Week 1 HW: Principles and Practices

1

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

I would like to develop a biological engineering solution that enables fast-food and beverage chains to produce biodegradable packaging made from their own food waste. The idea is to create a closed-loop system in which organic waste generated by restaurants—such as coffee grounds, food scraps, or plant-based residues—can be processed through bioengineering techniques (such as microbial fermentation, mycelium growth, or biopolymer extraction) and transformed into functional, compostable packaging materials.

My motivation for developing this solution comes from two main concerns. First, many fast-food chains such as McDonald’s, Luckin Coffee, and other takeaway brands still rely heavily on conventional plastic packaging. While plastic is durable, its longevity far exceeds what is actually needed for single-use food packaging, which typically serves its purpose for only minutes or hours. As a result, these materials accumulate in landfills and natural environments, causing long-term pollution. I believe that packaging designed to biodegrade naturally after use would be a more environmentally responsible alternative.

Second, while some existing eco-friendly solutions—such as paper straws or certain plant-based plastics—are already on the market, they often provide a poor user experience. For example, paper straws tend to absorb liquid quickly, become soft, and lose structural integrity, which makes them inconvenient for consumers. Therefore, I aim to develop a hybrid biodegradable material that balances environmental sustainability with practical usability, ensuring that the packaging is both pleasant to use and significantly less harmful to the planet.

Overall, this project would not only reduce plastic waste but also encourage circular use of resources within the food industry, turning waste into valuable materials rather than pollution.

2

Describe one or more governance policy goals related to ensuring this application contributes to an ethical future & prevents harm.

In developing a biodegradable food packaging solution made from restaurant food waste, I believe that strong and thoughtful governance is essential to ensure that this innovation contributes to an ethical future while minimizing potential harm. In particular, I would align my work with three key policy goals: ensuring safety and security, promoting constructive use, and protecting equity and consumer autonomy.

First, with regard to safety and security, my application must align with and operate within existing regulatory frameworks that govern plastic use and food contact materials in China. China has already introduced important policies to limit plastic pollution, such as the “Opinions on Further Strengthening Plastic Pollution Control” issued by the National Development and Reform Commission and the Ministry of Ecology and Environment, as well as the so-called “Plastic Ban Order” (限塑令), which restricts or phases out certain single-use plastic products in the catering and retail sectors. These policies signal a clear national commitment to reducing environmental harm from plastics. My proposed biodegradable packaging should therefore not only comply with these regulations but actively support their goals by offering a viable, lower-impact alternative to conventional plastics.

At the same time, because my solution involves transforming food waste into materials that may directly contact food, a critical governance priority is to ensure strict compliance with food safety standards. In China, food contact materials are regulated under standards such as GB 4806.1 (General Safety Requirements for Food Contact Materials and Articles) and GB 4806.7 (Food Contact Plastics), which define permissible substances, hygiene requirements, and safety testing protocols. A key policy goal for my application would be to establish clear certification pathways, standardized testing procedures, and transparent quality benchmarks so that producers can reliably demonstrate that their materials are safe, non-toxic, and free from harmful contamination. This reduces health risks for consumers and increases trust in innovative, sustainable materials.

Second, in terms of promoting constructive use, governance should encourage the responsible adoption of circular, waste-to-material systems within the food industry. Policies could support pilot programs, technical guidelines, and best-practice frameworks that help restaurants and manufacturers safely process food waste into packaging materials. By making production processes as simple, standardized, and reproducible as possible, governance can lower barriers to adoption while ensuring consistent quality and safety across different producers.

Third, regarding equity and autonomy, it is crucial that consumers have sufficient information to make informed choices. Because packaging derived from food waste may be unfamiliar or even concerning to some people, I believe there should be clear labeling requirements that explain what the material is made of, how it is processed, and how it meets food safety standards. Transparency and traceability empower consumers rather than exposing them to hidden risks. Additionally, governance should consider equity across different businesses: small restaurants and local vendors should receive support—such as subsidies, technical training, or shared processing facilities—so that sustainable packaging is not only accessible to large corporations but can be adopted more broadly across society.

In summary, my application would be guided by governance policies that:

Together, these policy goals would help ensure that my proposed biological engineering application contributes to a safer, more sustainable, and more ethically responsible future.

3

Describe at least three different potential governance actions by considering the purpose, design, assumptions, and risks of failures & “success”

In developing a biodegradable food-waste-derived packaging system for fast-food and beverage businesses, I propose at least three complementary governance actions. Each action addresses different points in the system: production, certification, and consumer engagement. Below, I describe their purpose, design, underlying assumptions, and potential risks of failure or unintended “success.”

Governance Action 1 — Mandatory Food-Waste Collection & Standardized Upcycling Protocols for Large Chains

Purpose — What is done now and what I propose Currently, most restaurant food waste is either discarded as general trash or handled through municipal waste systems, with little incentive for businesses to sort, store, or repurpose it. Even though some chains have adopted paper-based alternatives (e.g., pulp cup holders, paper straws, paper bags), many still rely heavily on plastic packaging, as I observed in my community research with students.

