Mondays 11:15-13:00 @Belfer auditorium
Course email (to send exercises, suggestions, errors, insights...): firstname.lastname@example.org
Main reading resource: "Cell Biology by the Numbers" book
Vignettes that reveal how numbers serve as a sixth sense to understanding our cells
Subject 1 (30/10/17): Quantitative reasoning in molecular and cell biology
Exercise 1 (due by 06/11/17)
Subject 2 (06/11/17): Size and mass
Exercise 2 (due by 13/11/17)
Subject 3 (13/11/17): Concentrations and absolute copy numbers
Exercise 3 (due by 20/11/17)
Subject 4 (20/11/17): Rates and durations
Exercise 4 (due by 27/11/17)
Subject 5 (27/11/17): Genomes and mutations
... To be continued ...
General info on the final assignment
- 5 minutes with calculation on white board, 2 minute extension for extra aids/features (multi-answer question presented to class, object for demonstration etc.)
- Pay attention to unit conversions, significant digits, big clear handwriting, keep it simple and elegant.
- Assignment of dates will be posted soon!
- 2-3 pages long, with introduction of the question, some background, the calculation, possible outcomes and interesting conclusions.
- To be submitted (after feedback from class peers) 2 weeks after the oral presentation.
Course description and syllabus:
Over the past decades, biology has evolved rapidly from a descriptive, qualitative discipline to a more analytical, data-driven and quantitative one. Our ability to collect numbers that describe the most basic molecular processes within the cell has increased significantly, and simple calculations based on these data can provide important insights and enrich our scientific intuition.
This course is aimed at exposing students to the practice of making back of the envelope calculations (so called Fermi problems) with key numbers in biology, and its useful applications in research. We will learn how to identify the major factors that determine the order of magnitude of the results, when to allow simplification, how to calculate them efficiently, and how to avoid common pitfalls.
The course is composed of weekly lectures on different aspects of quantitative cell biology through many examples of basic (yet often surprising) questions:
- Size and geometry (e.g. What is larger, mRNA or the protein it codes for? How many cells are there in a human?)
- Concentrations and absolute numbers (e.g. What is the elemental and macromolecular composition of a cell? How many virions result from a single viral infection?)
- Energies and Forces (e.g. What is the power consumption of a cell? How much does protein synthesis take out of the entire energy budget of a cell?)
- Rates and durations (e.g. How long does it take cells to copy their genomes? What is faster, transcription or translation? What are the time scales for diffusion in cells?)
- Information and errors (e.g. What is the mutation rate during genome replication? What is the error rate in transcription and translation?)
The last few meetings of the course will be dedicated to presentations of student calculations as a final assignment.
Course book is freely available at: bionumbers
Specific reading material will be given during the course.
* Those who did not take a molecular biology course should read the first few chapters of "Essential Cell Biology", Alberts et al, Garland Science
Other recommended readings (none compulsory, all for enrichment and fun):
- “Guesstimation” by Lawrence Weinstein and John Adam
- “Physical Biology of the Cell” by Rob Phillips, Jane Kondev, Julie Theriot and Hernan Garcia
- “Physiology by Numbers” by Richard Burton (and its partner book “Biology by Numbers” also by Richard Burton)
- “Consider a Spherical Cow” by John Harte (and its partner book “Consider a Cyclindrical Cow” also by John Harte)
- "Street fighting mathmatics" by Sanjoy Mahajan
Attendance and active participation is required.
50% - Weekly assignments
50% - Final assignment (presentation + written vignette)
Key numbers in cell biology (with reference links)
Physical Biology of the cell at Caltech - Rob Phillips group
Order of Magnitude Physics course (Prof. Nir Shaviv, in hebrew)