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:
Perform summary statistics
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.
Karen L. Sweazea, PhD, FAHA Arizona State University
As faculty, we often find ourselves juggling multiple responsibilities at once. Although many of us are interested in adding hands-on or other activities to our classes, it can be difficult to find the time to develop them. This is where more advanced students who have already taken the class or graduate students can help.
A couple of summers ago I requested the help of an extra teaching assistant in my Animal Physiology course. The role of the position I was requesting was unique as I was not seeking a student to help with grading or proctoring exams. Rather, the role of this student was to help develop in-class activities that would enhance the learning experience of students taking the course.
For each lesson, the special graduate student TA was tasked with finding an existing (ex: https://www.lifescitrc.org/) or creating a new activity that could be implemented in the classroom during the last 10-20 minutes of each session, depending on the complexity of the activity. This enabled me to begin converting the course into a flipped classroom model as students enrolled in the course were responsible for reading the material ahead of time, completing a content comprehension quiz, and coming to class prepared to discuss the content and participate in an activity and/or case study. Special TAs can also assist with developing activities for online courses.
While the benefits of having such a TA for the faculty are clear, this type of experience is also beneficial to both the TA as well as the students enrolled in the course. For the TA, this experience provides an opportunity to develop their own teaching skills through learning to develop short lesson plans and activities as well as receiving feedback from the faculty and students. For the students, this is a great way to build cultural competence into the course as TAs are often closer in age to the students and may better reflect the demographics of the classroom. Cultural competence is defined by the National Education Association as “the ability to successfully teach students who come from a culture of cultures other than our own.” Increasing our cultural competency, therefore, is critical to student success and is something that we can learn to address. Having special TAs is just one way we can build this important skill.
Karen Sweazea is an Associate Professor in the College of Heath Solutions at Arizona State University. Her research specializes in diabetes and cardiovascular disease. She received her PhD in Physiological Sciences from the University of Arizona in 2005 where her research focused on understanding glucose homeostasis and natural insulin resistance in birds. Her postdoctoral research was designed to explore how poor dietary habits promote the development of cardiovascular diseases.
Dr. Sweazea has over 40 publication and has chaired sessions and spoken on topics related to mentoring at a variety of national and local meetings. She has additionally given over 10 guest lectures and has developed 4 graduate courses on topics related to mentoring and professional development. She has mentored or served on the committees for undergraduate, master’s, and doctoral students and earned an Outstanding Faculty Mentor Award from the Faculty Women’s Association at Arizona State University for her dedication towards mentoring.
Suzan A. Kamel-ElSayed, VMD, MVSc, PhD Associate Professor, Department of Foundational Medical Studies Oakland University
In May 2019, the physiology faculty at the Oakland University William Beaumont School of Medicine Department of Foundational Medical Studies received an email from Dr. Rajeshwari, a faculty member in JSS in a Medical College in India.
While Dr. Rajeshwari was visiting her daughter in Michigan, she requested a departmental visit to meet with the physiology faculty. Responding to her inquiry, I set up a meeting with her and my colleagues where Dr. Rajeshwari expressed her willingness to invite the three of us to present in the 6th Annual National Conference of the Association of Physiologists of India that was held from Sept. 11-14, 2019, in Mysuru, Karnataka, India.
The conference theme was: “Fathoming Physiology: An Insight.” My colleague then suggested a symposium titled “Physiology of Virtue,” where I could present the physiology of fasting since I fast every year during the month of Ramadan for my religion of Islam. To be honest, I was surprised and scared at my colleague’s suggestion. Although I fast every year due to the Quranic decree upon all believers, I was not very knowledgeable of what fasting does to one’s body. In addition, I faced the challenge of what I would present since I did not have any of my own research or data related to the field of fasting. Another concern was the cultural aspect in talking about Ramadan in India and how it would be received by the audience. However, willing to face these challenges, I agreed and admired my colleague’s suggestion and went forward in planning for the conference.
After Dr. Rajeshwari sent the formal invitation with the request for us to provide an abstract for the presentation, I started reading literature related to fasting in general. Reading several research articles and reviews, I was lost in where to begin and what to include. I began to ponder many questions: How will I present fasting as a virtue? Should I bring in religious connections? Will I be able to express spiritual aspects from a Muslim’s perspective? I decided that the aim of my presentation would be to describe how a healthy human body adapts to fasting, and the outcomes that practicing fasting has on an individual level and on the society as a whole. In addition, I found that focusing on the month of Ramadan and etiquettes of fasting required from Muslims had many physiological benefits and allowed me to have a real-world example in which fasting is present in the world.
Visiting India and engaging with physiologists from all over India was a really rich experience. The hospitality, generosity and accommodation that were provided was wonderful and much appreciated. The conference’s opening ceremony included a speech from the University Chancellor who is a religious Hindu Monk, along with Vice Chancellors, the organizing chair, and the secretary. In addition, a keynote speech on the physiological and clinical perspectives of stem cell research was presented by an Indian researcher in New Zealand. I was also able to attend the pre-conference workshops “Behavioral and Cognitive Assessment in Rodents” and “Exercise Physiology Testing in the Lab and Field” free of charge.
For my presentation, I included the definition, origin and types of fasting. In addition, I focused on the spiritual and physical changes that occur during Ramadan Intermittent Fasting (RIF). Under two different subtitles, I was able to summarize my findings. In the first subtitle, “Body Changes During RIF,” I listed all the changes that can happen when fasting during Ramadan. These changes include: activation of stress induced pathways, autophagy, metabolic and hormonal changes, energy consumption and body weight, changes in adipose tissue, changes in the fluid homeostasis and changes in cognitive function and circadian rhythm. In the second subtitle, “Spiritual Changes During RIF,” I presented some examples of spiritual changes and what a worshipper can do. These include development of character, compassion, adaptability, clarity of mind, healthy lifestyle and self-reflection. To conclude my presentation, I spoke of the impacts RIF has on the individual, society, and the global community.
