Week 1 HW: Principles and Practices
W̵͈͛ḫ̶͗ą̵̔ṭ̸͌ ̴̩͝c̸̱̊l̶̬̄e̶̡̽a̸̙̚n̵̩͋ ̴̹̌W̷͈̃ả̴̯ẗ̶́ͅè̵͈r̶̲̆ ̵̝͐h̶̲̐ị̶̇ḏ̶͊e̷̼͆s̸̯̎
I would be interested in developing an environmental sensor (such as engineered bacteria) that detects hazardous contaminants like heavy metals (or possibly other pollutants) in water and responds by producing a strong, unpleasant smell. Many forms of modern pollution are dangerous but do not carry clear signs of danger with them. They are invisible, odorless, and difficult to !intuitively! recognize without specialized testing. This creates a disconnect between environmental harm and human perception, where water may appear clean while still being unsafe to consume.
In my idea, I would like to develope a system using engineered bacteria as a living warning interface, with smell as an intuitive signal. When the modified bacteria sense the presence of contaminants like heavy metals, they activate the production of compounds associated (for humans) with decay or spoilage. Instead of explaining risk through data or visual indicators of water quality, the system communicates directly through the sense of smell.
The goal is not to create a precise diagnostic tool, but rather to create an embodied, instinctive response. If the water smells bad, the water is bad!
We have a very power detector implemented in our body. Humans can sense/smell some molecules with a concentration of up to 0.1 ppt. These melocules furthermore get associated them with emotions, body sensations and danger. But recent (mainly human-made) changes to our environment have introduced new harmful components to which our danger-detection-module, aka our nose, has not yet adapted. This project tries to create a tool that makes these otherwise invisible hazards “erfahrbar” (tangible).
By using smell as one of the most immediate and emotionally charged senses, this project tries to reframe synthetic biology as a new tool to make sense of our environment again. We can you organisms so we can communicate with with our surround once again.
(As my background as an artist I would like to create a art-installation with different water veils containing waters of different areas and qualities all looking like drinking water inviting poeple to smell.)
Containment and Control:
Prevent accidental release of genetically engineered bacteria into natural water systems.
• Use of containment strategies (e.g.kill switches that trigger if bacteria leave controlled environments).
• Physical containment measures
• Regulatory oversight requiring testing in controlled environments before any field use!
Human and Ecological Safety:
Ensure that the compounds produced for smell signaling do not harm humans, animals, or microbes.
• Risk assessment of any volatile compounds released.
• Limits on concentration and exposure levels.
• Monitoring for unintended ecological impacts (e.g., affecting local microbial communities or wildlife).
Transparency and Public Trust:
Ensure communities understand the presence and purpose of engineered bacteria in their environment.
• Public disclosure of where, when, and why bacteria are used.
• Clear labeling of water systems using the technology.
• Education campaigns about benefits, risks, and safe interaction
