Week 1 HW: Principles and Practices

Part 1: Class Assignment

1. “The Big Idea”

In the world of Big Farm, nutrient pollution is a big problem, particularly near farms where fertilizers and manure release excess phosphorus and nitrogen into the environment. This leads to issues like eutrophication, dead zones, and human health impacts. This also leads to losses in other industries such as fishing or recreational activity. Paradoxically, we also frequently see cases of nutrient depletion, particularly in the context of agriculture. Monocropping and poor agricultural practices has led to the depletion of topsoil, making it one of the scarcest resources in the world. According to the UN Food and Agricultural Organization, 90% of our world’s topsoil is at risk by 2050. To combat this, I’m interested in seeing if a circular nutrient economy is possible:

A. Capture nitrogen & phosphorus from the water
B. Convert them to stable bioproducts
C. Capsulize them to regenerate soil

Phase 1 would involve pulling the nitrate and phosphate from the environment. There’s plenty of natural phenomenon that I can take inspiratino from in order to do so, but for this aspect I think I would have ot do more research. Some examples I can think of are just creating microbial biofilms on 3D-printed lattices, or mimicking natural filters.

Phase 2 would involve locking this biomass into soil-safe carriers, which would almost certainly involve microbiome engineering as well. Possible options include simple alginate/cellulose pellets, biopolymer beads, mycelium composites or mineralized granules. These would have to be designed to be slow release so that run-off is minimized and we don’t face the issue that inspired this project. One thing to note is that good soil is not just a few nutrients, and requires a balance of other factors, including microorganism diversity and organic matter. It might be possible that the final product is some sort of mixture rather than a homogeneous assortment of pellets.

I believe the development of Phase 2 would increase agricultural diversity across the globe and could also potentially allow for at-home growth in areas where soil generally is not necessarily suitable for doing so. This could reduce traditional lawns and increase area for people to garden in their yards, which is another added benefit for the environment.

2. Governing “The Big Idea”

There are a few goals I would want to target with this project. They can be further broken down into sub-components.

1. Environmental Protection
   The most optimistic outcome of the project is the hope that there is a beneficial environmental impact, and close to no environmental harm. To achieve this, there needs to be a couple of considerations:
   • Adequate testing
     • There should be field pilots and monitoring over multiple seasons before consideration for deployment
   • Protect biodiversity
     • Installation should not affect sensitive habitats, and any scenario where this could occur, impact assessments should be done
   • Chemicals and components used should not pose a risk to the environment
2. Environmental Justice & Transparency
   Potential risks should be addressed prior to the experiment. The project and its applications should also be placed in the correct cultural and social context.
   • Equitable access for all areas
     • Small farms and low-income areas need to be considered. In that case, affordability is also a concern
   • Transparency in historically polluted areas
     • Communities should be consulted on consent and opinions
   • Public reporting of data
   • Post-deployment monitoring
3. Responsible Innovation
   • Phased approvals
   • Liability frameworks
   • Frequent reassesment
   • Adaptive permitting
4. Long-term Sustainability
   • Maintain the circular economy
   • Ensure long-term benefits

3. Potential Actions

Scenario 1: Mandatory Environmental Performance Standards

1. Purpose
   Rather than self-reporting nutrient removal and soil impacts, minimum thresholds should be required with regards to things like nutrient capture efficiency, runoff/leaching rates, carbon footprint, etc.
2. Design
   • Federal & state regulators set standards
   • Companies certify products before sale
   • Universities and other R&D groups test prototypes under common protocols
   • Independent parties audit field trials
     This scenario could be analogous to emissions standards for vehicles
3. Assumptions
   • Metrics are measurable and cheap to do so
   • Lab results translate to real watersheds
   • Regulators can keep up with new designs
4. Risks of Failure & “Success”
   • “Success”:
     • Firms would try to optimize only for regulated metrics, rather than ecosystem complexity
     • Start-ups are crowded out by compliance costs
   • Failure:
     • Innovation is bottlenecked by strict rules
     • Loopholes leads to greenwashing
     • Slow approvals delay overall benefits

Scenario 2: Transparency & Public Accountability

1. Purpose
   There would likely be limited visisbility into field performance, thus it may be possible to create open data platforms and certification schemes that let different members of the community to evaluate systems
2. Design

• Univerities publish standard test protocols
• NGOs run registries
• Firms disclose performance data
• Local governments host dashboards

3. Assumptions

• Transparency will deter bad practice
• Communities are interested in engaging with data
• Transparency puts pressure on firms to improve

