Week 1 HW: Principles and Practices

1. Biological Engineering Application Proposal: “Bio-Filter Moss” — a genetically engineered moss that absorbs heavy metals (lead, mercury) from urban water sources and changes color (green to bright blue) when saturated. Why: To provide low-cost, visible water quality monitoring for communities without access to expensive lab testing.

2. Governance/Policy Goals To ensure an ethical future, the primary goal is Non-malfeasance (Preventing Harm). Sub-goal A (Biosafety): Prevent the moss from escaping into the local ecosystem and becoming an invasive species. Sub-goal B (Security): Ensure the moss cannot be modified by bad actors to create harmful environmental agents and release toxins.

3. Governance Actions I am comparing three different actions (Options) to achieve these goals:

• Option 1: Technical Biocontainment (Genetic Kill-Switch) Purpose: To prevent the moss from spreading outside the designated water treatment areas. Design: Engineer the moss to be auxotrophic, meaning it requires a specific synthetic nutrient (not found in nature) to survive. Assumptions: Assumes the moss won’t evolve to bypass this metabolic dependency through horizontal gene transfer. Risks: Risk of “leaky” expression where the moss survives at low levels, or the cost of the synthetic nutrient makes it too expensive for poor communities.

• Option 2: Regulatory Licensing and “Seed” Tracking Purpose: To control who has access to the modified organism and track its distribution. Design: A government agency (e.g., EPA) requires a permit for deployment. Each batch is “barcoded” with a unique synthetic DNA sequence for traceability. Assumptions: Assumes local authorities have the capacity to monitor and enforce these permits. Risks: Creates a bureaucratic barrier that might slow down the help for communities in need. Risk of a “black market” for the moss.

• Option 3: Open-Source Community Monitoring Protocol Purpose: To empower local users to report performance and any unexpected environmental spread. Design: A mobile app where users upload photos of the moss and GPS coordinates. “Citizen scientists” act as the first line of defense. Assumptions: Assumes users will be motivated to report and have access to smartphones/internet. Risks: Reporting might be inconsistent or inaccurate, leading to a false sense of security.

4. Does the option:	Option 1	Option 2	Option 3
   Enhance Biosecurity
   • By preventing incidents	1	2	3
   • By helping respond	3	1	2
   Foster Lab Safety
   • By preventing incident	1	2	3
   • By helping respond	3	1	2
   Protect the environment
   • By preventing incidents	1	2	3
   • By helping respond	3	2	1
   Other considerations
   • Minimizing costs and burdens to stakeholders	2	3	1
   • Feasibility?	3	1	2
   • Not impede research	2	3	1
   • Promote constructive applications	2	3	1
   —————————————————–	———-	———-	———-

5. Recommendation & Trade-offs: I prioritize Option 1 (Technical Kill-Switch) as the core safety strategy. While it ranks lowest in feasibility and cost due to complex genetic engineering, it provides the only reliable prevention of environmental escape (Rank 1). To balance the high costs and lack of tracking, I recommend combining it with Option 3 (Community Monitoring App). This creates a multi-layered governance system: biological containment for safety, and open-source monitoring for public transparency and rapid response. The main trade-off is the increased R&D cost, which I argue is a necessary investment for ethical environmental deployment.

Audience: This recommendation is directed to the United Nations Environment Programme (UNEP) to serve as a framework for low-cost, bio-based environmental monitoring.

Week 2 Lecture Prep

• Professor Jacobson:

  1. Question: 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? Answer: The intrinsic accuracy of DNA polymerase is approximately 1:10^6 (one error per million base pairs). The human genome is approximately 3.2 Gbp (billion base pairs). This means that without additional correction mechanisms, thousands of mutations would arise with each cell division. Biology solves this problem using proofreading mechanisms (the editing activity of the polymerase itself) and post-replication error correction systems, such as the MutS Repair System. This reduces the resulting error rate to a level that allows the genome to be copied virtually without distortion.
  2. Question: 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? Answer: The average human protein is approximately 345 amino acids long (~1036 bp). Due to the degeneracy of the genetic code (multiple codons per amino acid), the number of DNA sequence variants for a single protein is colossal (on average 3^345 or more). Not all variants are effective because of Secondary Structures (Incorrect sequence can form stable “hairpins” in mRNA that block the ribosome), GC Content (Too high (90%) or low (10%) levels of GC pairs makes synthesis or translation impossible) and codon bias (different organisms prefer different codons; use of rare codons slows down protein synthesis).

• Dr. LeProust:

  1. Question: What’s the most commonly used method for oligo synthesis currently? Answer: The most common method is Phosphoramidite DNA Synthesis
  2. Question: Why is it difficult to make oligos longer than 200nt via direct synthesis? Answer: This is due to the stepwise yield. Even at high efficiency (e.g. 99%), errors accumulate exponentially. For 200 nucleotides, the final yield of pure product becomes critically low (~37% or less), and the number of defective strands is too high.
  3. Question: Why can’t you make a 2000bp gene via direct oligo synthesis? Answer: With chemical synthesis, the error rate is about 1:10². For a 2000 bp fragment, this means that there are guaranteed to be many errors in each molecule. Instead of direct synthesis, such genes are assembled from short oligonucleotides using assembly methods such as Gibson Assembly or Whole Genome Assembly.

• George Church:

  1. Question: What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency”? Answer: Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Leucine, Lysine, Histidine, Arginine. The “Jurassic Park” movie claimed that dinosaurs couldn’t survive in the wild because they were dependent on lysine supplements. However, since lysine is essential for all animals (they can’t synthesize it anyway), this “defense” is meaningless: dinosaurs would have simply obtained lysine from their normal diet (plants or other animals), as all modern species do.