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. Videos: Night science (08:48)
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. Videos: Phenomenology of exploratory dynamics Chromosome segregation Geometric distributions
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. Videos: Representations An Introduction One of the most profound ways in which mathematics allows us to describe the world around us is through different REPRESENTATIONS of objects, processes and concepts. This vignette provides a number of examples of such representations. Vectors An Introduction The notion of vector is much broader than the simple idea of position vector we first encounter in physics. This vignette describes various generalizations of the notion of vector. The “Right” Variables and the Awesome Power of Data Collapse This vignette describes the deep and important question of what degrees of freedom we should use in describing a given problem. After illustrating this with several examples, we describe the notion of data collapse. The “Right” Coordinates for the Harmonic Oscillators - Part 1 The “Right” Coordinates for the Harmonic Oscillators - Part 2 This vignette describes the all-important notion of finding the right coordinates in the concrete situation of coupled mass-spring systems. Though this sounds like it is far from biology, there are few examples that are more potent for showing the essence of ideas such as PCA.
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. Videos: The Cell as a Bag of X This vignette describes the convenient and illuminating abstraction of pretending that cells are bags of genes or proteins or alleles. The Cell as a Bag of mRNA This vignette describes the modern tools of transcriptomics and then borrows from our earlier study of the coupled oscillators to illustrate how the covariance matrix helps us find natural coordinates and perform dimensional reduction. Eigenworm This vignette uses all of our tools about vectors, representations and collective coordinates to examine a brilliant case study in the motion of the worm C. elegans.
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.