In conclusion, not only was this the first time I visited India, but it was also the first time for me to present a talk about a topic that I did not do personal research on. Presenting in Mysuru not only gave me a chance to share my knowledge, but it allowed me to gain personal insight on historical aspects of the city. It was a unique and rich experience that allows me to not hesitate to accept similar opportunities. I encourage that we, as physiology educators, should approach presenting unfamiliar topics to broaden our horizons and enhance our critical thinking while updating ourselves on research topics in the field of physiology and its real-world application. Physiology education is really valued globally!
Suzan Kamel-ElSayed, VMD, MVSc, PhD, received her bachelor of Veterinary Medicine and Masters of Veterinary Medical Sciences from Assiut University, Egypt. She earned her PhD from Biomedical Sciences Department at School of Medicine in Creighton University, USA. She considers herself a classroom veteran who has taught physiology for more than two decades. She has taught physiology to dental, dental hygiene, medical, nursing, pharmacy and veterinary students in multiple countries including Egypt, Libya and USA. Suzan’s research interests are in bone biology and medical education. She has published several peer reviewed manuscripts and online physiology chapters. Currently, she is an Associate Professor in Department of Foundational Medical Studies in Oakland University William Beaumont School of Medicine (OUWB) where she teaches physiology to medical students in organ system courses. Suzan is a co-director of the Cardiovascular Organ System for first year medical students. Suzan also is a volunteer physiology teacher in the summer programs, Future Physicians Summer Enrichment Program (FPSP) and Detroit Area Pre-College Engineering Program (DAPCEP) Medical Explorers that are offered for middle and high school students. She has completed a Medical Education Certificate (MEC) and Essential Skills in Medical Education (ESME) program through the Association for Medical Education in Europe (AMEE) and Team-Based Learning Collaborative (TBLC) Trainer- Consultant Certification. She is also a member in the OUWB Team-Based Learning (TBL) oversight team. Suzan is an active member in several professional organizations including the American Physiological Society (APS); Michigan Physiological Society (MPS); International Association of Medical Science Educators (IAMSE); Association of American Medical Colleges (AAMC); Team Based Learning Collaborative (TBLC); Egyptian Society of Physiological Sciences and its Application; Egyptian Society of Physiology and American Association of Bone and Mineral Research (ASBMR).
My students, like me, enjoy a challenge. Occasionally this challenge comes in the form of staying on track, using our lab time efficiently to achieve the learning outcomes and staying engaged with the material. There are specific topics that we cover in our undergraduate human anatomy and physiology course, such as the skeletal system, that had become a little dry over time. Classes occasionally included students sitting at desks looking disinterestedly at disarticulated bones glancing at their lab manual and then checking their phones. I felt that the students were not getting enough out of our laboratory time and weren’t nearly as excited as I was to be there!
With other faculty members I recently devised some new laboratory activities that include a series of quests that closely resemble a mental obstacle course, to try to encourage engagement with the material and make our learning more playful and memorable. There may also be some healthy competition along the way.
I teach an undergraduate two semester combined anatomy and physiology course, in which I lead both the lecture and laboratory portions. Students who are enrolled in this course are majoring in Biology, Neuroscience, Public Health and Health Promotions. Many of the enrolled students are destined for graduate school programs such as Medicine, Nursing, Physical Therapy, Physicians Assistant and PhD Programs. An example of the quest format we used recently in a bone laboratory is described here.
The laboratory is set up with multiple quest stations that each represent a multi-step task on areas within the overarching laboratory topic. All of the tasks are designed to enable students to achieve the learning outcomes of the laboratory in an engaging way. The quest stations are designed to encourage the students to physically move around the laboratory in order to interact with other students, touch the exhibits, explore case studies, complete illustrations and build models. Each student begins with a quest guide which provides instructions and upon which they take notes, answer questions and complete drawings. Students move at their own pace and work in self-selected pairs or groups of three. They are able to ask for assistance at any stage of a quest from either of two faculty members present.
Clinical case studies
Because of the students’ interest in patient care, we use clinical case studies as a major component of the obstacle course. X-ray images of a variety of pathological conditions as well as healthy individuals challenged students’ ability to identify anomalies in bone structure and surgery outcomes. The images that we used included a skull of a newborn showing clearly the fontanelles, an example of osteoporosis and joint replacement surgery. Students are required to identify anatomical location of the image as well as any anomalies, pathology or points of interest. Because of the student demographic of this class, many of them are destined to enter healthcare professions, they are particularly interested in this quest and are invested in solving the mystery diagnoses.
The Creative Part
The coloring pencils and electric pencil sharpener have come into their own in the laboratory and like Grey’s Anatomy illustrator Henry Vandyke Carter created before them, amazing anatomically accurate drawings are appearing on the page. Histology has been a particularly challenging aspect of our course for students with little previous exposure to sectioned specimens. In an attempt to allow students to really process what they are looking at and reflect on the tissue function I have asked students to draw detailed images of the histological specimens, label cell types and reflect on specific cell functions. This exercise aims to elevate the student’s ability to look closely at histological specimens and gain a better understanding of what they are observing and contemplate specific cell function.
Another quest involves categorizing bones and making illustrations of them, making note of unique identifying features and their functions.
Reminiscent of scenes from my three year old’s birthday party, I brought out the modeling clay and tried to stifle the reflex instruction to “don’t mix the colors”! Students were tasked with creating a 3-dimensional model of structures such as synovial joints. This is a particularly successful exercise in which students work with colored modeling clay to construct models of joints and label parts of the joint and describe the function of each part. This allows students to consider the relationship between the structure and function and move beyond looking at two-dimensional images from their textbooks and lecture slides. Students submit images of their completed models to the faculty for successful completion of the quest.
Other quest stations that were part of this particular laboratory session included Vertebrae Organizing, Mystery Bone Identification and Bone Growth Mechanisms.