I propose a governance policy requiring large fast-food and coffee chains (e.g., national or regional franchises) to separate and store suitable organic waste streams (such as coffee grounds, plant residues, or food scraps) and follow standardized protocols for safe collection and transfer to approved bio-processing facilities that convert waste into packaging materials.

Design — What is needed to make it work

Actors who must opt in / implement: restaurant chains, third-party waste processors, and certified bio-manufacturers.

Government role: define which waste streams are acceptable, set storage standards (temperature, contamination control), and license approved upcycling facilities.

Funding: could involve a mix of corporate investment and government incentives (e.g., tax reductions or subsidies for participating businesses).

Infrastructure: shared regional processing hubs to reduce the burden on individual restaurants.

Assumptions — What could be wrong

I may be overestimating restaurants’ willingness or capacity to participate; some may see sorting and storing waste as operationally burdensome.

I assume that enough usable food waste can be collected consistently, which may not be true in smaller or less standardized outlets.

I also assume that centralized processing facilities would be economically viable at scale.

Risks of Failure & “Success”

Risk of failure: Restaurants might comply only superficially (minimal sorting, poor quality separation), leading to contaminated inputs that undermine material safety.

Unintended risk of “success”: If demand for “packaging-grade” food waste grows too quickly, businesses might overproduce or prioritize waste generation rather than reduction—similar to how some recycling systems have historically created perverse incentives.

Analogy: This is similar to e-waste or battery recycling mandates, where success depends not just on collection rules but on real downstream processing capacity and quality control.

Governance Action 2 — A Dedicated Food-Contact Certification System for Bio-Derived Packaging

Purpose — What is done now and what I propose Existing food-contact regulations are primarily designed for conventional plastics or paper products. However, materials derived from food waste or biofilms (such as the SCOBY-based biofilm my students and I experimented with) fall into a grey area. In our project, although SCOBY films were highly eco-friendly, users worried about hygiene because of their uneven texture and slight acidity.

I propose a new, dedicated certification category for bio-derived and upcycled food packaging, integrated with existing standards (such as GB 4806.1 and GB 4806.7) but tailored to materials made from biological processes.

Design — What is needed to make it work

Actors involved: government regulators, independent testing laboratories, material scientists, and manufacturers.

Key elements:

Clear definitions of acceptable biological inputs.

Standardized testing for microbial safety, chemical leaching, durability, and user safety.

A visible labeling system (e.g., a “Certified Bio-Upcycled Food Contact Material” mark).

Approval process: materials must pass both lab tests and real-world pilot trials before commercial use.

Assumptions — What could be wrong

I assume that scientific testing can fully capture real-world risks; however, novel materials may behave unpredictably in different temperatures, humidity levels, or food types.

I also assume that certification costs will not be prohibitively expensive for smaller innovators, which may not be realistic without subsidies.

Risks of Failure & “Success”

Risk of failure: If certification is too strict or slow, innovation could be stifled, discouraging companies from developing sustainable alternatives.

Risk of “success”: If certification becomes a marketing tool rather than a meaningful safety benchmark, companies might “greenwash” their products while still producing suboptimal materials—similar to some issues seen with vague “biodegradable” labels in plastics.

Analogy: This is comparable to drone certification or medical device approval—necessary for safety, but potentially slowing innovation if poorly designed.

Governance Action 3 — Consumer Transparency, Labeling, and Public Engagement Program

Purpose — What is done now and what I propose Currently, most consumers have little understanding of what their takeaway packaging is made of, where it comes from, or how it decomposes. Based on my student project interviews, users often reject alternatives like paper straws because of poor experience, and they were even more hesitant about SCOBY-based materials due to perceived hygiene concerns.

I propose a governance action that combines mandatory transparent labeling with public education campaigns about circular materials and responsible consumption.

Design — What is needed to make it work

Actors: government agencies, restaurants, packaging manufacturers, schools, and NGOs.

Key components:

Clear on-package labels explaining:

source of the material (e.g., “made from upcycled food waste”),

biodegradability conditions,

and food-safety certification status.

Public campaigns (e.g., in schools, cafés, and social media) explaining why these materials matter and how to dispose of them properly.

Pilot programs in selected cities to test consumer acceptance before national rollout.

Assumptions — What could be wrong

I assume that better information will lead to more responsible consumer behavior; however, price and convenience may still dominate decisions.

I may also underestimate how skeptical some consumers will remain, even with clear labeling.

Risks of Failure & “Success”

Risk of failure: If labels are too technical or confusing, consumers may ignore them entirely.

Risk of “success”: If awareness rises but affordable alternatives remain limited, consumers could feel frustrated or morally burdened without real choices—similar to debates around ethical fashion or carbon labels in food.