_̸̙͐͑̀́͐̀͠_̸͉̖͊̐̂͛͊̊͋͛͝_̴̧̨̞̖͎̞̆̀͑͝_̷̭̼͇̻̹̣͙̏̀͌_̵̣͉̘͖̦̺̣̼̔̎͗̉̓̚̚_̶͈̮̟͙̾̋̾̈_̶̣̮̟͍̬̣͉͖̒̓̋͆̚_̶͓̀̓_̶̨̥̗̥̭̯̖̐͊͝ͅ_̷̛͓̪̬̗̬̣̣̻̤͑̈̽̓́͝_̴̙͑̏͑̑̂̍_̴͚̥̾̃͗̈́̈̿̎͂_̷̰̦̟̹̩͍́_̸̥͕̏́̽̍̚ͅ_̸̲̬̬̩͑̋̈̆͝_̸̨̰̦̝̺̥͑̈́̌̕_̸̺̭̟̟͈̼̑́̋_̸̺͚̜̣̪̱̳̊̉̃̆͊͌̽͗͝_̴̻̘̲̬̓͋͗͐̊ͅ_̸͙̿̒̌͐͛_̷͎̝̝̮̬̘͆̀_̶̗̪̣͍̞́̒̀̽_̷̨͕̘̥̻͎̬̗̲̃̑̄͌̽̌͘͠_̴̥͆͛́̀̒_̵̡̥͈̺̩̫̊̾̐̒̒́̈̕͘_̶͓̤̮̲̰̳̑̋̆̂̈́̓͌̅͝_̵̛͖̤̿̇͑̓͘͝ͅ_̸̡͎͕͍̳̤̭͖̆̾̈́̿̎͊̕ͅ_̷̛̰̻̌͆͗̍̆͝͠_̷̙̱̯͑̑͒͑̓̽͌̆̚_̷̛̦̾̊̆̓̐̏́_̵̤̣̏̀̄̅͝͝_̸͈̰̹̝̭͔͖̓́̂̃͝_̸̨͓̯̖̜̳͊͜_̷̡̙̰͕̤̠̦̋͜_̵̧̳̬͍͇̱̟̓̋̾̏̈́̾́̚_̸͉͍̭̾͌͊͑̃̋͠_̴̬̪͛̀͆̂̓͠_̷͉̬̺̂́̅̚_̵͙̙̦̑̏͋͗_̶̹͈̼̮̯̾̈̽̀̇̅̿̀̉_̷̡̘͍͓͈͂͛̅͊͐̀͐̒͜͜͜͝_̵̮̰̱͈̖͍̲̼̉̈́̎͗̐_̸̰̠̪͕͊͝_̴̢͖̦̥̖̗̇̐̉̋_̸̢̞̻̣̜͑
Purpose
Currently, water contamination by hazardous substances such as heavy metals is primarily detected through technical, invisible methods: chemical test kits, laboratory analysis, sensors, and regulatory monitoring. These systems are effective but require infrastructure, expertise, time, and most importantly trust in abstract data. For everyday users, contaminated water frequently remains sensory-neutral. It smells, looks and tastes clean while still being unsafe. This project proposes a shift from data-driven warning systems to sensory communication. By engineering bacteria that recognize specific contaminants in water and respond by producing a strong, unpleasant odor, the system acts as a living warning interface. Rather than explaining risk through numbers, labels, or visual indicators, it communicates danger through smell. The proposed change is not to replace existing testing infrastructure, but to add an direct, embodied layer of perception that reconnects environmental risk with human intuition.
Design
Biological Design
• Engineered bacteria capable of sensing specific contaminants
(e.g. heavy metals, toxins, or microbial byproducts)
• Genetic circuits linking detection to the production of unpleasant odor compounds
• Built-in containment strategies
(e.g. kill switches, nutrient dependency, physical encapsulation)
Technical & Contextual Design
• Deployment in controlled environments
(testing vessels, installations, water interfaces rather than open ecosystems)
• Clear sensory thresholds so the smell is noticeable but not harmful
• Systems for safe disposal of contaminated bacterial material
Actors Involved
• Researchers design, test, and validate the sensing and odor-response mechanisms
• Manufacturers produce the engineered bacteria under controlled conditions
• Users (e.g. communities, institutions, artists)
opt in to using the system as a warning tool
• Organizations and regulators approve use cases, set safety standards,
and oversee containment and disposal
• Funders (academic, public, or artistic) support development, testing, and evaluation
Participation must be opt-in, and use would require approval by biosafety and ethics committees.
Assumptions
This project relies on several assumptions that may be incorrect:
• That it is even possible to engineer such a bacteria
(I am an artist and don’t have any experience with synthetic biology)
• That containment systems will fully prevent unintended environmental release
• That smell is universally interpreted as a warning signal
(cultural differences may alter perception)
• That bacteria can be engineered to respond specifically
enough without too many false positives
• That odor production can be strong, stable, and controllable across different environments
• That users will trust sensory feedback over invisible data,
or understand it as a warning rather than contamination itself
Risks of Failure & Success
Risks of Failure
• False alarms could cause unnecessary panic or water avoidance
• Odor production may be too weak, inconsistent, or overwhelming
• Bacteria could die or mutate, reducing reliability
