Week 1 HW.1: Principles and Practices

1. Describe my biological engineering project

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

I propose to engineer a strain of soil bacteria (likely Bacillus subtilis, a common benign soil bacterium) to act as a “search and sequester” tool for agricultural soil. Heavy metal contamination (like Arsenic and Lead) in soil is a major global issue because plants absorb these toxins, which then end up in our food.

How it works:

• Sensing: The bacteria will be engineered with a biosensor promoter that detects specific heavy metals.
• Reporting: When metal is found, the bacteria will express a colorimetric protein (turning the soil a specific color) to alert farmers of contamination.
• Action: The bacteria will produce “chelating agents” (molecules that bind to metals) to lock the toxins in a form that plant roots cannot absorb, effectively cleaning the soil for crops.

Why: To increase global food safety and reclaim polluted arable land without using harsh chemical washes that destroy soil health.

2. Describe governance/policy 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

Primary Goal: Ecological Non-Malfeasance (Do No Harm)
My overarching goal is to ensure that the introduction of this bacteria cleans the heavy metals without becoming a pollutant itself. The solution must not become a problem by permanently disrupting the native soil microbiome.

Sub-Goals:
To achieve Ecological Non-Malfeasance, we must meet these three specific sub-goals:

1. Ensure Spatiotemporal Containment (Don’t Spread):
   The engineered bacteria must be restricted to the specific geographic area (the contaminated field) and a specific timeframe (the growing season). They must not escape into surrounding ecosystems or persist after the job is done.
2. Prevent Horizontal Gene Transfer (Don’t Share Genes):
   Soil is dense with microbes that swap DNA. We must ensure the synthetic genes (specifically the metal-binding genes and antibiotic resistance markers) do not “jump” from our engineered bacteria to native pathogens, potentially creating “super-bugs.”
3. Enable Traceability & Accountability (Know the Source):
   If an environmental issue arises (e.g., a crop failure in a neighboring field), regulators must be able to definitively prove whether the bacteria was the cause. This ensures accountability and allows for targeted cleanup rather than guessing.

3. Describe governance actions

describe at least three different potential governance “actions” by considering the four aspects below (Purpose, Design, Assumptions, Risks of Failure & “Success”)
Purpose: What is done now and what changes are you proposing?
Design: What is needed to make it “work”? (including the actor(s) involved - who must opt-in, fund, approve, or implement, etc)
Assumptions: What could you have wrong (incorrect assumptions, uncertainties)?
Risks of Failure & “Success”: How might this fail, including any unintended consequences of the “success” of your proposed actions?

Action 1: Mandatory Genetic “Kill Switch” (Technical Governance)
Purpose: Currently, GMOs released into the wild can reproduce indefinitely. I propose mandating that all soil-remediation bacteria must contain a “biocontainment circuit” (kill switch) that causes the bacteria to die once the specific heavy metal is gone or after a set number of cell divisions.
Design:

• Actors: Scientists (must design it), Regulators (must verify it works).
• Mechanism: A genetic circuit that requires a specific synthetic nutrient (not found in nature) to survive (auxotrophy). The farmer sprays this nutrient during treatment. When they stop spraying, the bacteria die.

Assumptions: We assume the kill switch is 100% effective and that evolution will not mutate the bacteria to bypass the switch (escape mutants). Risks of Failure & “Success”:

• Failure: The switch breaks, and the bacteria take over the field, disrupting the nitrogen cycle.
• Success Risk: The bacteria die too quickly before cleaning the soil, wasting money.

Action 2: The “Sandbox” Licensure Model (Policy Governance)
Purpose: Currently, approval is often binary (yes/no). I propose a tiered “Sandbox” approach where the bacteria are approved only for specific, geologically contained test sites before general farm use.
Design:

• Actors: EPA/Environmental Agencies (issuing licenses), Third-party auditors (testing soil run-off).
• Mechanism: A limited license allowing use only on plots of land with physical run-off barriers and no connection to groundwater tables.

Assumptions: We assume that physical barriers can effectively contain microscopic bacteria during heavy rains or floods.

Risks of Failure & “Success”:

• Failure: A flood washes the bacteria out of the sandbox into a local river.
• Success Risk: The regulation is so strict and expensive that only massive corporations can afford to develop the tech, stifling innovation.

Action 3: Genetic Barcoding and Public Registry (Transparency Governance)

Purpose: Currently, if a GMO spreads, it is hard to identify the source. I propose a mandatory unique DNA “watermark” inserted into the bacteria’s genome, registered in a public database.

