for educators to learn new teaching skills, and design and evaluate meaningful, high-quality projects.

In light of Covid-19

The importance of self-directed learning has only become more prominent with the advent of the Covid-19 pandemic. It has necessitated the adaptation and evolution of educational systems through distance and virtual learning. ‘Unfinished learning’, a term coined by McKinsey & Company, is used to demonstrate that students have missed out on opportunities that they normally would have had during a typical academic year, as a result of the Covid-19 pandemic. Be it schedule disruptions, unreliable internet connectivity, Zoom fatigue, Covid-19, or overall well-being, the pandemic set students back in some form or the other.

In India, there is a lack of robust data on the impact of the pandemic on the education system but according to the ‘Covid-19 Learning Loss in Higher Education’ by TeamLease, India has an estimated learning loss ranging between 40-60%. It is evident that the closure of educational institutions triggered a shift to technological and remote learning methods, which raised challenges, such as access to such technology, sustaining motivation to learning, and incorporating reliable assessment methods. In the case of disciplines that require hands-on practical classes, such as life sciences and engineering, there have been limitations imposed on access to classes and the nature of assessments.

It is with this novel scenario in mind that researchers called the need for innovative alternative education and assessment strategies. The pandemic has therefore acted as an opportunity for higher education providers to recalibrate the way they deliver their teaching styles. A study conducted at Aalborg University, Denmark, which has a long tradition of applying PBL in their educational activities, found that a digital PBL approach was able to mitigate some of the negative consequences of online learning. Digital PBL enabled students to work in a productive manner without the feeling of isolation and was effective in achieving positive learning outcomes when group collaborative online tools were used.

The way forward

Problem-based learning encourages students to give importance to evidence, formulate opinions, develop skills to justify their well-founded opinions, work as part of a team, improve written and oral communication skills, and actively engage in issues that are relevant in today’s society. Bearing this in mind, the incorporation of a PBL approach into the classroom can greatly motivate students to challenge themselves and develop transferable skills for higher education, such as doctoral programmes. Moreover, as education delivery methods are becoming dynamic, it is prudent for educators to incorporate innovative teaching styles, such as PBL, in their classrooms.

The discipline of Molecular Biology investigates information processing pathways in living cells, identifying the key players that synthesize our genetic blueprint – the deoxyribonucleic acid (DNA) molecule – and subsequently ‘express’ it into ribonucleic acid (RNA) and protein molecules – a process termed ‘gene expression’. While it is fascinating to explore nature’s information-processing pathways, reading through molecular biology textbooks could be a daunting task for a rookie undergraduate not acquainted with the terminology used.

Different books use synonymous nomenclature interchangeably, making it difficult to differentiate between terms like ‘sense/ antisense’, ‘coding/ non-coding’, ‘template/ non-template’. The complementary base pairing of nucleotides and the anti-parallel nature of DNA strands add a further layer of complexity. This especially poses a challenge for students referring to multiple textbooks in their course of study. Those unable to make the right connections run the risk of incorrectly interpreting the fundamental processes of life. This article is the first in a two-part series that addresses some of the most common misconceptions in undergraduate molecular biology.

Misconception 1:

Only one strand of DNA is used to synthesize RNA.

This statement occurs in most textbooks leaving students with the notion that at all times, only one entire strand of DNA from the two strands in the duplex is transcribed into RNA, while the other strand is inert and has no role to play. This leads to an incorrect understanding of the process of ‘transcription’. I first realized this when a student, having completed the assigned reading, asked me, “So, if only one strand of DNA is used for making RNA, what does the other strand do? Are there no genes present on this strand?” Since then, I make it a point to ask this very question in class to check whether students have thought about it at all and ensure to fill the gap in their understanding by means of a simple blackboard exercise.

Correct Concept:

Only one strand of the DNA duplex is used to synthesize RNA at a given time in a given region of the DNA.

Different regions of the DNA express at different stages in the life of a cell. Nucleic acid hybridization experiments have provided evidence for the same. When a particular region of the DNA is being transcribed, the strand of the DNA that is used to make a complementary RNA is termed the ‘template’ strand. At the same time, the other strand in the same region is NOT transcribed, and is therefore termed the ‘non-template’ strand. The latter strand may, however, act as the template strand in a different region of the DNA or at a different time in the same region.

