Inimary Toby-Ogundeji, PhD Assistant Professor University of Dallas
The use of JupyterLab notebook provides a user-friendly method for learning data analysis. It is easy to work with and also provides a variety of datasets for direct use and case study data discussions. One example follow-up task that can be used to extend this data analysis activity is performing logistic regression. An example approach using Firth’s logistic regression method is provided here (https://bit.ly/31gb7vG). JupyterLab provides a temporary workspace to accomplish basic tasks in R. One consideration is that it doesn’t maintain the user’s data and/or work once they close the browser. Analysis performed in JupyterLab cannot be saved to the virtual platform, however files from the work session can be exported out and saved externally. For users wanting to have the capabilities of saving work sessions and transferring between JupyterLab sessions in a streamlined manner, they can establish a freely available account.
The activity described in this article highlight a user-friendly method to learn some basic data analysis skills. It is ideal for students with little to no experience in Biostatistics, Bioinformatics or Data Science. The article provides an opportunity for students to reflect and practice analysis of data collected from biological experiments within an online learning environment. The activity is suitable for an instructor led session (using an app with screen sharing capabilities). This article provides basic knowledge about how to use R for simple data analysis using the JupyterLab virtual notebook platform.
The goal of this activity is to familiarize the user with the basic steps for importing a data file, retrieval of file contents and generating a histogram using R within a JupyterLab environment. The workflow steps to accomplish these tasks are outlined below:
Access JupyterLab
Access “R”
Access datasets
Perform summary statistics
Data visualization
Workflow Step-by-Step instructions and screenshots from JupyterLab
Dr. Toby holds a PhD in Biomedical Sciences (specialization in Organ Systems Biology) from Ohio State University, College of Medicine. Her postdoctoral training was in Functional Genomics at the FAA-Civil Aerospace Medical Institute in Oklahoma City. She is currently an Assistant Professor of Biology at University of Dallas. She teaches several courses including: Human Biology, Bioinformatics and Biostatistics. She enjoys mentoring undergraduate students and is an active member of The APS. Dr. Toby’s research program at UD is focused on cell signaling consequences that occur at the cellular/molecular interface of lung diseases. She is also leveraging the use of computational methods to assess immune sequencing and other types of high throughput sequencing data as a means to better understand lung diseases.
Gregory J. Crowther, PhD Everett Community College
On June 23, Dr. Chaya Gopalan of Southern Illinois University spoke at the APS Institute of Teaching and Learning on the topic of “The Flexibility of Using the Flipped Classroom as a Virtual Classroom During the COVID-19 Pandemic.” The presentation was great — full of empirical data, practical tips, and audience participation.
One of the questions that arose was, assuming that one is flipping a class with video lectures, how long should those video lectures be? I can’t remember what Chaya said about this at the time, but many others used the chat window to weigh in. They mostly argued that shorter is better, with 10-12 minutes being a commonly prescribed upper limit.
The author droning on during a long video lecture.
I had heard this “shorter is better” mantra many times before, and believed that it was well-supported by the literature. Still, I had resisted any impulse to shorten my own videos. I was already generating one video per chapter per course — 50 videos per quarter in all. If I divided each video into four shorter videos, that would be 200 videos per quarter to manage. Couldn’t my students just hit “pause” and take breaks as needed?
Thus, the video-length issue was making me increasingly uncomfortable. I think of myself as an evidence-based teacher, yet I seemed unwilling to go where the evidence was pointing.
Having battled myself to an impasse, I decided to email Chaya. I wrote:
…If you — as an expert flipper who has read the literature and published your own papers on this — were to tell me, “Come on, Greg, the evidence is overwhelming — for the good of your students you just need to make your videos shorter — stop whining and do it!” then I probably would comply. So … what do you think?
Chaya declined to respond with an ultimatum, but she did note that her own videos vary greatly in length — from 8 minutes to an hour! A lot of this variation is topic-specific, she said; some “stories” need to be told as a single chunk, even if it takes longer to do so.
Chaya’s point about chunking the material according to natural breakpoints was exactly what I needed to hear. While the idea of shortening videos because “shorter is better” did not itself inspire me, the idea of finding those breakpoints and reorganizing the material accordingly seemed utterly worthwhile. Maybe this would help my students more easily track their progress within each chapter. And off I went — I was finally ready to shorten my videos!
So, what lessons can be extracted from this bout of navel-gazing?
The thing that jumps out at me is this: my long-held resistance to a fairly mild idea (“make your videos shorter!”) was suddenly overcome not by conclusive new research, but by a subtle shift in perspective. When Chaya made a particular point that happened to resonate with me, I now wanted to make the change that I had been guiltily avoiding for months.
This was — for me, at least — a valuable reminder that, while evidence-based teaching is undoubtedly a good thing, behavior is rarely changed by evidence alone. There’s just no substitute for direct conversations in which open-minded people with shared values can stumble toward a common understanding of something.
It may be slightly heretical for me to say so, but I’ll take a good conversation over a peer-reviewed paper any day.
Greg Crowther teaches human anatomy and physiology at Everett Community College (north of Seattle). He is the co-creator of Test Question Templates, a framework for improving the alignment of biology learning activities and summative assessments.
Jennifer Ann Stokes, PhD Assistant Professor of Kinesiology Southwestern University
In my previous blog post, I outlined the lessons learned in my first run teaching a year-long integrated upper-division human anatomy and physiology course. It has been about a year and a half since the original post and after having taught the course for a second time I will review and add to my list of initial lessons learned. Additionally, this spring semester brought new challenges with a very swift move to online coursework due to COVID-19, so I will also comment on the resulting course alterations. As a reminder, this course sequence (A&P I and II) is an upper-division junior and senior level course at my college and class sizes are very small (20-24 students) allowing for maximum time for interaction, questions, and instructor guidance both in lecture and lab.
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First, I will review the previous lessons learned and add additional commentary based on what I learned in my second year. If you haven’t yet, I would check out the previous blog for the initial notes.
1) Use an integrative textbook.
My textbook of choice is still Physiology: An Integrated Approach by Dee U. Silverthorn. For anatomy, I continued to supplement the anatomy information, such as the specifics of the skeletal system and joints, muscles, histology, etc., through the use of models and other reference material in hands-on lab activities. One addition made in the second year was the use of AD Instrument’s Lt online learning platform. I discuss the addition of Lt in more detail later in this post, but I think it is important to note here too since the Lt lessons directly complemented the textbook material and helped bridge the gap between lecture and lab for the students.
