Syllabus

BIOE/ENGR.80 - Spring 2020

Introduction to Bioengineering (Engineering Living Matter)

Students successfully completing BIOE/ENGR.80 will have a working understanding for how to approach the systematic engineering of living systems to benefit all people and the planet. Our four main goals for the quarter are (1) to help you learn ways of thinking about engineering living matter, (2) to empower you to explore and do bioengineering starting from DNA, and (3) for you to become more capable of learning and explaining bioengineering to yourself and others, including discussing the broader ramifications of engineering the living world. (4) Specific to Spring 2020, in the time of COVID-19 and at the dawn of a decade, we also aim to enable you to devise and express your wishes for bioengineering as might be made true by or before 2030, and to develop practical plans for making you wishes real.

When

6 April to 10 June 2020

MWF, 1:30-2:20p, Lectures & Activities via Zoom

Where (Class & Office Hours, same link)

Zoom: https://stanford.zoom.us/j/861034342?pwd=NkVXNUcwNVBKb1RCWnk3aTVydWJFQT09

Instructors

Course Lead, Prof. Drew Endy; Office Hours (PST) Mon/Wed/Fri 14:20-15:00 (after class) (after class) and by appointment via endy@stanford.edu (can also schedule by emailing marc4@stanford.edu)

Co-Instructor, Dr. Siavash Ahrar; Office Hours Tue 11:30-12:30, Sat 09:30 AM-10:30; sahrar@stanford.edu

Co-Instructor, Prof. Michael Specter; Office Hours Wed 16:00-17:00; specterm@stanford.edu

Teaching Assistants

Jon Calles; Office Hours Fri 15:00-16:00; jecalles@stanford.edu

Nicolai Ostberg; Office Hours Fri 15:30-16:30; nostberg@stanford.edu

Naomi Pacalin; Office Hours Tues 10:00-11:00; npacalin@stanford.edu

Julisia Chau; Office Hours Mon 09:00-10:00; jhchau@stanford.edu

Brianna Chrisman; Office Hours Wed 09:00-10:00; briannac@stanford.edu

Victor Tieu; Office Hours Mon 16:00-17:00; vtieu@stanford.edu

If the schedule does not work well for you, please contact us on Piazza with suggestions on how we can better accommodate your circumstances. All times in PST. Office hours are held on the same zoom link as class.

Grading

The course is designed to operate on a S/NC basis. To earn a S grade a student must satisfy the following two conditions:

(1) Earn an average grade of 70% or above on the PSETS.

(2) Earn a cumulative grade of 70% or above on the Final Project (team-based).

Please note your lowest PSET grade will be dropped from your PSET average.

Please also note that we will offer quizzes throughout the quarter that will accrue points. You can apply your cumulative quiz points to reduce the threshold for (1) and (2) to as low as 60% given sufficient quiz points.

Key Dates

6 April 2020; first class

25 May 2020; no class

10 June 2020; last class

Honor Code

We expect you will uphold Stanford’s Honor Code. Discussion among peers and with the teaching staff is strongly encouraged. All submitted work must be completed individually unless explicitly noted otherwise.

Students with Documented Disabilities:

Students who may need an academic accommodation based on the impact of a disability must initiate the request with the Office of Accessible Education (OAE). Professional staff will evaluate the request with required documentation, recommend reasonable accommodations, and prepare an Accommodation Letter for faculty. Unless the student has a temporary disability, Accommodation letters are issued for the entire academic year. Students should contact the OAE as soon as possible since timely notice is needed to coordinate accommodations. The OAE is located at 563 Salvatierra Walk (phone: 723-1066).

Office of Accessible Education site

Week 1: Getting Started

Day	Title
Mon 6 April	Why engineering biology?
Wed 8 April	What makes living matter unique?
Fri 10 April	How to read a bioengineering research paper

Week 2: People, Planet, & Political Health

Day	Title
Mon 13 April	People health (what do people need of bioengineers?)
Wed 15 April	Planet health (what does everything else “need”?)
Fri 17 April	Political health (what does it mean to engineer biology at social scales)

Week 3: Analysis & Design of Molecules & Genetic Systems

Day	Title
Mon 20 April	Activity – Tools for seeing biology (Foldscope)
Wed 22 April	Analysis and design of molecules
Fri 24 April	Analysis and design a genetic systems

Week 4: Engineering Abstraction in Biology

Day	Title
Mon 27 April	Engineering abstraction in living matter – synthetic genetic logic
Wed 29 April	Engineering abstraction in living matter – generic system architecture
Fri 1 May	Team Project: Brainstorming + project introduction

Week 5: DNA Reading & Writing

Day	Title
Mon 4 May	DNA sequencing (read) and synthesis (write), core concepts
Wed 6 May	DNA read/write strategy, from exponentials to interconvertibility of matter and information
Fri 8 May	Team Project – Project priorities + story spine

Week 6: From Diffusion to Programmed Development

Day	Title
Mon 11 May	Molecular diffusion and spontaneous behaviors
Wed 13 May	Activity – Dancing droplets
Fri 15 May	Programming morphogenesis (could you grow an arm?)

Week 7: Project

Day	Title
Mon 18 May	Team Project – Planning
Wed 20 May	Team Project – Story (Play.1)
Fri 22 May	Team Project– Story (Play.2)

Week 8: Evolution as Tool for Engineering

Day	Title
Mon 25 May	No class
Wed 27 May	Evolution as an algorithm
Fri 29 May	Evolution as a service

Week 9: Bioengineering Futures

Day	Title
Mon 1 June	Bioengineering futures related to planet health
Wed 3 June	Bioengineering futures related to human health
Fri 5 June	Bioengineering futures related to Political health

Week 10: Bioengineering Futures & Charge to Class

Day	Title
Mon 8 June	Closing discussion and charge -1
Wed 10 June	Closing discussion and charge -2

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