Week 1 HW: Principles and Practices

Describe a biological engineering application or tool you want to develop and why

I want to develop a soft material actuator powered directly by living cells rather than electronics or mechanical pumps. The system would use microbial metabolism, specifically gas produced during fermentation, to generate pressure inside a flexible chamber, allowing the material to inflate and perform mechanical work. Instead of using batteries, compressors, or microcontrollers, the material would respond to environmental conditions such as temperature or moisture because those conditions naturally regulate cellular activity. In this way, the environment becomes the control signal and biology becomes both the energy source and the actuator. If metabolic activity can reliably produce mechanical motion, it opens pathways toward deployable biohybrid interfaces, such as agricultural materials that respond to weather, environmental monitors that operate without batteries, or wearable materials that adapt to the human body. The goal is not to replace traditional machines but to investigate whether biological processes can serve as power, sensing, and control within soft matter systems.

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)

Design the system to fail safely (loss of function, not uncontrolled release) with proper precautions

Ensure transparency about the potential risks involved in the prototype, especially with the use of gas produced

Understand the material lifecycle

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. Biosafety Regulation

• Purpose: Ensuring there’s no uncontrolled release and exposure of cells

• Design, Actors: Biosafety staff, public health agencies, trained researchers

• Assumptions: There will likely be minimal risks in my proposal, but just in case

• Risks: Improper handling, out of control containment of yeast or other actives

2. Education and Trust

• Purpose: Have clear documentation of the work and be transparent about its effects.

• Design, Actors: Conference participation, community outreach/engagement programs

• Assumptions: Educating the public and sharing knowledge would allow for acceptance of living materials

• Risks: Informal attempts to replicate without proper lab set up, misinformation, not enough market adopting the product

3. Sustainability in Design and Environment

• Purpose: Figure out the material lifecycle of the product, whether the biohybrid material actually help to reduce environmental impact or is it creating a new waste stream. How to properly dispose of this? How can we make this material more resilient?

• Design, Actors: Recycling centers, waste systems, manufacturers

• Assumptions: Bio materials are not automatically environmentally friendly

• Risks: May risk creating new class of waste or contaminating the waste stream, materials may degrade faster than ideal in certain environmental conditions

Score (from 1-3 with, 1 as the best, or n/a) each of your governance actions against your rubric of policy goals

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

This was a close scoring, but I would prioritize option 2 (Education & Trust) since communities must be open minded to living materials and we can assume that early engagement can improve long-term adoption and safer use. This is important not only for obtaining data for continuous research and evaluation but also understand the true impact of the system. Prioritizing Education & Trust means relying more on public understanding and voluntary compliance rather than strict control. This can make research participation, feedback, and acceptance easier, but it may reduce enforceability compared to formal regulation. Extensive communication takes time and resources that could otherwise be spent on technical development.

Assignment (Week 2 Lecture Prep)

1. Homework Questions from Professor Jacobson:

• Nature’s machinery for copying DNA is called polymerase. What is the error rate of polymerase? How does this compare to the length of the human genome. How does biology deal with that discrepancy?

Error rate of polymerase is 1:10^6, length of human genome is 3.2 billion base pairs, biology deals with this discrepancy through a repair system (to be cont.)

• How many different ways are there to code (DNA nucleotide code) for an average human protein? In practice what are some of the reasons that all of these different codes don’t work to code for the protein of interest?

2. Homework Questions from Dr. LeProust:

• What’s the most commonly used method for oligo synthesis currently?

Phosphoramidite

• Why is it difficult to make oligos longer than 200nt via direct synthesis?

Depurnification, more prone to error

• Why can’t you make a 2000bp gene via direct oligo synthesis?

It would be difficult to achieve with error rates

3. Homework Question from George Church • What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency”?

The 10 essential amino acids in animals are Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine, Arginine. The takeaway for Lysine Contingency is that animals didn’t reinvent it and that it evolved only after plants and microbes.

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