Week 1 HW: Principles and Practices
Describe a biological engineering application or tool you want to develop and why.
I want to engineer a bacteria to produce enzymes to convert plastic and glass wastes to a fertilizer. Microbes secrete extracellular enzymes—such as PETase, MHETase, cutinases, lipases, and esterases—to hydrolyze (break) the chemical bonds of plastics, releasing monomers (e.g., ethylene glycol, terephthalic acid) and oligomers. For glasses (phosphate-based), bacteria such as Bacillus ascheri and Burkholderia eburnea can aid in dissolving and releasing silicon and other plant-growth-promoting nutrients. I want to create a bacteria that can combine these two functions by engineering it to produce enzymes for break down of both plastics and glasses and convert to useful biofertilizers for plants. I want to develop such an organism because both plastic and glass seem to pose serious threats as being non biodegradable for ages.
Describe one or more governance/policy goals related to ensuring that this application or tool contributes to an “ethical” future, like ensuring non-malfeasance (preventing harm). Break big goals down into two or more specific sub-goals.
The main goal to make this enzyme produced by engineered bacteria an ethical and safely managed product with minimal risks to environment,responsible use of it and a proper containment of the engineered organism.
This main goal can be broken down to sub goals: Protect the environment:
- As the product is being created to reduce environmental pollution of plastics and glasses, release of these organisms in the soil should not harm the natural ecosysytem of soil bacteria - prevent horizontal transfer of genes.
- Auxotrophs of the engineered bacteria dependent on unnatural amino acids should be created so that in their absence the bacteria die.
- Farmers should be well informed about the fertilizer created by the bacteria, concentration to be used to prevent any harm to natural ph of the soil while maintaining its fertility.
Responsible and Receptive Approach
- Companies or industries producing the product should meake the information about the product available to the public
- Awareness about the product to the end user (farmer)and government should provide susbsidy to promote the product.
Future Research
- Encourage researchers in the area to innovate better strains to produce an optimised enzyme for production of the fertilizer from such waste.
- Government funding to such projects which aims at decreasing the environmental pollution and giving back useful products to nature.
Next, describe at least three different potential governance “actions” by considering the four aspects below (Purpose, Design, Assumptions, Risks of Failure & “Success”).
1.A new law on the manufacturing of “Fertilizers from plastic waste and glass” should be created Purpose: The main aim of this law would be to involve a regulatory body to check the safety standards of the fertilizers before application to soil- check the amount of contaminants present in the end product, concentration application limits of the fertilizer, safety levels for the end user.
Design: The regulatory body will decide on the threshold levels of the fertilizer used, also the soil ecosystem on which it is applied should not be affected. The government agricultural department should ensure the end user be fully informed about the product. The product should have a quality check inspection before release into the market.
Assumptions: The law is accepted at the same level in all countries.The run off from these fertilizers are assumed to be low in heavy metals.
Risks of Failure and Success: Risks of failures: The end users may not be receptive to the idea of using such fertilizers produced out of waste. Risks of success: The law decreases the burden of plastic waste in landfills and provide a sustainable alternative to chemical fertilizers.
- Government subsidies to farmers using the fertilizer and also incentives to companies Purpose: These strategies will promote the product and also make people aware and be receptive to such sustainable approaches.
Design: The government can conduct awareness camps and demonstrate its application. Tax benefits can be provided to companies that sell these products.
Assumptions: While initial setup requires high capital investment, the government assumes long-term savings in waste management and lower fertilizer costs for farmers.
Risks of Failure & Success: Risks of Failures: Subsidies may be subject to change, and if environmental regulations on microplastics in fertilizer tighten, current products might become non-compliant. Risk of Success: Many startups might adopt these fertilizers quickly without thinking for the benefit of obtaining incentives, without tginking about the long term impacts.
- Handling of the engineered bacteria
Purpose: Proper protocol should be followed to handled these “superbugs”(genetically engineered) to prevent them from mixing with natural biota in the ecosystem.This can lead to creating a pathogen by horizontal gene transfer.
Design: The organisms created should be created as auxotrophs so that in the absence of the desired nutrient kills the microbe. incorporate genes in bacteria that kill it in specific environmental conditions- create a suicidal circuit.
Assumption: It is assumed that the genetic modification does not significantly impair the growth rate or metabolic function of the bacteria, allowing for sufficient yield.
Risks of Failure & Success: Risks of Failures: The engineered genes may be lost or mutated over successive generations, causing the bacteria to lose their intended function or gain unintended traits. Risk of Success:The survival and effectiveness of GEB in the field depend on factors like temperature, pH, and nutrient availability.
| Policies and Action | Biosafety Law | Government Subsidies | Handling GE Bacteria |
|---|---|---|---|
| Protection of environment | |||
| Prevention of environmental hazard | 1 | 3 | 2 |
| Product quality and Safety | 1 | 3 | 2 |
| Responsible and Receptive Approach | |||
| Public awareness | 2 | 1 | n/a |
| Government subsidy | 1 | 2 | n/a |
| Future Research | |||
| R&D for such innovative strains | 2 | 3 | 1 |
| Government funding projects | 2 | 3 | 1 |
| Other considerations | |||
| Minimizing costs and burdens to stakeholders | 3 | 1 | 2 |
| Feasibility? | 2 | 3 | 1 |
| Promote constructive applications | 1 | 3 | 2 |
Last, drawing upon this scoring, describe which governance option, or combination of options, you would prioritize, and why. Outline any trade-offs you considered as well as assumptions and uncertainties.
