Project Description The biological engineering technology I would like to develop is a modular cellular biosensor system for agricultural monitoring, based on non-pathogenic cells encapsulated in closed devices that respond to specific chemical signals in soil or environmental samples.
These biosensors are designed to detect indicators such as nutrient imbalance, plant stress, early-stage plant pathogens, or chemical contaminants. Importantly, the cells are not intended to be released into the environment. Instead, they operate within physically contained and biodegradable cartridges or microdevices, producing a measurable output such as a colorimetric, fluorescent, or electrical signal.
Subsections of Homework
Week 1 HW: Principles and Practices
1. Project Description
The biological engineering technology I would like to develop is a modular cellular biosensor system for agricultural monitoring, based on non-pathogenic cells encapsulated in closed devices that respond to specific chemical signals in soil or environmental samples.
These biosensors are designed to detect indicators such as nutrient imbalance, plant stress, early-stage plant pathogens, or chemical contaminants. Importantly, the cells are not intended to be released into the environment. Instead, they operate within physically contained and biodegradable cartridges or microdevices, producing a measurable output such as a colorimetric, fluorescent, or electrical signal.
The goal of this technology is to support more informed and sustainable agricultural decision-making, reducing excessive use of fertilizers and agrochemicals, minimizing environmental damage, and improving crop health—especially in contexts where access to laboratory testing or advanced monitoring infrastructure is limited.
This project is motivated by my interest in applying biological engineering to real-world problems while ensuring that emerging biotechnologies are developed in a safe, ethical, and environmentally responsible manner.
2. Governance / Policy Objectives
Primary Objective
To ensure that the development and deployment of cellular biosensors in agriculture contribute to an ethical, safe, and equitable future, while minimizing risks to human health, ecosystems, and social systems.
Sub-objectives
2.1. Biosecurity and Non-maleficence
Prevent accidental release of living cells into the environment.
Avoid misuse or repurposing of biosensors beyond their intended function.
2.2. Environmental Protection
Ensure that sensor materials and outputs do not introduce toxic residues.
Prevent ecological interference with native soil microbiota.
2.3. Equity and Responsible Access
Enable access for small-scale and resource-limited farmers.
Avoid technological dependence on a small number of proprietary providers.
2.4. Transparency and Accountability
Ensure traceability of design, testing, deployment, and disposal.
Communicate clearly what the biosensor measures—and its limitations.
3. Governance Actions
Opt 1: Mandatory “Encapsulated and Non-replicative” Design Standards
Purpose Currently, agricultural biosensing technologies do not always distinguish between deployable organisms and contained sensing systems. This action would require that cellular biosensors used in agriculture rely on non-replicative cells fully encapsulated in closed systems**.
Opt 3: Technical Strategies for Traceability and Biological Shutoff
Purpose Reduce risks through embedded technical safeguards rather than relying solely on regulation.
Design
Built-in biological shutoff mechanisms activated outside the device.
Lot-based labeling and basic usage records.
Actors: developers, manufacturers, local authorities.
Assumptions and Uncertainties
Assumes correct usage and handling by end users.
Technical reliability under diverse field conditions is uncertain.
Risks
Potential technical failure of shutoff systems.
Increased system complexity and cost.
Does the option:
Option 1
Option 2
Option 3
Enhance Biosecurity
• By preventing incidents
1
2
1
• By helping respond
2
3
1
Foster Lab Safety
1
2
2
• By preventing incident
• By helping respond
Protect the environment
1
2
1
• By preventing incidents
• By helping respond
Other considerations
• Minimizing costs and burdens to stakeholders
3
1
2
• Feasibility?
2
1
2
• Not impede research
3
1
2
• Promote constructive applications
2
1
2
Based on this evaluation, I would prioritize a combination of Option 2 (safe-by-design incentives) and Option 3 (technical safeguards), complemented by minimal baseline requirements from Option 1.
This combined approach:
Encourages innovation without unnecessarily restricting early-stage research.
Integrates ethical considerations directly into technical design.
Is adaptable to agricultural contexts with uneven regulatory capacity.
Target Audiences
Institutional level: universities and research centers.
National level: agricultural and environmental agencies.
International level: sustainable biotechnology consortia.
6. Ethical Reflection
This week’s class highlighted that the risks of biological engineering technologies are not purely technical, but deeply shaped by how they are deployed, interpreted, and governed in real-world contexts.
A new ethical concern for me was recognizing that even “contained” or “passive” biosensing technologies can cause harm if they lead to misinterpretation of data, overconfidence in technological solutions, or exclusion of local knowledge.
To address these concerns, additional governance actions are needed, including:
User training and community engagement.
Clear communication of uncertainty and limitations.
Overall, this assignment reinforced the idea that ethical governance is not an add-on to biological engineering, but a prerequisite for its legitimacy and long-term sustainability.
Lecture 2 – Prep
Jacobson — DNA Replication & Coding
Q1. What is the error rate of DNA polymerase? How does this compare to the length of the human genome? How does biology deal with this discrepancy?
DNA polymerase with proofreading has an error rate of approximately **1 mistake per 10⁶ nucleotides copied**. The human genome is about **3.2 × 10⁹ base pairs** long.
If replication relied only on polymerase accuracy, this would result in thousands of errors per genome replication, which would be incompatible with life.
Biology resolves this discrepancy through multiple layers of error correction:
- Proofreading activity of DNA polymerase (3’→5’ exonuclease).
Mismatch repair systems that correct errors after replication.
