Syllabus

2023 Spring Quarter 

Monday, Wednesday, & Friday 

Time 1:30-2:20p, Packard 201

To email the entire teaching team please use: <redacted>

STUDENT HOURS

Come chat with us! This is time set aside by the instructors and TAs to work with you. Use it for help on assignments or to ask any questions about bioengineering or anything at all!

Times: <redacted>

The entire teaching team stands with you, ready and eager to help you learn. Should you need assistance outside of regular student hours, please just email the teaching team! We will find time to meet with you (intro_bioe_team@lists.stanford.edu).

COURSE GOALS

Students completing BIOE/ENGR.80 should have a working understanding for how to approach the engineering of living systems to benefit all people and the planet. Our three main goals for the quarter are: (1) to help you learn ways of thinking about engineering living matter, (2) to empower you to understand and practice engineering biology through DNA reading and writing, and (3) for you to become more capable of learning about and discussing bioengineering with others, including broader societal issues and ethical considerations.  

SPRING 2023 SCHEDULE

WEEK 1 -- Bionauts Assemble!  (Literature Parsing; Fermi Estimation)

3 April - Why engineer biology?

5 April - Introduction to bionaut essentials: reading research papers & estimating solutions

7 April - What makes living matter unique?

WEEK 2 -- Improving People Health via Innovation in Medicine (Molecular Structure Analysis)

10 April - Design and production of new small molecule drugs

12 April - How to analyze & design protein-based therapeutics

14 April - Cells as medicines: How living organisms can be used to treat disease

WEEK 3 -- From Diffusion to Programmed Behaviors (DNA Sequence Wrangling; Functional Abstraction)

17 April - Molecular diffusion and spontaneous behaviors

19 April - Genetic control over biological systems

21 April - DNA as a programming language: How to change DNA sequence to alter a living organism's behavior

WEEK 4 -- DNA Reading and Writing (Sequencing and Synthesis Chemistries and Hardware)

24 April - DNA sequencing and synthesis technologies

26 April - How to measure the abundance of other biological molecules (proteins and metabolites)

28 April - Leading through quantitative and qualitative change: Applications of next generation sequencing and synthesis tools

WEEK 5 -- Evolution as a Tool for Engineering (Data Analysis; Directed Evolution; Abstraction reprise)

1 May - DNA mutations: From bug to feature

3 May - Harnessing evolution in the lab: Rationale and methods underpinning directed evolution

5 May - What's a GMO and how will the next generation of GMOs be different?

WEEK 6 -- Improving Planet Health via Innovation in Biodiversity Conservation (Imaging; Computational Inference)

8 May - Tools for seeing biology: A $1 microscope

10 May - What can bioengineers do to help endangered species?

12 May - De-extinction through genetic engineering: how does it work and should we be doing it?

WEEK 7 -- Tackling Cancer & Organ Shortages (Immunology Basics; Bioinks; Dancing Droplets)

15 May - Getting to know your immune system: a primer on human innate and adaptive immunity

16 May - Addressing the organ donor shortage through 3D printing human organs

19 May - Cutting edge therapies that use your immune system to fight cancer

WEEK 8 -- Bioengineering Project Week (Design Thinking)

22 May Project Day 1 (Thing from the Future; Framestorm/Brainstorm)

24 May Project Day 2 (Futures Wheel; Un-naming)

26 May Project Day 3 (Story Spine; Story Telling)

WEEK 9 -- Bioengineering Beyond the Bench

29 May - no class - Memorial Day

31 May - Biosecurity  

2 June - Bioeconomy 

WEEK 10 -- Bioengineering Beyond the Bench and Wrapup

5 June - Bioculture

7 June - Bioengineering Projects Showcase

SPRING 2023 GRADING

Your grade will be based on three components: weekly problem sets, a bioengineering project, and an instructor-evaluated participation grade. The overall grade breakdown is as follows:

Weekly problem sets – 70% total

Weekly problem sets will introduce you to the essential and fundamental skill of reading and interpreting bioengineering papers. You will practice estimating solutions to bioengineering problems and demonstrate proficiency in basic bioengineering skills, such as genetic design, protein structure analysis, and imaging. 

