Quantitative Learning apps for Plant Physiology

Purpose: to help other instructors teaching the same course

Common Course ID:  BOT310 General Plant Physiology
CSU Instructor Open Textbook Adoption Portrait

Abstract: This open bank of educational apps is being utilized in a plant physiology course for upper division undergraduate students by Alana Chin at Cal Poly Humboldt. The OERs presented here are a series of web-based phone-optimized apps allowing students to explore photosynthesis and key physical laws through equations by manipulating parameters with intuitive sliders. Each app has a unique visualization to help student understanding and allows them to make and test assumptions by changing one factor while holding others constant. The main motivation to make and use these apps was to allow students who may not have an intuitive grasp of algebra to learn to look at equations with with calm and understand what they represent. Most student access the apps through a QR code during lecture or study. I hope making them an OER helps other faculty teaching this course.

BOT310 General Plant Physiology 
Brief Description of course highlights:  Plant growth, development, reproduction, metabolism, photosynthesis, soil/water relations, inorganic nutrition, and translocation. Quantitative analysis of physiological functions.
https://catalog.humboldt.edu/preview_course_nopop.php?catoid=10&coid=55909 

Student population: Pre-requisite: BIOL 105, BOT 105, and PHYX 106, or their equivalents. All with a grade of C- or higher. Students are required to take this class in the Botany major, and can choose to take it to meet specific requirements for range and biochemistry majors, or as an elective for general biology students. Most students are seniors.

Learning or student outcomes: 
- Understanding the essentials of plant function from a biophysical, ecological, and chemical perspective
- Competence in the use of essential equipment and associated study designs and analyses
-  Ability to design meaningful experiments in the context of the literature and communicate them in writing.

Key challenges faced and how resolved:  A key challenge is “equation blindness”. Students blank when confronted with something like Ficks Law if diffusion and cannot picture in their mind what will happen to diffusion when the parameters change. These apps attempt to help with this challenge and have been popular with the students.

Textbook or OER/Low cost Title:  Quantitative Learning apps for Plant Physiology 
Brief Description: These OERs are web-based Shiny Apps written in R, they take inputs from sliders, calculate outcomes, and provide responsive visualizations. I use them because many students cannot look at an equation and tell me how changing one parameter influences the others. This lets them explore visually in class: I can pose a challenging question, have them think through an answer (for example draw a curve) with neighbors, then test their assumptions with the app. Using their phone takes advantage of a familiar information input mode and supports different learning styles and less mathematically prepared students.

Please provide a link to the resource
Sun vs shade leaves with real data: https://alana.shinyapps.io/photosynthetic/ 

Photosynthesis types and climate change, manipulation of temperature at different CO2 levels https://alana.shinyapps.io/Photosynthesis_Temperature/ 

Fick’s law with parameter visualization https://alana.shinyapps.io/FicksLaw/
Hagen-Poiseuille relationship https://alana.shinyapps.io/Hagen-Poiseuille/ 

Ohm’s law https://alana.shinyapps.io/OhmsLaw/
Gas law explorer https://alana.shinyapps.io/GasLaw/ 

Grows fractal trees and leaf veins to study the geometry of plant development: https://alana.shinyapps.io/fractaculous_fractals/

Authors:  Alana RO Chin

Student access:  QR codes and hyperlinks are given to students on slides in class and are available on the class Canvas site.

Provide the cost savings from that of a traditional textbook.  Textbooks are not required for this course and not used in my version, however others may find that they supplement rather than replace texts. 

License: CC BY-NC 

OER/Low Cost Adoption Process

Provide an explanation or what motivated you to use this textbook or OER/Low Cost option. Customizing materials to the contemporary needs and learning modes of students without adding cost.

How did you find and select the open textbook for this course? I was inspired by the Ecology apps of Ruben Manzanedo to make some for plant physiology.

Sharing Best Practices: I wish I knew how easy it was to make these! They only look fancy - the code is super simple. I encourage others to make more for other biology classes. Let me know if you’d like the source code!

Describe any key challenges you experienced, how they were resolved  and lessons learned. Initial lack of web hosting and lack of knowledge. 

Instructor Name: Alana Chin
I am a Botany assistant professor at Cal Poly Humboldt. 

Please provide a link to your university page.
https://www.humboldt.edu/biological-sciences/alana-chin
Please describe the courses you teach 
General botany is part of our three semester introductory course program taken by nearly all Humboldt science students. We walk through the plant tree of life introducing cellular and ecological concepts following vision and change and LOC based guidelines through the lens of plants. Students take three hours of lecture and three hours of lab per week.

Plant physiology is an intense upper division course taken by botany, range, and biochemistry students. The class is split into three sections, physics, structure, and climate. Tests are essay exams with 8 potential questions provided at the beginning of each section. The core writing assignment is a GRFP style proposal. Labs focus on a mix of demonstrating concepts through apparatus construction and engineering thinking and learning key skills and equipment. Students are introduced to coding, sensor building, thermal and fluorescent imaging, 3 forms of spectroscopy, rehydration kinetics, osmotery, porometry, pressure chambers, SPADs, IRGAs, as well as advanced field skills in our adjacent forest. This course has two hours of lecture and six hours of lab work per week.

Describe your teaching philosophy and any research interests related to your discipline or teaching.  I focus on hands on learning to develop career relevant skills that prepare students for technical jobs or graduate school. I appreciate organsimal biology as well as the biophysics underlying plant functional ecology. My research interests focus on tall trees and climate change and I bring this into my teaching through lectures and an emphasis on plant-climate interactions in physiology labs.