Syllabus
Required text: Physical Biology of the Cell (2nd ed) by Phillips, Kondev, Theriot and Garcia (ISBN: 0815344503)
The syllabus is tentative and subject to change. During the pandemic, Rob gave a series of related vignettes found here: the Physical Biology of the Cell YouTube channel .
| Date | Topic |
|---|---|
| Week of Jan. 05 (#1) |
The wonder and mystery of Life A feeling for the organism. What sets the scale of X? The cell as a bag of X! Teaching the order of magnitude thinking protocol. Reflection on what is life. |
| Week of Jan. 12 (#2) |
Stuff(t) and dynamical systems. Unity of dynmical phenomena and Newton's gift. mRNA(t), ligand-receptor(t), enzyme/product(t). Rate equation protocol, chemical master equation protocol and putting space in the picture. |
| Week of Jan. 19 (#3) |
Biology's unique dynamics. Phenomenology of exploratory dyamics; microtubule search, development of vasculature, the immune system and animal foraging. The mathematics of exploratory processes. |
| Week of Jan. 26 (#4) |
Null hypotheses What they are, how to formulate them, examples, and how they have implications for dangerous prediction. The great probability distributions. |
| Week of Feb. 02 (#5) |
The real secret of life. The rules of spontaneous change - an ode to the laws of thermodynamics. Defiance. Biological batteries. Case studies in life needing energy. Forming gradients. Pumping sugar up a gradient. Fidelity in biological polymerization. |
| Week of Feb. 09 (#6) |
Weird vectors, big data, regression, thinking big about data, etc. Jiggling and coupled vibrations (covariance matrices), shapes, transcriptomes, the Eigenworm as an example. |
| Week of Feb. 16 (#7) |
Adapatation across scales; signaling and regulation The rules of chemotaxis. Variations on the theme of gene regulation. Graph theory as a big piece of mathematics that is pervasive and powerful. |
| Week of Feb. 23 (#8) |
The science of engineering life. Reflections on engineering. Manipulating atoms, energy and information. |
| Week of Mar. 02 (#9) |
The dreamer's toolkit. Why we are here. Summary of our adventure, the place of life in the universe, the place of biology in science, the place of curiosity and joy in our lives. |