Readings mentioned specifically in class will be listed here as the course progresses.
Bionumbers website by Intenational effort (Maintained by Ron Milo’s lab) ** 2015. The bio numbers website is a portal into biological numeracy. Many of the key numbers of biology can be found here
The Biomass Distribution on Earth by Yinon M. Bar-On, Rob Phillips, and Ron Milo PNAS 2018. This paper examines the distribution of biomass on planet Earth, challenging many of our preconceptions about biological numeracy.
Re-examination of the relationship between marine virus and microbial cell abundances by Charles H. Wigington, et al. Nature Microbiology 2016. This paper gives a modern description of the measured virus to bacterium ratio. Figure 2 gives the key data that led to our 10:1 ratio of viruses to microbes
One at a time, live tracking of NGF axonal transport using quantum dots by Bianxiao Cui, et al. PNAS 2007. This paper gives a flavor of how the dynamics of transport has been measured in neurons. We will make a big deal out of this topic when discussing diffusive time scales
The tragic matter by G. Schatz FEBS 2003.
Polymerases and the Replisome: Machines within Machines by Tania A. Baker and Stephen P. Bell Cell 1998. This paper discusses the incredible fidelity of the DNA polymerase by comparing it with a FedEx truck delivering packages along the road.
Models in biology: ‘accurate descriptions of our pathetic thinking’ by Jeremy Gunawardena BMC Biology 2014. This incredible opinion piece by Jereme Gunawardena discusses the role that models play in science.
The quantitative and condition-dependent Escherichia coli proteome by Alexander Schmidt et al. Nature Biotechnology 2016. This paper proposes a very interesting method to take a census of E. coli’s conent under different growth conditions.
A Mathematician’s Lament by Paul Lockhart ** 2009.
On the growth and form of the gut by Thierry Savin, et al. Nature 2011. This paper describes how the chicken gut gets its characteristic folding
The starry messenger by Galileo Galilei ** 1610.
Physical limits to magnetogenetics by Markus Meister eLife 2016. Harsh critique of high profile papers that don’t obey the laws of physics
Macroscopic equations for pattern formation in mixtures of microtubules and molecular motors by Ha Youn Lee and Mehran Kardar Physical Review E 2001.
The Hydrodynamics of Active Systems by Julia M Yeomans ArXiv 2016.
Are theoretical results ‘Results’? by Raymond E Goldstein eLife 2018.
These are some useful links that can become handy as you explore deeper each of the topics discussed during the course.
Cell Biology by the numbers. This is the online version of “Cell Biology by the Numbers”, a resource that you will find helpful both for understanding the data that characterizes modern biology and for how to construct order-of-magnitude estimates to understand that data.
BE/APh 161 : Physical Biology of the Cell (Caltech). This website contains the material used for teaching a 10 week version of the same course. Here you will find useful problem sets to flex those quantitative biology muscles.
Stat 110: Probability (Harvard). This excellent course by Joe Blitzstein is a great resource to learn probability theory.
Video about dating humans and chimpanzees divergence. This great video talks about how Allan Wilson used molecules to date the divergence between humans and chimpanzees.