# BIOL 1940T (CRN 14871) Synthetic Biological Systems

Mondays and Wednesdays 3.30pm - 5.00pm, CIT Room 227
First class is Wednesday August 5th 2007

Date         Instructor    Topic
1. Sept 5  (W)  Gary Wessel   Introduction, perspective and ethical implications    Brown, MCB
2. Sept 10 (M)  Tom Knight    Foundations of synthetic biolog,                      MIT, Computer Science and AI Laboratory
3. Sept 12 (W)  John Savage   Nanocomputing                                         Brown, Computer Science
4. Sept 17 (M)  John Cumbers  The engineers approach, modularity, abstraction       Brown, BioMed
5. Sept 19 (W)  Jamie Gagnon  Synthetic biology literature review,                  Brown, MCB
Ethics essay due
6. Sept 24 (M)  Jeff Morgan   Techniques in synthetic biology                       Brown, Biomedical Engineering
7. Sept 26 (W)  John Cumbers  Isolation, characterized behavior, interfaces         Brown, Biomed
8. Oct  1  (M)  Wolfgang Peti Protein engineering 1                                 Brown, MPPB
9. Oct  3  (W)  Hasan Demirci Protein engineering 2                                 Brown, MCB
Take Home exam 1 given out
Oct 8 (M)  Columbus Day, no class
10.Oct 10 (W)  Jamie Gagnon, Literature review                                      Brown, MCB
Take Home exam 1, Due at beginning of class
11.Oct 15 (M)   Nicola Neretti Deterministic models 1                               Brown, Physics
12.Oct 17 (W)   Nicola Neretti Deterministic models 2                               Brown, Physics
13.Oct 22 (M)   Anubhav Tripathi     Microfluidics                                  Brown, Engineering
14.Oct 24 (W) Jason Sello      Metabolic engineering                                Brown, Chemistry
Modeling exercise due
15.Oct 29 (M) Pam Silver       Designing Biological Systems                         Harvard, Systems Biology
16.Oct 31 (W) Sherief Reda  Cellular logic motifs                                 Brown, Engineering
17.Nov 5  (M) Christina Smolke Metabolic engineering and RNA logic devices          Caltech, Chemical Engineering
18.Nov 7  (W) Jim Collins      Engineering Gene Networks:Integrating Synthetic Biology & Systems Biology
BU
1 page outline of final project due
19.Nov 12 (M) Suzanne Sindi    Stochastic Modeling                                  Brown, Applied Math
Take home exam 2 given out
20.Nov 14 (W) Suzanne Sindi    Stochastic Modeling                                  Brown, Applied Math
21.Nov 19 (M) Chris Voigt      Programming bacteria: wiring synthetic sensors and circuits to heterologous outputs                                                                                               Pharmaceutical Chemistry, UCSF
Take home exam 2 due
Nov 21 (W) Thanksgiving, no class
22.Nov 26 (M) Jay Tang         Biophysics of bacteria                               Brown, Physics
23.Nov 28 (W) Group Presentations and Discussion
24.Dec 3  (M) Marc Johnson     Bioenergetics and biofuels                           Brown, MCB
25.Dec 5  (W) Jim Head         Exploring Planetary Environments: Earth and the Solar System
Brown, Geology
26.Dec 10 (M) Final project oral presentations 1
27.Dec 12 (W) Final project oral presentations 2


## Outline

A multidisciplinary course that combines seven areas of science and engineering giving undergraduates a solid foundation in a cutting edge field of biological engineering. Synthetic biology is a mixture of biology, chemistry, engineering, genetic engineering and biophysics. It builds on recent work in systems biology which involves the modeling of biological systems, but goes further in that it involves the construction and standardization of biological parts, that fit together to form more complex systems.

## Background

In 1978 the Nobel Prize in Medicine was awarded to Daniel Nathans and Hamilton Smith and it was predicated that "the new era of synthetic biology” had arrived , where genes could be cut up, changed around and put back together again to form novel function. However it was not until 2000 that the first examples of an engineered biological circuits were published in Nature. One was a synthetic oscillator; an engineered strain of E.coli capable of cyclic expression of green fluorescent protein, the other was a bacterial toggle switch capable of switching the protein to be expressed into one of two states. Since then engineers’ interest and contributions to biology have created a completely new field of ‘synthetic biology’.

Synthetic biology is a mixture of biology, chemistry, engineering, genetic engineering and biophysics. It builds on recent work in systems biology which involves the modeling of biological systems, but goes further in that it involves the construction and standardization of biological parts, that fit together to form more complex systems. One of the key factors that is making synthetic biology a reality is the falling cost of two key technologies, sequencing of DNA (now just $7 per read) and synthesis of novel DNA (now$0.69 per base pair). This fall in price continues to halve about every 18 months and was recently compared to the doubling of the number of processors being put onto computer chips which also happens every 18 months. If this pace of development continues then not only is a new field of science and engineering forming but also a new industrial revolution, based on smaller, cleaner biological machines.

## Course aim

This course will aim to you a thorough grounding in the theory and current literature of synthetic biology as well as provide you with an up-to-date framework in modeling and systems biology. It will include the fundamental principles of engineering such as abstraction, modularity, standardization and composition and how these are being applied to biology. You will get an overview of the biological techniques specific to experts in biology and engineering at Brown. The course will also include a number of visiting lectures, experts in the field from outside of Brown.

## Notes

• Taught by interdisciplinary faculty
• There may be opportunity for individual or group practical projects in Spring 2008.