Powering up Graduate Science Education:

Author: Benjamin Heifetz
Date: Jan 21, 2023

Many of us who grew up in the era of the dot-com bubble (and its subsequent crash) carry a persistent optimism for the latest technology as it can be applied in our day-to-day lives. Over this optimism, however, looms a dark cloud of disinterest fueled by the many instances in which we’ve been told a technology will be life-changing only to find that it is more convenient to accomplish a task without, rather than with the new tech. This is especially widespread in the world of science education. I have innumerable memories from middle and high school of teachers structuring a lesson or a project around the use of a software program that was supposed to enrich our understanding of a subject but instead proved itself to be a speed bump in acquiring the material in the first place.

Of course, the intentions of the educators were never in question. Some things just aren’t easy to learn from two-dimensional textbook images and the verbose descriptions accompanying them. The use of new and advanced resources to facilitate student’s understanding of difficult-to-grasp subjects in mathematics and science is absolutely necessary, but the lack of an intuitive user interface, customizable features, limited content, and technological literacy has stunted the efficacy of these resources and left a bad taste in the mouth of many of us who were the first to try them.

This problem has certainly not left us, but in the elementary, middle, and high school world, there are many websites and computer programs that have caught up and are able to effectively teach students simple topics in science and math through interactive lessons and avant-garde techniques in a manner more efficient than traditional textbooks and lectures. An excellent example is the University of Colorado, Boulder’s PHET simulations, which provide simple and accurate depictions of many natural phenomena that are able to be interacted with and can both complement and sometimes even supplant textbooks. One area of education in which technology has not caught up, however, is graduate science education.

As I’ve continued tutoring graduate and medical students in physiology, I’ve noticed that there is a serious deficit in the number of resources for learning and conceptualizing important information outside of the traditional use of scientific journals, textbooks, lectures, and PowerPoint presentations.

A few of the main reasons I suspect why graduate education lacks a larger network of tools for learning outside of scientific journals, textbooks, lectures, and PowerPoint presentations are:

The high degree of specificity of the topics taught
The relatively low number of students trying to learn these topics
The fact that many of us were taught first and foremost to refer to text sources when learning a new subject

The convergence of these realities provides little to no market for resources outside of the aforementioned widely available ones. While there are some software programs for graduate education, they tend to be nonspecific and expensive as a result of the relatively diffuse number of students who will actually purchase them.

Luckily, the barriers to entry into the development of educational tools have reduced over the past few years and there are a number of very simple ways in which we can design and implement our own customized tools without having a degree in computer science and without spending any more time than we would be working on drawing a diagram or creating a PowerPoint presentation. Find a few of my favorite resources below, along with a brief description of how they might be useful to you in your teaching or self-learning journey.

1. Integrate manipulatable 3D models using Blender, the free and open-source modeling software:

Blender can be run on nearly any computer and provides an open canvas for creating quality three-dimensional models of anything you can think of! While intimidating at first glance, it is actually quite intuitive once you’ve acquainted yourself with the basic functions. You can even animate creations if you want to highlight a concept over a time sequence. Blender can be used to open and manipulate 3D models made by other people as well (just make sure you’ve got permission). I often use Blender to create simple models to explain abnormal anatomies and pathologies to my students. They can click around, point to things, and highlight specific areas using the cursor. Additionally, Blender can export the file in almost any format you could practically need. In fact, the models on this website were originally made on Blender! While you won’t be making Pixar-quality animations immediately, you can absolutely make serviceable and helpful educational models using Blender after just a couple of hours of practice. It has paid dividends for me in my tutoring and I have found that it makes it much easier to explain things that are difficult to present in two dimensions. The model to the left was created using Blender! click and drag to manipulate and scroll to zoom!

2. Utilize industry-used tools like Pymol

Pymol provides an excellent resource for students to explore molecular structures. This is a free resource for students and can help visualize structures and their relationship to charge. One of the most difficult concepts to grasp for students of organic chemistry (or students who reluctantly have to take an organic chemistry class) is visualizing molecular structures in 3D space. Pymol makes this quick and easy and takes only minutes to learn. Better yet, if a student downloads Pymol, you can send them files of molecules for them to manipulate themselves. Previously dreaded topics like stereochemistry and enantiomerization become a breeze to explain with tools like Pymol. People in the biology world may similarly find the program useful for visualizing proteins. Find below an example of a molecule that can be rendered using Pymol. Simple molecules like water and acetic acid can also easily be created

The model shown above is the EAAT3 transport protein, which is used found at the presynaptic terminal of a neuron and transports two K+ ions out of the neuron in exchange for one H+ ion, two Na+ ions and one glutamate molecule.

3. Host more than just text and images for students to access anytime with Quarto

While services like Google Classroom, WordPress, and Canvas can be useful for hosting files and class information, they don’t provide a particularly customizable or interactive way to present information. Luckily, Quarto, a free service, allows you to create a highly customizable website using an easy-to-learn markdown language and minimal HTML. Quarto is especially good for educational purposes because it has LatEX integration, syntax highlighting, and integration of interactive elements using widgets, extensions, and Shiny, which I will explain below.

Quarto features syntax highlighting, which is especially useful for teaching data-science related topics! See below a simple example of syntax highlighting in some R code:

Code

mean(c(2, 4, 6)) # This will calculate the mean of these

4. Go beyond data presentation with Shiny

Oftentimes, simple diagrams aren’t enough to get a point across. Furthermore, when teaching a concept to students it can be useful for them to be able to manipulate the data presentation themselves to better grasp the information being presented. This is where Shiny comes in. Designed to be used in the Rstudio IDE, Shiny can be seamlessly integrated into Quarto presentations, websites, and blogs. With Shiny, students will be able to interact with sliders, text boxes, buttons, and plots, and other controls to explore data, run statistical models, or perform other computations and analyses. This is also particularly useful for presenting and teaching remotely, as one Shiny web app can provide information that would otherwise take many PowerPoint slides. Furthermore, Shiny web apps are extremely customizable. Check out their website for examples of some of the most creative Shiny projects people have created.

5. Use augmented reality simply and easily with Modelviewer

While intimidating at first, augmented reality for the purposes of education is only as enigmatic as you make it. Free and open-source programs like Google’s Modelviewer allow simple 3D models (saved as .glb files from Blender or any other program) to be viewed in augmented reality using only basic HTML code (no knowledge of WebGL or WebXR or any other javascript libraries necessary!). Read more about this on the Modelviewer website. Visit my homepage and click the “augmented reality demo” tab to see simple AR in action. I will devote later blog posts to showing how to create a simple model and put it in AR.