2) Start building and assessing students’ A&P knowledge from the ground up, and build incrementally.
Laying the foundation for the core concepts is critical to the student’s understanding, application, and mastery of the complex integrative content that this course builds. I took this foundation building more seriously the second time around and, in the end, I did not have to spend more time on the basic content but instead I provided more formative assessment opportunities. This helped the students who did not have as strong a background or understanding of the basic material to recognize that they needed additional assistance. In addition to the weekly homework assignments which were graded for completion only, I added weekly low-stake quizzes using our learning management system (LMS). At first I thought the students would dislike the extra work, but an end-of-the-year survey indicated that they appreciated the extra practice and that the quizzes helped them feel better prepared for the exams.
3) Create a detailed course outline, and then be prepared to change it.
This lesson holds true for just about any course, but I found it especially true for an integrated A&P course – even when teaching it a second time. And it is even more important when you have to switch to online delivery. In the second year, I learned to appreciate that no two cohorts of students are the same and what took the previous cohort a day to master took the next cohort up to two days in some cases. Having the “flex days” at the end of each section was crucial for concept review and content integration. These are days where no new content is introduced, but instead we review and practice together.
4) Constantly remind your students of the new course format.
I cannot emphasize this enough: students will want to revert back to what they are comfortable with and what has worked for them in the past. I constantly remind students that their “cram and forget” method will not serve them well in this course and provide them with ample opportunity to practice this both on the formative and summative assessments. In the second year I continued the individual meetings with each student after their first exam to discuss study strategies and new ways to approach this material, but I also implemented additional check-ins throughout the year particularly with those students who were struggling. I continued to remind the students that the course content not only builds throughout the entire semester but also the entire year! I hammered this point home a bit more with the addition of “retention” quizzes which were delivered unannounced throughout the year and tested major core concepts and application.
5) Solicit student feedback.
Students can be brutally honest, so use that to your advantage. A lot of the new things I added in my second year teaching this course came from the first year-student feedback. I send out my own surveys with specific questions throughout the year which the students fill out anonymously. I find that students are happy to help, especially when they can see a course alteration mid-semester which was based on their feedback.
6) Be prepared to spend a lot of time with students outside of the classroom.
Still very true, but that’s probably my favorite part of this job. Even when we switched to online course delivery the virtual office hours were busy and students took advantage of the extra review and time to ask questions.
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In this second section, I will add additional lessons learned in my second year of teaching this course and comment on the changes made when the course moved online mid-way through the second semester.
7) Over-communication.
One of the things I am known for with my students is consistent and clear communication, probably to the point of over-communication. I also emphasize that communication is a two-way street, so just as I am constantly communicating information to them, I expect them to do the same to me, including any accommodations, sports travel, or general course questions. I model this behavior with regular use of our LMS announcement page and I use the start of each class to review important deadlines and open the floor for questions. The move to online instruction only made this over-communication even more important. Early on in the transition period I checked in often to let them know the new plan and opened discussion pages to allow them to ask questions and express any concerns. I checked in multiple times a day using the LMS announcement page, posted a “live” course schedule and tables of new homework and quiz due dates all in one central location, and I added silly memes to the discussion boards to up engagement. I also added resource pages on the basics of Zoom and how to be an online student since this was very new territory for them (and me). Looking back this was a lot of information that was constructed and disseminated very quickly, but an end-of-the-year survey indicated they appreciated the information and that it told them that I was prepared and willing to help them during the transition.
8) More assessments. More practice. More activity.
In my second year, I assigned more practice problems from the textbook to help the students prepare for the exams and held problem sessions outside of class for review. This additional time and practice was well received even when it was a greater time commitment for the students. With the move to online instruction I was thankful that I had already established a fairly homework-heavy course as these assignments became even more important. The assigned “lecture” time was switched to virtual problem solving sessions and the course moved even more toward a flipped-classroom model. Since the switch to online occurred after I had already built a pretty solid reputation with this class (about a semester and a half) they were used to reading and problem solving before class, even if that class was now online. All homework and quizzes moved online which allowed for quicker feedback to the students on their progress and, thus, more time for questions before the exams. The switch to fully online homework and quizzes I plan to keep even when the course moves back to in-person as the quick feedback for the students and less time spent hand-grading by me is worth the extra time it takes to set-up the online modules.
9) Utilization of LMS Discussion Forums.
Honestly, the use of the LMS discussion forums did not start until the course moved online, but their quick success made me question why I had not taken advantage of this tool earlier. When the course moved online I added discussion pages with titles such as “What is going on?!? General course questions.” and “What I am most nervous about with the course moving online is…” The goal was to provide an outlet for students to ask questions and share their concerns. I always started the discussion myself, giving them a sort of “jumping off” point and an example. These discussion pages were utilized by almost all members of the course and were rated very highly in the end. Students could comment any time of day enhancing the accessibility of the discussion. I will modify these to be used in my courses moving forward for both in-person and online courses.
10) Online presence for both lecture and lab.
I actually increased my A&P online presence prior to the mandatory switch to online coursework with the implementation of AD Instruments Lt learning platform in the fall semester. My students received free access to both the anatomy and physiology modules thanks to an award from the American Physiological Society. The Teaching Career Enhancement Award supported a year-long study assessing the use of the ADInstruments Lt learning platform and its interactive and immersive lessons aimed at enhancing knowledge, retention, and practical application of the integrative course content. The Lt platform was fully customized to the course material and was used both in the lecture classroom and in the lab. In the lab, students were able to interact with a data acquisition system that is more “game-like” and familiar, while still collecting high-level human physiology data. Lt also allowed for the creation of new lessons that engaged students with the use of embedded questions in multiple formats, including drag-and-drop labeling, drawing, short answers, and completion of tables. These lessons were used in many ways: for pre-lab preparation, in-lab and post-lab assessment, and for active learning activities in the classroom. Lessons were completed individually or in small groups, and questions were set up with hints, immediate feedback, multiple tries, and/or automatic grading.