• Containment failure could lead to environmental or regulatory concerns
Risks of Success
• Smell-based warnings could stigmatize certain water sources or communities
• The technology could be misused to intentionally create fear or disruption
• Sensory warning systems might be adopted without adequate regulation due to their simplicity
_̸̙͐͑̀́͐̀͠_̸͉̖͊̐̂͛͊̊͋͛͝_̴̧̨̞̖͎̞̆̀͑͝_̷̭̼͇̻̹̣͙̏̀͌_̵̣͉̘͖̦̺̣̼̔̎͗̉̓̚̚_̶͈̮̟͙̾̋̾̈_̶̣̮̟͍̬̣͉͖̒̓̋͆̚_̶͓̀̓_̶̨̥̗̥̭̯̖̐͊͝ͅ_̷̛͓̪̬̗̬̣̣̻̤͑̈̽̓́͝_̴̙͑̏͑̑̂̍_̴͚̥̾̃͗̈́̈̿̎͂_̷̰̦̟̹̩͍́_̸̥͕̏́̽̍̚ͅ_̸̲̬̬̩͑̋̈̆͝_̸̨̰̦̝̺̥͑̈́̌̕_̸̺̭̟̟͈̼̑́̋_̸̺͚̜̣̪̱̳̊̉̃̆͊͌̽͗͝_̴̻̘̲̬̓͋͗͐̊ͅ_̸͙̿̒̌͐͛_̷͎̝̝̮̬̘͆̀_̶̗̪̣͍̞́̒̀̽_̷̨͕̘̥̻͎̬̗̲̃̑̄͌̽̌͘͠_̴̥͆͛́̀̒_̵̡̥͈̺̩̫̊̾̐̒̒́̈̕͘_̶͓̤̮̲̰̳̑̋̆̂̈́̓͌̅͝_̵̛͖̤̿̇͑̓͘͝ͅ_̸̡͎͕͍̳̤̭͖̆̾̈́̿̎͊̕ͅ_̷̛̰̻̌͆͗̍̆͝͠_̷̙̱̯͑̑͒͑̓̽͌̆̚_̷̛̦̾̊̆̓̐̏́_̵̤̣̏̀̄̅͝͝_̸͈̰̹̝̭͔͖̓́̂̃͝_̸̨͓̯̖̜̳͊͜_̷̡̙̰͕̤̠̦̋͜_̵̧̳̬͍͇̱̟̓̋̾̏̈́̾́̚_̸͉͍̭̾͌͊͑̃̋͠_̴̬̪͛̀͆̂̓͠_̷͉̬̺̂́̅̚_̵͙̙̦̑̏͋͗_̶̹͈̼̮̯̾̈̽̀̇̅̿̀̉_̷̡̘͍͓͈͂͛̅͊͐̀͐̒͜͜͜͝_̵̮̰̱͈̖͍̲̼̉̈́̎͗̐_̸̰̠̪͕͊͝_̴̢͖̦̥̖̗̇̐̉̋_̸̢̞̻̣̜͑
Prioritized Governance Options
The highest priority should be given to Organizations and regulatory bodies as the primary actors for response, particularly in the areas of biosecurity and environmental protection. Because this project involves engineered organisms clear institutional oversight is essential. Regulatory and ethics organizations are best positioned to establish safety standards, define acceptable use cases, and respond to unintended consequences such as misuse, misinterpretation, or containment failure.
At the same time, Researchers should play a central role in monitoring, as they are most capable of evaluating long-term biological behavior and possible ?kill-switches?(I don’t know excactly how and if they are possible). Research institutions are also critical for containment strategies and for openly communicating limitations and uncertainties of the system.
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?
Polymerase error rate: ~1 error per 10⁶ base pairs Human genome size: ~3.2 × 10⁹ base pairs (3.2 Gbp)
This would result in ~3,200 errors per genome replication which would be too many! To deal with it biology work with Error Correcting Polymerase, which lowers the error rate to ~10⁹.
2
The average Average Human Protein is made out of ~ 1036 bp.
With an average of around 3 bp per codon ≈ 333–345 amino acids. Number of DNA sequences≈3^345 different ways.
Changing a codon to a synonymous one often results in a non-functional or misfolded protein.
Homework Questions from Dr. LeProust:
1
The most commonly used method for oligonucleotide synthesis today is solid-phase phosphoramidite synthesis. Typically controlled-pore glass (CPG), carried out in a standard automated 96-well format.
2
Every cycle has an yield less than 100%. The error rate occurs with each synthesis cycle and accumulates exponentially over successive cycles.
3
The error rate ist still at around 1:2000 nt and it scale exponentially! There would be too many errors! :D
Homework Question from George Church:
1
Histidine (H) Isoleucine (I) Leucine (L) Lysine (K) Methionine (M) Phenylalanine (F) Threonine (T) Selenocysteine (U) Tryptophan (W) Valine (V)
It’s possible to engineer organisms that require supplemental lysine to survive. If lysine isn’t supplied, the organism cannot grow. For microbes, lysine dependency can act as a containment mechanism, but only under strict conditions:
• The environment must lack lysine.
• Cross-feeding from other organisms must be prevented.
• Alternative biosynthesis pathways must not evolve.