Week 1 HW: Principles and Practices

Class Assignment

1. 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.

I would like to develop solid electrolytes based on chitosan for lithium-ion batteries, aiming to enhance ionic conductivity and electrochemical stability while minimizing environmental impact. Chitosan serves as a renewable polymer matrix that can be chemically and structurally tuned to facilitate ion transport and improve mechanical and thermal robustness. This application applies principles of bio-inspired material design to energy storage, with the integration of chitosan targeting the creation of more sustainable and environmentally friendly batteries.

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 - Safety and Harm Prevention

• Minimize thermal and fire risks compared to conventional liquid electrolytes.
• Avoid toxic additives or solvents.
• Ensure long-term stability and safe degradation.

Goal B - Environmental Sustainability

• Prioritize renewable and low-impact materials.
• Assess environmental impacts across synthesis, use, and disposal.
• Design for recyclability and recovery of bio-derived components.

Goal C - Responsible Use and Equitable Access

• Promote responsible use and equitable access to sustainable battery technologies.
• Encourage knowledge sharing across academia, industry, and public sectors.

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

Safety and Performance Standards:

• Establish mandatory testing for ionic conductivity, electrochemical stability, and thermal resistance prior to commercialization.

Sustainability Incentives:

• Provide government support for renewable, bio-derived materials, including lifecycle assessment requirements and fiscal incentives.

Open Collaboration and Data Governance:

• Create shared databases of material properties and failures, reproducible protocols, and interdisciplinary research collaborations.

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 a combined approach of Safety and Performance Standards and Open Collaboration and Data Governance. Safety standards are essential for preventing incidents and ensuring lab and commercialization safety, while open data and collaboration improve incident response and reduce barriers to research. Also, sustainability incentives contribute to long-term environmental goals but are less critical for immediate risk reduction. The main trade-off is higher costs and potential delays from mandatory testing versus greater safety and transparency. This recommendation assumes adequate testing capacity and willingness to share data and is best directed at national-level agencies that can coordinate regulation and data infrastructure effectively.

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, and the human genome is about 3 × 10⁹ bases long. Biology resolves this mismatch through multiple layers of error correction, post-replication mismatch repair systems, and cellular checkpoints that eliminate heavily damaged cells. These reduce the effective error rate, which is low enough to maintain genome stability.

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 due to codon redundancy, approximately 3ᴸ for a protein of length 𝐿. In practice, most of these sequences do not function well because of codon bias, unfavorable mRNA secondary structures, extreme GC content, unintended regulatory motifs, and disrupted translation kinetics.

Homework Questions from Dr. LeProust:

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

The most common method is solid-phase phosphoramidite chemistry.

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

Oligos longer than roughly 200 nucleotides are challenging to synthesize because small, step by step errors build up exponentially as the length increases.

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

2000bp gene cannot be directly synthesized because the efficiency drops and errors accumulate.

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: phenylalanine, histidine, isoleucine, leucine, lysine, methionine, arginine, tryptophan, tryptophan, and valine. The need for lysine offers a possible containment approach, since organisms unable to produce lysine cannot survive without it supplied externally."

Week 1 HW: Principles and Practices