Week 1 HW: Principles and Practices

Question Responses

1. I am highly interested in biologically engineering a type of bacterial that efficiently consumes plastics like polyethylene terephthalate (PET) and converts them to harmless byproducts. I am aware that there already exists some form naturally growing bacteria the does this, however, it is not scalable for large-scale goals. The reason for my interest in engineering such type of bacteria is to at least mitigate the harmful effects of hundreds of millions of tons of plastics that are thrown each year in oceans and landfills, destroying the biosphere in these places and causing some global effects.

2. The main policy to make is to ensure the saftey of this large scale operation by first mandating thorough lab tests and closed containment trials prior to releasing it to the open environment. Secondly, design the bacteria with a built-in safeguard as a kill-switch and hand it to a head comitte as a third party that is its own seperate entity and is resposibile for monitoring the status of the bacteria and initiating the kill-switch when it is deemed necessary.

3. Governance Action 1: Mandatory Genetic Safeguards for Plastic-Degrading Bacteria Actor(s): Academic researchers, biotech companies, funding agencies, regulators Purpose: This action would require all engineered plastic-eating bacteria to include at least one validated containment mechanism before research funding, publication, or deployment. Design: Funding agencies will require safeguard documentation in grant proposals. Institutional Biosafety Committees then verify compliance before approval. Journals require disclosure of safeguards as a condition of publication. Assumptions: We assume that genetic safeguards remain stable over time and that researchers can implement safeguards without major performance loss. Risks of Failure & Success: The proposed safeguards could be lost through mutations or selective pressure and there would be no way of stopping the bacteria.

Governance Action 2: Incentives for Use in Controlled Waste-Processing Facilities Actor(s): Governments, industry, environmental agencies Purpose: This action shifts deployment towards a more controlled settings rather than open ecosystems. Design: Governments offer tax credits or grants for bioreactor-based plastic degradation. Facilities must meet containment and disposal standards, and the environmental agencies will oversee compliance and inspections. Assumptions: We assume that controlled facilities can scale plastic degradation effectively and that it is feasable to provide finantial incentives to drive the growth of this industry. Risks of Failure & Success: High infrastructure costs may limit participation. And usually, countries who have a big issue with landfills, cannot sustain to give incentives at a large scale.

Governance Action 3: Phased Environmental Release Approval Process Actor(s): Federal regulators, environmental agencies, researchers Purpose: This action introduces a standardized, stepwise approval process. Design: Sequential stages: lab testing, then contained field trials, then limited environmental release. Progression requires independent ecological risk review. Long-term monitoring required for post-deployment. Assumptions: We assume that short-term trials can predict long-term ecological effects, and that regulators have sufficient expertise and resources and there are no unpredictable consequences. Risks of Failure & Success: Long-term impacts may emerge after approval. Lengthy approval timelines could delay urgent environmental interventions.

5. I would priortise the 3rd option of staged testing. While, it’s true that the other options are still important and play a role in the feasability of this project. However, this is the only measure that is impelented in the environment and can test the safety of the bacterial and quickly stop it through measures that were prepared prior to thr testing. Because the engineered safeguard could be mutated and stop working causing the bacteria to go rogue, so this is by far the safest and most realistic option that allows us to predict the safety of the bacteria. This recommendation is most relevant for national environmental regulators, such as the Environmental Protection Agency (EPA), because they have the authority and infrastructure to evaluate ecological risk and enforce compliance. Federal funding agencies should also support this framework by requiring phased testing as a condition of research support. The biggest tradeoff to this approach is that a staged approval process may slow deployment. Applying these measures when this industry is still new would harm the opportunity for rapid growth of this industry and severly limit participation due to the tedious required tests. The approach also requires significant regulatory resources and scientific expertise, which may not be equally available across countries. Additionally, since this is practically a new field, there will always be uncertainties about the safety even after tests, because no one witnessed a project of this scale before, so it’s unpredictable especially at first and there has to be long term tests continually done even after the release of the bacterial into the environment to not be blindsighted by something harmful.