Additional DNA repair pathways (base excision repair, nucleotide excision repair, recombination).
Together, these reduce the effective mutation rate to a level compatible with genome stability and evolution.
### Q2. How many different ways are there to code (DNA nucleotide code) for an average human protein? Why don’t all of these codes work in practice?
An average human protein is encoded by ~1036 bp, corresponding to ~345 amino acids. Because the genetic code is degenerate (most amino acids have multiple synonymous codons), the number of possible DNA sequences that could encode the same protein is astronomically large (on the order of 10¹⁷⁰ or more).
However, most of these theoretical codes do not work in practice due to:
Codon bias and tRNA availability, which affect translation speed and accuracy.
mRNA secondary structure, influencing stability and ribosome access.
Unwanted sequence motifs, such as cryptic splice sites, promoters, or polyadenylation signals.
GC/AT extremes, repeats, and hairpins, which interfere with DNA synthesis and assembly.
Protein folding assumptions, since translation kinetics can affect folding outcomes.
Thus, biological and manufacturing constraints dramatically reduce the usable coding space.
LeProust — DNA Synthesis
Q3. What is the most commonly used method for oligo synthesis today?
The most commonly used method is solid-phase phosphoramidite chemical synthesis, where nucleotides are added one at a time in a cyclic process (coupling, capping, oxidation, deprotection).
Q4. Why is it difficult to make oligos longer than ~200 nucleotides by direct synthesis?
Each synthesis step has less than 100% efficiency. As length increases:
Errors accumulate exponentially.
The yield of full-length correct product drops sharply.
Truncations and side reactions become dominant.
As a result, purification becomes impractical beyond ~200 nt.
### Q5. Why can’t you make a 2000 bp gene via direct oligo synthesis?
Direct synthesis of a 2000 bp molecule would require ~2000 consecutive high-efficiency steps, leading to:
Near-zero yield of full-length product.
Extremely high error rates.
Impossible purification.
Instead, long genes are built by assembling many shorter oligos using enzymatic methods (e.g., PCR assembly, Gibson assembly), followed by error correction and sequence verification.
Church — Essential Amino Acids & the Lysine Contingency
Q6. What are the 10 essential amino acids in animals, and how does this affect the “lysine contingency”?
A commonly cited list of 10 essential amino acids in animals is:
Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Threonine
Tryptophan
Valine
Arginine
Because lysine is already essential, animals cannot synthesize it and must obtain it from their diet.
This undermines the idea of the “lysine contingency” as a biocontainment strategy: withholding lysine is ineffective because lysine is widely available in natural ecosystems via food webs and microbes.
Implication: Effective biocontainment must rely on stronger strategies, such as:
Dependence on noncanonical amino acids not found in nature.
Q. [Given slides #2 & #4 (AA:NA and NA:NA codes)] What code would you suggest for AA:AA interactions?
Given that nucleic acids have a simple pairing rule (A=T, C=G) :contentReference[oaicite:0]{index=0} and that biology also uses an AA→tRNA “AARS code” as a mapping layer :contentReference[oaicite:1]{index=1}, I would propose an AA:AA “interaction code” that is not a single fixed pair rule, but a small alphabet of interaction types + a pairing matrix.
A practical AA:AA code should capture the *dominant physical forces* that drive protein structure and binding. I’d encode each amino acid by a short “interaction signature,” then define allowed/strong pairings between signatures (analogous to base-pair compatibility).
1) Define a compact interaction alphabet (example: 6 symbols)
Assign each residue its primary interaction mode(s):
H = Hydrophobic packing (V, L, I, M, A, F, W, Y*)
+ = Cationic (K, R, H*)
− = Anionic (D, E)
D = H-bond donor (K, R, H, N, Q, S, T, Y)
A = H-bond acceptor (D, E, N, Q, S, T, Y, H*)
S = Special covalent/coordination (C for disulfide; H/C/D/E for metal binding)
(*H and Y can be context-dependent; histidine switches charge state, tyrosine is amphipathic.)
Each amino acid can be written as a 2–3 character code, e.g.
Leu = H
Asp = −A
Lys = +D
Asn = DA
Cys = S (and weak H)
2) Define the pairing “grammar” (interaction matrix)
Instead of one-to-one pairs, AA:AA uses a set of preferred pairings:
Hydrophobic core:H ↔ H (packing / van der Waals)
Salt bridges:+ ↔ − (strong, directional at suitable distance)
Hydrogen bonds:D ↔ A (directional geometry; backbone or side-chain)
Aromatic stacking:H(aromatic) ↔ H(aromatic) (π–π; subset of H)
Covalent lock:S(Cys) ↔ S(Cys) (disulfide)
Metal/ligand hubs:S ↔ S and S ↔ (D/A/+/−) (context-specific coordination)
This is conceptually parallel to the slides’ emphasis that biology uses codes and that interactions are a core idea (e.g., “Codes … Interactions”) :contentReference[oaicite:2]{index=2}, but it reflects the reality that protein interactions are multi-constraint (geometry + environment), not a single deterministic pairing like Watson–Crick.
3) Why this code is useful
It is small and learnable (like NA:NA base-pair rules), but expressive enough for AA chemistry.
It supports design and prediction: you can scan a sequence or interface and immediately see what interaction types are “available” and what partners they prefer.
It generalizes to non-standard amino acids (NSAA) by assigning them to the same interaction symbols (or adding one new symbol if truly novel), consistent with the slides’ theme of expanding/engineering codes. :contentReference[oaicite:3]{index=3}