Week 1 HW: Principles and Practices

Class Assignment

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

I want to optimize PETase (polyethylene terephthalate hydrolase). PETase is an enzyme that can break down PET plastics, which are widely used in packaging. By optimizing PETase, we can enhance its efficiency in degrading PET and increase its stability under various conditions. This could lead to more effective recycling processes and help reduce plastic pollution.

I plan to use AI models such as ProteinMPNN to propose mutations and test them in the lab.

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.

One governance goal for optimizing PETase is to ensure that the enzyme does not have unintended consequences on the environment or human health, such as producing harmful byproducts.

Possible sub-goals:

• Identify possible byproducts in the lab.
• Test the toxicity of the byproducts.
• Ensure that there are no byproducts that could be harmful to environment and health.

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

• [Option 1] As researchers, we could conduct comprehensive testing of the optimized PETase to identify any potential harmful byproducts and assess their toxicity.

  • Purpose: To ensure that the optimized PETase does not produce harmful byproducts.
  • Design: Conduct experiments to identify all the products produced by the PETase.
  • Assumptions: We know what it looks like when there’s no unexpected byproducts.
  • Risks of Failure: If harmful byproducts are not identified, it could lead to environmental or health issues.
  • Success: The optimized PETase is found to be safe and does not produce harmful byproducts.

• [Option 2] Companies that produce the enzymes should provide detailed information about the enzyme’s properties, including any potential risks and safety measures.

  • Purpose: To sufficiently inform users about the potential risks associated with the enzyme.
  • Design: Disclose information about the enzyme’s properties and potential risks.
  • Assumptions: Companies will comply with the reporting requirements and provide accurate and sufficient information.
  • Risks of Failure: Could lead to mishandling of the enzyme.
  • Success: Users are well-informed about the enzyme and can use it safely.

• [Option 3] Regulators could establish guidelines for safe use and disposal to minimize potential impact.

  • Purpose: To ensure that the enzyme is used and disposed of properly to minimize potential environmental impact.
  • Design: Develop guidelines of best practices for the use and disposal.
  • Assumptions: Users will follow the guidelines.
  • Risks of Failure: If users do not follow the guidelines, it could lead to negative consequences.
  • Success: Environmental and health impact are minimized.

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.

I would prioritize Option 1, because this option is our responsibility as researchers, and it is the most direct way to ensure safety by eliminating risks at the source.

Lab Preparation

• Complete Lab Specific Training in Person.
• Complete Safety Training in Atlas

Week 2 Lecture Prep

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: $1:10^6$

Human genome length: 3.2 Gbp (billion base pairs)

Mechanisms to deal with the discrepancy: proofreading and repairing (MutS)

2. 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?

Average human protein: 345 amino acids. Number of different ways to code: $3^{345}$.

Reasons that not all codes work: codon bias among species and mRNA secondary structure.

Questions from Dr. LeProust

1. What’s the most commonly used method for oligo synthesis currently?

Phosphodiester method.

2. Why is it difficult to make oligos longer than 200nt via direct synthesis?

Because the yield decreases exponentially with length, and the error rate increases with length as well.

3. Why can’t you make a 2000bp gene via direct oligo synthesis?

Because the cumulative error rate would be too high leading to practically zero yield.

Question from George Church

What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency”?

Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Leucine, Lysine, Arginine.

Lysine is essential for protein synthesis and enzyme production, which is critical for survival.

Your HTGAA Website

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