Homework

Weekly homework submissions:

  • Week 1 HW: Principles and Practices

    Does the option: Option 1 Option 2 Option 3 Enhance Biosecurity • By preventing incidents • By helping respond Foster Lab Safety • By preventing incident • By helping respond Protect the environment • By preventing incidents • By helping respond Other considerations • Minimizing costs and burdens to stakeholders • Feasibility? • Not impede research • Promote constructive applications

week-01-hw-principles-and-practices/_index.md

*Final project idea > I cannot see my Individual final project anymore as I probably messed up the code but this is my idea: *

For my final project, I want to build and adapt a bioreactor to grow bacterial cellulose in different shapes and manifestations. In the end, I would like to see if there is any cross-over possible with a desktop spinning machine. Not sure how - but that is what I want to explore.

Inspiration for the bioreactor design: the Innocell bioreactor by Caradt, who built the open-source model of the Design Friction Lab. PhD candidate Emma Sicher (connected to the Innocel project of the Design Friction Lab) focuses on hyperlocal fermentation with scoby cultures, which I want to incorporate as well.

Inspiration for the desktop spinning machine: Lazaro Vasquez, E. et al.(2024) Desktop Biofibers Spinning: An Open-Source Machine for Exploring Biobased Fibers and Their Application Towards Sustainable Smart Textile Design.

Inspiration for applications:

Homework week 1: Governance Policy Goals I looked up governance policy goals in this document: Government of the Netherlands (2025) Government’s vision on biotechnology 2025-2040 to see what kind of ethical future regarding biotechnology the Dutch goverment is endorsing.

My project idea aligns with the Dutch government aim to establish the Netherlands as a global leader in biotechnology by 2040, specifically leveraging it to achieve a climate-neutral, circular economy and sustainable industrial production. The government’s strategy focuses on using industrial biotechnology to substitute fossil-based materials with sustainable biobased alternatives, such as textiles and high-quality secondary raw materials. To support this, the government is committed to creating a resilient, forward-looking regulatory framework that reduces administrative burdens while ensuring high standards for human, animal, and environmental safety.[based on introduction text in document].

Zooming in, my project addresses the governance policy goals outlined in the document in the following ways: [overview made with Gemini - prompt: **can you summarise the governance policy goals related to ensuring this application -my project idea- contributes to an ethical future & prevents harm. Assessment is my own.]

Governance Policy Goals
1. Ensure Safety & Security
Adherence to the Precautionary Principle: The government emphasizes that actions should not be taken if there is a real possibility of harm to human health or the environment, even without full scientific certainty.Bacterial cellulose is non-toxic, can have anti-bacterial properties, wound healing properties, decomposes naturally, and is relatively safe. The bioreactor functions as an extended controlled environment.
Biosafety and Biosecurity Preconditions: Biotechnology must be developed and used safely, considering both the safety of people, animals, and the environment (biosafety) and national security interests (biosecurity).The production of bacterial cellulose can be done in safe conditions, e.g. food and beverages such as nata de coco, kombucha.
Mitigation of Dual-Use Risks: Policy goals include increasing resilience against the misuse of biological capabilities by malicious parties, such as the creation of pathogens or the theft of sensitive data.open-source project, building on open source data, widely available cultures, old knowledge and techniques.
Safe and Sustainable by Design (SSbD): A key goal is to ensure that safety and sustainability are integrated right from the design stage of an innovation to reduce the need for risk management later on.Biosafety protocols are followed, risk assessment is executed, I work with locally available cultures.
2. Promote Constructive Uses
Contribution to Societal Goals: Innovations are steered toward achieving the United Nations’ Sustainable Development Goals (SDGs), focusing on health, a circular economy, and sustainable food production.Contributes directly to circular economy, sustainable food production.
High-Standard Circularity: For applications like bio-based materials, a primary goal is to use industrial biotechnology to substitute fossil raw materials and process them into high-quality secondary products.Project focuses on developing bio-based materials, incorporates scaling up metrics and is geared towards high-quality secondary products.
Transdisciplinary Research: To ensure practical and social relevance, the government promotes research where industry, civil society, and end-users collaborate to solve societal challenges.By incorporating hyperlocal cultures, the project ensures that societal challenges are adressed on a local and immediate level.
3. Promote Equity & Autonomy
Justice and Fair Distribution: A fundamental principle is that the costs and benefits of biotechnology must be shared fairly across society, ensuring applications promote wellbeing regardless of socioeconomic position.By focusing on hyperlocal cultures and ingredients, the projects is not dependent on global production chains of tea.
Freedom of Choice: Especially regarding genetically modified products, the government aims to ensure the public can choose between modified and non-modified products through mechanisms like transparent labeling.Not directly applicable, needs to be further assessed.
Public Engagement and Legitimacy: Policy goals include involving the public in dialogues to understand their concerns, expectations, and values (like “naturalness”) to ensure technological developments have broad social support.The design of the reactor and the involvement of others in hyperlocal cultures ensured public engagement and dialogue on the legitimacy of working with this material.
Open Strategic Autonomy: By reducing high-risk strategic dependencies on foreign actors for critical technologies, the government aims to ensure the Netherlands and Europe maintain their own capacity for innovation and decision-making.Is accounted in the culture, needs to be critically assessed in the materials needed to built the tools - e.g. through a thorough Bill of Materials
PurposeDesignAssumptionsRisks of Failure & “Success”
What is done now and what changes are you proposing?What is needed to make it “work”?What could you have wrong?How might this fail, including any unintended consequences of the “success” of your proposed actions?
Lot of research, scattered from academic, grassroots, industrial. Image of bacterial cellulose for students is not very appealing. By focusing on manipulating properties and tools that have a clear link to application domains, I aim to make working with bacterial cellulose more interesting for students.Clear demonstrator in a research product and a business case. A good design of the bioreactor will be essential to convince design students.Societal acceptance and student’s willingness to work with a safe bacteria. I could also be wrong in my assumption that this is a relatively beginner-friendly culture to work with.As a pedagogical project, it fails if students don’t see the relevance of learning to work with a bioreactor or with a nano-cellulose growing culture, but only see a sour-smelling slimy pellicle on a acidic drink. Succes factors would be if students spontaneously start to build their own bioreactors modified for their project’s purpose.