One of the primary things that I learned from this exercise was that designing game-like scenarios in the classroom is far more enjoyable and entertaining for me as well as for the students, a win-win scenario. Overall from the perspective of the teaching faculty, the level of engagement was significantly increased compared with previous iterations of the class. The quality of the work submitted was high and in addition, this quest-based laboratory design is suitable for a wide range of topics and activities. I am currently designing a muscle physiology laboratory in a similar format that will include an electromyogram strength and cheering station as well as a sliding filament muscle contraction student demonstration station. In reflection I feel that my personal quest to find a novel and interesting way for the students to learn about bones was successful. Now onto the next quest……
Sarah Knight Marvar received her BSc in Medical Science and
PhD in Renal Physiology from the University of Birmingham, UK. Sarah is
currently a Senior Professorial Lecturer and Assistant Laboratory Director in
the Biology Department at American University in Washington DC. Sarah teaches
undergraduate Anatomy and Physiology, general biology classes as well as a
Complex Problems class on genetic modification to non-majors as part of the AU
Core program. Sarah’s research interests include using primary research
literature as a teaching tool in the classroom, open educational resources and
Alice R. Villalobos, BS, PhD Texas Tech University
As teachers we hope students remember and apply all the physiology they learned in our class. However, many undergraduate students hope simply to get through this semester of physiology and their other courses. They dread the amount of material and that ‘so many things go on in the body at one time.’ I asked myself what could be integrated into lecture or lab to help students better learn material in class, study more effectively on their own and ideally, improve recall when taking exams. Around this time, I attended a teaching workshop focused on short activities and simple tools that could be incorporated into lectures to facilitate learning and recall. One tool was the ‘bumper sticker’.
Similar to an actual bumper sticker, the teaching bumper sticker is a short memorable phrase or slogan that encapsulates a thought, principle, or concept. In this case, a bumper sticker helps students learn and remember a concept or principle. In all areas of life, we use short sayings or one-liners often of unknown derivation that convey a profound or funny, classic or clever, instructional or encouraging thought. ‘Righty tighty, lefty loosey.’ means turn the screw to right to tighten and left to loosen. “I before E except after C.” with the addendum, “… and in words, such as protein or weight.” Could bumper stickers work in a physiology course? I already borrowed “Water follows sodium; sodium doesn’t follow water.” from my undergraduate professor. We all develop short phrases while working on lectures, reading physiology papers and books, or on the fly during lecture.
Recently, I began using bumper stickers in a more organized manner. I took a sheet of lined paper, wrote ‘Bumper Stickers for A&P-II’ on the top, and made plenty of copies. On the first day of class I discussed tips to improve learning and study habits. I explained the bumper sticker was a teaching/learning tool and gave each student a sheet. I admitted it was an experiment, but my intention was to give them short phrases to refer to and contemplate when studying on their own or spark a memory on an exam. That very day we started glycolysis. The first bumper sticker was “You must spend an ATP to make ATP.” I explained the first step in glycolysis is phosphorylation, using a phosphate from ATP. Despite some initial skepticism, bumper stickers caught on and helped many students.
Rather than repeating your explanation verbatim, students must accurately explain concepts to themselves and others in their own words. When students study with a partner or in groups, they can refer back to the bumper sticker along with lecture notes, diagrams and textbook to explain the respective concept to each other in their own words and peer-correct. When students are teaching each other, they are truly ‘getting it’. Granted, it is essential that students use more exact and scientific vocabulary to describe a mechanism or concept, as is true for any discipline. For most students this won’t happen the very first time they explain the concept. Learning physiology or any subject is a process; developing the vocabulary is part of that process. A memorable bumper sticker is a prompt for stimulating discussion – verbal communication in the context of learning a given physiological mechanism and developing the vocabulary of physiology.
There is no established technique for the initial delivery of a bumper sticker phrase. However, its two-fold purpose as a teaching/learning tool is to help students understand and remember a concept; thus, the phrase and initial proclamation must be memorable. Based on my hits and misses, here are several tips. First, keep it short, ideally 10 words or less. Second, timing is key. Similar to a joke, timing is important but varies with topic and teaching style. Some use the phrase as a teaser to introduce a topic; others use it to summarize key points. Third, be as direct as possible and capture students’ full attention. Some write the phrase on the board or slide and make an announcement, “Listen up. Write this down.” Fourth, look directly at your students and state the phrase clearly with meaning, effective voice inflection, dramatic tone, appropriate pause, facial expression, hand gesturing, and/or a little physical comedy. Fifth, use accurate and scientific terms to explain the meaning of the phrase as it applies to the physiological concept. This is absolutely critical. Left to interpretation, students might misunderstand the actual physiological concept.
Bumper stickers for better study and testing strategies
*Use common sense at all times, especially on test day.* At times, students forget obvious and intuitive things. For example, when applying Boyle’s Law to respiration, don’t forget to breathe. I remind students that lung volume and intrapulmonary pressure will change such that when we inhale air flows in, and when we exhale air flows out. Physical laws applied to physiological mechanisms explain relationships among different components of a mechanism, e.g., the pressure of a quantity of gas to its volume. I assure them, they can and will learn the fundamental physics on which Boyle’s law is based, but keep it simple and remember – when you inhale air flows in, when you exhale air flows out.
*Understand the question, before you answer it.* My PhD advisor shared this pearl of wisdom before my qualifying exam. I encourage students to calmly, slowly and deliberately read the entire question. On any multiple choice or essay exam, they must be certain of what is being asked, before answering a question. Do not stop reading the question until you come to a period, question mark or exclamation point. Students are concerned about wasting precious time. Slowing down just a bit to answer correctly is worth the time and decreases the odds of second guessing or having to go back to the question. I make another pitch for reading the text book. It is a way to practice reading calmly and deliberately and catching differences in font or formatting, e.g., print style, italics, bold, underline, that may indicate key terms for an exam question.
Bumper stickers for general principles in physiology
*Enough, but not too much.* Many students think every physiological end point is maintained at a constant value. I explain that various parameters are regulated such that they gently fluctuate within a narrow range. Plasma sodium must be ‘enough’; if it drops too low osmolarity decreases. If sodium is ‘too much’, osmolarity increases; plasma volume increases; blood pressure increases. If an endpoint falls below range, regulatory mechanisms bring it back up into range; should it increase above normal range, regulatory mechanisms bring it back down into range.
