Biology is being revolutionized by new experimental techniques that have made it possible to measure the inner workings of molecules, cells and multicellular organisms with unprecedented precision. The objective of this short module is to explore this deluge of quantitative data through the use of biological numeracy. We will survey exciting research examples from our department and beyond in order to develop theoretical models that make precise predictions about biological phenomena. These predictions will be tested through the handson analysis of experimental data and by performing numerical simulations using Matlab.
Physical biology will be introduced as an exciting new tool to complement other approaches within biology such as genetics, genomics and structural biology. The module will introduce students to the enabling power of biological numeracy in scientific discovery and make it possible for them to use these tools in their own research.
Course instructor: Hernan Garcia (hggarcia@berkeley.edu). Office hours: Wednesdays 1:30pm to 2:30pm @ 501C LSA. Please, see announcement on Piazza for updated office hours.
Course GSI: Elizabeth Eck (eeck@berkeley.edu, Office hours: Mondays 11:00am to 12:00pm @ 349 LSA) & Gabriella Martini (martini@berkeley.edu, Office hours: Tuesdays 4:00pm to 5:00pm @ 349 LSA).
Class materials:
 Course syllabus (subject to change)
 Download and install Matlab by logging on to the UC Berkeley Software Central. It is very important you do this at least a week before classes start!
Schedule: Class meets Tuesdays from 24 PM in 107 Genetics & Plant Biology Building and Thursdays from 24 PM in 103 Genetics & Plant Biology Building. There are no independent Discusison sections as Lectures, Labs and Discussions are integrated within the weekly lectures.
Homework policy: Homeworks are due at the beginning of class one week after they are posted. Solutions will be posted two days after the homeworks are submitted, and homeworks will be returned a week after they are submitted. NO late homeworks will be accepted (late means anytime after class starts the day the homework is due) unless you have a note from someone like a doctor or a Dean. You may discuss the homework with others, but your explanations and derivations must be your own. Your logic and the significance of your results should also be explained.
Lecture 
Date  Topics  Materials 
1 
1/22 
A feeling for the numbers in biology: Estimation and biological numeracy E. coli by the numbers 
A feeling for the numbers: Powerpoint Presentation Papers: Mathematics Is Biology’s Next Microscope, Only Better; Biology Is Mathematics’ Next Physics, Only Better (Cohen2004), Theory in Biology: Figure 1 or Figure7? (Phillips2015b), Distribution of biomass on Earth (BarON2018 and SI) and Number of genes in human genome, The Tragic Matter (Schatz2003), Polymerases and the Replisome (Baker1998) Reading material: PBoC chapters 1 through 3 Making simple plots: Matlab code (in class) 
2 
1/24 
Temporal scales in biology Bacterial Growth: Simulations using the Euler method 
Homework 1 out, due 1/31: Sender2016, Li2014 E. coli by the numbers  Bacterial growth: Powerpoint Presentation Simulating bacterial growth: Matlab code (in class) Papers: An obsession with dN/dt (Neidhardt1999) Reading material: PBoC chapters 2 and 3 Matlab tutorials: 2 and 3 
3 
1/29 
Bacterial Growth: Limits to bacterial growth, Part I 
E. coli by the numbers  Limits to bacterial growth, Part I: Powerpoint Presentation Papers: Stouthamer1973 Reading material: PBoC chapters 2 and 3 
4 
1/31 
Bacterial Growth: Limits to bacterial growth, Part II 
Homework 1 due Homework 2 out, due 2/7: Schmidt2016, Mass spec data on ATP synthase, Cai2006 E. coli by the numbers  Limits to bacterial growth: Part II: Powerpoint Presentation Papers: VanOijen2006 Reading material: PBoC chapters 2 and 3, MBoC chapters XX (ATP Synthase, Mass spectrometry) 
5 
2/5 
Diffusion: Axonal transport and deriving the diffusion equation

Diffusion, Part I: Powerpoint Presentation Papers: Lipps2011, Hochbaum2014, Droz1962, Cui2007, Morfini2011, Yildiz2003 Reading material: PBoC chapter 13 
6 
2/7 
Bacterial Growth: Analyzing movies of growing colonies and fitting data 
Homework 2 due Homework 3 out, due 2/14 Measuring bacterial growth using microscopy: Data, MatlabCode Reading material: PBoC chapters 2 and 3 
7 
2/12 
Diffusion: Solving the diffusion equation using coin flips 
Diffusion by coin flips: Matlab code Reading material: PBoC chapter 13 
8 
2/14 
Diffusion and FRAP: Solving the diffusion equation using master equations, Part I 
Homework 3 due (send abstract for estimate over email to Hernan, Gabriella and Liz) Homework 4 out, due 2/21 Diffusion, Part II: Powerpoint Presentation 
9 
2/19 
Diffusion and FRAP: Solving the diffusion equation using master equations, Part II 
Diffusion, Part III: Powerpoint Presentation Spread the butter for diffusion: Matlab code 
10 
2/21 
Flies by the Numbers: The physical limits to DNA replication and transcription in development, Part I 
Homework 4 due Homework 5 out, due 2/28: Gregor2007a, Gregor2007b Flies by the Numbers: Powerpoint Presentation Recombination and the first mapping of a chromosome: Sturtevant1913. 
11 
2/26 
Flies by the Numbers: The physical limits to DNA replication and transcription in development, Part II