Ethical concerns that arose + proposed governance actions

  • Juxtaposition between hyperlocal cultures and dependency on global materials - look for circular, local, regenerative materials or building principles.
  • Public Engagement and Legitimacy - make sure the project has relevance beyond the lab space, actively consider how societal transitions can be linked (agriculture, food, bioeconomy)
  • Mechanistic worldview on more-than-human collaboration - critically question paradigms of production and decision-making.

week-02-hw-dna-read-write-and-edit/_index.md

**Preparatory homework for week 2 **

Homework Questions from Professor Jacobson: [Lecture 2 slides]

  1. Nature’s machinery for copying DNA is called polymerase. What is the error rate of polymerase? 1:10^6 How does this compare to the length of the human genome. How does biology deal with that discrepancy?** ?**
  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? ?

Homework Questions from Dr. LeProust: [Lecture 2 slides]

  1. What’s the most commonly used method for oligo synthesis currently? ** Oligionucleatide Synthesis = a. Functionalized SiO2; b. Coupling with phosphoramidite; c. Capping unreacted sites; d. Oxidation; e. Deblock; Repeat b. to e. N times. Based on timeline I would say Khorana > Letsinger > Caruthers’ Phosphoramidite method is now mostly used. **
  2. Why is it difficult to make oligos longer than 200nt via direct synthesis? PCR
  3. Why can’t you make a 2000bp gene via direct oligo synthesis?

Homework Question from George Church: [Lecture 2 slides] Choose ONE of the following questions to answer; and please cite AI prompts or paper citations used, if any.

  1. [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”?

Amino Acids =

Lysine Contingency = my first hit in trying to understand what this is brings me to Jurassic Park fandom. I already love it

[question answered with ChatGPT5 - prompt: **Hi chat, can you help me answer this question: What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency". I do not have the knowledge (yet) to assess the legibility of the answer.*]

  • Observations that I find interesting but don’t completely understand > Chat nuances ‘all animals’ into ‘most animals’, and that they’re not identical in all animals, and for humans we mostly discuss 9 essential amino acids (minus arginine).

The 10 essential amino acids in many animals (esp. monogastric animals)

In animal nutrition (e.g., pigs, dogs, many mammals), the commonly listed 10 essential amino acids — meaning the animal cannot synthesize enough of them and must obtain them from diet — are:

  1. Arginine
  2. Histidine
  3. Lysine
  4. Isoleucine
  5. Leucine
  6. Methionine
  7. Phenylalanine
  8. Threonine
  9. Tryptophan
  10. Valine