Analogy: This resembles nutrition labeling or carbon labeling in food systems—powerful for awareness, but insufficient without systemic change.

Overall Reflection: What Success Would Mean (and Why It Matters)

If these governance actions work together, I believe the “success” would be more than just reduced plastic waste—it would cultivate a culture where citizens see consumption as a shared responsibility rather than a disposable act. Restaurants would become active participants in circular systems, and consumers would be more mindful of what they use and discard.

At the same time, I recognize that the biggest risks lie in business resistance to additional costs and labor, and potential health or hygiene concerns if bio-derived materials are poorly regulated. Strong, thoughtful governance is therefore essential to balance environmental ambition, practical usability, and public safety.

4

Score each of your governance actions against your rubric of policy goals.

5

Based on scores, describe which governance option or combination of options, you would prioritize, and why.

Based on my scoring and risk assessment, I would prioritize a combined approach in this order:

(1) Food-contact safety certification (Option 2) — first priority. Safety is the prerequisite for adoption. In my student project, even highly eco-friendly materials (e.g., SCOBY-based biofilm) triggered hygiene concerns due to uneven texture and slight acidity, which reduced user trust. A dedicated certification pathway (aligned with standards such as GB 4806.1/GB 4806.7 but tailored to bio-derived materials) would reduce health risks and give restaurants and consumers confidence.

Trade-off: certification can slow innovation and raise compliance costs. Uncertainty: current tests may not fully capture long-term or real-world variability across foods, temperatures, and storage conditions.

(2) Standardized food-waste collection and upcycling protocols for large chains (Option 1) — second priority. Even with safe materials, the system cannot scale without reliable, uncontaminated inputs. However, I see a major risk that restaurants will resist the added labor and logistics of sorting and storing food waste, so incentives and shared processing infrastructure may be necessary.

Trade-off: increased operational burden and cost for businesses. Uncertainty: whether consistent, high-quality waste streams can be collected in everyday operations.

(3) Consumer transparency and labeling (Option 3) — third priority. Labeling and public engagement are essential for autonomy and trust, but they are most effective once safe, scalable products exist. Implemented too early, awareness without affordable options could create frustration rather than adoption.

Trade-off: early transparency may increase skepticism; late transparency may slow trust-building. Uncertainty: how much consumer behavior changes when price and convenience remain dominant.

Overall, I prioritize safety → supply scalability → consumer trust, because failures in safety or supply would undermine the entire system, while consumer education works best when credible alternatives are already available.

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?

The natural DNA replication machinery (DNA polymerases with proofreading) has an extremely low error rate — approximately 1 mistake per 10⁶ to 10⁸ base pairs copied due to both base selection and 3’→5’ exonuclease proofreading.

The human genome is about 3.2 billion base pairs long (≈3.2 × 10⁹ bp).

If polymerase made errors at the high end of ~1 in 10⁶, that would still be thousands of mistakes per whole genome replication. If at ~10⁸, it would be tens of mistakes per genome. Biology deals with this discrepancy through multiple error-correcting and DNA repair systems (proofreading by polymerase and post-replication repair mechanisms) that catch and fix mismatches before they become permanent mutations.

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?

A DNA “codon” is 3 nucleotides long, and there are 4 possible bases (A, T, C, G), giving 4³ = 64 possible codons.

Of these: 61 code for amino acids, 3 are stop signals that terminate translation.

Because there are 20 amino acids, many amino acids are encoded by multiple codons.

So in theory, there are many different ways (often dozens to hundreds) to encode the same amino acid sequence by swapping one codon for a synonymous one. Even though multiple codons can code for the same amino acid:

So while the genetic code is redundant, not all theoretically possible codings are biologically equivalent or work well to produce functional proteins.

Homework Questions from Dr. LeProust

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

The most commonly used method is phosphoramidite solid-phase synthesis.

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

Direct chemical synthesis has stepwise inefficiency:

Each addition cycle isn’t 100% perfect.

Even small inefficiencies compound exponentially over many steps.

If each coupling step is ~99% efficient, then by 200 bases the chance that every step succeeded becomes very low. This leads to a mixture of truncated sequences and errors dominating the product. Hence, oligos longer than ~200 nt become low yield, low purity, and difficult to purify.

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

Errors and truncations accumulate over too many steps — must assemble from shorter oligos

Homework Question from George Church

1. What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency"?

For humans and most animals the amino acids that must be obtained from the diet (because they cannot be synthesized fast enough internally) are: Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine, and (for some definitions) Arginine (especially in young animals).

Because lysine is one of the essential amino acids that animals cannot synthesize on their own, the “Lysine Contingency” highlights a real biological dependency rather than a hypothetical one. It shows that organisms are fundamentally constrained by their metabolic capabilities and must rely on their environment (diet or microbes) for certain critical building blocks, making lysine availability a potential evolutionary and ecological vulnerability.