Week 1 HW: Principles and Practices
- First, describe a biological engineering application or tool you want to develop and why.
Engineered bacteriophage as a delivery vector or indicator. Factors such as selective host range, ability to integrate, infection of drug-resistant bacteria, reproducibility, and more would make them a versatile tool.
- 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.
(slightly edited from example framework)
Enhance Biosecurity • By preventing incidents • By helping respond
Foster Lab Safety • By preventing incidents • By helping respond
Protect the environment • By preventing incidents • By helping respond
Ensure Equitable Use • Regulation • Education
- Next, describe at least three different potential governance “actions” by considering the four aspects below (Purpose, Design, Assumptions, Risks of Failure & “Success”).
Considering actors like researchers, industry/corporations, governments and health organizations, manufacturers, and users/general public.
Goals include:
• Education (best practices, use, risks, etc.)
• Guidelines (patenting, manufacturing, use cases, who can buy, development, etc.)
• Monitoring (phage resistance, environmental impact, health impact, logging use, etc.)
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: Education Guidelines Monitoring Enhance Biosecurity • By preventing incidents 2 1 3 • By helping respond 3 2 1 Foster Lab Safety • By preventing incident 1 2 n/a • By helping respond n/a 2 1 Protect the environment • By preventing incidents 2 1 n/a • By helping respond 3 2 1 Ensure Equitable Use • By preventing incidents 2 1 n/a • By helping respond 3 1 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 would prioritize guidelines for industry and manufacturing actors, education for the general public/users and for researchers, and monitoring by governments and health agencies. Preventative measures (guidelines/education) are important to preventing misuse, unequal use, or dangerous impacts, while monitoring and having response plans are important for responding to problems. There needs to be a balance of governance for all actors, with most of my three categories being utilized for each group in different ways.
- Reflecting on what you learned and did in class this week, outline any ethical concerns that arose, especially any that were new to you. Then propose any governance actions you think might be appropriate to address those issues.
Ethical concerns surround the use and possible misuse of synthetic biology. Governance actions in a lot of emerging areas are seen on the research side and health agency sides, but I believe that as use becomes broader, it will be important to have regulation for industry and education for the general public (for example, a lot of people have never heard of phage therapy).
Assignment (Week 2 Lecture Prep)
Homework Questions from 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?
Error rate is 1:10^(6) while the human genome is about 3.2 Gbp. Biology deals with this through error checks and correction methods, including proof reading, redundancy, and cell self-destruction.
- 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?
There are many different ways to code for the same protein due to multiple codons leading to the same amino acid (redundancy). In practice, all of those different codes don’t work or aren’t seen creating the protein due to base pair and tRNA bias in different organisms.
Homework Questions from Dr. LeProust:
- What’s the most commonly used method for oligo synthesis currently?
Solid-phase oligonucleotide synthesis using phosphoramidite chemistry.
- Why is it difficult to make oligos longer than 200nt via direct synthesis?
Due to the accumulation of small errors.
- Why can’t you make a 2000bp gene via direct oligo synthesis?
It is difficult to make oligos longer than 200nt via direct synthesis due to error accumulation.
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”?
The 10 essential amino acids are Arginine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, and Valine. This is interesting for the “Lysine Contingency” since animals cannot synthesize any of these essential amino acids (in high enough quantities), so they have to get them through their diet. Making dinosaurs reliant on external Lysine is just making them like any normal animal.