Course Syllabus

BIOE.80/ENGR.80 - Spring 2016       Engineering Living Matter (aka, Introduction to Bioengineering)

 

Students completing BIOE.80/ENGR.80 should have a working understanding for how to approach the systematic engineering of living systems to benefit all people and the planet. Specific skills and fundamental concepts covered are summarized at the end of this document, starting on page 3. Our two main goals for the quarter are to (1) help you learn ways of thinking about engineering living matter and (2) empower you to explore and discuss the broader ramifications of engineering the living world.

 

Handy Details

 

When: March 28 to June 1, 2016

Lectures & Demos, MWF, 1:30-2:20p


Where: Lecture location (Monday, Wednesday): Shriram Center, Room 104

Demo location (Friday): Shriram Center, Rooms 112 and 132

In class exams: Final Exam, 12:15-3:15p, Friday 3 June 2016, Room TBD

Assignment Pickup. After initial delivery in lecture, graded assignments can be found in the cubbies outside of Shriram 361.   The cubbies are labeled "BioE 80 Outbox".

Instructors

Drew Endy (OH, Monday 3p, Friday 10a, or by appointment); endy@stanford.edu; OH for Prof. Endy are in Shriram Room 252 (2nd floor, Blue Atria)

Jan Liphardt (OH, Monday 10a; Friday 3p, or by appointment); jan.liphardt@stanford.edu; OH for Prof. Liphardt are in Shriram Room 005 (just below Lecture room)

Teaching Assistants. Office Hours for TAs to be determined and confirmed with students during Week 1.

All Office Hours will take place in Shriram Tea Room (basement level)

Da Yoon No   <dayoonno@stanford.edu> Monday 10-11AM

Nathan Kipniss <kipniss@stanford.edu> Monday 11AM-12PM

Shivani Torres <shivant@stanford.edu> Monday 2:30-3:30PM

Celine Liong <cliong@stanford.edu> Wednesday 2:30-3:30PM

Sibel Sayiner <ssayiner@stanford.edu> Thursday 1-2PM

Mathias Voges <mvoges@stanford.edu> Friday 11-12PM 

TA Mentoring Groups and Case Studies. TA Mentoring Groups will be assigned during Week 1. Each week we will provide one or two articles, links, and other materials for further investigation and thought. You are encouraged to discuss these materials with your TA and your colleagues during your weekly mentoring meeting. Attendance is not mandatory and you will not be graded by your TA mentor – this is purely an additional resource for you. In general, discussion materials will focus on a big problem and technologies or startups most relevant to the selected topic.

 

MUD. Everything in class clear as mud? Write your question on anything, anonymously, and turn in at the end of class to a TA or Professor. Hours later there will be an answer on the course site.

 

Grading. The following items will determine your grade – 9 puzzles (64%), 6 lab demos starting in week 3 (6%), a final essay (15%), & a final exam (15%)

 

Puzzles. ~1 per week (two lowest grades dropped); 70% total grade. NOTE: Puzzles are due at start of class period as noted; ZERO CREDIT IF LATE. Must be turned in as a PHYSICAL COPY for rapid grading and comments.

 

Demos. ~1 per week starting in Week 3; 6% total grade.  Note: 2-3 short questions that can be completed during Friday demos or over the weekend.  Due by the start of lecture on Monday following each demo. ZERO CREDIT IF LATE. Must be turned in as a PHYSICAL COPY for rapid grading and comments. 

If you are going to miss a demo, download the handout when it's uploaded to Canvas. Answer the questions and turn it in at the beginning of lecture on Monday following the demo. If you are unclear on any of the concepts from the demo, contact the head TAs (whoever uploaded the demo handout) for help.

 

Final Essay. 3 pages (3 pages “I’d like”; 1 page “I’d wish”; 1 page “What if?”); 15% total grade; due as late as allowed during quarter.

 

General Assignment Policy. Any assignment that is turned in without a name will not be graded, and given a zero.

 

Final Exam. Questions similar to the Puzzles; 15% total grade. Last year’s exam will be provided as a practice exam.

 

Honor Code. Uphold Stanford’s Honor Code. Puzzles must be completed individually unless explicitly noted otherwise. The Final Essay must be your own but can drawn upon conversations with others. The Final Exam must be your own work.

