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Introduction to Biological Engineering Design
A class for first-year MIT undergraduates who are interested in the engineering of biology.
[NK, can we renumber to 20.001A, allowing for a future in which 20.001B and 20.001C might cover engineering aproaches applied to biological science and engineering approaches applied to biomedical work, respectively?]
[DE, we can call it whatever the hell you want but I kinda liked the 20:20 number...it's the vision thing...the other niche versions sound great though...how many can we teach?]
Key Concepts
- Understand the operation of genetic programs in prokaryotes and eukaryotes.
- Describe key enabling technologies that support the engineering of biology, including synthesis, abstraction and standardization.
- Develop awareness of issues of human practice that result from the development and application of biological technologies.
Organiziation
End of term project will be specification of the design of a system, allowing for a smooth transition to iGEM summer undergraduate research experience if desired.
Class tentative setup as 4-0-8
- 2x1hr lecture
- 2x1hr recitation (one to cover journal articles and other as Q/A time with TA)
- eight hours of work outside of class
Assessment
- 2x1hr in class exams
- final design project
- no final exam
Draft Syllabus
WEEK | DAY | Lecture topic | Recitation article | For Next Time |
1 | 1 | Welcome | BioText/DesignText | |
1 | 2 | NASCAR tour of the cell [1] | Lives of a Cell [2] | DNA structure refresher |
2 | 1 | Bacterial gene expression | Sigma description/Jacob and Monod | Standards:digital vs analog Measurements: PoPS vs Northern |
2 | 2 | Noisy gene expression | Weiss/van Oudenaarden | Measurements: cell vs bulk |
3 | 1 | Genetic switch | Mark P-tashne | Standards: transfer curve |
3 | 2 | Genetic circuit design | Toggle/Repressilator | Standards: genetically encoded logic functions |
4 | 1 | Registry: parts, devices, systems | Composition | Measurements: device (bacterial photography system?) characterization |
4 | 2 | Composition: physical vs functional | Standard assembly | |
5 | 1 | Review session | Q/A with TA | |
5 | 2 | Exam I | break | |
6 | 1 | Evolution | Darwin-lite | Standards: comment on ID ruling |
6 | 2 | Synthesis technologies | ||
7 | 1 | Forward genetics Reverse engineering |
Design of genetic screens [3] | read: genetics text, plus genetics problem set |
7 | 2 | Sequencing projects | Systematic analysis of yeast genome [4][5] | Standards: Registry vs SGD Measurements: SGD Project Task A |
8 | 1 | Foundations for engineering: abstraction | ||
8 | 2 | Foundations for engineering: decoupling | Project Task B | |
9 | 1 | Reverse genetics Forward engineering |
T7.1 [6] | |
9 | 2 | Application: engineering therapeutics | JK's work [7] CV's work [8] | Preliminary project description due |
10 | 1 | Application: engineering for bioremediation/of bioresponsive agents | ||
10 | 2 | Review session | Q/A with TA | |
11 | 1 | Exam II | no recitation | |
11 | 2 | Socially responsible engineering | Help session for final project | |
12 | 1 | Final project presentations (poster session if class large?) | ||
12 | 2 | class evaluation |