*It’s not a mathematical equation; it’s a relationship.* Many students confess they are ‘really bad at math’ or ‘hate math’. CO, MAP, renal clearance, alveolar ventilation rate – all math. Understanding and passing physiology requires math. I tell students math describes physiological relationships between different factors that regulate or dictate a given endpoint, similar to interactions and relationships among friends or a team. Actual equations represent precise relationships, e.g., CO = HR x SV. In that case, cardiac output will increase and decrease in direct proportion to heart rate and stroke volume. Then there is Poiseuille’s Equation. Students are not required to memorize that equation, but they must learn and apply the principles of the equation: F α DP, F α1/R and F α r4. I clarify the α symbol means ‘in proportion to’, not equals. I repeat, ‘It’s not a mathematical equation; it’s a relationship.” I suggest they view a as a hug, and embrace the dependence of blood flow on the pressure gradient, vascular resistance, and the luminal radius. The 4 means when radius changes even just a little, flow changes a lot! I provide a more technical explanation of how blood flow can decrease significantly with gentle vasoconstriction and increase with gentle vasodilation; this showcases the essential regulatory role of vascular smooth muscle. This particular bumper sticker serves to remind them math is critical to our understanding of physiology and hopefully, ease their anxiety. More math awaits in respiratory physiology, and they revisit and apply F αDP, F α1/R and F α r4 to air flow.
*Know what abbreviations mean, and don’t make up abbreviations.* I explain the names of hormones, especially, are rich in information. These names indicate source, stimulus for release, and mechanism of action. For example, atrial natriuretic peptide, ANP, is a peptide hormone secreted from atrial tissue when plasma volume increases that increases urine output (-uretic) and sodium (natri-) excretion. Not too creative, but self-explanatory. Couple it with “Water follows sodium …”; problem solved.
Bumper stickers for chronological order or sequence
For many cellular and organ mechanisms, there is a strict chronological order of events. During the cardiac cycle, there is a distinct chronological order for each of several different phenomena that occur simultaneously and interdependently. I use bumper stickers to teach a basic concept of cardiac physiology that help students learn the cardiac cycle – the electrical~mechanical relationship. First, I show the entire Wiggers diagram and explain it tracks the series of interrelated electrical and mechanical events as they occur in the same timeline of one heartbeat. I assure them we will take one panel at a time and pull it altogether at the end. I start with the relationship of the ECG to the 4 ventricular phases, using a set of bumper sticker phrases that I write on the board. We review the electrical events of P (atrial depolarization), QRS (ventricular depolarization) and T (ventricular repolarization) deflections. Then, I say, “Pay attention. Write down each phrase.”
*Electrical then mechanical.* I explain emphatically that first an electrical signal is transmitted and received, then the atrial or ventricular muscle responds. In the cardiac cycle, electrical events P, QRS, and T each precede atrial or ventricular responses.
*Depolarizeàcontract. Repolarizeàrelax.* I explain depolarization triggers contraction; repolarization leads to relaxation. P wave signals atrial contraction; QRS complex signals ventricular contraction; T wave signals ventricular relaxation.
*Depolarizeàcontractàincrease pressure. Repolarizeàrelaxàdecrease pressure.* I remind them changes in pressure gradients across the atrioventricular and semilunar valves determine whether valves open or close and consequently, whether blood flows into or out of the ventricle. Depolarization leads to ventricular contraction and in turn, an increase in pressure; repolarization leads to ventricular relaxation and in turn, a decrease in pressure.
*The AV valve is the fill valve; the semilunar valve is the ejection valve.* A student thought of this phrase! She explained, “When the AV valve – tricuspid or mitral – is open during diastole, the ventricle fills with blood from the atrium. When the semilunar valve – pulmonary or aortic – is open during systole, blood is ejected.” In that moment I thought my work as a teacher was done; my student is teaching herself and others. I give her full credit, but use her bumper sticker. I further explain when the ventricle relaxes and pressure drops below the atrial pressure, the AV valve will open, and blood enters the ventricle; when it contracts ventricular pressure exceeds atrial pressure and the AV valve closes; as it continues to contract, eventually ventricular pressure exceeds aortic pressure, the aortic valves opens, and blood is ejected into the aorta.
Bumper stickers might not be the right tool for every teacher, student, or topic, or be appropriate for undergraduate versus graduate course. If you decide to implement this tool, you might not have a bumper sticker for every basic or general physiology concept or mechanism or a set of bumper stickers for every organ system. You might only use a bumper sticker phrase once or twice in a whole semester. When used appropriately, they truly can make a difference. On the other hand – if how you teach is working just fine and your students are getting it – then all I have to say is, “If it ain’t broke, don’t fix it!”
Alice Villalobos received her Bachelors of Science in biology from Loyola Marymount University and her PhD in comparative physiology from the University of Arizona-College of Medicine. For the past several years, she has taught Anatomy & Physiology-II and Introduction to Human Nutrition in the Department of Biology at Blinn College and guest lectured at Texas A&M University on the topics of brain barrier physiology and heavy metal toxicology. She recently relocated to Texas Tech University to join the Department of Kinesiology & Sport Management where she teaches Physiological Nutrition for Exercise.
Monica J. McCullough, PhD Western Michigan University, Department of Biological Sciences
After attending the 2018 APS – ITL conference for the first time,
I walked away with so many actionable ideas to implement in my large classes.
One valuable experience was practicing active learning techniques as part of a
session. “Doing” helps many to learn much more than “hearing” about best practices.
I not only learned much from the active sessions offered at APS-ITL but
transferred that experience into my own classroom upon returning.
I decided to try a semester-long project for my Intro to Bio for
majors, modifying a project I learned about from Dr. Beth Beason-Abmayr (http://advan.physiology.org/content/41/2/239) from
Rice University. Dr. Beason-Abmayr introduced ‘The Fictitious Animal
Project’ during her session at APS-ITL as one she uses in her Vertebrate
Physiology for non-bio majors, averaging around 30 students per semester.