These modules were also incorporated in the active-learning lecture component of the course, providing additional exposure and practice with the content. The Lt lessons directly complemented the textbook material and helped bridge the gap between lecture and lab for the students. When the course moved fully online I was incredibly thankful that Lt was already in use in my course and that the students were already comfortable and familiar with the platform. I used Lt exclusively for the online labs and supplemental lecture content for the remainder of the spring semester. Just as before, the lessons and modules were customized by me to fit my course learning objectives and prepare the students for their new online assessments. Students could complete the online coursework at their leisure and stop by the virtual office hours for help or post questions on the discussion boards for feedback. Student feedback indicated that the addition of Lt to this course enhanced accessibility of the course content, provided extra practice and exposure to the material, and overall was rated highly by the students.
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And just as I did before, now I turn the conversation over to the MANY seasoned educators who read this blog. What did you learn in your quick move to online coursework? Did you implement any new pedagogical tools which you will continue to use even with in-person instruction? Please share!
Jennifer Ann Stokes is a soon-to-be Assistant Professor of Kinesiology at Southwestern University in Georgetown, TX, after spending the last three years at Centenary College of Louisiana. Jennifer received her PhD in Biomedical Sciences from the University of California, San Diego (UCSD) and following a Postdoctoral Fellowship in respiratory physiology at UCSD, Jennifer spent a year at Beloit College (Beloit, WI) as a Visiting Assistant Professor of Biology to expand her teaching background and pursue a teaching career at a primarily undergraduate institution. Jennifer’s courses include Human Anatomy and Physiology (using an integrative approach), Nutritional Physiology, Exercise Physiology, Medical Terminology, and Psychopharmacology. Jennifer is also actively engaged with undergraduates in basic science research (www.stokeslab.com) and in her free time enjoys cycling, hiking, and yoga.
Kristen L.W. Walton, PhD Biology Department Missouri Western State University
COVID-19 (Coronavirus Disease 2019) is caused by infection with SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus-2). Current evidence suggests that this zoonotic coronavirus originated in China in late 20191, and it subsequently spread rapidly across the globe, causing significant morbidity and mortality. To help contain the spread of this virus, many countries have implemented policies and orders aimed at reducing contact between people. The terms “social distancing” and “flatten the curve” have been rapidly imbued in our culture. Indeed, a Google Trends search shows a significant surge in searches for “social distancing” between the week of March 1-7, 2020 and the week of March 29-April 4, 20202. In the United States, to help mitigate the rapid spread of SARS-CoV-2, a few colleges and universities began to announce in early March that they would be suspending face-to-face classes and shifting to all-online instruction, and soon most postgraduate institutions in the USA followed suit, including my institution.
In early March, as the situation became recognized as increasingly urgent by the higher education institutions in our region, the administration at my institution, Missouri Western State University (MWSU), made a decision to extend spring break by one week, through March 22. Then, in the middle of that second week of spring break, the university administration announced that MWSU would cancel all face-to-face classes for the rest of the semester, and students would have several options regarding their grades for the spring 2020 semester3. Higher education institutions across the USA have grappled with how to handle grades in this unprecedented time. Students who did not sign up for online classes are finishing their face-to-face courses, in many if not most cases, as hastily-constructed online versions. Many institutions have chosen to make all classes pass/fail, others have opted to keep letter grades as the only option, and still others, including MWSU, have given students flexible options to choose a pass/fail option or a letter grade. The MWSU administration also gave faculty flexibility in determining whether to create a “culminating experience” for students who elected to complete their courses. This could mean anything from reducing the amount of content and/or assessments, changing the format of assessments (for example, a final paper in lieu of a final exam), or essentially continuing as originally planned but with online course delivery and assessments. This flexibility for faculty was intended to recognize that some types of classes are more amenable than others to a shift to online delivery. Students whose midterm grade was a C or higher could elect to choose the “credit” (pass) grade option for the course if they chose not to complete the culminating experience; students who chose to complete the culminating experience earned a letter grade based on their course grade at the end of the semester. To increase flexibility for students, this option was available to students up until the last day of classes, April 24. The deadline for a withdrawal from the class was also extended to April 24.
For me, as a biology faculty member, the flexibility allowed by our administration in how to structure the last five weeks of my classes led to a lot of thought about my courses and how to best achieve the course objectives for each of them. I spent many hours considering this, discussing options with my colleagues in a socially distant manner, through emails and our first Zoom department meeting, a somewhat difficult transition for our close-knit group of faculty used to frequent in-person conversations. I also spent time reading a flurry of articles and blog posts about the importance of being understanding of the major disruption to our students’ lives and college experience4; the importance of recognizing the difficulty in creating a high-quality online course experience with a few days’ notice5; and, not to be overlooked, the importance of tending to one’s own needs, both professional and personal, in this high-stress time.
Depending on one’s personal situation, a faculty member could also be dealing with changes in family schedules and responsibilities due to children who were suddenly not attending school or day care. Illness could strike any of us or our friends and family members, certainly adding to the stress and anxiety experiences. Partners could be furloughed as businesses shuttered their doors due to the pandemic. While some academics touted their ability to be highly productive during the quarantine and even cited the invention of calculus by Sir Isaac Newton during the black plague as inspiration, others pointed out that quarantine is not universally a time when one can focus solely on work and scientific discovery. This is true for me, on a personal level. I have two elementary school-aged children whose school closed a week after my university suspended face-to-face classes. I have had sole responsibility for child care and helping them with their school work at home, while also moving my classes online and maintaining other work responsibilities. Many of the students in my classes are non-traditional and have similar child care and “home school” responsibilities. Others have financial stress due to job layoffs, or, conversely, increased work stress and time demands for those working in the health care field. Another concern is that many of our students have poor access to broadband internet and technology to access class materials online. Several of my students emailed me during the transition stating that they were using only a smartphone to access course materials and had no access to a laptop or desktop computer, printer, or other technology, and no high-speed internet.
