Week 1 HW: Principles and Practices

1. First, describe a biological engineering application or tool you want to develop and why.

I am interested in developing materials that recover over time by mimicking fungal evolutionary conservatism and continuity. I am currently developing a pollen sensor intended to be placed in children’s playgrounds, while simultaneously reading Merlin Sheldrake’s Entangled Life. Together, these are inspiring me to think about design in a different way.

In Entangled Life, Sheldrake describes how certain fungi infect insects, such as ants, causing them to veer off the trajectory of their own evolutionary story and onto the evolutionary path of the fungus. This blurring of where one organism ends and another begins, prompted me to reflect on how can other objects operate in similar ways.

From this, I began to brainstorm how a pollen sensor, a public infrastructure where durability and reparability govern its sustainability and performance, could behave more like a fungus. How might it heal itself? How could it detect air quality and sense its environment without relying solely on electronic monitoring of pollen, carbon, dust, or humidity? What might be gained from infrastructure that is self-regenerative, adaptive, or even slowly evolving into another living organism?

2. Next, 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.

In considering material that recovers especially public infrastructure, some governance that relates are environmental responsibility, ecological integration, public trust and safety standards regarding to public infrastucture utilities.

3. Next, describe at least three different potential governance “actions” by considering the four aspects below (Purpose, Design, Assumptions, Risks of Failure & “Success”).

1. Environmental responsibility

• Purpose: Self-recovering material used in public infrastructure does not introduce harm to surrounding environment and affect original biodiversity.
• Design: Require environmental impact assessments for all materials and define acceptable interactions between the infrastructure and local ecosystems.
• Assumptions: That materials designed to recover or regenerate will affect ecosystems and hence has to be carefully governed.
• Risks of Failure & “Success”:Failure is that the regenerative materials will alter local ecosystems in unpredictable or harmful ways. Success is that regenerative material will improve circularity in resources.

2. Public safety and infrastructure standards compliance

• Purpose: Maintaining public trust by ensuring the material meets established safety stands especially as it begins to repair
• Design: Require regular inspection protocols that account for material change, aging, or regeneration over time. Establish clear thresholds for intervention.
• Assumptions: Public acceptance depends on reliability, when the infrastructure completely regnerates it is well integrated back into nature.
• Risks of Failure & “Success”: Failure is that the material recovery will compromise the structrual integrity and introduce new safety hazards. The success is that the infrastructures remains safe, reliable over a period of time until original functionality is overtaken by new identity.

3. Ecological impact

• Purpose: The public infrastructure with regnerative material operates within ecological limits
• Design: Ensure ecological integration rather than disruption
• Assumptions: The rate of regeneration is influenced greatly and different location to location hence different types of material must be used, not a one size fits all.
• Risks of Failure & “Success”: Success is that the regenerative material will allow ecological compatibilty and creative positive interaction with its surroundings. Failutre is that failed integration between the organisms and their environment.

4. Next, score (from 1-3 with, 1 as the best, or n/a) each of your governance actions against your rubric of policy goals. The following is one framework but feel free to make your own:

5.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. Drawing upon this scoring, I would prioritise priortise Public safety and infrastructure standards compliance because this goverance option addresses the risks associated with materials and installation, it ensures the regulations and compliances are met with industry standards which together contribute and build public trust. Some trades offs are safety may constrain certain material properties where it cannot completely replicate the conservatism or continuity like fungus. Key assumptions are that current safety standards do not yet provide a framework for selfregenerative materials, and there is uncertainty regarding how the materials will behave under rapdily changing conditions.

In preparation for Week 2’s lecture on “DNA Read, Write, and Edit,"

In addition, answer these questions in each faculty member’s section:

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? Error Rate: 1:10¹⁶
   Throughput: 10 mS per Base Addition

Compared to length of human genome 3 x 10⁹ base pairs Biology deal with that discrepency through error correcting gene sythesis.

3. 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? 10¹⁴³ possible DNA sequences, and not all work to code for protein of interest because of codon usage bias and mRNA stability.

Homework Questions from Dr. LeProust:

1. What’s the most commonly used method for oligo synthesis currently? Most common use is each nucleotide addition has a small failure rate (~0.5–1%).
2. Why is it difficult to make oligos longer than 200nt via direct synthesis? It is difficult because loner sequences have more opportunities for incomplete coupling and other chemical damages.
3. Why can’t you make a 2000bp gene via direct oligo synthesis? Direct oligo synthesis only reliably produces ≤200 nt sequences

Homework Question from George Church: [Using Google & Prof. Church’s slide #4] What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency”?

1. Arginine
2. Histidine
3. Isoleucine
4. Leucine
5. Lysine
6. Methionine
7. Phenylalanine
8. Threonine
9. Tryptophan
10. Valine It shows how the Lysine contingency is a noraml universal biologcal contstraint. All aniamsl need certain amino acids from food.