During her session at APS-ITL, we divided into groups, ranging from 2-10,
and mimicked the project. I instantly saw the value of this activity and had to
add it to my teaching repertoire. Dr.
Beason-Abmayr’s project was to create a fictitious animal that had certain
physiological characteristics. Students had categories, such as cardiovascular
system, respiratory system, that were randomly selected and answer sets of
questions that students would answer about the integration of them, including
benefits and trade-offs for the fictitious animal. They completed
scheduled homework sets after topics were discussed in class. The students
worked in groups and would present their creations to the class with drawings
of their animals. What really piqued my interest was that since students had to
create an animal that does not exist in nature, they couldn’t just Google it to
create this project, and the potential to bring out their ingenuity to the
Since I was going to teach biological form and function the
upcoming Fall, and mind you for the first time, I thought I’d start with this
semester-long project for 290 students, which were primarily freshmen. A major
component that I wanted to maintain was the student presentations, as this is
an important skill for these budding scientists. Obviously, the logistics to
maintain this was the first decision, and when factoring in around 75 groups (averaging
4 students per group), I decided that the group presentations would span a
total of 4 days at the end of the semester, in a gallery-style presentation.
Presenters would line the room with their visual aid and the rest of the class
would visit each group with designated rubrics. (Presentation
Rubric) Additionally, the individual group members would submit a peer
evaluation of their group mates at the end of the day of their presentation. (Group
Peer Evaluation). My next modification was to adapt the category options so that
the students would create a species that yielded both plant and animal
components, as we would be learning about both. There were 5 overall
anatomical/physiological categories, including size, circulation, sensory
environmental interaction, structure and motility. These
too would be randomized with the use of Google by “rolling the dice” to assign
each characteristic. (Project
directions) I continued with Dr. Beason-Abmayr’s project checkpoint of
homework sets throughout the semester where students work on a subset of the
categories and continue to build their species, as we learn about the topics in
class. Each group submitted electronically to Dropbox, and allow time for
feedback with rubrics. (HW set
1 rubric example) To end, there was a final wrap-around short answer portion on
the final exam where students described each category and how it was
incorporated with their own species. This allowed
me to check for individual understanding of the project as we all know some
group projects allow for ‘moochers’ to do and understand little.
For me, this project is a keeper. It helped reinforce the
essential concepts during the semester and practice soft skills needed to excel
in the workforce. It was exciting to see how some students really embraced the
project, including creating a costume of their species, 3-D print outs, live
plants they’ve modified and sculptures. While difficult, there were also some
group conflicts that did occur, yet, these emerging adults were able to work
through their differences. A key factor to this was each group developing their
own contract at the very beginning of the semester and was open for adjustments
for the duration of the semester. (Team
Contract) The big take-away for me is, it is worth the risk to try
something new in the classroom, no matter how large or small the size. This
project helped student gains with the material, and practice throughout the
semester. As an educator, I feel it is pivotal to find ways that help our
students feel confident with the material and keep them curious and innovative.
Just as at the top presentations at our conference, doing
science makes concepts stick much more than just hearing about it.
J. McCullough, PhD joined as a Faculty Specialist in the Department of
Biological Sciences and Western Michigan University in 2016, prior to which she
was faculty at Adrian College. She currently teaches large introductory
courses, including Anatomy, Physiology and Biological Form and Function. Dr.
McCullough received her BS and PhD from Western Michigan University and studied
regulation of neurotrophic factors. Dr. McCullough has 4 young children and has
found a great interest in doing science demo’s in her elementary children’s’
Scientific literacy allows citizens to get involved in issues and ideas related to science as a reflective citizen. A scientifically literate person can:
Recognize, offer and evaluate explanations for a variety of scientific and technological phenomena
Describe and evaluate scientific research and propose ways to answer questions and solve problems following the scientific method
Analyze and evaluate data, concepts and arguments in a variety of contexts, reaching appropriate conclusions for the data received
Quality education is the key to achieving literate societies. Unfortunately, scientific literacy is generally very low in most developing countries. Results of the PISA tests, for example, reveal that competencies in mathematics and sciences in developing countries are below the average of the countries evaluated. This has enormous consequences for the communities by negatively impacting their political, economic and social decision-making.
Figure 1. Performance in mathematics and science of different countries in the 2015 Pisa tests. Images Taken from http://www.oecd.org/pisa/.
It is very important to open spaces for the general community in developing countries to learn about the practice of science. Many scientific organizations develop training activities that are usually directed at specialized audiences. For this reason, it is important to highlight the task of scientific associations that are concerned with bringing science to the general community such as the American Physiological Society through events such as PhUn week. In the particular case of Colombia, the Colombian Association for the Advancement of Science (ACAC) organizes every two years a very large science fair “Expociencia” that is visited by more than 40,000 elementary, middle and high school students.
These science fairs have several objectives:
Allow students to present the results of scientific projects. Students are exposed to an essential component of science, sharing and communicating research. In addition, they have the opportunity to learn from their peers and receive feedback from more experienced researchers.
Open the doors of academic, governmental or industry laboratories to the community. Visitors have the opportunity to know what scientists do, interact with them, expose their visions about science. In addition, visitors can express doubts they have about different concepts, and sometimes they can find answers to their questions.
Generate academic spaces so that researchers can discuss how to work with the community, address their most pressing needs and communicate their results to the public.
Figure 2. Participation of students in academic activities at Expociencia 2018. Images courtesy of Deiryn Reyes, ACAC.
Recently with the support of the Faculty of Medicine of the Universidad de los Andes, I had the opportunity to participate in Expociencia. It was gratifying to see how the children ran from one side to the other having the opportunity to learn about electronics, physics, programming, biology, medicine and anthropology. These children are like sponges that quickly absorb the information they receive and are willing to ask questions without filtering them through mechanisms that adults have learned. In addition, Expociencia promotes spaces for university students to share their experiences and for a moment to be role models for school students. I believe that many lives are changed thanks to the experience of living science.
