Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
- A biological engineering application: A biological tool I would like to develop is a sensor for detecting banned pesticides in agriculture. This tool would be low-cost and affordable, readily deployable in the field, and capable of providing reliable results. The sensor would be highly sensitive, able to detect trace levels of pesticides, and would serve as a first-line screening tool to monitor a large number of agricultural plots. 2. Governance/policy goals: This sensor would contribute to the implementation of Peru’s National Policy on Sustainable and Safe Agricultural Production and to efforts to monitor and regulate the use of agricultural pesticides. 3. Potential governance “actions” (AI assistance was used to organize governance concepts) Governance Action 1: Regulatory Screening Requirement There is insufficient monitoring for banned pesticides. A regulatory approach would require field-level screening using low-cost sensors. This assumes that sensors are reliable for screening purposes. Risks include false positives or, if successful, excessive reliance on sensors instead of laboratory verification.
Questions from Professor Jacobson: 1. The polymerase error rate is 10⁻⁶. A mammalian genome is 3,000 Mbp, so in a hypothetical continuous replication of DNA it could result in 3000 mutations. Most of the genome is non-coding, in addition, most replication errors are corrected by polymerase proofreading mechanisms. 2. With four nucleotides in DNA and codons made of triplets of these, there could potentially be 64 combinations to form amino acids. However, there are only 20 amino acids in practice. This is because the genetic code is degenerated, which makes it more robust to mutations. Questions from Dr. LeProust: 1. What’s the most commonly used method for oligo synthesis currently? Phosphoramidite chemistry synthesis. 2. Why is it difficult to make oligos longer than 200nt via direct synthesis? Because of accumulation of errors. 3. Why can’t you make a 2000bp gene via direct oligo synthesis? Because of accumulation of errors. Questions from George Church: The Smart Red Blood Cells (Smart-RBC) project aims to improve the body’s natural capabilities. Since it does not involve human experimentation but only organ prototypes, ethical barriers would not apply. One potential application would be improving performance in low-oxygen environment