Consideration of my students’ access to technology, stress, and other burdens, as well as the other factors described above led me to make different choices for each of my three classes this spring. For my honors colloquium, titled, ironically enough, Plagues That Changed the World, my co-instructor and I decided not to try to coordinate the student-led presentations that were scheduled for the last 6 weeks of the semester and instead only required a final paper. Seven of 13 undergraduates in this course chose the credit grade based on their midterm grade, and did not complete this rather minimal culminating experience. For my upper-division biology majors course, Molecular Basis of Disease, which is a capstone-type elective course that is not a prerequisite for any other classes, I chose to culminate the lab portion by keeping a scheduled lab quiz, but not attempt to recreate the planned five-week group research project. For the lecture portion of that class, students who elected to complete the culminating experience wrote a literature review article as originally planned and were given one online exam instead of two in-class exams. Even with this reduced workload, 6 of the 15 undergraduates enrolled in the course chose to take a credit grade and did not complete the course. My third course this spring, Pathophysiology, is primarily populated by pre-nursing majors and population health majors, with a few pre-health-professions biology majors. It would not have been appropriate to drop content or assessments of content knowledge from this course, because the overwhelming majority of students in the course needed to learn that content for success in later coursework. As it happens, I have taught this lecture-only course in an online format in the summer for several years, so transitioning it to an online delivery mode was relatively easy, with a few exceptions: increased modes of accessing the material, and exams. I have structured the all-online previous version of that class to be asynchronous, based on knowledge of my student population, many of whom work full time while also taking classes. I felt that was still the best choice in these uncertain times. However, in addition to posting video lectures, I downloaded the audio-only podcasts and posted them separately for students who did not have regular high-speed internet access or were working solely from a smartphone with a small screen. I also made additional course notes available.
As for the exams, I have always required proctored exams in the online version of this course, and structured them similarly to the written exams taken by students in the traditional, face-to-face version of the course. Proctored online exams would not have been feasible in the COVID-19-induced chaos that ensued in late March and early April, as some of my students were moving home many states away, finding themselves under self-quarantine, caring for family members, etc., and I myself had schedule considerations to juggle with children and their school work and Zoom meetings which competed for our limited bandwidth home internet. I tried to strike a balance between several considerations: best practices for online unproctored exams, such as making them open-book and not easily Google-able; the format and level of rigor students were used to from the first two written, face-to-face exams; and being mindful of unequal access to technology among my students. In this class, 81 of 86 undergraduates completed the culminating experience, a high proportion driven largely by the requirement of their specific majors for a letter grade in this required course.
As I write this, I still have several papers to grade and final course grades to enter. I can say with certainty, however, that the choices for assessments and content coverage that I made for my Pathophysiology course did not appear to substantially disadvantage the majority of students, and the course grade distribution will be noticeably higher than usual, aside from the small number of students who did not complete the course. Several of my colleagues have observed similar increases in their course grades this semester. In that course, I erred on the side of leniency with the exams, but since I could not in good conscience drop content from that course – pre-nursing students still need to have learned about diseases of the digestive tract, even if COVID-19 interrupted their semester! – I am comfortable that they will at least have a reasonable degree of preparation for their subsequent courses. For my other two courses, grades will not be higher and in some cases students submitted work that was of lower quality than I expected from their work earlier in the semester. I strongly suspect that many students who chose to complete those courses did not have the focus or the ability to do so as well as they would have in the face-to-face courses. I do not have survey data to help clarify what the students were thinking, but I suspect the students who needed the letter grade for subsequent coursework approached this altered, online part of the semester differently from those who were only taking an elective where a credit grade would suffice or a GPA issue was not anticipated. Informal feedback from all three of my classes included several students commenting about how they did not sign up for online classes because they prefer traditional-format classes, comments about family issues (helping children with school work, moving back home because of job loss, stressful quarantine situations), and comments about missing deadlines because of work or other outside responsibilities.
Although I still need to submit my final course grades for the spring 2020 semester, the summer session is already looming. My institution chose a few weeks ago to offer only 100% online summer classes, so my usual summer online Pathophysiology class will need to have exam structure revamped away from the written, proctored format that I have previously used. In addition, many institutions including my own are having discussions about the fall semester. At this time, we just don’t know what the COVID-19 situation will be in late August. We have been told to prepare for something unusual, whether it will be a fully online semester, a restructured semester with two or three shorter block sessions, or some other plan. In preparing for that, I will be considering these questions for each of my classes:
1. How can the course learning objectives best be accomplished in an altered course format?
2. What are the best ways to transition a heavily hands-on lab course to an online or shortened course format?
3. What are the needs of the student population in this course?
4. What is the appropriate balance between flexibility versus maintaining appropriate expectations in the course?
Considering the course goals and learning objectives is a critical component of any course design or transition to a different format, and the course may need to change if the different format is not amenable to the original goals and learning objectives. In this time of forced transitions to altered course structures and the impacts of COVID-19 mitigation strategies on us and our students, choices might be different from the choices we would otherwise make. It’s also important for faculty, administrators, and students to recognize that different types of courses may be more or less easy to convert to an all-online format. And while online instruction can be excellent and perhaps this experience will encourage broader use of certain online course components in future face-to-face classes for many faculty, it is not the “college experience” that many students expect and there is speculation among higher education administrators that enrollments will be down this fall, adding to the financial distress that many universities and colleges are already experiencing. Although I have read some opinion pieces that higher education should use this spring as a springboard to shift to more online courses permanently, I would argue that it’s also important to recognize that a large proportion of our students and faculty, myself included, strongly prefer those face-to-face classes and hope to return to them as soon as we can. I am certain that as a global community of physiology educators we will continue to interact and support each other as we navigate all of the upcoming transitions.
References:
Coronaviridae Study Group of the International Committee on Taxonomy of Viruses. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol. 2020;5:536–44.
Kristen Walton is a Professor in the Biology Department at Missouri Western State University. She earned her PhD in Physiology from the University of North Carolina-Chapel Hill in 2001 and was a SPIRE (Seeding Postdoctoral Innovators in Research and Education) Postdoctoral Fellow at UNC-Chapel Hill from 2001-2006. In 2006, she began her current position at Missouri Western State University, a primarily undergraduate institution. She has taught a variety of undergraduate courses including animal physiology, pathophysiology, immunology, molecular basis of disease, introductory cell biology, public health microbiology, and human anatomy & physiology. Her research interests are in intestinal inflammation and inflammatory bowel disease, and in discipline-based education research.
