Week 1 HW: Principles and Practices

Lab Documentation

Pipetting Lab

Objective: Practice accurate pipetting techniques and proper laboratory handling.

Procedure:

• Identified pipettes (P20, P200, P1000) and their volume ranges.
• Set desired volumes and aspirated/dispensed liquids correctly.
• Changed tips between samples to avoid contamination.
• Held pipettes vertically during aspiration and at a slight angle during dispensing.

Challenges and Fixes:

• Initially inconsistent volumes due to air bubbles and hand instability.
• Fixed by slowing plunger release and maintaining steady posture.

Reflection: Accurate pipetting is critical in biological experiments; small mistakes can significantly affect results.

Class Assignment: Ethics, Governance, and Biotechnology

1. Biological Engineering Application

I am interested in developing patient-derived cancer organoids from stem cells to support personalized oncology treatment. These organoids replicate a patient’s tumor properties and can be used to test multiple therapies in vitro before applying them clinically. This approach aims to reduce trial-and-error in cancer treatment, lower side effects, and improve outcomes.

2. Governance and Policy Goals

Primary Goal: Ensure that organoid technologies are used ethically, safely, and equitably.

Sub-goals:

• Protect sensitive genetic data.
• Ensure informed consent for current and future uses.
• Prevent unethical commercialization of patient materials.
• Promote equitable access to treatments.

3. Governance Actions

Option 1: Expanded Informed Consent

Purpose: Patients fully understand long-term use of their organoids. Design: Clear consent forms, IRB oversight, opt-in for secondary research. Assumptions: Patients can understand complex biomedical information. Risks: Consent fatigue; complexity may discourage participation.

Option 2: Genetic Data Governance

Purpose: Protect patient genetic data from misuse. Design: Secure storage, anonymization, restricted access, audits. Assumptions: Institutions maintain strong security systems. Risks: Higher administrative cost; smaller labs may struggle.

Option 3: Regulation of Commercial Use

Purpose: Prevent profit without patient consent. Design: Rules for academic-industry partnerships; transparency in commercialization. Assumptions: Regulations balance ethics and innovation. Risks: Slower translation to clinic; reduced private investment.

5. Recommended Governance Strategy

I recommend combining Option 1 (Expanded Informed Consent) and Option 2 (Genetic Data Governance). This ensures patient protection and ethical use of organoids without impeding research. Option 3 can be selectively applied to prevent unethical commercialization. Audience: academic medical centers, hospital ethics committees, and national health regulators.

Ethical Reflection

Organoids contain personal genetic information, raising privacy and ownership concerns. Ethical responsibility extends beyond technical feasibility. Ensuring proper consent, secure data handling, and equitable access is essential to maintain trust in biotechnological innovation.

Week 2 Lecture Preparation

Professor Jacobson

Polymerase error rate: ~1 error per 10⁹–10¹⁰ nucleotides after proofreading. Human genome size: ~3 × 10⁹ bp. Biological solution: DNA proofreading and mismatch repair mechanisms.

DNA coding variability: Codon redundancy exists, but factors like codon bias, mRNA stability, and translation efficiency limit practical coding options.

Dr. LeProust

Oligo synthesis method: Solid-phase phosphoramidite. Difficulty >200 nt: Accumulated errors and incomplete coupling. Why 2000 bp gene can’t be made directly: Error rate too high; must assemble from shorter oligos.

George Church

Essential amino acids: His, Ile, Leu, Lys, Met, Phe, Thr, Trp, Val (Arg conditionally). Reflection: Essential amino acids highlight vulnerabilities that influence engineering decisions.