Figure 1 depicts a scenario where genes A and C partially overlap with genes B and D, respectively, on the opposite strand. Strand–1 is the template strand for genes A and C, whereas strand–2 is the template strand for genes B and D. When strand–1 is being used for RNA synthesis from gene A, its complementary region on strand–2 cannot be used to transcribe gene B. However, strand–2 can be used at the same time to transcribe gene D (Fig.1, Possibility–1). Alternatively, when gene A is being transcribed from strand–1, at the same time, a different region on strand–1 can be used to synthesise gene C (Fig. 1, Possibility–2). Further, gene B can be transcribed at a different time when gene A is not being transcribed. The possible combinations of simultaneous gene transcriptions are listed in Table 1.

Why is this so?

If the complementary regions on both strands of DNA were to be transcribed simultaneously, the two RNA molecules thus formed would pair with each other due to their complementary nature. They would thus not be available for protein synthesis (translation) (Figure 2a).

Further, if such regions were to be transcribed and translated, the two proteins synthesized would have completely different amino acid sequences (Figure 2b). They would be two completely different proteins with distinct functions. If nature were to optimize the function of one protein by modifying the DNA sequence encoding it, this would result in a corresponding change in the nucleotide sequence on the complementary DNA strand, thus changing the sequence and modifying the function of the protein encoded by that strand. Hence, a change in the coding region of one DNA strand would be possible only at the expense of a corresponding change in the coding region of the other strand. It would therefore not be possible to optimize the function of both proteins simultaneously – an evolutionary disadvantage to the cell. These are probably the reasons why nature favours transcription from only one strand of a region of DNA at a time and the occurrence of overlapping genes (like genes A and B in Fig. 1) is rare.

To aid visualization of these concepts, I write actual nucleic acid sequences on the blackboard and walk students through DNA –> RNA –> polypeptide synthesis (Figures 2a and 2b). Given a duplex DNA sequence, students are expected to transcribe it to the corresponding mRNA and translate the mRNA to the corresponding peptide sequence using the standard genetic code. This in-class exercise has helped greatly in clarifying doubts.

Misconception 2:

The ‘sense’, ‘coding’ and ‘template’ strands of DNA are the same.

The ‘antisense’, ‘noncoding’ and ‘non-template’ strands of DNA are the same.

Students incorrectly interpret that the ‘sense’ strand of DNA is used to synthesize mRNA that finally encodes the protein, therefore it is called the ‘template’ or ‘coding’ strand. The other strand is the ‘non-template’ or ‘antisense’ or ‘non-coding’ strand and has no role to play in the transcription process.

This is apparent from a simple exercise of presenting the sequence of a DNA duplex and the mRNA sequence corresponding to any one strand, and asking students to appropriately name the strands (Figure 3). In my experience, most students confuse the nomenclature since their understanding of the concept behind the definitions is not clear.

Correct Concept:

This is a classic example of ‘too many cooks spoil the broth’ wherein the use of several alternative terms interferes with the correct understanding of the associated concept. Further, the terms are not all synonymous. Students mistakenly club them together – all positive-sounding terms in one group and their opposites in another.

As defined earlier, in the region being transcribed, the ‘template’ strand refers to that strand of DNA being used to synthesize RNA. The sequence of the newly synthesized RNA is, therefore, complementary to that of the template strand.

On the other hand, the non-template strand is also termed the ‘sense’ strand since its nucleotide sequence is identical to that of the synthesized RNA, with the exception of U replacing T in RNA. Nature makes ‘sense’ of the information coded in the DNA. In turn, the sequence of RNA (if it is mRNA), read as triplet codons, dictates the specific sequence of amino acids in the protein being translated from it. Extrapolating back to DNA, the ‘sense’ strand contains the genetic code for making the RNA and the corresponding protein, and hence, is also known as the ‘coding’ strand. It is important to note that the sense/ coding strand of the DNA is not transcribed. It is the same as the ‘non-template’ strand discussed above. By corollary, the ‘template’ strand is known as the ‘antisense’ or ‘non-coding’ strand.

The equalities in terms of nomenclature, therefore become:

• Template = Transcribed = Antisense = Non-coding strand = complementary in sequence to the synthesized RNA

• Non-template = Non-transcribed = Sense = Coding strand = same sequence as synthesized RNA (T replaced with U in RNA)

This can be understood better using actual nucleotide sequences (Figure 3).

The above are only a couple of common misconceptions that students of molecular biology have with respect to the transcription process. In the next article in the series, we will discuss some of the misconceptions about protein translation.