In the nineteenth century lived a poet who wrote and translated from other languages several of the best-known stories that are known by children and adults in Colombia. His influence on Colombian literature is similar to that of the Grimm brothers in Europe. The name of this writer was Rafael Pombo. A few weeks ago, thanks to my son, I had the opportunity to learn that he also wrote about the importance of knowledge and science. On this occasion I want to share a personal translation of one of Rafael Pombo´s poems, that can be used to discuss with small children and adults the importance of science in our lives.
THE CHILD AND THE OX
Rafael Pombo (1833-1912)
-What do you think about all day
Lying on the grass?
You seem to me a great doctor
Enraptured in his science.
-The science, dear child
It is not what feeds me;
That is the fruit of study,
With what God gives humans.
Out thinking for me,
Poor animal, hard enterprise;
I prefer to make thirty furrows
Before learning two letters.
Chewing well, I care more
that a lesson at school.
With the teeth, I chew,
You, child, with your head.
But if you want to be wise
Hopefully seeing me you´ll learn
To ruminate, and ruminate a lot,
Every bit of science.
Digesting, not eating,
It is what the body takes advantage of,
And the soul, invisible body,
has to follow such a rule.
Without ruminating it well, do not swallow
Not a line, not a letter;
The one who learns like a parrot,
Ignorant parrot stays.
National Academies of Sciences, E., and Medicine., Science Literacy: Concepts, Contexts, and Consequence. 2016.
Ricardo A. Peña-Silva M.D., PhD is an associate professor at the Universidad de los Andes, School of Medicine in Bogota, Colombia, where he is the coordinator of the physiology and pharmacology courses for second-year medical students. He received his doctorate in Pharmacology from The University of Iowa in Iowa City. His research interests are in aging, hypertension, cerebrovascular disease and medical education. He works in incorporation and evaluation of educational technology in biomedical education.
He enjoys spending time with his kids. Outside the office he likes running and riding his bicycle in the Colombian mountains.
Society has moved into the age of virtual reality. This computer-generated trend has wide-sweeping implications in the classroom. Specific to anatomy, impressive 3D modeling programs permit students to dissect simulated bodies pixel by pixel. It is exciting and often more cost-effective. Virtual dissection, without doubt, can play a significant role in the current learning environment. However, as stated by Rene Descartes, “And so that they might have less difficulty understanding what I shall say about it, I should like those who are unversed in anatomy to take the trouble, before reading this, of having the heart of a large animal with lungs dissected before their eyes (for it is in all respects sufficiently like that of a man)”. This idea leads me to my argument; there is no replacement for the real thing.
We as teachers must incorporate a variety of learning tools for a student to truly understand and appreciate anatomical structure. Anatomical structure also needs to be related to physiological function. Is there anyone reading this that has not repeated the mantra “form determines function” hundreds or thousands of times during their teaching? The logistical and financial restrictions to human cadavers, necessitates the frequent incorporation of chemically preserved specimens into our laboratory curriculum. Course facilitators often employ a cat or a pig as a substitute for the human body. I am not advocating against the use of preserved specimens or virtual programs for that matter (and kudos to my fellow facilitators who have learned the arduous techniques required to dissect a preserved specimen). However, it is my opinion that it is a time consuming assignment with limited educational end points. Not to mention the rising specimen costs and limited vendor options. The cost of a preserved cat is now ~$40, while the average cost of a live mouse is only ~$5. Two very important components necessary to understand the concept that form determines function are missing from preserved specimens (even cadavers). These two components are: texture and color. With respect to color, the tissues of preserved specimens are subtle variations of gray, completely void of the Technicolor show of the living organism. Further, texture differences are extremely difficult to differentiate in a preserved specimen. Compare this to a fresh or live specimen and the learning tools are innumerable. You might argue that mice are much smaller, but dissecting microscopes can easily enhance the dissection and in my experience far outweigh the noxious experience of dissecting a chemically preserved organism.
To further convince you of the value of dissecting fresh tissue I would like to present a couple of examples. First, why is the color of tissue important? One of the most important bodily pigments is hemoglobin. Hemoglobin, as we all know, is the pigment that gives blood its red color. Therefore the color of a tissue often reflects the level of the tissue vascularity and often (but of course not always) in turn the ability of that tissue to repair or regenerate. Simply compare the color of the patellar tendon (white) to the red color of the quadriceps. Muscles being highly vascularized have a much greater ability to regenerate than non-vascular connective tissue such as the patellar tendon. In addition, muscles contain myoglobin, a red protein very similar to hemoglobin. Two clear examples of teaching opportunities that would be missed with the traditional use of preserved specimens.
Texture is completely lost with chemical preservation as tissues become hardened and rubbery. My students are always blown away by the fact you can completely eliminate the overall structure of the brain by pressing it between their two fingers. The tactile experience of holding the delicate brain allows students to explore how form begets function begets pathology. Traumatic brain injury (TBI) has become a hot topic in our culture. We no longer see children riding bicycles without helmets, the National Football League has new rules regarding tackle technique and my 8-year-old soccer player is penalized for headers during game play. What better way to educate a new generation of students just how delicate nervous tissue is than by having them “squash” a mouse brain? Regardless, of the amazing skull that surrounds the brain and the important fluid in which it floats, a hit to the head can still result in localized damage and this tactile experience emphasizes this in a way no virtual dissection could ever accomplish.
Finally, I would like to discuss a topic close to my heart that does require a non-preserved large animal specimen. The function of arteries and veins is vastly different based on the structure of elastic or capacitance vessels, respectively. For example, the deer heart allows easy access to the superior or inferior vena cava (veins that are thin and easily collapsed) and the aorta (thick and elastic artery) permitting valuable teaching moments on vessel structural variability for divergent physiological function. These structures on a preserved specimen are usually removed just as they enter the heart making them very difficult to evaluate.
