User:Nkuldell:20.020 working page

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?
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.

End of term project will be specification of a system, allowing a smooth transition to iGEM 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 via

• 2x1hr in class exams
• final design project
• no final exam

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