Casimir Course - Biology for Physicists 2017



Mondays: 15:45-17:45 hrs, Thursdays: 10:45-12:45 hrs


C1.110 (final session: A1.100), building 58, Van der Maasweg 9, Delft


Instructor: Greg Bokinsky

Teaching Assistant: Mathia Arens

Guest Lecturers: Mathia Arens, Franklin Nobrega, Marek Noga, Carsten Blom

Description: Our goal is to introduce scientists with little biological background to several basic topics in molecular biology, as described from a biologist’s perspective. We will also discuss related papers from the recent literature. This will provide a taste of not only how biology works, but also how biological experiments are performed, and the sorts of complications biology experiments often encounter. 

Please read the Background Reading before you come to class, as you will learn a great deal more from the lecture. Attending the lectures alone will not teach you biology!

Each class (after the first class) will start with a 45 minute lecture given by the instructor, which will be followed by a student presentation of a scientific paper drawn from the literature. The paper will be relevant to the previous lecture’s topic (see Syllabus for paper list and order). All participants will read the paper and prepare two questions for the discussion. 

Topics include: Evolution and Horizontal Gene Transfer; Gene Expression; Proteins and Enzymes; Metabolism; Genetic Engineering and synthetic biology; TBA.

Assessment: Pass/Fail grades will be given based on the student presentation and discussion (50%), discussion preparation (25%); and passing quizzes covering the background reading assignments (25%). Attendance at all sessions is required to pass, though absences due to exceptional circumstances are allowed.

Biology for Physicists 2017: Syllabus

  1. October 12. Course introduction, Lecture 1: Life in 30 minutes;
  2. Lecture 2: Evolution and horizontal gene transfer Background reading: General cell biology; Overview of Modern and New Evolutionary Synthesis (pp. 1-12) Optional background reading: Overview of Modern and New Evolutionary Synthesis (pp. 13 – 48), Moran models of drift (nice quantitative treatment of evolution)
  3. October 16. Lecture 3: Gene expression Background reading: From DNA to Protein (pages 231-238); Control of gene expression  (pages 244-260) Student paper presentation: “Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer” Sorek et al. Science 318, 1449 (2007).
  4. October 19. Lecture 4. Proteins and Enzymes Background reading: Proteins (pages 119-130, 133-135, 140-143, 146-152). Student paper presentation: “Optimality and evolutionary tuning of the expression level of a protein” Dekel & Alon, Nature 436, 588 (2005).
  5. October 23. Lecture 5. Metabolism Background reading: Chemistry and Metabolites 1, 2, 3. Student paper presentation: “The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters” Bar-Even et al. Biochemistry 50, 4402 (2011).
  6. October 26. Lecture 6. Genetic engineering Background reading: Foundations for Engineering Biology”; “A brief history of synthetic biology” Student paper presentation: “Functioning of a metabolic flux sensor in Escherichia coli” Kochanowski et al. PNAS 110, 1130 (2013).
  7. October 30. Lecture 7. Bacteriophages. Guest lecturer: dr. Franklin Nobrega. Student paper presentation: “A Synthetic Genetic Edge Detection Program” Tabor et al., Cell 137, 1272 (2009).
  8. November 2: Lecture 8. General bacterial stress response.  Guest lecturer: Mathia Arens. Student paper presentation: “Membrane fusion during phage lysis” Rajaure et al., PNAS 112, 5497 (2015).
  9. November 6: Lecture 9. “Metabolism 2.” Guest lecturer: dr. Marek Noga. Student paper presentation: “Dps Protects Cells against Multiple Stresses during Stationary Phase” Nair and Finkel, J. Bact. 186, 4192 (2004).
  10. November 9: Lecture 10. Charge transport and nanowires in bacteria. Guest lecturer: Carsten Blom. Student paper presentation: “Systems-level analysis of mechanisms regulating yeast metabolic flux” Hackett et al., Science 384, 432 (2016).
  11. November 13: Course wrap-up: 5 minute presentations of your PhD work. Student paper presentation: “Probing single- to multi-cell level charge transport in Geobacter sulfurreducens DL-1” Nature Communications 4, 2751 (2013).


Course dates: Every Monday afternoon (15:45-17:45 hrs) and Thursday  morning (10:45-12:45 hrs) between October 12 and November 13.

Location: C1.110, building 58, Van der Maasweg 9, Delft. NB: Nov. 13: room A1.100.

Credits: 5 GSC.

Registration: The course already started - it is not possible to register anymore.


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12 October - 13 November 2017

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