Week 1 HW: Principles and Practices

9th February 2026

Tammy Sisodiya

Figure 1: Diagram of how the biocartridge works

QUESTION 2

I chose ensuring environmental and public health safety (Non-Maleficence) as the governance / policy goal. I defined some subgoals.

Subgoals:

Microbial competition for natural resources like food, space and nutrients due to invasive bacteria entering water bodies, and due to selective, evolutionary advantages such as faster growth and being able to use nutrients efficiently compared to native microbial populations .

Policy requirement: We can use multi-layered biocontainment for bio-cartridges. For example, we can engineer the bacteria to metabolically require a nutrient for their growth and development which is not found in natural water bodies, therefore it will not outgrow and compete with native microbes. We can also use a environmental condition resistant, hydrogel based system to encapsulate the bacteria, ensuring it cannot escape into the water bodies.

Specific metric to assess the policy: If there is no detergent or clothes washing chemicals used, it should automatically trigger the genetic kill-switch which conditionally over expresses the toxic essential gene in toxin-antitoxin systems or activates selective nutrient dependency.

Traceability: We must use DNA barcoding for bacterial species identification. The bacterial strain will have a inoperative genetic sequence which allows regulators to trace bacteria to its manufacturer.

Horizontal gene transfer occurrence - plastic recycling enzyme and antibiotic resistance genes transferring into pathogenic bacteria. The plastic degrading enzymes may, if released, also affect objects composed of PET of importance, such as in dashboards, door panels, engine covers, ignition components, gear housings and connector housings in the automotive industry and in pill bottles, for example, in the pharmaceutical industry.

Policy requirement: We can ensure bacteria do not contain antibiotic resistance genes in their genome which can be evolutionarily selected for horizontal gene transfer.

Specific metric to assess the policy: We can use gene editing technologies like CRISPR-Cas9 to ensure no antibiotic resistance genes remain to be transferred to pathogenic microbes. Policies need to elucidate that PETase’s plastic breakdown ability doesn’t create harmful chemicals which are more toxic than the microplastic.

When I asked Gemini, “What should I measure for governance/policy goals related to ensuring that this application or tool contributes to an ‘ethical’ future for a bacteria coculture based project?” the AI suggested Safety and Biocontainment Metrics, Environmental Justice & Sustainability & Equity and Global Governance (Google, 2026).

3) QUESTION 3

Proposed Governance Action	Aspect	Description & Implementation
Regulating and approving the genetic kill and selective nutrient dependency mechanisms in bacteria (e.g., Synthetic Auxotrophy) Actor: Federal regulators	Purpose	If there is damage or destruction to the bio cartridge causing escape of the microbes, the microbial survival rate can be set at <10−8 (Cell Biology by the Numbers, 2015) to ensure that if an organism escapes, it is highly likely to not survive almost immediately, reducing the biosafety threat to ecosystems.
	Design	Federal regulators will need to approve the: genetic kill switch mechanism with toxin-antitoxin systems to kill bacteria and the gene editing to make engineered PETase plastic degrading bacteria with a metabolic dependency mechanism by selective nutrient dependency.
	Assumptions	We know the microbial composition of our existing water bodies and the nutrient dependencies they have compared to our engineered microbe.
	Risks of Failure & “Success”	Risk: Mutations may occur to avoid selective nutrient dependency gene editing. Success: Manufacturers can identify bacteria they’ve edited compared to natural microbial populations and can understand and control their growth.
Providing an incentive for the sustainable upcycling of bio cartridges Actor: Private companies and device manufacturing companies (Miele, Bosch, Hotpoint)	Purpose	Companies at present that produce filters do not provide incentives for users combined with promoting sustainability measures. Users will receive money off their energy bill or new cartridges when they return old cartridges for commercial sterilisation and nutrient reuse.
	Design	Companies will finance the cartridge returning program, from the user’s home to the bio cartridge manufacturing / sterilising and nutrient reuse depot.
	Assumptions	We can assume users will keep the cartridge until they receive confirmation to return it back instead of disposing in the bin.
	Risks of Failure & “Success”	Risk: High fossil fuel and carbon dioxide emission production from transporting cartridges would exceed the environmental advantageousness of the textile microplastics degradation and byproduct upcycling. Success: Promotes a Circular economy.
Providing the no marker policy for bacteria Actor: Academic researchers	Purpose	Researchers will use gene editing to make a unique short genetic sequence in the engineered bacteria genome to identify it when it escapes by researchers and federal regulators, and we can trace back to the institution where it was produced.
	Design	We will create a database to add all of the engineered bacteria genetic sequences so they can be differentiated and identified as escaped microbes.
	Assumptions & Risks of Failure & “Success”	Assumption: We can assume the unique sequence in the bacterial genome will not mutate over time. Risks of Failure & “Success”: Failure: Selective pressures to remove DNA which does not serve a function in their genome. Success: Chances are the no marker trait may be selectively picked.

