Cell Biology By the Numbers

 

Course given on fall semester by Ron Milo, teaching fellows: Maya Voichek, Yinon Bar-On

Mondays 11:15-13:00 @Belfer auditorium

Course email (to send exercises, suggestions, errors, insights...): cellbiologybythenumbers@gmail.com


Main reading resource: "Cell Biology by the Numbers" book

Vignettes that reveal how numbers serve as a sixth sense to understanding our cells

Course outline

Subject 1 (30/10/17): Quantitative reasoning in molecular and cell biology

Exercise 1 (due by 06/11/17)

A filmed version of the lecture from the class of 2014-15

 

Subject 2 (06/11/17): Size and mass

Exercise 2 (due by 13/11/17)

Slides from the lecture - photo gallery of sizes in cell biology

A filmed version of the lecture from the class of 2014-15

 

Subject 3 (13/11/17): Concentrations and absolute copy numbers

Exercise 3 (due by 20/11/17)

Slides from the lecture - photo gallery of concentrations in cell biology

A filmed version of the lecture from the class of 2014-15

 

Subject 4 (20/11/17): Rates and durations

Exercise 4 (due by 27/11/17)

A filmed version of the lecture from the class of 2014-15 

 

Subject 5 (27/11/17): Genomes and mutations

... To be continued ...

General info on the final assignment 

Oral presentation

  • 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!

 

Written vignette

  • 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.

 

Deadlines 
04/12/17  - Send us an email with your chosen subject as 1-2 lines for approval.
25/12/17 - Start of student presentation sessions.

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.

Accompanying texts:

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):

 

Grading:

Attendance and active participation is required.

50% - Weekly assignments

50% - Final assignment (presentation + written vignette)

Interesting links:

BioNumbers Database

BioNumber of the month

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)