These are just some elementary examples. Numerous concepts can be enhanced with the added illustrations of texture and color. When presented with both options, my students always choose the fresh tissue! The wonder and excitement of handling fresh tissue has become a hallmark of our Anatomy and Physiology course and is regularly mentioned as student’s favorite example of hands-on learning in the classroom.
I have to end this with a special shout-out to my dear lab adjunct Professor Elizabeth Bain MSN, RN. Liz has made access to deer heart and lungs an easy task for me.
April Carpenter, PhD is an Assistant Professor in the Health and Exercise Physiology Department at Ursinus College. She received her PhD in Molecular and Cellular Physiology at Louisiana State University Health Sciences Center and completed two postdoctoral fellowships at the Hospital for Special Surgery in New York and Cincinnati Children’s Hospital Medical Center. Her research interests include the molecular regulation of endothelial function and its impact on all phases of skeletal muscle injury. Dr. Carpenter currently teaches Anatomy and Physiology, Research Methods and a new Pathophysiology course.
In June I attended the American Physiological Society’s Institute on Teaching and Learning (ITL) for the first time. It was a fantastic week of presentations, workshops, and networking, from the opening keynote address on “Student-instructor interactions in a large-group environment” by Prem Kumar (University of Birmingham, UK) to the closing plenary talk on “Inclusive practices for diverse student populations” by Katie Johnson (Beloit College).
The week is hard to summarize concisely, yet I can easily identify my most memorable moment. That occurred on Wednesday morning (June 20th). Robert Bjork, a UCLA psychologist, had just delivered a fascinating plenary talk on learning, forgetting, and remembering information. He had reviewed several lines of evidence that the memorization process is more complicated than tucking facts into a mental freezer where they persist forever. Instead, the timing and context of information retrievals can profoundly affect the success of subsequent retrievals.
At the end of the lecture, I stood up with a question (or possibly a monologue masquerading as a question). “It seems that maintaining long-term memories is a really active, dynamic process,” I said. “The brain seems to be constantly sorting through and reassessing its memory ‘needs,’ somewhat like the way the kidney is constantly sifting through the plasma to retain some things and discard others. Is that a reasonable analogy?”
“Yes it is,” he answered politely. “Perhaps,” he added, “you could write a paper on the ‘kidney model’ of how the brain learns.”
The audience clapped along in time, then erupted with wild applause! That’s how I prefer to remember it, anyway; perhaps others who were there can offer a more objective perspective.
In any case, singing is not just a mechanism for hijacking Q&A sessions at professional development conferences; it can also be done in the classroom. And this example of the former, while unusual in and of itself, hints at several useful lessons for the latter.
Unexpected music gets people’s attention. In truth, I have no idea whether most ITL attendees found my song fun or helpful. Still, I’m quite sure that they remember the experience of hearing it. Now think about your own courses. Are there any particular points in the course where you desperately need students’ undivided attention? Unexpected singing or rapping is amazingly effective as an attention-grabber, even (especially?) if the performer is not a gifted musician. Don’t be afraid to use this “nuclear option.”
Music is not just for “making science fun” and memorizing facts. Many teachers and students who support the integration of music into science courses do so because they think it’s fun and/or useful as a mnemonic device. Both reasons are legitimate; we do want our courses to be fun, and our students do need to memorize things. But music can be much more than an “edutainment” gimmick. “Neurons Like Nephrons” (http://faculty.washington.edu/crowther/Misc/Songs/NLN.shtml), for example, develops an analogy between the way that the brain processes information and the way that the kidney processes plasma. It’s not a perfect analogy, but one worthy of dissection and discussion (https://dynamicecology.wordpress.com/2016/11/14/imperfect-analogies-shortcuts-to-active-learning/). Songs like this one can thus be used as springboards to critical thinking.
The effectiveness of any musical activity is VERY context-specific. After my musical outburst at ITL, I was flattered to receive a few requests for a link to the song. I was happy, and remain happy, to provide that. (Here it is yet again: http://faculty.washington.edu/crowther/Misc/Songs/NLN.shtml.) But here’s the thing: while you are totally welcome to play the song for your own students, they probably won’t love it. To them, it’s just a weird song written by someone they’ve never heard of. They won’t particularly care about it unless the production quality is exceptional (spoiler: it’s not) or unless they are going to be tested on the specific material in the lyrics. Or unless you take other steps to make it relevant to them – for example, by challenging them to sing it too, or to explain what specific lines of lyrics mean, or to add a verse of their own.
In conclusion, music can function as a powerful enhancer of learning, but it is not pixie dust that can be sprinkled onto any lesson to automatically make it better. As instructors, for any given song, you should think carefully about what you want your students to do with it. That way, when the music begins, the wide-eyed attention of your incredulous students will be put to good use.
Gregory J. Crowther, PhD has a BA in Biology from Williams College, a MA in Science Education from Western Governors University, and a PhD in Physiology & Biophysics from the University of Washington. He teaches anatomy and physiology in the Department of Life Sciences at Everett Community College. His peer-reviewed journal articles on enhancing learning with content-rich music have collectively been cited over 100 times.
As adults of ever increasing age, I am sure almost every one of you has had a conversation lamenting your loss of physical abilities over the years. “I used to be able to do that.” “I used to be good at that.” As a parent to two young, energetic, fearless boys I hear (and think) these sentiments almost daily. While watching children play on a playground, sprinting for hours, hanging upside down, contorting their bodies into nearly impossible positions, jumping (and falling), twisting and turning, and literally bouncing off walls, parent conversations almost always include incredulous statements about children’s’ physical capacity followed immediately by a statement of the parents’ lack thereof. More than once I’ve heard a parent say, “If I did that, I’d be in the hospital.”
But have you ever actually thought, “Why can’t I do that anymore?” The answer isn’t just “I’m too old”. Obviously the physiologic changes of age are undeniable, but it’s a more complicated reason. At some point in your life, you stopped playing like children play. You stopped running and jumping and twisting and turning. You move in straight lines. You sit for hours. You don’t try that new move. It looks too hard. You might hurt yourself. As physiologists, we all know about homeostasis and adaptations, and it’s no surprise that our lifestyles have contributed to our physical inability in adulthood. Of course you would hurt yourself if you tried ‘that’, but only because you haven’t tried anything like that in years. Start trying ‘that’ though, and over time you’ll find yourself much more physically capable despite the aging process.