One ethical concern that became more apparent this week is the unpredictability of releasing engineered organisms into natural ecosystems. Even when designed for environmental benefit, plastic-eating bacteria could disrupt microbial communities, transfer genes to other organisms, or evolve in unintended ways. Another issue is governance consistency. Regulations for environmental biotechnology vary widely across regions, raising the possibility that research or deployment could shift to areas with weaker oversight. This creates uneven safety standards and increases the chance of poorly monitored releases. To address these concerns, several governance actions would be appropriate. First, regulators should require phased testing before environmental release so that risks can be evaluated in controlled stages. Second, mandatory genetic containment mechanisms should be incorporated into engineered organisms to reduce the likelihood of uncontrolled spread. Third, governments and research institutions should establish standardized reporting systems for environmental incidents to ensure rapid response and shared learning. Finally, international coordination on biotechnology guidelines would help promote consistent safety expectations and reduce regulatory gaps.

HTGAA Website Assignment I personalized my website page, added an image for me, filled a brief describtion of myself, and added my email in my contact info. I learned how to use and properly edit my HTGAA website pages through trial and error.

Week 2 Pre-Lecture HW: DNA Read Write and Edit

Pre-lecture 2 homework questions:

Question 1: 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? Response: The error rate of DNA polymerase varies between 1 in 10^{4 to 1 in 10}5. The length of the human genome is 3 * 10^{9 base pairs, this would mean hundereds of mutations every cell division. However, biology dealt with that discrepancy through proofreading, which decreases the error rate to about 1 in 10}7, along with other correcting methods like mismatch repair, DNA damage checkpoints, and if there is still severe mutation detected, the cell will go into apoptosis.

Question 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? Response: The genetic code is degenerate, meaning multiple codons can encode the same amino acid. With 61 codons specifying 20 amino acids, each amino acid is encoded by about three codons on average. For a typical human protein of roughly 400 amino acids, this results in approximately 3^{400 (about 10}190) possible DNA sequences that could produce the same protein. In practice, many of these sequences do not function effectively. Cells exhibit codon bias, preferring certain codons because the corresponding tRNAs are more abundant, which improves translation efficiency. Some sequences also create mRNA structures that hinder ribosome movement or reduce stability, leading to lower protein production. also, specific nucleotide patterns can unintentionally introduce regulatory signals such as premature stop cues or splice sites. For these reasons, although many DNA sequences are theoretically possible, only a subset will reliably generate the desired protein within a biological system.

Questions from Dr. LeProust:

1. Most commonly used oligo synthesis method? response: The most commonly used oligonucleotide synthesis method is solid-phase phosphoramidite synthesis.
2. Why it’s hard to make oligos >200 nt directly? Response: It is difficult to synthesize oligos longer than about 200 nucleotides because each nucleotide addition is not perfectly efficient. Even with ~99% coupling efficiency, small errors accumulate at every step, causing many strands to be truncated or contain mistakes by the end of the process. Longer sequences also become harder to chemically handle and purify, reducing overall yield and quality.
3. Why you can’t make a 2000 bp gene by direct oligo synthesis? Response: A 2000 bp gene cannot be made directly through oligo synthesis because the stepwise chemical process introduces small errors during each nucleotide addition. As the sequence length increases, these errors accumulate, leading to a very low proportion of full-length, correct DNA strands. The resulting mixture would contain many truncated or incorrect sequences, making purification impractical. Instead, long genes are typically assembled from shorter, high-quality oligos using methods such as PCR or gene assembly.

Question from Dr. George Church: What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency”? Response: The ten essential amino acids in animals are histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine, and arginine (arginine is especially essential during growth). They are considered essential because animals cannot synthesize them in sufficient amounts and must obtain them through diet. This weakens the idea behind a “lysine contingency,” which proposes engineering organisms to depend on lysine so they cannot survive outside controlled environments. Since lysine is already common in many natural environments and diets, relying on it alone would not provide strong containment. An organism could potentially obtain lysine from surrounding biological material, making the safeguard less reliable. Effective biocontainment typically requires dependencies on nutrients that are rare or entirely synthetic rather than widely available amino acids.

Sources used for homework: Google searches and slides for Lecture 2