Bioengineering project – 25% total

Each team will design a genetic device to solve a societal need. To help you thoughtfully design and develop your project, we have divided it into specific subtasks which will support the progress of your project from conception, to DNA and experimental design, and reporting of your idea. All assignments are collaborative team assignments with a single submission. 

Instructor/TA assessment of participation, effort, and teamwork – 5%

This score assesses your individual participation in the course. The score incorporates attendance, pre-lecture conceptual questions at the start of each class, and contributions to your team project.

Total course score Letter grade

90-100% A- to A+

80-89% B- to B+

70-79% C- to C+

60-69% D- to D+

<60% NP

LATE POLICY

Late assignments will see a score reduction of 10% each day late up to 5 days, no credit after 5 days. Every student has one 24h extension of an assignment free from score reduction. Please note that you are using your extension in the Canvas assignment comments when the late work is turned in. 

HONOR CODE

We expect you will uphold Stanford’s Honor Code on academic integrity. The honor code articulates university expectations of students and faculty in establishing and maintaining the highest standards in academic work.

1. The Honor Code is an undertaking of the students, individually and collectively:

   • that they will not give or receive aid in examinations; that they will not give or receive un-permitted aid in class work, in preparation of reports, or in any other work that is to be used by the instructor as the basis of grading;

   • that they do their share and take an active part in seeing to it that others as well as themselves uphold the spirit and letter of the Honor Code.

2. The faculty on its part manifests its confidence in the honor of its students by refraining from proctoring examinations and from taking unusual and unreasonable precautions to prevent the forms of dishonesty mentioned above. The faculty will also avoid, as far as practicable, academic procedures that create temptations to violate the Honor Code.

3. While the faculty alone has the right and obligation to set academic requirements, the students and faculty will work together to establish optimal conditions for honorable academic work.

Violations of the Honor Code

Examples of conduct that have been regarded as being in violation of the honor code include:

• Copying from another's examination paper or allowing another to copy from one's own paper

• Unpermitted collaboration

• Plagiarism

• Revising and resubmitting a quiz or exam for regarding, without the instructor's knowledge and consent

• Giving or receiving unpermitted aid on a take-home examination

• Representing as one's own work the work of another

• Giving or receiving aid on an academic assignment under circumstances in which a reasonable person should have known that such aid was not permitted

Observation of Stanford's Honor Code should not impact discussion of course material among peers and with the teaching staff. Discussion and debate is strongly encouraged. All submitted work must be completed individually unless explicitly instructed and noted otherwise.

Repercussions for Violating the Honor Code

In recent years, most student disciplinary cases have involved Honor Code violations; of these, the most frequent arise when a student submits another’s work as their own, or gives or receives unpermitted aid. The standard sanction for a first offense includes a one-quarter suspension from the University and 40 hours of community service. In addition, most faculty members issue a "No Pass" or "No Credit" for the course in which the violation occurred. The standard sanction for multiple violations (e.g. cheating more than once in the same course) is a three-quarter suspension and 40 or more hours of community service.

Common Misconceptions

If asked what constitutes a violation of the Honor Code, most students might say "copying," "cheating" or "plagiarism." As examples, they may think of someone purchasing a paper and submitting it for class, or looking over someone’s shoulder during an exam.

However, some Honor Code concerns are more subtle. They may seem perfectly OK to the person committing violation. They may even be OK in non-academic settings. Unfortunately, merely having benign intentions is not enough. Here are some examples.

LEARNING IN A TIME OF (PARTIAL) CHAOS

It’s not been an easy time and the SARS-CoV-2 pandemic is still ongoing.  We are blessed to be able to learn together this quarter. The teaching team is here with you to enable you to learn as much as you wish. We are also here to listen or help with anything we can.  Please let us know. We are WITH you, not AT you.  

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: 650-723-1066).