BE 262 - Physical Biology Bootcamp
About
This course provides an intensive introduction to thinking about the beauty and mystery of the living world from a quantitative perspective. Our first foray into this approach will be to use “street fighting mathematics” to perform order of magnitude estimates on problems ranging from how many photons it takes to make a cyanobacterium to the forces that can be applied by cytoskeletal filaments. These modeling efforts will be complemented by the development of physical models of phenomena such as gene expression; collective behaviors like flocking enabled by energy; and cytoskeletal polymerization. We will also use Python to write computer code to analyze real-world quantitative experiments. No previous experience in coding is presumed, though for those with previous coding experience, advanced questions will be available.
Where and When?
Our first meeting will take place on Tuesday, September 3th, 2024: please arrive promptly at 8:50am in the Chen Building, Lecture Hall 100. Subsequently, we will begin days at 9am. Sunday, September 8th is a day off (possibly with an optional group hike in the morning), and the course will conclude on Tuesday, September 10th.
On the first day, there will be a brief introduction to the course, and then each of you will have 60 seconds to deliver a lightning talk in which you quickly tell us who you are, where you are from, and what you are excited about. (Out of respect, we will enforce this cadence.) For these talks, send your single-slide presentation as a PDF to Rob and Sara (smahdavi [at] caltech [dot] edu) no later than 5pm on Sunday, Sept. 1 in PDF FORMAT (no exceptions).
Each day will have a schedule roughly of the form:
| Time | Session |
|---|---|
| 9am - noon | Lectures from Rob |
| noon - 1:00 pm | Lunch Break |
| 1:00 pm - 2:00 pm | Guest Talk |
| 2:00 pm - 4:00 pm | Lectures from Rob |
| 4:00 pm - ~5:30 pm | Computation sessions with Sara |
| 6:00 pm - 10:00 pm | Evening lab session (each student only does this for two of the nights: your schedule TBA) |
Course Syllabus
Below is a tentative outline of the topics we plan to explore. However, some material may be taught earlier or later—and omitted or amplified—if discussions invite.
| Day | Lecture Topics | Computation Topics |
|---|---|---|
| Day 1 (Tuesday, September 3rd) | A feeling for the organism. What sets the scale of X? Order of magnitude thinking as a tool for understanding the world. Examples from the energy scale to form a spindle to the amount of poop created per year by whales. | Forward Euler applied to bacterial growth |
| Day 2 (Wednesday, September 4th) | Stuff of t and biology’s unique laws of dynamics. Dynamical phenomena in both the nonliving and the living. The great principles of dynamics and their biological consequences. Biology’s unique answer to purposeful dynamics. | Master Equation of 1D diffusion applied to FRAP |
| Day 3 (Thursday, September 5th) | Making our guesses precise: null hypotheses. When guesses become probability distributions. The great distributions: binomial, Poisson, exponential and their important biological consequences. | Stochastic 1D diffusion applied to FRAP and application to a diffusing element reaching a target |
| Day 4 (Friday, September 6th) | What is life? Various musings on the secret of life. Defiance as the secret of life. Biological batteries and paying for the processes of life. Setting up membrane gradients. Biological fidelity. | Master equation for consitutive gene expression |
| Day 5 (Saturday, September 7th) | Representing and Approximating Life. Rethinking the idea of a vector: from Descartes (x,y) to ChatGPT. Weird vectors, from personality type to cell shape to fluorescence recovery after photobleaching experiments. | Understanding Taylor expansions and defining the error of an approximation |
| Sunday, September 8th | ** day off ** | None |
| Day 6 (Monday, September 9th) | The Value and Values of Science. The mystery of the world and the value of wonder. Loving the questions. Research as exploratory dynamics. | Bacterial growth |
| Day 7 (Tuesday, September 10th: half day) | Order of magnitude computations in groups. | None |
Experimental Sessions
- Building a microscope from scratch [Ana, Heun Jin, Rosalind, & Minakshi]: Using a few rules-of-thumb about geometric optics, you will learn how to a microscope works and put your knowledge to the test by building one from scratch. You will learn the art of aligning lasers, laying down lenses, and testing your craftsmanship on biological samples. Further options for builds for the night may include optical tweezer, TIRF, or line-scan confocal.
- Live fly gene expression [Bruno & Vinu]: In this experiment you will learn how to test theoretical models of transcriptional dynamics using confocal microscopy to image live fly embryos. You will learn how to design experiments to measure the elongation rate of mRNA and the input-output relationship between transcription factors and mRNA and how these experiments have been used to test theoretical models.
Experimental Schedule
| Date | Optics | Fly |
|---|---|---|
| Tues, Sep 3rd | A | D |
| Wed, Sep 4th | B | E |
| Thurs, Sep 5th | C | F |
| Fri, Sep 6th | D | A |
| Mon, Sep 9th | E | B |
| Tues, Sep 10th | F | C |
Session at the Mt Wilson Telescope
As part of the bootcamp, all of you will be building a microscope – either an optical trap, a TIRF microscope or a confocal microscope. To give you an inspiring example of the ambition of optical instruments, every student will take a field trip to the famed Mt Wilson Hooker telescope, used by Edwin Hubble to discover the expanding universe. This will be a 7pm – 1am field trip either on Thurs, Sep 5th or Fri, Sep 6th evening. In preparation for that visit and to give you a sense of the massive ambition and technical achievement of the telescope you will use, please read “The Day We Found the Universe” by Marcia Bartusiak.
Mt Wilson Telescope Schedule
| Group | Date |
|---|---|
| 1 | Thurs, Sep 5th |
| 2 | Fri, Sep 6th |