QUESTION 4

5) PRIORITIES, TRADE-OFFS, ASSUMPTIONS AND ETHICAL CONCERNS

1 - Our audiences - The audiences are the United Nations Environment Programme (UNEP) Global Plastics Treaty and Industry Consortia. I prioritise regulation and extended producer responsibility (EPR) (OECD, 2001) as a combination of options. Why? Companies do not take liability for the ocean microplastics pollution problem, as it is not owned by anyone solely (regulation). Therefore, EPR gives the incentive to use products like PHA to make other important products like sustainable packaging and agricultural films.

Bio Cartridges once filled can be sent back and with the circular economy approach, the PHA collected can be used for other purposes such as sustainable packaging, agricultural films, medical devices and consumer goods. Therefore, EPR can be used by manufacturers, as if the consumer’s cartridge is full they can send it back for free and can receive a discount for a new bio cartridge. A loyalty program will ensure with 3 uses, that they receive a cartridge for free.

2 - Trade Offs include the cost of buying and receiving new cartridges by transport, transporting old cartridges for cartridge cleaning and reuse and sending back for households with less income.

The bio cartridge if attached to the machine will make the price more expensive. We can mitigate this if we make the bio cartridge addition optional but a recommended action for reducing microplastic pollution. The government may also support with subsidies.

Another tradeoff is the biosecurity risk associated with bacteria like B. subtilis and P. putida being used in the home. We mitigate this by using the immobilisation technique of anchoring the bacteria to a solid cellulose membrane, which increases biosafety and decreases risk of contamination in water bodies in the event the cartridge is damaged/broken.

3 - Assumptions and Uncertainties

Assumptions we make is:

Our PETase enzyme can survive the high alkalinity of detergents in the washing machine, even when optimised in silico. We must also assume users will return bio cartridges back and will not dispose in the bin, as the circular economy approach using P. putidain layer 2 will be missed. The cost of harvesting PHA will far outweigh the cost of cartridge returning, sterilisation and nutrient recycling processes and sending back to the consumer. But we do not know if P. putida will overcome the upcycling ability by mutating over multiple generations.

4 - Ethical concerns we may have

Possibility of microbe leakage in natural water bodies, biocontainment hazard.

Is all microplastic pollution the individual’s responsibility? The cost of using the biocartridge may be a disadvantage to lower income households if not used as an addition and shifts all liability from manufacturers to individuals. Laundry must be affordable for all.

What are the proposed governance actions for these ethical concerns?

We can use genetic kill switches to kill bacteria if grown on a selective nutrient to ensure metabolic dependency on it.
Cartridges are funded by manufacturers to be sent back by consumers and cleaned thoroughly to send back, so the cost is not upon the consumer
Biosafety regulators will ensure all bio cartridges are certified to make sure they are tested for breaking/damage and the non functional DNA watermark is added in the bacterial genome and was added to the DNA barcoding database (is all open source).

Week 2 Lecture Prep

Homework Questions from Professor Jacobson:

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? The error rate of DNA polymerase is between 10^{-4 to 10}-6. The human genome is composed of 3 billion base pairs, and every cell division ends up with 3,000–6,000 mistakes. Biology deals with the discrepancy by allowing 3′→5′ exonuclease activity, which proofreads the DNA for errors and takes off wrong bases straight away. After DNA is replicated, mismatch repair occurs, the freshly replicated DNA is checked for mismatches which have occurred, and will removes the incorrect base, to replace it with the right one.
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? Total variations which are possible with 4 base pairs and 1036 human base pairs = 4^1036.