Ida T. Fonkoue, Ph.D. Post-Doctoral Fellow, Renal Division Emory University School of Medicine
Ramon A. Fonkoue, Ph.D. Associate Professor, French and Cultural Studies Michigan Technological University
The COVID-19 pandemic has led to a total and sudden reshaping of the academic landscape across the country, with hundreds of institutions moving administration entirely online and shifting to online instruction for the remainder of the spring semester or for both spring and summer. This sudden transition with practically no time to prepare has major implications for students and faculty alike, and poses serious challenges to a smooth transition as well as effective online teaching on such a large scale. Out of these challenges, two issues in particular are examined here:
By Phil Hill, licensed under CC-BY. See URL in references.
the disparity in resources and preparedness for effective online teaching
the implications of the migration to virtual classrooms for diversity and inclusion
Disparity in resources and preparedness for effective online teaching
Teaching an online course requires just as much, if not more, time and energy as traditional classroom courses. It also requires specific IT skills to be effective. Some teachers have managed to achieve great success engaging students online. However, many challenges remain for the average teacher. While online teaching has now been embraced by all higher education institutions and the number of classes offered online has seen a steady growth over the years, it should be noted that until now, instructors and students had the choice between brick and mortar classes and virtual ones. Each could then choose based on their personal preferences and/or circumstances. What makes the recent changes so impactful and consequential is that no choice is left to instructors or students, as the move to online classes is a mandate from the higher administration. Whether one is willing, prepared or ready is irrelevant. It is from this perspective that the question of the preparedness to migrate online is worth examining.
With academic units ordered to move classes online, instructors who had remained indifferent to the growing trend of online teaching have had a difficult reckoning. They have had to hastily move to online delivery, often with a steep learning curve. This challenge has been compounded in some cases by the technology gap for instructors who haven’t kept their IT skills up to date as well as the school’s preparedness to support online teaching. But even instructors who had some familiarity with learning management systems (LMS) and online delivery have faced their share of challenges. We will only mention two sources of these difficulties:
First, students’ expectations in a context of exclusive online teaching are different from when most online classes took place in the summer, and were attractive to students because of convenience and flexibility. With online classes becoming the norm, students in some universities are taking steps to demand that school administrators pay more attention to quality of instruction and maintain high standards to preserve teaching effectiveness.
Second, instructors can no longer use LMS resources just for the flexibility and benefits they afforded, such as in blended classes or flipped classes. Moving everything online thus requires extra work even for LMS enthusiasts.
For students, there have been some interesting lessons. Until now, it was assumed that Generation Z students (raised in the boom of the internet and social media) we have in our classes have tech skills in their DNA and would be well equipped and ready to migrate online. Surprisingly, this hasn’t been the case across the board, and these first weeks have revealed real discrepancies in student IT equipment with varying consequences for online classes. Equipment failure and problems with access to high speed internet emerge as the most serious difficulties on the students’ side. Furthermore, online learning requires independence and often more self-discipline and self-motivation. Most online courses are not taught in real time, and there are often no set times for classes. While this flexibility makes online classes attractive, it can also be a drawback for students who procrastinate and are unable to follow the course pace. If left to themselves, only the most responsible students will preserve their chances of performing well. On this last point, one unexpected issue has been students who have virtually disappeared from their classes since the migration of courses online amid the COVID-19 pandemic. The current transition has thus presented major challenges for teachers and students alike.
Implications of the migration to virtual classrooms for diversity and inclusion
The second issue we think deserves attention is the way in which educational institutions’ commitment to diversity and inclusion would play out in virtual classes. While they are now among the professed core values of all colleges and universities across the country, implementing diversity and inclusion in an online environment presents a different set of challenges for both instructors and students. In traditional classrooms, the commitment to diversity and inclusion typically translates into the following:
A diversity and inclusion statement from the school must be included in the course syllabus.
Instructors must remind students a few rules at the beginning of the course, including: recognition that the classroom is an environment where diversity is acknowledged and valued; tolerance of and respect for diversity of views in the classroom.
Sensitivity to and respect for diversity (gender, age, sexual orientation, etc.).
Students are asked to be courteous and respectful of different opinions.
In moving into a virtual environment, instructors have to think about the challenges of virtual classrooms and their potential impact on diversity and inclusion. For instance, the faceless nature of course participation and asynchronous delivery may make it easier for participants to disregard or neglect diversity and inclusion rules. Teachers need to reflect on ways to ensure that the virtual space of online classes remains an environment that fosters diversity and inclusion. One drawback of online classes is the potential impact of the relative anonymity on social engagement. In a traditional classroom, participants are constrained by the physical presence of their peers in the confined space of the classroom. The closed physical space of the classroom, combined with the instructor’s authority and peer pressure contribute to fostering discipline. Reflecting on the way online teaching impacts the instructor, one faculty noted: “I didn’t realize how much I rely on walking around the room and making eye contact with students to keep them engaged.” As an online teacher, one lacks the ability to connect physically with students, to read emotional cues and body language that might inform about the individuality of a student. Moreover, a good grasp of the diversity in the classroom and of students’ learning abilities is needed to plan instruction, and give each of them the opportunity to learn and succeed.
Drawing from the above considerations, here are some key questions that instructors should consider as they migrate online: What skills do instructors need to properly address diversity and inclusion online? How do instructors include diversity and inclusion requirements in online course design? How to create an inclusive online classroom? How do instructors attend to diverse students’ needs during instruction? How do they monitor behaviors and enforce diversity and inclusion rules during instruction?
While the migration might have been abrupt, instructors need not seek perfection in moving their courses online. As in traditional classes, what matters the most, from the student’s point of view, is constant communication, clear directions and support from their teachers. Students understand the challenges we all face. They also understand the rules in virtual classes, provided we emphasize them.
Dr Ida Fonkoué is a post-doctoral fellow at Emory University School of Medicine in the Laboratory of Dr Jeanie Park. She trained under Dr Jason Carter at Michigan Technological University, where she graduated with a PhD in Biological Sciences in December 2016. She teaches renal physiology classes and lead small groups in the School of Medicine. Her long-term research goal is to understand how the sympathetic nervous system, the vasculature and inflammation interplay to contribute to the high cardiovascular disease risk of patients living with chronic stress, such as those with post-traumatic stress disorder.
Dr. Ramon A Fonkoué is an Associate Professor of French and Cultural Studies and the Director of Graduate Studies in the Department of Humanities at Michigan Technological University. He is also a Visiting Scholar in the department of French and Italian at Emory University. He has been teaching online for 9 years and has experience with blended, flipped and full online classes.
I always had this curiosity about life. Since the very beginning, always wanting to understand how animals’ breathe, how they live, how they move. All that was living was very interesting. – Dr. Ibarra
“I always had this curiosity about life and I wanted to
become a doctor, but my parent told me it was not a good idea,” Lise
Bankir explained in her interview for the Living
History Project of the American Physiological Society (APS). The video interview (video length: 37.14
min.) is part of a rich collection over 100 senior members of the APS who have
made outstanding contributions to the science of physiology and the
profession.
