Week 1 HW.1: Class assignment

1. Describe an application

Identify a biological engineering tool or application you wish to develop and explain your motivation.

I would like to develop a way to make plants grow 100x faster. I find this a very interesting and ambitious question. Perhaps you reverse-engineer the genome, morphological development and constraints, proteins/enzymes/catalysts for growth. Perhaps you design a separate organism (two bacterium?) which produces biomass - a combination of a carbon sequester and a cellulose printer. Perhaps you attempt to design a minimal artificial cell, like a Xenobot / JCVI minimal cells - using new AI design software, you create a minimal genome/DNA, design your own morphological topology through simulation, which is compiled down to gene regulatory networks (GRN’s), transcription factors/thresholds, and DNA.

Why? Because trees and plants are great. They are calming, they look beautiful, they are functionally useful. Originally I wanted to build my own house, and was wondering - why is wood so expensive? If we could grow wood more quickly and effectively, that would be useful. It would also be fun to rapidly green certain areas of the world to produce arable land - the Australian desert, for example.

2. Establish governance goals

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.

• Enhance biosecurity (prevent misuse and uncontrolled spread)

  • Prevent incidents

    • Restrict access to engineered strains, protocols, and enabling tools
    • Use genetic containment (kill-switches, auxotrophy, sterility)
    • Avoid traits that increase invasiveness or persistence outside intended settings

  • Help respond

    • Establish monitoring and reporting systems for unexpected dissemination
    • Maintain traceability (registries, audit logs, chain-of-custody)

• Foster lab safety (reduce accidents during development)

  • Prevent incidents

    • Standard biosafety training and conservative organism/chassis selection
    • Physical containment and phased testing (lab → greenhouse → controlled trials)
    • Explicit evaluation of failure modes in growth and developmental pathways

  • Help respond

    • Clear spill/escape response protocols and emergency shutdown procedures
    • Regular safety reviews and independent oversight

• Protect the environment (minimize ecological externalities)

  • Prevent incidents

    • Ecological risk assessment: gene flow, non-target effects, ecosystem disruption
    • Prohibit open release until long-term impacts are understood
    • Prefer reversible or self-limiting designs over permanent alterations

  • Help respond

    • Post-deployment surveillance and remediation plans
    • Defined liability and responsibility for environmental harms

• Equity, autonomy, and constructive use (ensure benefits are fairly distributed)

  • Minimizing burdens to stakeholders

    • Community consultation for land-use and deployment decisions
    • Avoid shifting risks onto local ecosystems or vulnerable populations

  • Feasibility without blocking research

    • Clear regulatory pathways that enable safe experimentation
    • Transparency and documentation to support responsible scaling

  • Promote beneficial applications

    • Prioritize reforestation, sustainable materials, and climate-positive outcomes
    • Discourage purely extractive or destabilizing commercial deployment

3. Design governance actions

Describe at least three different potential governance “actions” by considering the four aspects below (Purpose, Design, Assumptions, Risks of Failure & “Success”)

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?

1. Containment-by-design + staged release

• Actors: Institutional Biosafety Committees (IBC), national GMO regulators (e.g., OGTR/USDA), lab leads, funders
• Design: engineered sterility/kill-switches, greenhouse-only trials, stepwise permits before field testing
• Assumptions: containment works reliably; lab phenotypes predict outdoor behavior
• Risks: safeguard failure, gene flow, invasive advantage, unexpected ecosystem effects

2. Access control + biosecurity screening

• Actors: DNA synthesis firms, biosecurity agencies, research institutions, grant/journal oversight
• Design: sequence screening, restricted strain distribution, dual-use review processes
• Assumptions: misuse is limited by controlling access to key materials/information
• Risks: leakage, uneven enforcement globally, slowing benign research

3. Environmental monitoring + liability framework

• Actors: environmental agencies, local governments/landholders, independent ecologists, insurers/courts
• Design: required impact studies, long-term surveillance, clear remediation liability
• Assumptions: harms are detectable early and manageable with monitoring
• Risks: underfunded surveillance, delayed ecological damage, liability discouraging deployment

4. Score against rubric

Evaluate each action against objectives including:

• Biosecurity enhancement
• Lab safety
• Environmental protection
• Cost/burden minimization
• Feasibility and research impact

5. Prioritize options

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.

I would prioritise Containment-by-design + staged release. Given that there is immense uncertainty in how this project could be achieved, it is a waste of resources to consider other governance actions for now. Rapid iteration to reduce uncertainty is the path towards achievement. As part of this - a scalable safety protocol throughout this process facilitates rapid experimentation without risk of ruin, until the project can achieve milestones necessary for unlocking funding and revenue.