Week 1 HW: Principles and Practices

Assignment (Class - Ethics)

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

• I want to develop a bioengineered architectural substrate that accelerates coral colonization and marine habitat formation on submerged structures. I call this system Reef-Transition Building Skin (RTBS) - a modular “living interface” that can be attached to coastal buildings, seawalls, piles, and pier foundations, biologically tuned to support coral settlement and marine habitat formation once those structures are periodically or permanently submerged. Sea-level rise guarantees that many coastal structures will eventually enter the water, yet most existing hard infrastructure is ecologically sterile or actively harmful. RTBS responds to this reality by operationalizing the idea that architecture can also serve non-human systems. It is based on the idea that architecture should be designed for more than its period of human occupation: structures that serve people today should be capable of transforming into productive marine habitat in the future, so that when they are submerged they contribute to ecological life rather than becoming inert debris or pollution.

2. 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.

• Goal A — Prevent harm to ecosystems and people

  • Avoid invasive impacts: Check local ecological compatibility before deployment to prevent disrupting existing species and habitats.
  • Avoid toxic pollution: Set strict limits on harmful chemicals and materials that could leach into the water.
  • Avoid false ecological claims: Require measurable evidence before projects can claim environmental benefits.

• Goal B — Ensure real ecological benefit

  • Prove habitat improvement: Measure ecological conditions before and after installation to confirm actual gains.
  • Design for local conditions: Adapt structures to each site’s water quality, climate, and wave patterns.
  • Plan for long-term care: Require maintenance and repair plans if systems fail or cause harm.

• Goal C — Support fairness and local control

  • Benefit local communities: Ensure projects create jobs or ecological benefits for nearby residents.
  • Include local decision-making: Involve community stakeholders in design and approval.
  • Share information openly: Publish monitoring results, including failures, not just successes.

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

• Action 1 - Habitat-based permitting rule

  • This action would change coastal permits so projects must help marine ecosystems, not just avoid damage. Regulators would require new seawalls, piers, and coastal structures to show measurable ecological benefit, such as increased coral growth or biodiversity, supported by surveys before construction and monitoring for several years after installation. Independent reviewers would verify results, and projects that fail would need to be repaired or redesigned. This assumes ecological performance can be measured fairly and that communities can support monitoring. The risk is weak enforcement, where monitoring becomes symbolic. Even if it works, developers might focus on easy metrics instead of long-term ecosystem health.

• Action 2 - Eco-material certification standard

  • This action creates a certification system to ensure coastal building materials are safe for marine life. Materials would be tested for toxicity, chemical leaching, and durability, and proven in real-world pilot projects before approval. Certified materials would be labeled and traceable, and public infrastructure projects would prioritize their use. This assumes companies are willing to share information and certification bodies stay independent. The risk is greenwashing if standards are weak. Even success could create problems if certification becomes expensive and excludes smaller producers.

• Action 3 - Financial incentives for transition-ready architecture

  • This action makes ecological coastal design financially attractive. Governments and insurers would provide grants, insurance discounts, and performance-based funding to projects that demonstrate real ecological benefits. Funding would depend on monitoring results and require open data and local job training. This assumes insurers accept ecological performance as reducing risk and that ecosystem benefits can be valued financially. The risk is funding projects that don’t actually help ecosystems. Even if successful, incentives could unintentionally encourage more development in vulnerable coastal areas.

4. 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. 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.

• Based on the scoring, I would prioritize the habitat-based permitting rule as the primary governance action, supported by certification and financial incentives. Permitting is the strongest safeguard because it directly prevents ecological harm and sets enforceable minimum standards. Without a regulatory baseline, certification and incentives risk becoming optional or symbolic. A permitting framework ensures that every coastal project must meet habitat-performance thresholds, making environmental protection non-negotiable rather than market-dependent.

• Certification and incentives still play important supporting roles. Certification reduces uncertainty about material safety, making compliance easier and more consistent, while incentives help offset costs and encourage adoption. However, relying too heavily on financial incentives could unintentionally encourage risky development in vulnerable coastal areas. Permitting acts as the necessary boundary that keeps ecological goals from being undermined by economic pressures.

• The main trade-off is feasibility: strong permitting requires institutional capacity, reliable monitoring, and long-term enforcement. It assumes ecological performance can be measured fairly across diverse sites and that regulators have resources to enforce standards. Uncertainty remains around scaling this system globally and maintaining political support over time. Still, prioritizing permitting creates a stable ethical foundation, with certification and incentives functioning as tools that operate within those ecological limits rather than replacing them.

Assignment (Lab Preparation)

• Complete Lab Specific Training in Person.
• Complete Safety Training in Atlas

Assignment (Your HTGAA Website)

• Personalizing your HTGAA website

Assignment (Week 2 Lecture Prep)

Homework Questions from Professor Jacobson:

1. 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?
   • DNA polymerase makes about one error per 10⁴–10⁵ bases, while the human genome is about 3 × 10⁹ bases long. Cells correct this mismatch through proofreading and mismatch repair, reducing the final mutation rate to roughly one error per genome replication.
2. 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?
   • An average human protein can be encoded by an astronomically large number of DNA sequences because of codon redundancy, roughly 3ᴸ for a protein of length L. Most of these sequences do not work well in practice due to codon bias, unstable mRNA structure, extreme GC content, hidden regulatory motifs, or disrupted translation kinetics.

Homework Questions from Dr. LeProust:

1. What’s the most commonly used method for oligo synthesis currently?
   • The most common oligo synthesis method is solid-phase phosphoramidite chemistry.
2. Why is it difficult to make oligos longer than 200nt via direct synthesis?
   • Oligos longer than about 200 nucleotides are difficult because small stepwise synthesis errors accumulate exponentially with length.
3. Why can’t you make a 2000bp gene via direct oligo synthesis?
   • A 2000 bp gene cannot be made by direct synthesis because yield collapses and errors dominate, so long genes must be assembled from shorter oligos.

Homework Question from George Church:

1. 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 arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. Lysine dependence highlights a potential containment strategy because organisms that cannot synthesize lysine cannot grow without an external supply.