User:Nkuldell:20.020 working page

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Contents

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
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