I think a combiantion of biosafety law o fertilizers made from plastic and glass waste and governemnt subsidies I would prioritize because that would help in the promotion of the new innovative product as well as use it efficiently. The awareness about the product would also make the public receptive towards new technology and adopt sustainable practices.
Here many assumptions are made about the engineered bacteria beinga safe organism which will not be a hazard to the ecosystem and would prevent nutrient leaching and will not undergo mutation in the processto become pathogenic.These uncertainties can be mitigated by some of the methods mentioned above.the handling of the GE bacteria becomes important when you consider the soil ecosystem with its natural organisms. There are also uncertainties regarding process of conversion of fertilizer from plastic and glass waste.
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 typically ranges from 10-4 to 10-6 errors per base pair during initial nucleotide insertion. While proofreading the accuracy improves to 10-7 to 10-8 errors per base pair. The human haploid genome is 3.5 billion base pairs long so roughly 6.3 billion pairs long, so the DNA polymerase has an estimated error rate of 1 error per 109to 1010 nucleotides. Biology has a very efficient way of solving this discrepancy by using proofreading method in (3’- 5’ Exonuclease Activity) and mismatch repair mechanisms.
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?
The standard genetic code uses 64 codons for 20 amino acids and 3 stop signals. Calculation for Average Protein For a 375-amino-acid protein, the total number of coding DNA sequences is the product of codon choices per position: 1×1×29×31×45×63 =3.2 × 10195 So roughly 3374 =10^179.
In reality the codon usage varies from species to species meaning the organism prefers a certain codon over the otehr to produce the same amino acid which is used in protein engineering as codon optimization. Synonymous codon variants often fail to produce functional, equivalent proteins in practice due to cellular biases and kinetic effects during gene expression.
Codon usage bias matches tRNA availability in human cells, so rare codons slow ribosome speed, reducing protein yield. Optimal codons boost expression up to 15-fold, while mismatched ones drop levels dramatically. Codon swaps can change protein structure, solubility, or stability, even if the amino acid sequence stays identical.
Dr.LeProust:
What’s the most commonly used method for oligo synthesis currently? Phosphoramidite solid-phase synthesis is the most commonly used method for oligonucleotide (oligo) synthesis today. This technique builds oligos stepwise on a solid support like controlled pore glass (CPG), adding protected nucleoside phosphoramidite monomers one at a time. Key steps include detritylation (removing the 5’-protecting group), coupling (adding the next nucleotide), oxidation (stabilizing the phosphite linkage), and capping (blocking failed sequences).
Why is it difficult to make oligos longer than 200nt via direct synthesis?
Each nucleotide addition has a coupling yield of about 99%, but errors compound exponentially; a 200-mer requires roughly 200 cycles, dropping full-length product yield below practical levels (e.g., ~36% theoretical at 99% efficiency, far lower in practice). Longer sequences amplify deletions, truncations, and depurination from repetitive harsh cycles (oxidation, capping, deprotection)
Failure sequences (n-1 mers, mutations) dominate output, and no standard method like HPLC or gel electrophoresis resolves the tiny full-length fraction from closely related byproducts.
Longer strands form secondary structures that sterically hinder reagent diffusion and coupling, especially on porous solid supports like CPG, where diffusion slows dramatically.
Why can’t you make a 2000bp gene via direct oligo synthesis?
Deletions, insertions, and substitutions build up rapidly beyond 100-200 nt, as there’s no proofreading like in enzymatic replication. Long sequences form stable hairpins or folds that sterically hinder reagent access and coupling.
Professor Church
What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency”? The 10 amino acids often referenced for many animals (e.g., swine, dogs, rats) are those animals cannot synthesize sufficiently: lysine, methionine, tryptophan, threonine, valine, isoleucine, leucine, arginine, histidine, and phenylalanine.
The lysine contingency refers to a fictional genetic failsafe from the Jurassic Park franchise. In Jurassic Park, geneticist Henry Wu engineered dinosaurs unable to synthesize the essential amino acid lysine, making them dependent on external supplements provided by park staff. Without lysine, the dinosaurs would enter a coma and die, preventing their survival if they escaped Isla Nublar and disrupted ecosystems. Lysine is abundant in nature—found in plants like soy, bacteria, and prey animals—allowing dinosaurs (or any organism) to obtain it through diet. Humans and animals can’t synthesize lysine either but thrive without supplements by eating lysine-rich foods, undermining the contingency’s viability. Lysine is an essential amino acid critical for protein synthesis, collagen formation, and carnitine production, with deficiencies linked to anemia or impaired metabolism. Information coutesy: perplexity pro lysine as essential amino acid and lysine contingency