Week 1 HW: Principles and Practices
Describe a biological engineering application or tool you want to develop and why. One application that might be worth exploring would be in the realm of data storage for an imagined, hypothetical semi-exposed media. For this context special proteins could be designed in applications that bind to sequences that code for hidden malware or faulty sequences and or act for preserving media. I imagine that both this media design and this protein use would be niche but nonetheless fun to design for. Modalities could be as a gentle spray or as a settled solution that could be extracted.
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).
A policy goal to ensure that this application contributes to an ethical future could be ensuring transparent design and standardization of these proteins (and their stats per context) so there is a way to validate their production and application prior to use. This could reduce the chance of bad actors sabotaging batches or distributing lower quality batches.
- Describe at least three different potential governance “actions” by considering the four aspects below (Purpose, Design, Assumptions, Risks of Failure & “Success”)
| Governance Action | Purpose | Design | Assumptions | Failure and Success Risks |
|---|---|---|---|---|
| Standardized Libraries | Educates communities on proteins available and safe designs | Create a library to hold these designs, as well as protocols for their manufacture to spec | That communities will agree on these standards and that there are not unnecessary inequities holding these standards | Success means that manufacture paths are straightforward. Failure means that design paths are too numerous to account for and fragmentation possibilities are higher |
| Blue-teaming Design | To build a community line of protection of designs and applications | Design blue teaming frameworks and recruit educators to practice | That there is sufficient interest for funding | Success means that it is easier for production and share. Failure means that this pipeline has an established line of people who |
| Red-teaming Design | To identify means of sabotaging to proteins to protect libraries and distributors | Design blue-teaming framework and recruit educators to practice | That there is sufficient interest for funding | Success means that it is easier for production and share. Failure means that this pipeline has less visibility on sabotage routes |
- Next, score (from 1-3 with, 1 as the best, or n/a) each of your governance actions against your rubric of policy goals.
| Does the option: | Option 1 | Option 2 | Option 3 |
|---|---|---|---|
| Enhance Biosecurity | 3 | 3 | 3 |
| • By preventing incidents | 3 | 3 | 3 |
| • By helping respond | 3 | 3 | 3 |
| Foster Lab Safety | 3 | 3 | 3 |
| • By preventing incident | 3 | 3 | 3 |
| • By helping respond | 3 | 3 | 3 |
| Protect the environment | 3 | 3 | 3 |
| • By preventing incidents | 3 | 3 | 3 |
| • By helping respond | 3 | 3 | 3 |
| Other considerations | 3 | 3 | 3 |
| • Minimizing costs and burdens to stakeholders | 3 | 2 | 2 |
| • Feasibility? | 3 | 3 | 3 |
| • Not impede research | 3 | 3 | 3 |
| • Promote constructive applications | 3 | 3 | 3 |
- 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 would prioritize library standardization. All operations, from that educators to users, can be facilitated from having a common reference frame. Further, among the options, this appears the most neutral. Overall, proper security requires practitioners from both sides of the spectrum: training in protecting and disrupting systems, and being willing to document for the good of the community.
Homework
Answers for Homework Questions from Professor Jabson:
- Error rate - 1: 10^6. This is dwarfed by the length of the human genome. The body has numerous selectivity and repair mechanisms to deal with mitigate issues from mutations.
- 64 / Some codes might not work due to chemical incompatibility and structural reasons.
Answers for Homework Questions from Dr. LeProust:
- Phosphoramidite DNA Synthesis Cycle
- Increasing inefficiency of reactions with greater length
- Extremely high inefficiency Error rates
Answers for Homework Question from George Church:
- Arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine
I’m still forming my thoughts on how this affects my view of the Lysine Contingency.