Introduction to Biological Engineering Design

Syllabus

Course Meeting Times

Lectures: 2 sessions / week, 1.5 hours / session

Studios: 1 session / week, 3 hours / session

Course Overview

This class is project-based introduction to the engineering of synthetic biological systems. In this subject, you will have an opportunity to develop projects that are responsive to real-world problems, using solutions that depend on biological technologies. Through interactive lectures and studio time, you will learn techniques, strategies and vocabulary to enable the engineering of your synthetic biological system. These will be gained by considering:

• how biology can be made easier to engineer, including the use of DNA synthesis, standards, and abstraction in biological engineering
• the consequences of success, introducing issues of human practice, including (a) biological safety, (b) security, (c) ownership, sharing, & innovation, and (d) ethics
• the clever solutions that nature has found to solve physical challenges, specifically examining the components that control cellular behavior
• the ways nature innovates, examining the evolution and reuse of good components as well as the reboot of living systems after catastrophic collapse

It is hoped this subject will provide an engaging introduction for would-be biological engineers as well as a foundational framework for anyone interested in the responsible and reliable programming of genetic material.

Introducing Synthetic Biology

Poetry

Not long ago when biology meant
looking and prodding and fixing what’s bent
there were armies of scientists working away
to list what they found
and to know life’s display

But not all was well as they tried to discover
how life could be programmed since some but not other
experiments worked and each person designed
their template for learning
as they were inclined

“Share!” said the engineers “and try to remember
that others will use your work only whenever
the tools you develop are standard and simple
think of most screwthreads and
think of the wheel.

Maybe in this way life by design
could work out of the box and others will find
lots of interesting ways to build up from the bottom
making useful new parts
then new systems. No problem!”

By combining devices in new and fun ways
the biologists builders could spend their workdays
learning what’s out there and making new widgets
to responsibly meet
the needs of our planet.

Video

Do-It-Yourself Biology: Natalie Kuldell and Reshma Shetty at the MIT Museum, January 14, 2009

This video was produced and provided by MITWorld, and is not covered under our Creative Commons license.

This presentation and audience discussion briefly covers some of the synthetic biology concepts introduced in this class, and especially speaks to how amateurs and self-learners can work on this subject.In this 1 hour 10 minute program, the first 24 minutes are presentation;  then a group discussion is initiated by considering two questions:

• If you could build anything out of biology, what would you build and why?
• What would you ask your neighbors if they were building this organism in the house next door to you?

The Implications of Synthetic Biology: Drew Endy at the MIT Museum, March 21, 2006

This video was produced and provided by MITWorld, and is not covered under our Creative Commons license.

Course Details

Policies

Students in 20.020 should:

1. Do great things
2. Do their best
3. Come to class with an open mind and some energy to engage with the challenges
4. Work collegially and constructively
5. Tell people who need to know if there is a problem

What You’ll Work On

1. Design a plausible and compelling synthetic biological system
2. Develop a detailed design plan and construction roadmap
3. Evaluate ownership, commercial, and ethical aspects of the project

Learning Objectives

1. Understand the operation of genetic programs in prokaryotes and eukaryotes
2. Describe key enabling technologies that support the engineering of biology, including synthesis, abstraction and standardization
3. Develop awareness of issues of human practice that impact and result from the development and application of biological technologies

Joint Meetings with 20.902 Advanced Topics in Synthetic Biology

An advanced undergraduate course 20.902 Advanced Topics in Synthetic Biology meets with 20.020. 20.902 is a reading/journal club class in which the students also act as mentors for the 20.020 project teams, and give weekly presentations on their readings for the combined 20.020 / 20.902 group.

Course catalog description of 20.902:

“Provides an in-depth understanding of the state of research in synthetic biology. Critical evaluation of primary research literature covering a range of approaches to the design, modeling and programming of cellular behaviors. Focuses on developing the skills needed to read, present and discuss primary research literature, and to manage and lead small teams. Students mentor a small undergraduate team of 20.020 students.”

Two particular aspects of 20.902 are woven into the 20.020 OCW site.

• Papers on the readings page are assigned only to the 20.902 students. However, 20.020 students are exposed to these papers through the weekly in-class presentations and discussions.
• The project mentoring roles and expectations for 20.902 students are included on the projects page

Requirements and Grading

• Personal Design Portfolio (individual grade, up to 25% of your final grade)
  • A sequence of eight short homework assignments during the first half of the term.
• Project Development Notebook (team grade, up to 10% of your final grade
  • Includes the team facebook page, team contract, and project log
  • The project log is worth 20 points, and the other two components are worth 10 points each
• Team Project Presentations (team grade, up to 60% of your final grade)
  • 3 Ideas Presentation (15%)
  • Technical Specification Review (15%)
  • Final Presentation
    • technical documents (20%)
    • presentation (10%)
• Instructor Leverage (individual grade, up to 5% of your final grade)

Calendar

L = Lecture

S = Studio

WEEK	SES #	TOPICS	ACTIVITIES	KEY DATES
1	L1	Design, build, test	Paper airplane
	S1	Sampling of past projects	iGEM project review
	L2	Science as a take-apart	Take apart a tape recorder	Homework PDP1 due
2	L3	Engineering as a rebuild	Reassemble the tape recorder	Homework PDP2 due
	S2	Broader project landscapes	Scripts and storyboards	Homework PDP3 due
	L4	Decide what’s worth doing	Play “Decide” (an exercise in policy and team dynamics)
3	S3	Sorting hat into project camps	Temporary teams brainstorm project ideas	Homework PDP4 due
	L5	Knowns vs. unknowns	The Clock of the Long Now	Homework PDP5 due
4	L6	Backyard biology	Kitchen DNA, Lego™Phoresis
	S4	Project teams assigned	Work on team contract and Facebook page	Team contract and Facebook page due Homework PDP6 due Homework PDP7 due
	L7	FooCampers guide to bioengineering	More Lego™Phoresis
5	L8	Scientist as activist	Video of DNA experimentation hearings, 1976	Homework PDP8 due
	S5	Design day 1	MIT Libraries research guide webpage Work on projects
	L9	Interface between scientific/engineering community and the broader public	Guest lecture by Prof. Jonathan King, MIT
6	L10	Project work day		3 ideas presentation due
	S6	3 ideas presentations
	L11	3 ideas feedback	Final project selection
7	L12	System overviews	Flip books, iGEM “bacterial buoy” project
	S7	Design day 2 Abstraction in action part 1: systems to devices	Work on projects
	L13	Abstraction in action part 2: devices to parts
8	L14	Parts and registry
	S8	Design day 3	Test and debug; data-driven decision making
	L15	Hypothesis-driven engineering	Validate system operation, learn from modes of failure
9	L16	Project work day		Tech spec review due
	S9	Tech spec review presentations
	L17	Tech spec feedback	Plan project re-design
10	L18	Reliability	Failures of materials, system performance and human sources
	S10	Re-design day 1	Join registry of standard biological parts
	L19	Ownership and sharing	Inventor vs. investor role playing
11	S11	Re-design day 2	Drew Endy teaching
	L20	Project work day	Drew Endy teaching
12	L21	Project work day (cont.)
	S12	Consultations on projects
	L22	Tips on oral presentations
13	L23	Project work day
	S13	Final presentations day 1	Three teams present
	L24	Q&A and project work	Class evaluation
14	L25	Q&A and project work (cont.)
	S14	Final presentations day 2	Three teams present	Final reports due
	L26	Wrap-up and celebration		Project log due