So log10 (4^{1036) = 1036 * log10 (4)
1036 * 0.60206 = 623.734.
This results in: approx 5.42 * 10}623 possible DNA sequences. Some codons encode for stop codons which terminate the sequence, there may be a hairpin structure which blocks polymerases and the ribosome cannot bind and make any protein. Codon choice may be important for an organism (bacteria and humans use different codons), as if a sequence uses codons for which the cell has few transfer RNAs, the ribosome will stop and produce no protein.

Homework Questions from Dr. LeProust:

What’s the most commonly used method for oligo synthesis currently? The most common method used is solid phase phosphoramidite chemistry.
Why is it difficult to make oligos longer than 200nt via direct synthesis? The quality and the amount of product obtained from the chemical synthesis is poor as the sequence length exceeds longer than 200nt.
Why can’t you make a 2000bp gene via direct oligo synthesis? 2000bp gene is not possible to create via oligo synthesis as it will be error prone, amount obtained will be less and the quality will be reduced. Sequences should be between <150–200 bases.

Homework Question from Prof. Church:

What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency”? Histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine. Mammals cannot directly produce lysine in their bodies and rely on getting lysine from consuming foods such as beef, pork, chicken, fish (cod, sardines), dairy and soy products which contain it, as opposed to what was insinuated in the Lysine Contingency where dinosaurs are genetically modified with the inability to produce lysine (Lopez & Mohiuddin, 2024).

References

Bao, T., Qian, Y., Xin, Y., Collins, J. J., & Lu, T. (2023). Engineering microbial division of labor for plastic upcycling. Nature Communications, 14(1), 5712. https://doi.org/10.1038/s41467-023-40777-x

Cell biology by the numbers. (2015). Garland Science. https://doi.org/10.1201/9780429258770

Federley, R. G., & Romano, L. J. (2010). DNA polymerase: Structural Homology, Conformational Dynamics, and the Effects of Carcinogenic DNA Adducts. Journal of Nucleic Acids, 2010, 457176. https://doi.org/10.4061/2010/457176

Google. (2026). Gemini (Feb 10 version) [Large language model]. https://gemini.google.com

“Kill switch” design strategies for genetically modified organisms | Physical and Life Sciences Directorate. (n.d.). Retrieved 10 February 2026, from https://pls.llnl.gov/article/26016/kill-switch-design-strategies-genetically-modified-organisms

Lopez, M. J., & Mohiuddin, S. S. (2025). Biochemistry, essential amino acids. In StatPearls. StatPearls Publishing. http://www.ncbi.nlm.nih.gov/books/NBK557845/

Microfibres: The plastic in our clothes | Friends of the Earth. (n.d.). Retrieved 10 February 2026, from https://friendsoftheearth.uk/plastics/microfibres-plastic-in-our-clothes

Microfiber filter. (n.d.). PlanetCare. Retrieved 10 February 2026, from https://planetcare.org/pages/microfiber-filter-washing-machine

OECD. (2001). Extended producer responsibility: A guidance manual for governments. OECD. https://doi.org/10.1787/9789264189867-en

Planetcare | the most effective solution to stop microfiber pollution. (n.d.). PlanetCare. Retrieved 10 February 2026, from https://planetcare.org/

Team:Exeter/Hardware—2019.igem.org. (n.d.). Retrieved 10 February 2026, from https://2019.igem.org/Team:Exeter/Hardware

Vassilenko, K., Watkins, M., Chastain, S., Posacka, A., & Ross, P. S. (2019). Me, my clothes and the ocean: The role of textiles in microfiber pollution (Ocean Wise Science Feature). Ocean Wise Conservation Association. https://assets.ctfassets.net/fsquhe7zbn68/4MQ9y89yx4KeyHv9Svynyq/8434de64585e9d2cfbcd3c46627c7a4a/Research_MicrofibersReport_191004-e.pdf

World Health Organization. (2022). Global guidance framework for the responsible use of the life sciences: Mitigating biorisks and governing dual-use research. https://www.who.int/publications/i/item/9789240056107

DNA Animation from LottieFiles: https://lottiefiles.com/free-animation/genetics-iHhxPhbgLp