The archive gives us great insight into how these scientists
chose their fields of study. As Dr.
Bankir, an accomplished renal physiologist, explain how she ended up “studying
the consequences of vasopressin on the kidney.”
She describes her work in a 1984 paper realizing “high protein was
deleterious for the kidney, because it induces hyperfiltration,” which of
course now we accept that high protein accelerates the progression of kidney
disease. Later she describes her Aha! moment, linking a high protein diet to
urea concentration, while on holiday.
“It came to my mind that this adverse effect of high protein
diet was due to the fact that the kidney not only to excrete urea (which is the
end product of proteins), but also to concentrate urea in the urine. Because the plasma level of urea is already
really low and the daily load of urea that humans excrete need that urea be
concentrated about 100-fold (in the urine with respect to plasma).”
Other interviews highlight how far ahead of their time other
scientists were. As is the case when it
comes to being way ahead of teaching innovations and active learning in
physiology with Dr. Beverly
Bishop. In her video interview, you
can take inspiration from her 50 years of teaching neurophysiology to physical
therapy and dental students at SUNY in New York (video length: 1 hr. 06.09
min.). Learn about how she met her
husband, how she started her career, and her time in Scotland. Dr. Bishop believed students could learn
better with experimental laboratory activities and years ahead of YouTube, she
developed a series of “Illustrated Lectures in Neurophysiology” available
through APS to help faculty worldwide.
She was even way ahead of others in the field of
neurophysiology. Dr. Bishop explains, “everyone
knows that they (expiratory muscles) are not very active when you are sitting
around breathing quietly, and yet the minute you have to increase ventilation
(for whatever reason), the abdominal muscles have to play a part to have active
expiration. So, the question I had to
answer was, “How are those muscles smart enough to know enough to turn on?” Her
work led to ground breaking work in neural control of the respiratory muscles,
neural plasticity, jaw movements, and masticatory muscle activity.
Another interview shed light on a successful career of
discovery and their implications to understanding disease, as is the case with
the video interview of Dr. Judith S.
Bond. She describes the discovery of meprins proteases as her most
significant contribution to science (video length: 37.38 min.), “and as you
know, both in terms of kidney disease and intestinal disease, we have found
very specific functions of the protease.
And uh, one of the functions, in terms of the intestinal disease relates
to uh inflammatory bowel disease. One of
the subunits, meprin, alpha subunit, is a candidate gene for IBD and
particularly ulcerative colitis. And so that opens up a window to – that might
have significance to the treatment of ulcerative colitis.”
Or perhaps you may want to know about the life and research
of Dr.
Bodil Schmidt-Nielsen, the first woman president of the APS (video length:
1 hr. 18.07 min.) and daughter of August and Marie Krogh. In her interview, she describes her
transition from dentistry to field work to study water balance on desert
animals and how she took her family in a van to the Arizona desert and while
pregnant developed a desert laboratory and measured water loss in kangaroo
rats. Dr. Schmidt-Nielsen was attracted
to the early discoveries she made in desert animals, namely that these animals
had specific adaptations to reduce their expenditure of water to an absolute
minimum to survive.
The Living History Project managed to secure video
interviews with so many outstanding contributors to physiology including John B. West,
Francois
Abboud, Charles
Tipton, Barbara
Horwitz, Lois Jane
Heller, and L.
Gabriel Navar to name a few. For
years to come, the archive provides the opportunity to learn from their
collective wisdom, discoveries, family influences, career paths, and entries
into science.
As the 15th anniversary of the project
approaches, we celebrate the life, contributions, dedication, ingenuity, and
passion for science shared by this distinguished group of physiologists. It is my hope you find inspiration, renewed
interest, and feed your curiosity for science by taking the time to watch a few
of these video interviews.
Dr. Jessica M. Ibarra is an Assistant Professor of Physiology at Dell Medical School in the Department of Medical Education of The University of Texas at Austin. She teaches physiology to first year medical students. She earned her B.S. in Biology from the University of Texas at San Antonio. Subsequently, she pursued her Ph.D. studies at the University of Texas Health Science Center in San Antonio where she also completed a postdoctoral fellowship. Her research studies explored cardiac extracellular matrix remodeling and inflammatory factors involved in chronic diseases such as arthritis and diabetes. When she is not teaching, she inspires students to be curious about science during Physiology Understanding Week in the hopes of inspiring the next generation of scientists and physicians. Dr. Ibarra is a native of San Antonio and is married to Armando Ibarra. Together they are the proud parents of three adult children – Ryan, Brianna, and Christian Ibarra.
Recently I was faced with a teaching challenge: how to incorporate active learning in a huge Introductory Biology lecture of 400+ students. After searching for methods that would be feasible, cost effective, and reasonably simple to implement in the auditorium in which I was teaching, I came up with clickers. Our university has a site license for Reef Polling Software which means I wouldn’t add to the cost for my students—they could use any WiFi enabled device or borrow a handset at no cost. I incorporated at least 4 clicker questions into every class and gave students points for completing the questions. 10% of their grade came from clicker questions and students could get full credit for the day if they answered at least 75% of the questions. I did not give them points for correct answers because I wanted to see what they were struggling to understand.
I’m now a clicker convert for the following 3 reasons:
Clickers Increase Student Engagement and Attendance
In a class of 400+, it is easy to feel like there is no downside to skipping class since the teacher won’t realize you are gone. By attaching points to completing in-class clicker questions, about 80% of the class attended each day. While I would like perfect attendance, anecdotally this is much better than what my colleagues report for similar classes that don’t use clickers. Students still surfed the internet and slept through class, but there was now more incentive to pay a bit of attention so you didn’t miss the clicker questions. In my opinion, getting to class can be half the battle so the incentive is worth it. In my small classes I like to ask a lot of questions and have students either shout out answers or vote by raising their hands. Often, students won’t all vote or seem to be too embarrassed to choose an answer. I tested out clickers in my small class and found an increased response rate to my questions and that I was more likely to see the full range of student understanding.
