Week 1 — Principles & Practices

This week lays the foundation for ethics, safety, and governance in biotechnology — and we get hands-on with lab basics.

Homework — DUE BY START OF FEB 10 LECTURE

Documentation

Make sure to document every step of the in-silico and lab experiments. Make sketches, screenshots, notes, drawings - anything that helps you - and others understand the experiment.

Your Documentation should help you - and others - to understand the topic. Don’t be afraid to add things that don’t work. Show your failures - and how you overcame them. Your Documentation should be a description of the amazing journey you are on!

Overview

Ethics, safety, and security are essential considerations throughout (and beyond!) this class. We have therefore designed the Class Assignment this week to give you a strong foundation, and then will ask you to reflect each week and in the design of your final project.

Class Assignment — DUE BY START OF FEB 10 LECTURE

1. First, describe a biological engineering application or tool you want to develop and why. This could be inspired by an idea for your HTGAA class project and/or something for which you are already doing in your research, or something you are just curious about.
2. Next, describe one or more governance/policy goals related to ensuring that this application or tool contributes to an “ethical” future, like ensuring non-malfeasance (preventing harm). Break big goals down into two or more specific sub-goals. Below is one example framework (developed in the context of synthetic genomics) you can choose to use or adapt, or you can develop your own. The example was developed to consider policy goals of ensuring safety and security, alongside other goals, like promoting constructive uses, but you could propose other goals for example, those relating to equity or autonomy.
3. Next, describe at least three different potential governance “actions” by considering the four aspects below (Purpose, Design, Assumptions, Risks of Failure & “Success”). Try to outline a mix of actions (e.g. a new requirement/rule, incentive, or technical strategy) pursued by different “actors” (e.g. academic researchers, companies, federal regulators, law enforcement, etc). Draw upon your existing knowledge and a little additional digging, and feel free to use analogies to other domains (e.g. 3D printing, drones, financial systems, etc.).
   1. Purpose: What is done now and what changes are you proposing?
   2. Design: What is needed to make it “work”? (including the actor(s) involved - who must opt-in, fund, approve, or implement, etc)
   3. Assumptions: What could you have wrong (incorrect assumptions, uncertainties)?
   4. Risks of Failure & “Success”: How might this fail, including any unintended consequences of the “success” of your proposed actions?
4. Next, score (from 1-3 with, 1 as the best, or n/a) each of your governance actions against your rubric of policy goals. The following is one framework but feel free to make your own:

5. Last, drawing upon this scoring, describe which governance option, or combination of options, you would prioritize, and why. Outline any trade-offs you considered as well as assumptions and uncertainties. For this, you can choose one or more relevant audiences for your recommendation, which could range from the very local (e.g. to MIT leadership or Cambridge Mayoral Office) to the national (e.g. to President Biden or the head of a Federal Agency) to the international (e.g. to the United Nations Office of the Secretary-General, or the leadership of a multinational firm or industry consortia). These could also be one of the “actor” groups in your matrix.

Reflecting on what you learned and did in class this week, outline any ethical concerns that arose, especially any that were new to you. Then propose any governance actions you think might be appropriate to address those issues. This should be included on your class page for this week.

Assignment (Final Project) – Due as part of your Final Project presentation (not Feb 10)

As part of your final project, design one or more strategies to ensure that your project, and what it enables, contributes to growing an ethical biological future.

Assignment (Lab Preparation) — DUE BY START OF FEB 10 LECTURE

Lab Training (failure to complete this will jeopardize your acceptance into the course)

• Complete Lab Specific Training in Person.
• Complete Safety Training in Atlas
  • Navigate to atlas.mit.edu and on the right-hand side, click “Learning Center”
  • Head to the Course Catalog and find the following two courses:
    • General Biosafety for Researchers (EHS00260w)
    • Managing Hazardous Waste (EHS00501w)

Assignment (Week 2 Lecture Prep) — DUE BY START OF FEB 10 LECTURE

In preparation for Week 2’s lecture on “DNA Read, Write, and Edit," please review these materials:

1. Lecture 2 slides as posted below.
2. The associated papers that are referenced in those slides.

In addition, answer these questions in each faculty member’s section:

Homework Question from Professor Jacobson:

(To be added soon)

Homework Questions from Dr. LeProust: [Lecture 2 slides]

1. What’s the most commonly used method for oligo synthesis currently?
2. Why is it difficult to make oligos longer than 200nt via direct synthesis?
3. Why can’t you make a 2000bp gene via direct oligo synthesis?

Homework Question from George Church: [Lecture 2 slides]

Choose ONE of the following three questions to answer; and please cite AI prompts or paper citations used, if any.

1. [Using Google & Prof. Church’s slide #4]   What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency”?
2. [Given slides #2 & 4 (AA:NA and NA:NA codes)]   What code would you suggest for AA:AA interactions?
3. [(Advanced students)]   Given the one paragraph abstracts for these real 2026 grant programs sketch a response to one of them or devise one of your own:
   • https://arpa-h.gov/explore-funding/programs/boss
   • https://www.darpa.mil/research/programs/smart-rbc
   • https://www.darpa.mil/research/programs/go

Assignment (Your HTGAA Website) — DUE BY START OF FEB 10 LECTURE

1. Begin personalizing your HTGAA website in in https://edit.htgaa.org/, starting with your homepage — fill in the template with information about yourself, or remove what’s there and make it your own. Be creative!
2. As with all assignments in HTGAA, be sure to write up every part of this Homework on your HTGAA website in order to receive credit.