🧬 Week 1: Principles & Practices

🌊 Biological Engineering Project

Genetically waterproof mycelium surfboards from olive waste.

Prior research: Polyester/pine resin coatings (6-12 months)

HTGAA innovation: CRISPR hydrophobins → permanent waterproofing

📊 Governance Table

Governance Options

Option 1: Regulatory Notification Requirement

Purpose: Currently no specific EU regulation targets mycelium GMM composites for consumer products. Propose mandatory notification to national authority (Hellenic Ministry of Rural Development) before production begins. Design: Manufacturer submits safety dossier; authority reviews within 90 days. Assumptions: Assumes regulatory capacity exists; may underestimate review backlog. Risks: Overregulation could stifle innovation; under-review could miss risks.

Option 2: Open-Source Safety Certification Incentive

Purpose: Incentivize producers to publish biosafety protocols openly in exchange for fast-track certification and reduced liability. Design: EU-funded certification body reviews open-source designs; certified producers get market access priority. Assumptions: Assumes industry willing to share IP; assumes certification body can be funded. Risks: IP concerns may limit participation; certification quality may vary.

Option 3: Technical Containment Standard

Purpose: Require validated thermal inactivation (≥60°C/48h) as a technical standard for all mycelium GMM products before market release. Design: ISO-style standard developed with industry; enforced via product testing. Assumptions: Assumes thermal inactivation is universally applicable. Risks: Some products may require different inactivation methods not covered.

Scoring Table

1 = best, 2 = moderate, 3 = poor

Recommended Governance Approach

A combination of Option 1 + Option 3 is recommended. Mandatory notification ensures regulatory oversight without excessive burden, while a technical thermal inactivation standard provides a clear, measurable safety requirement applicable to all mycelium GMM products.

Audience: Hellenic Ministry of Rural Development and Food + EU Commission DG Health and Food Safety.

Trade-offs: Option 2 (open-source incentive) is desirable long-term but requires industry buy-in that may not exist at early stages. Option 1+3 can be implemented immediately with existing regulatory frameworks.

Uncertainties: Thermal inactivation standards need validation across different mycelium composite formulations.

Ethical Concerns from Week 1

The pipetting lab raised awareness of how even basic lab work requires careful attention to precision and contamination control.

Key ethical concerns for the mycelium surfboard project:

1. Environmental release: Engineered G. lucidum must never be released into natural environments — containment protocols are essential.
2. Skin safety: Hydrophobin SC16 coating on a consumer product requires toxicological testing before market release.
3. Equity: Advanced biotechnology should not remain exclusive to well-funded labs — open-source protocols can democratize access.

Governance action proposed: Establish a community biolab safety protocol for mycelium composite GMM work, modeled on iGEM biosafety guidelines, accessible to all nodes globally.

Week 2 Lecture Prep

Professor Jacobson Questions

1. Error rate of DNA polymerase vs human genome: DNA polymerase has an error rate of ~1 in 10⁷ bases. The human genome is ~3×10⁹ base pairs, meaning ~300 errors per replication cycle. Biology addresses this through proofreading (3’→5’ exonuclease activity) and mismatch repair systems, reducing effective error rate to ~1 in 10¹⁰.

2. Ways to code for an average human protein: An average protein of 300 amino acids could be encoded by ~3×10¹⁴⁸ different DNA sequences (since most amino acids have 2-6 codons). In practice, codon bias (organism-specific preferred codons), RNA secondary structure, and ribosome binding efficiency mean most sequences don’t work equally well.

Dr. LeProust Questions

1. Most commonly used method for oligo synthesis: Phosphoramidite chemistry — sequential addition of protected nucleotides on a solid support, with ~98-99% coupling efficiency per step.

2. Why difficult to make oligos >200nt: Each synthesis step is ~99% efficient. For a 200nt oligo: 0.99²⁰⁰ = ~13% full-length product. At 300nt: ~5%. Errors accumulate multiplicatively, making longer sequences increasingly impure and costly.

3. Why can’t you make a 2000bp gene via direct oligo synthesis: A 2000bp gene would require ~0.99²⁰⁰⁰ = ~2×10⁻⁹ yield — essentially nothing. Instead, shorter overlapping oligos (~60nt) are synthesized and assembled via PCR or ligation into longer genes.

Professor Church Question

Selected: What are the 10 essential amino acids and the Lysine Contingency?

The 10 essential amino acids (cannot be synthesized by humans) are: Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine, and Phenylalanine.

The “Lysine Contingency” refers to the idea that if organisms lost the ability to synthesize Lysine, they would become dependent on dietary sources — creating a vulnerability. This has implications for biosecurity (engineered auxotrophs as containment), agriculture (Lysine-enriched crops), and synthetic biology (orthogonal organisms dependent on non-natural amino acids).