4. Risks of Failure & “Success”
   • “Success”:
     • Pressure of reputation stifles experimentation
     • Surveillance burdens small operaors
     • Politicization of environmental metrics
   • Failure:
     • Data mishandling or misinterpretation
     • Firms selectively report
     • Continued public mistrust

Scenario 3: Market-Driven Scaling

1. Purpose
   Nurient recovery would probably struggle economically. To counteract this, there could be subsidies provided, nutrient-credit markets and public procruement to accelerate deployment once systems meet safety threshoulds.
2. Design
   • Governments pay for nutrient removal
   • Farmers get rebates for recycled fertilizers
   • Cities host infrastructure for the capure
   • community boards approve projects
     This system could be analogous to current renewable energy tax credits.
3. Assumptions
   • Price signals will drive adoption
   • Farmers would accept the recyled inputs
   • Monitoring would prevent abuse of the system
4. Risks of Failure & “Success”
   • “Success”:
     • Dependence on incentives
     • Nutrient extraction from ecologically sensitive waters
     • Monoculture of this technology
   • Failure:
     • Gaming of credits
     • Inequitable deployment
     • Political instability

4. Scoring

The following scale is used to score these strategies:

1 = Weak
2 = Moderate
3 = Strong

5. Prioritization

I believe the most important to value here would be the environmental performance standards. It seems that none of the other strategies quite work without solid thresholds and protocols. It also most supports my idea of aligning innovation with environmental protection rather than letting it fall into the hands of the market and the public.

By requiring these thresholds, regulators can ensure these technologies genuinely make a beneficial impact in reducing pollution instead of just shifting risks from waterways to soils or communities.

6. References

https://news.un.org/en/story/2022/07/1123462
https://www.unep.org/news-and-stories/story/five-reasons-why-soil-health-declining-worldwide
https://www.epa.gov/nutrientpollution/sources-and-solutions-agriculture

Part 2: Lab Preparation

I have completed:
A. Lab Specific Training
B. Safety Training in Atlas

Part 3: Week 2 Lecture Prep

1. Questions from Professor Jacobson

Q1: The error rate of polymerase is 1:10^2. Compared to the length of the human genome, this is 300 S per base addition. To deal with this, biology adds quality control steps. For example, proofreading, mismatch repair systems, damage repair pathways and cell-cycle checkpoints. This is necessary to copy the human genome effectively.

Q2: Most amino acids have multiple codons. An average human protein is around ~400 amino acids long (https://bionumbers.hms.harvard.edu/bionumber.aspx?s=n&v=4&id=106445). This means the total number of possible DNA sequences could be on the order of 10^100 or more, so in theory, many different DNA strings could lead to the same amino-acid chain.

In practice, most of these codes don’t work that well because different codon choices can fail or perform poorly for different reasons. Examples could be codon bios, folding effects or other constraints.

2. Questions from Dr. LeProust

Q1: Currently, the most common method for oligo synthesis is: Coupling with phophoramidite –> Capping the unreacted sites –> Oxidizing it –> Deblocking it. In this case, the deblocking step is preparing it for the next nucleotide.

Q2: It is difficult to make longer than 200nt as compounding errors lead to truncated molecules.

Q3: A 2000 bp gene would require 2000 flawless coupling cycles with near-perfect chemistry every time. This involves a lot of effort and this level efficiency is unrealistic. Additionally, this scenario would probably lead to accumulating chemical damage and costs.

3. Questions from George Church

The ten amino acids generally considered essential for animals are arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. Essential amino acids cannot be sufficiently synthesized in an animal’s carbon skeleton, so they must be obtained from diet or symbionts.

The “lysine contingency” is the fact that animals in particular have lost the ability to make lysine. Given that it’s an essential amino acid, it now seems that this may be more of an evolutionary constraint that allows an ecosystems to create reliance between species. Our drive for this amino acid has led to unique agricultural systems and food webs that may not exist if we could produce it. For example, lysine production for animal feed is currently a major industry for optimizing livestock growth. If it were non-essential to animals, this industry may not exist, and we may not feel the need to farm so extensively.

I also wonder if it would be possible that animals have developed into lysine dependent over millions of years, in the sense that it was once possible non-essential. In this case, it would’ve been just a self-imposed evolutionary change.

Reference:
https://www.ncbi.nlm.nih.gov/books/NBK546575/table/glutaric-a1.T.nutritional_requirements_f/
https://www.ncbi.nlm.nih.gov/books/NBK557845/

Part 4: MY HGTAA WEBPAGE

As you can see, I’ve done my best to personalize this page so far. Yippee!