Clickers Help Identify Student Misconceptions in Real Time
Probably the biggest benefit of clickers to my teaching is getting a better sense of what the students are understanding in real time. Many times I put in questions that I thought were ‘gimmes’ and was surprised to see half the class or more getting them wrong. When that happens, I can try giving them a hint or explaining the problem in a different way, having them talk with their group, and then asking them to re-vote. Since I don’t give points for correctness, students don’t feel as pressured and can focus on trying to understand the question. I’m often surprised that students struggle with certain questions. For instance, when asked whether the inner membrane of the mitochondria increases surface area, volume, or both, only half of the students got the correct answer the first time (picture). Since this is a fundamental concept in many areas of biology, seeing their responses made me take time to really explain the right answer and come up with better ways of explaining and visualizing the concept for future semesters.
Clickers Increase Student Learning (I hope)
At the end of the day, what I really hope any active learning strategy I use is doing is helping students better understand the material. To try to facilitate this, I ask students to work in groups to solve the problems. I walk around the class and listen while they solve the problem. This can help me get an idea of their misconceptions, encourage participation, and provide a less scary way for students to ask questions and interact with me. While working in groups they are explaining their reasoning and learning from each other. Interspersing clicker questions also helps to reinforce the material and make sure students stay engaged.
I’m convinced that clickers are helping to improve my teaching and students seem to agree. Of the 320 students who filled out course evaluations one semester, 76 included positive comments about clicker questions. Here are two of my favorites:
“I like how we had the in-class clicker questions because it made me think harder about the material we were learning about in that moment.”
“I enjoyed doing the clicker questions. If the class disagreed with something she would stop and reteach the main point and hope we would understand. That was really helpful on her part.”
I would be remiss if I didn’t end by thanking the many researchers who have studied how to incorporate clickers into your class to maximize learning. I decided to try them after hearing Michelle Smith talk at the first APS Institute on Teaching and Learning and highly recommend seeing her speak if you have the chance. If you only want to read one paper, I suggest the following:
Smith, Michelle K., et al. “Why peer discussion improves student performance on in-class concept questions.” Science 323.5910 (2009): 122-124.
I hope you will comment with how you use clickers or other strategies to engage large lecture classes. For more resources I’ve found helpful designing my classes click here.
Katie Wilkinson, PhD is a newly minted Associate Professor of Biological Sciences at San Jose State University. She completed her undergraduate work in Neuroscience at the University of Pittsburgh and her PhD in Biomedical Sciences at the University of California, San Diego. She was an NIH IRACDA Postdoctoral Fellow in Research and Scientific Teaching at Emory University. At SJSU her lab studies the function of stretch sensitive muscle proprioceptors. She teaches Introductory Biology, Vertebrate Neurophysiology, Integrative Physiology, Pain Physiology, and Cardiorespiratory Physiology to undergraduate and masters students.
When I was approached to write a blog for PECOP I thought I could bring a slightly different perspective on classroom technology as I am not a full-time classroom educator. My primary role for the past dozen years with ADInstruments has been to work with educators who use our products to get the most from their investment in our technology. This has led to thousands of conversations about use and misuse of technology in the classroom and teaching laboratories. I would like to share some of my insights here.
Early in my academic career I was tasked with a major overhaul of the introductory Biology curriculum at Louisiana Tech, and incorporating technology was part of this mandate. I have always been a bit of a tech geek, but rarely an early adopter. I spent quite a bit of time and effort taking a good hard look at technology before implementing it in my classrooms. I was fortunate enough to participate in T.H.E. QUEST (Technology in Higher Education: Quality Education for Students and Teachers). Technology was just beginning to creep into the classroom in the late nineties. Most courses were traditional, chalk and talk; PowerPoint was still a new thing, and this three-week course taught us how to incorporate this emerging technology appropriately. PowerPoint worked better for many of us than chalk and talk, but also became a crutch, and many educators failed to use the best parts of this technology and applied it as a panacea. Now PowerPoint has fallen out of favor and has been deemed to be “Killing Education”(1). When used improperly, rather than curing a problem, it has backfired and reduced complex concepts to lists and bullet points.
I was fortunate enough to have been on the leading edge for a number of technologies in both my graduate and academic careers. Anybody remember when thermocyclers were rare and expensive? Now Open PCR can deliver research quality DNA amplification for around $500. Other technologies became quickly obsolete; anybody remember Zip drives? Picking the tech that will persist and extend is not an easy task. Will the Microscope go the way of the zip drive? For medical education this is already happening (2). While ADInstruments continues to lead the way with our PowerLab hardware and software packages for education (3); there are plenty of other options available. Racks of very specialized equipment for recording biological signals can now be replaced with very affordable Arduino based electronics (4,5). As these technologies and their supporting software gets easier to use, almost anyone can collect quality physiological data.
One of the more interesting technologies that is evolving rapidly is the area of content delivery or “teaching and learning” platforms. The most common of these for academia are the Learning Management Systems. These are generally purchased by institutions or institutional systems and “forced” upon the faculty. I have had to use many different platforms at different institutions. Blackboard, Desire 2 Learn, Moodle, etc. are all powerful tools for managing student’s digital records, and placing content in their “virtual” hands. Automatic grading of quiz questions, as well as built in plagiarism detection tools can assist educators with large classes and limited time, when implemented properly. This is the part that requires buy in from the end user and resources from the institution to get the faculty up and running (6). While powerful, these can be cumbersome and often lack the features that instructors and students who are digitally savvy expect. Many publisher digital tools integrate with the University LMS’s and are adopted in conjunction with, or more frequently now instead of a printed textbook. McGraw Hill’s Connect and LearnSmart platforms have been optimized for their e-textbooks and integrate with most LMS’s (7). Other purpose-built digital tools are coming online that add features that students expect like Bring Your Own Device applications; Top Hat is one of these platforms that can be used with mobile devices in and out of the classroom (8).
So what has endured?
In my almost 20 years in higher education classrooms and labs, lots of tools have come and gone. What endures are passionate educators making the most of the technology available to them. No technology, whether digital or bench top hardware, will solve a classroom or teaching laboratory problem without the educator. While these various technologies are powerful enhancements to the student experience, they fall flat without the educator implementing them properly. It’s not the tech, it’s how the tech is used that makes the difference, and that boils down to the educator building out the course to match the learning objectives they set.
My advice to educators can be summed up in a few simple points:
Leverage the technology you already have.
Get fully trained on your LMS and any other digital tools you may already have at your institution. The only investment you will have here is your time and effort.
Check the cabinets and closets, there is a lot of just out of date equipment lying around that can be repurposed. Perhaps a software update is all you need to put that old gear back in rotation.