Transcriptional elongation in flies: Data and Matlab code 
12 
2/28 
Developmental patterning: The French Flag model and how to make morphogen gradients, Part I Dimensionless numbers and dimensional analysis 
Homework 5 due Homework 6 out, due 3/7: Abouchar2014 (SI), GarciaBellido1979. The French Flag model: Powerpoint Slides Papers: Testing the French Flag model (Driever1989 and 2013); measuring Bicoid degradation (Drocco2011), diffusion (AbuArish2011), bicoid localization (Little2011), and translation (Petkova2014) Testing the French Flag model: Bicoid dosage mutant sample image, Bicoid dosage full data set, MatlabCode 
13 
3/5 
Developmental patterning: The French Flag model and how to make morphogen gradients, Part II Discussion: Thinking about concentrations and ATP in the cell 

14 
3/7 
Regulatory biology and the constitutive promoter, Part I: Phase diagrams and solving for mean mRNA levels 
Homework 6 due No homework this week  Time to work on your estimate vignettes (due 3/14) Dynamics of the constitutive promoter: Matlab code The constitutive promoter: Powerpoint Slides 
15 
3/12 
Regulatory biology and the constitutive promoter, Part II: Master equations and transcriptional noise, an analytical approach Discussion: Diffusion estimates 
Clarke1946: Flyingbomb attacks on London and the Poisson distribution Jones2014: Transcriptional noise in the lac operon 
16 
3/14 
Regulatory biology and the constitutive promoter, Part III: Master equations and transcriptional noise, a numerical approach 
Estimate vignettes due (email them to Hernan, Gabriella and Liz) Homework 7 out, due 3/21: Taniguchi2010, Petkova2014, Gunawardena2014 (Models in biology: `accurate descriptions of our pathetic thinking') Solving the master equation for the constitutive promoter: Matlab code 
17 
3/19 
Regulatory biology: Simple repression, Part I 
Simple repression: Powerpoint Slides 
18 
3/21 
Regulatory biology: Simple repression, Part II

Homework 7 due
Homework 8 out, due 4/4: A First Exposure to Statistical Mechanics for Life Scientists (Garcia2007b). Voltagegated ion channel data and paper (Keller1986). Dissection of simple repression: Garcia2011c Matlab: Sample microscopy images of bacteria, Full bacterial gene expression data set, Extractting fluorescence from bacterial cells 
19 
4/2 
The forces of evolution: Mutation  LuriaDelbruck, Part I 
Nothing in biology makes sense except in the light of evolution: Dobzhansky1973 LuriaDelbruck experiment: Powerpoint Slides, Luria1943 Exploring the adaptive mutation hypothesis (Poisson distribution): Matlab code 
20 
4/4 
The forces of evolution: Mutation  LuriaDelbruck, Part II 
Homework 8 due Homework 9 out, due 4/11 Simulating the LuriaDelbruck experiment: Matlab code 
21 
4/9 
The forces of evolution: Genetic drift  Buri experiment, Part I 
Genetic drift: Buri1956, Powerpoint Slides Simulating genetic drit by coin flips: Matlab code 
22 
4/11 
The forces of evolution: Genetic drift  Buri experiment, Part II

Homework 9 due (send abstract for estimate over email to Hernan, Gabriella and Liz)
Homework 10 out, due 4/18: Buri data Genetic drift by spreading the butter: Matlab code 
23 
4/16 
Study Hall to prepare for presentations  
24 
4/18 
Dynamical systems: A genetic switch, Part I 
Homework 10 due Homework 11 (extra credit) out, due 5/2

25 
4/23  Dynamical systems: A genetic switch, Part II  
26 
4/25  Physical Biology of the Cell 
Bring a smartphone or computer to fill out the official course survey as well as Hernan's survey: Hernan's survey, Berkeley's survey 
27 
4/30 
Presentations of second estimate (1/2 of the class)  
28 
5/2  Presentations of second estimate (1/2 of the class)  Homework 11 (extra credit) due 
Matlab tutorials: We will assume no previous Matlab experience. These are small tutorials that introduce the different concepts we'll use in each class.
 Variable and arrays, and plotting.
 Forloops.
 Loading and displaying images (sample image).
 Ifstatements.
If you want to go beyond our introductory Matlab tutorials, here are some other great sources:
Bibliography:
Phillips, R., et al. (2013). Physical Biology of the Cell, 2nd Edition. New York, Garland Science. (PBoC)
Alberts, B. (2015). Molecular Biology of the Cell. New York, NY, Garland Science. (MBoC)
Milo, R. and Phillips, R. (to be published in 2016, can be downloaded from http://book.bionumbers.org/). Cell Biology by the Numbers. New York, NY, Garland Science.
Mahajan, S. (2010). StreetFighting Mathematics: The Art of Educated Guessing and Opportunistic Problem Solving. MIT Press (2010).
Weinstein, L. and Adam, J.A. (2008). Guesstimation: Solving the World's Problems on the Back of a Cocktail Napkin. Princeton University Press.
Bring a smartphone or computer to fill out the official course survey as well as Hernan's surve