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 6th: please arrive promptly at 8:30am in the Chen Building, Lecture Hall 100. Sunday, September 11th is a day off, and the course will conclude on Tuesday, September 13th.
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 Gabe (gsalmon [at] caltech [dot] edu) no later than 5pm on Sunday, Sept. 4 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 |
| 4:00 pm - ~5:30 pm | Computation sessions with Gabe |
| 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 6th) | A feeling for the organism: what sets the scales of X? order of magnitude thinking; simple estimates | Cell growth rates: image analysis, regression |
| Day 2 (Wednesday, September 7th) | Dynamics across scales in biology: chemical master equations, applications in diffusion, morphogenesis, cytoskeletal length control | Simulating diffusion, chemical master equations and coin flips, applications to FRAP experiments |
| Day 3 (Thursday, September 8th) | Probability as the language of biology: probability distributions and their applications | Gene expression and stochastic simulations: counting proteins through coin flips; Gillespie sampling |
| Day 4 (Friday, September 9th) | The secret of life as defiance: case studies in energetic rebellion | Quantifying dynamic flagellar length control |
| Day 5 (Saturday, September 10th) | X without Y, beyond the atoms: coarse-grained views of living matter | *[evening bootcamp gathering!]* |
| Sunday, September 11th | ** day off ** | TBA |
| Day 6 (Monday, September 12th) | X without Y, beyond the atoms: coarse-grained views of living matter | TBA |
| Day 7 (Tuesday, September 13th: half day) | The dreamer's toolkit: closing provocations | None |
Experimental Sessions
- Building an optical trap or TIRF microscope from scratch [Ana, Heun Jin, & Soichi]: 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 craftsman ship on biological samples. Options for builds for the night are optical tweezer, TIRF, or line-scan confocal.
- Measuring the rate of transcription in Drosophila embryos [Yasemin, Yovan, & Andres]: Using a clever single-transcript fluorescent reporter, you will measure the rate of transcription of a morphogen protein during the development of Drosophila embryos. You will be doing so using the state-of-the-art confocal microscopes available to all Caltech researchers in the Biological Imaging Facility.
Experimental Schedule
Visit this link for your group assignments (for privacy, password-protected, expiring file).
| Experimental Group | Optics | Gene transcription in flies |
|---|---|---|
| Group A | Tues, Sep 6th | Wed, Sep 7th |
| Group B | Wed, Sep 7th | Thurs, Sep 8th |
| Group C | Thurs, Sep 8th | Tues, Sep 6th |
| Group D | Fri, Sep 9th | Tues, Sep 13th |
| Group E | Mon, Sep 12th | Fri, Sep 9th |
| Group F | Tues, Sep 13th | Mon, Sep 12th |
- See this paper for a relevant paper connecting to the fly transcription experiments.