Choose technology that matches your course objectives.
Small and inexpensive purpose-built tech is becoming readily available, and can be a good way to add some quantitative data to the laboratory experience.
Top of the line gear may have many advantages for ease of use and reliability, but is not necessarily the best tool to help your students accomplish the learning objectives you set.
Investigate online options to traditional tools.
eBooks, OpenStax, and publisher’s online tools can be used by students for a lot less money than traditional texts and in some cases these resources are free.
Wes Colgan III is the Education Project Manager for ADInstruments North America. He works with educators from all over the world to develop laboratory exercises for the life sciences. He conducts software and hardware workshops across North America, training educators to use the latest tools for data acquisition and analysis. He also teaches the acquisition and analysis portion of the Crawdad/CrawFly courses with the Crawdad group at Cornell. He has been a Faculty for Undergraduate Neuroscience member since 2007, and was named educator of the year for 2014. Prior to Joining ADInstruments, he was an assistant professor at Louisiana Tech University where he was in charge of the introductory biology lab course series.
This summer has been a uniquely exciting time for me as I prepare to teach my very first course, Human Physiology! What are the steps you take for preparing your courses? If it is your first time teaching, preparation seems overwhelming, and a challenge to figure out where to even begin. In this blog, I will be describing the steps I’ve taken to get ready for teaching my first course at our nearby minority-serving community college this fall. Full disclosure — I am definitely not an expert in course preparation, but I’ve included some tips and resources for what has worked for me.
Step 1: Reflection and determining my teaching philosophy
Reflecting on my time as an undergraduate student, I realize that learning how to learn did not come easy. It took me more than half way through my undergraduate years to figure out how to do it, and it was not until I was a graduate student that I mastered that skill. Thinking about my future students, I sought training opportunities to aid me in becoming a teacher who effectively facilitates student learning. I especially am interested in teaching practices that foster learning in first-generation college students who are not yet experienced with knowing how to learn and study. I want to make sure that my teaching style is inclusive of as many diverse student populations as possible. To do this, I have to educate myself on learning theories and effective teaching methods.
Early this summer, I attended the West Coast National Academies’ Summer Institute on Scientific Teaching to educate myself on teaching methods, and went home with understanding of the practices that fit my style and my philosophy. I highly recommend others to take advantage of these types of events or workshops (such as those offered by CIRTL) to familiarize yourself with various techniques. Aside from formal workshops, informal meetings with teaching mentors or experienced teachers gives valuable insight into the kinds of things to expect, things to avoid, suggestions and tips, teaching experiences, and inspirational words of wisdom. Use your network of mentors! Overall, inward reflection, formal workshops, and informal conversations with experienced mentors are ways that have helped me formulate the teaching practices that I will use for the course.
Step 2: Book and technology selection for the course
This sounds like an easy task, however, it can be a challenge if it is the first time you learn how to deal with choosing a book and the technology for your course. Luckily, one of my teaching mentors introduced me to the publisher’s local representative who met with me for several hours to discuss various book options and the technological tools that could be combined with my order. The rep helped me register my course in their online tool (Mastering A&P) and trained me to use this technology for creating homework, quizzes, interactive activities, rosters and grading. Thus far, I’ve spent countless hours exploring and learning how to use this technology before class starts. After all, I can’t expect my students to maneuver it if I can’t do it myself!
Step 3: Creating a syllabus, alignment table, and rubrics
The most important, hence time-consuming, task thus far is selecting the major topics and level of depth for the course while deciding the most important concepts, ideas, and skills for students to take away from the course. In order for students to meet expectations and become successful learners in the course, both the instructor and students should have this information clearly written out and understood at the very start of the course. The course syllabus is the first place where overall learning goals, outcomes, and expectations for the students for this course is presented. Furthermore, the syllabus should include information about grading, and any institutional policies on attendance, add/drop deadlines, and disability services.
Fortunately, the course that I am preparing has been offered multiple times previously, and thus I do not need to completely design a new course from scratch. However, I am re-designing and modifying sections of the course to include active and interactive teaching techniques. To guide this process during the semester, creating an alignment table for the course is beneficial to effectively execute learning activities and teach key concepts, ideas and skills. The components included in this table are: course learning goals, daily learning objectives, assignments, summary of activities, and assessments for each class period.
Take note that assessments should be determined first in order to prepare the content and activities for the class period accordingly (backwards design). Assessments could include an in-class activity, post-class assignments, exam and quiz questions. Rubrics of assessments should be made without ambiguity to formally assess students and to make sure the class period addresses the major points that students will be expected to learn. Preparing each class period, with flexibility for modifications based on gauging student grasp of the material, will help the semester run more smoothly and with less difficulties.
Step 4: Preparing content presentation and materials for activities
The last step I will take for course preparation is making and uploading any PowerPoint slides, handout materials, assignments, quizzes and exams, and any other material required for activities. With an alignment table already made, this portion of preparation should be relatively easy, but it will still take a significant amount of time.
Final Tips
Overall advice, plan ahead!! At minimum, it should take an entire summer to successfully prepare for a new course. With a well-planned course ahead of time, the hope is to be able to spend more energy throughout the semester to transfer and translate faculty enthusiasm for teaching into student enthusiasm for learning physiology!
Angelina Hernández-Carretero is an IRACDA Postdoctoral Fellow at UC San Diego and is an adjunct faculty member at San Diego City College. She earned her Ph.D. in Cellular & Integrative Physiology from Indiana University School of Medicine. Her research interests involve diabetes, obesity, and metabolism. Angelina has a passion for mentoring, increasing diversity in STEM education and workforce, and inspiring the next generation through outreach.
For my other two courses, grades will not be higher and in some cases students submitted work that was of lower quality than I expected from their work earlier in the semester. I strongly suspect that many students who chose to complete those courses did not have the focus or the ability to do so as well as they would have in the face-to-face courses. I do not have survey data to help clarify what the students were thinking, but I suspect the students who needed the letter grade for subsequent coursework approached this altered, online part of the semester differently from those who were only taking an elective where a credit grade would suffice or a GPA issue was not anticipated. Informal feedback from all three of my classes included several students commenting about how they did not sign up for online classes because they prefer traditional-format classes, comments about family issues (helping children with school work, moving back home because of job loss, stressful quarantine situations), and comments about missing deadlines because of work or other outside responsibilities.
