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Physical Biology of the Cell
Summary
Biology has been revolutionized by experimental techniques that have made it possible to quantitatively query the inner workings of molecules, cells and multicellular organisms in ways that were previously unimaginable. The objective of this short, intensive course is to respond to this deluge of quantitative data through quantitative models and the use of biological numeracy. The course will explore the description of a broad array of topics from modern biology using the language of physics, mathematics and computation. One style of thinking we will emphasize imagines the kinds of simple calculations that one can do with a stick in the sand. The course draws examples from across modern biology, including cell biology (signaling, regulation, and motility), physiology and metabolism, developmental biology (patterning of body plans and the control of organelle and tissue size and number), neuroscience (action potentials and ion channel gating), and all the way to biology at the planetary scale. These examples are used to develop theoretical models that make precise, testable predictions about living systems. Those predictions are then tested through hands-on analysis of experimental data and through numerical simulations performed using Python. Quantitative biology will be introduced as an exciting new tool to complement other approaches within biology such as genetics, genomics and structural biology. The course will introduce students to the enabling power of biological numeracy in scientific discovery and enable them to use these tools in their own future research. Note that no previous coding or advanced math skills are required. The course is designed with the objective of being widely accessible.
Course project
During the course, we will do many estimates about each biological phenomenon we address. To cement these skills, throughout the week, you will work on a short estimate individually or in groups. The idea is to present an interesting calculation about a biological phenomenon in the style of a vignette of Cell Biology by the Numbers. Some examples of interesting estimates are “How many proteins are in a viral capsid?”, “What is the energy cost to a host cell in order to create a new virus after it has been infected?”, “What is the cell-to-cell variability in the number of copies of the lacZ gene?”, “What is the largest osmotic shock a cell can suffer without bursting?”. Alternatively, you can write an estimate outside of biology. Some of our favorite examples are “MythBusters, Rapunzel”, where the student estimated how much weight Rapunzel’s hair could support and whether it could grow long enough, and “Cry me a River”, where the student estimated the total volume he had cried due to breakups over his life. Each evening, you will have 30 minutes to work on your estimate during our “study hall”. You will then present your estimate in a short talk at the end of the course.
Tentative Daily Rhythm
A typical day in the course looks like this:
| Time | Activity |
|---|---|
| 9:00am–9:30am | Breakfast |
| 9:30am–12:00pm | Lectures, hands-on activities, and copious amounts of coffee. |
| 12:00pm–1:00pm | Lunch |
| 1:00pm–2:00pm | Research talk from course faculty and invited guests on their research in quantitative biology. We aim for these talks to be of high pedagogical value, so interruptions and questions are encouraged! |
| 2:00pm–2:30pm | Breakout session between the students and the speaker. These sessions are perfect venues to ask follow up questions about the talk, but also to learn about the speaker’s career path. |
| 2:30pm–5:30pm | More lectures, hands-on activities, and copious amounts of coffee. |
| 5:30pm–6:00pm | Time to work on estimates for final presentation. |