Design:

• Actors: International Bio-safety Database (host), Biotech companies (submitters).
• Mechanism: A non-coding sequence of DNA that acts like a QR code. If strange bacteria appear in a neighboring farm, a PCR test can identify if it is our bacteria.

Assumptions: We assume that the watermark is stable and won’t be deleted by the bacteria as “junk DNA” over time.

Risks of Failure & “Success”:

• Failure: Bad actors could copy the barcode and use it on illegal releases to frame the company.
• Success Risk: Public knowledge of GMO testing locations might lead to vandalism or anti-science protests that destroy the research.

4. Rubric

1 = best, 3 = least or N/A

Does the option:	Kill Switch	Sandbox	DNA Barcoding
Ecological Non-Malfeasance
• Containment	1	2	3
• Prevents Gene Transfer	2	3	3
• Traceability	3	2	1
Other considerations
• Minimizing costs and burdens to stakeholders	2	3	1
• Feasibility?	2	1	1
• Not impede research	2	3	1
• Constructive Impact	3	2	2

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.

Recommendation:

Reasoning:
While Action 3 (Barcoding) is the easiest to implement and helps with accountability, it is purely reactive—it does nothing to stop an ecological disaster, it only helps you blame someone afterward.

To ensure an ethical future and “Non-malfeasance,” we must rely on Action 1 (Kill Switch) as the primary defense. Biological containment is essential when releasing engineered life into soil, as you cannot “recall” bacteria once they are released. However, because biological systems are prone to mutation and failure, we cannot rely on the kill switch alone.

Therefore, Action 2 (Sandbox Trials) is necessary as a secondary layer of defense. We must test the efficacy of the kill switch in a contained environment (the sandbox) to verify the assumptions (that the switch works and doesn’t mutate) before full agricultural release.

Trade-offs & Uncertainties:
The major trade-off here is Speed vs. Safety. Combining strict biological engineering requirements (kill switches take time to design) with strict physical testing permits (sandboxes take time to approve) will significantly delay the release of the project. This means soil remains polluted for longer. However, the risk of permanently destroying the soil microbiome with an invasive synthetic species outweighs the benefit of rapid deployment. The primary uncertainty remains the “evolutionary stability” of the kill switch over long periods in variable soil conditions.

Week 1 HW.2: Week 2 Preparation

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?

Polymerases have an initial error rate of roughly 1 in 10^4 to 10^5 nucleotides, which is extremely high compared to the ~3 billion 3 * 10^9 base pairs in the human genome. Without correction, this would lead to 100,000+ errors per cell division. Biology manages this through intrinsic proofreading exonucleases (reducing errors to 1 in 10^7 ) and post-replication mismatch repair, resulting in a final, remarkably low mutation rate of approximately 1 in 10^9 to 10^10 per base pair per generation.

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?

• 20 amino acids are encoded by 61 sense codons.
• An average human protein is around ~400 amino acids long.

Assuming each amino acid has ~3 possible codons on average, the number of possible DNA sequences encoding of the same protein is around 3^400 or 10^190

Homework Questions from Dr. LeProust

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

Solid-phase phosphoramidite synthesis. It works by adding one nucleotide at a time in a repeating chemical cycle.

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

Because coupling efficiency is <100% meaning its error will compound over and over. Even with 99% sucess rate, it is still around 13%. This means only ~13% of the final tube is the correct full-length product.

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

Even at 99.5% efficiency per step, the result is still around  ∼0.0045% which is nearly impossible.

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”?

• Arginine, histidine, methionine, isoleucine, leucine, lysine, phenylalanine, threonine, tryptophan, and valine.
• “This forced the dinosaurs to depend on lysine supplements provided by the park’s veterinary staff. In this way, dinosaurs could never escape from the park because they would never survive long without the food supplements.”

from https://jurassicpark.fandom.com/wiki/Lysine_contingency

If negative * negative = positive, then non-synthesizable * non-synthesizable = synthesizable lysine I guess

LLM Prompt:

• calculate coupling efficiency of 2000bp genes (via direct oligo synthesis) and 200nt long oligos

Week 1 HW.3: Setting up Website

https://pages.htgaa.org/2026a/arucha-khematharonon/

Might customize this more soon.

Week 1 Lab: Pipetting

Individual Final Project

Group Final Project