 

Schedule         Topics                                                                                                 Due Dates

 

(Week 1)          (Introduction, Motivation, & Framing)

28 March         Why Engineer Biology? – DE (Lecture 1)

30 March         What Makes Living Matter Special? – JL (Lecture 2)

01 April            Mushroom Making (Demo #1)

 

(Week 2)          (Restorative Medicine & Pattern Formation)

04 April            How to Grow an Arm – DE (Lecture 3)                      Puzzle 1 due

06 April            Something from Nothing (Pattern Formation) – JL (Lecture 4)

08 April            Dancing Droplets; Emergence (Demo #2)

 

(Week 3)          (Living Complexity plus Core Engineering Concepts)

11 April           My Microbiome and I – JL (Lecture 5)                       Puzzle 2 due

13 April           Fundamentals for Engineering Biology - DE (Lecture 6)

15 April            Meet Your Microbes (Demo #3)

 

(Internal Student Feedback @ End of Week 3)

 

(Week 4)          (What Makes DNA So Ripe for Engineering?)

18 April           DNA = Information = Data – JL (Lecture 7)          Puzzle 3 due

20 April          DNA Synthesis, Construction & Editing Tools – DE (Lecture 8)

22 April          Coding Messages & Synthesizing DNA (Demo #4)

 

(Week 5)          (How to Engineer Genetically Encoded Systems)

25 April          Engineering Molecular Machines & Systems – DE (Lecture 9) Puzzle 4 due

27 April          The Physics of Molecular Activity – JL (Lecture 10)

29 April          Virus Assembly & Molecular Ratchets (Demo #5)

 

(Week 6)          (Agriculture & Evolution)

02 May          From Breeding to Programming Food – DE (Lecture 11) Puzzle 5 due

04 May          System Design on Three Time Scales (Now, Learn, Evolve) – JL (Lecture 12)

06 May          Us vs. Them; Genetic Algorithms (Demo #7)

 

(Week 7)          (Neuro-Biology & Engineering)

09 May           What the Eye Tells the Brain – JL (Lecture 13) Puzzle 6 due

11 May           Programming Life with Light – DE (Lecture 14)

13 May           Opto/Neurogenetics Demo (Demo #6)

 

(Week 8)          (Ecosystems & Expansion)

16 May            Options for operating ecoystems – JL (Lecture 15) Puzzle 7 due

18 May            Genetic engineering to save nature?! – DE (Lecture 16)

20 May            BYO Microscope (PHONESCOPE) (Demo #8)

 

(Week 9)          (Engineering Health)

23 May            Lecture moved to Wed. May 25

25 May            Human Health in 2030 – JL (Lecture 17)  Puzzle 8 due

27 May            Living Longer; Living Forever? DE (Lecture 18)

 

(Week 10)        (Creative Design, Choices, Humanity)

30 May           Memorial Day - NO CLASS

01 June          Living Material as a Creative Medium – DE (Lecture 19) Puzzle 9 due

Fundamental Concepts & Core Skills

(Week 1)

- Capacities of natural life on Earth


- Existing scope of human-directed bioeconomy

- Matter that mixes and assembles itself

 

(Week 2)

- Deconstructing complicated problems


- How to choose among competing options

- Programmed pattern formation


- Reaction & diffusion systems

 

(Week 3)

- Microbial human anatomy


- Conceptualizing the engineering of biology (Sense, Compute, Actuate, Hack)

- Tools for engineering biology (Abstraction, Standards)

 

(Week 4)

- How atoms can be organized to make molecules

- How DNA has evolved to evolve (i.e., store data)

- How to print DNA from scratch
- Optimizing chemistry for accuracy

 

(Week 5)

- Programming genetic sensors, logic, and actuators


- Mass action kinetics (as applicable to engineering biology)


- Molecular thermodynamics (as applicable to engineering biology)

 

(Week 6)

- Natural diversity & phenotypic plasticity

- Time scale separations


- Integrated systems engineering

 

(Week 7)

- Biology beyond molecules (photons, electrons, etc.)

- Encoding of information in biological systems


- Genetic tools for biological input/output (Bio I/O)

 

(Week 8)

- What is an ecosystem?


- What constraints limit what life can do?

- Where else could we engineer life?


- What else might life look like? Should & can we use genetic engineering to protect natural biodiversity?

 

(Week 9)

- What will be the major human health challenges in 2030?


- What do possible solutions look like?


- Why are we not already pursuing and implementing those – what’s missing?

 

(Week 10)

- How does what we want and need shape bioengineering?


- Who should select, lead, and realize various competing bioengineering futures?