This childhood to adulthood performance decrement is not exclusive to physical capacity though. We are doing much the same to our mental capacity with age. A child will take physical risks on the playground, much as they also take mental “risks” in the classroom. Ask a group of 3rd graders a question, any question, almost all of them raise their hand hoping to answer…even if they don’t know the answer. And the student who got it wrong, will raise his hand again after the next question. Give them a challenge or a mystery to solve and they will dive right in. Let them touch and feel and manipulate. They don’t hesitate. They are on their mental playground. This is how they learn. As adults though, we aren’t going to the mental playground, because that’s not what adults do. We sit in chairs. We watch lectures. We make notecards. We read papers. We study the learning objectives and the PowerPoints.
Just as adults could physically benefit from some time on the playground every day, adults (and I’m including college students in this category) can also benefit from time on a mental playground. Even as educators of other adults, we need to remember this. We often forget the multitude of ways that we can put our students on the mental playground. We don’t do an activity, because the students might think it’s ridiculous. It might waste too much time, and there is too much material to cover today. I have found in my classrooms though, that activities that would work with kindergarteners can work equally well for college students.
To give examples of ways to put college students on the mental playground, I would like to share two activities that I have done in a physiologic assessment of health course that have been very effective. The course consists of juniors and seniors who have already taken several biology, chemistry, and physiology courses beyond anatomy and physiology. The first assignment that I give them is to work with a partner to draw a picture of a person with as many health risk factors as they can think of. I have found that most students who take this class (instructor included) are horrible artists, but this adds to the fun of the assignment. The students love it and come up with thousands of creative ways to represent health risk factors. We have a discussion over which drawings have incorporated the most “official” risk factors (as designated by national organizations like ACSM, AHA, etc.) and why some of the others are certainly not healthy (setting off fireworks indoors), but not listed as official risk factors. Something about taking the time to draw silly pictures on a specific topic really aids in student understanding (anecdotally in my class, but evidence exists that this is effective (Ainsworth S, Prain V, Tytler R. Drawing to Learn in Science. Science. 333 (6046),1096-1097, 2011.).
Another assignment I’ve had good results with to get students onto the mental playground is half mystery for the students to solve and half drawing pictures. I tell the class that we are going to learn about how the heart works and talk about the electrocardiogram. The first thing I ask them to do is to get out of a sheet of paper and to draw a picture of the house they grew up in as if they were looking at it from the road. Normally confusion ensues and the students want to know if it’s for a grade (yes), and why they’re doing it (trust me, it’ll make sense later). After giving the students time to sketch their house, I ask permission to show each to the class, and then ask the question to the class. “Whose house is bigger?” Ultimately the students come to the conclusion that it is nearly impossible to tell without knowing the perspective and distance from the artist and the other views of the house (the front view is only one of multiple views that would be needed to construct the 3-dimensional size of the house). Then, still without talking about the heart, I ask them to draw a picture of a baseball (just the baseball) being thrown. Once again I show the drawings to the class. All usually agree that everyone probably knows the approximate size of a baseball, but then I highlight how different people drew different sizes on the paper. Once again I discuss perspective and how large a baseball looks when it’s about to hit you in the face, because it takes up your entire field of vision, but if it were thrown at you, it would look smaller relative to your field of vision at the start. If you’re watching people playing catch equidistant from both, the ball might move back and forth without appearing to change size relative to the visual field. But all the baseballs are still the same size!
Finally, after the house and baseball drawings I ask, “what did all of that have to do with the heart and electrocardiograms?” After a few minutes, most students understand the theory behind the electrocardiogram without ever having analyzed one. I’ve even had a strong student who was finishing her clinical exercise testing degree that semester say that even though she had taken several courses on ECG analysis and knew how to read them to get good grades on ECG tests, this was the first time she truly “got it.”
Thousands of other ways to engage students on the mental playground are out there as well. Discussing muscle physiology? Hand out rubber bands before class starts and ask them to think about how muscles and rubber bands are remarkably similar yet not the same at all. Teaching about bones? Pass out a few models to let them hold and manipulate. Then ask the students to pretend they’re cavemen and they need to build all of their tools out of bones, which bones would make a good hammer? A good bowl? Spoon? Fork? Weapon? Teaching about brain physiology? Have the students invoke thoughts, memories, feelings or movements and then tell them which part of the brain is responsible. Be creative and remember that just like our bodies, our minds work best when they’re stretched and twisted and used in different ways on a regular basis.
I do not know enough about educational psychology to understand the underlying mechanisms by which these types of activities work (my PhD is in Kinesiology after all – a content expert told to teach well!). And admittedly most of my evidence that they work is anecdotal or comes by way of gradually improved student scores on final exam and practical questions related to my course objectives over several semesters in which I certainly adjusted more than one variable. However, I do know that in learning, students attend to touch and feel, emotion, and mystery. The same thing you’ll witness at an elementary school playground. Incorporating these into your lessons, even in the simplest of ways can be beneficial for all different types of learners. I’m asking you to turn your classrooms into intellectual playgrounds. Encourage risk taking. Validate atypical approaches. Make it fun. Make it engaging. All the memorized note cards might be forgotten by next semester if it’s not.
Ed Merritt is an assistant professor in the Department of Kinesiology at Southwestern University in Georgetown, Texas. Ed received his doctorate in Kinesiology from the University of Texas at Austin and completed a postdoctoral fellowship in Cellular and Integrative Biology at the University of Alabama at Birmingham. Ed was a faculty member at Appalachian State University until family ties brought him back to central Texas and Southwestern University. Ed’s research focuses on the molecular underpinnings of skeletal muscle atrophy after trauma and with aging, but he is also equally involved in the scholarship of teaching and learning and melding educational outreach activities with service learning.