Week 1 HW: Principles and Practices

Principles and Practices

Assignment 1

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

For this assignment, I want to explore the world of textile 3D printing with biomaterials. The fashion industry is one of the biggest polluters, with textile production generating massive amounts of waste, microplastic pollution, and toxic chemical runoff. A 3D-printable biomaterial textile could reduce waste, eliminate harmful processes, and allow for sustainable, on-demand production. I want to explore a way to produce garments and materials in a sustainable manner using synthetic biology principles. The materials and garments would be “grown”, and would be biodegradable, non-toxic, and could be engineered for properties like flexibility, durability, and even water resistance.

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.

• Goal 1: Ensure Safety & Environmental Protection
  • Sub-goal 1.1: Ensure that the biomaterials used are non-toxic and biodegradable.
  • Sub-goal 1.2: Prevent environmental damage from improper disposal or degradation by implementing regulations on material composition and end-of-life handling.
• Goal 2: Promote Ethical & Sustainable Industry Adoption
  • Sub-goal 2.1: Develop incentives for brands to transition to sustainable biomaterials.
  • Sub-goal 2.2: Establish transparency and labeling standards so consumers know the material origins and environmental impact.

3. Next, describe at least three different potential governance “actions” by considering the four aspects below (Purpose, Design, Assumptions, Risks of Failure & “Success”). Try to outline a mix of actions (e.g. a new requirement/rule, incentive, or technical strategy) pursued by different “actors” (e.g. academic researchers, companies, federal regulators, law enforcement, etc). Draw upon your existing knowledge and a little additional digging, and feel free to use analogies to other domains (e.g. 3D printing, drones, financial systems, etc.).

   • Purpose: What is done now and what changes are you proposing?
   • Design: What is needed to make it “work”? (including the actor(s) involved - who must opt-in, fund, approve, or implement, etc)
   • Assumptions: What could you have wrong (incorrect assumptions, uncertainties)?
   • Risks of Failure & “Success”: How might this fail, including any unintended consequences of the “success” of your proposed actions?

   Action 1: Certification & Regulation of Biomaterials

   • Purpose: Introduce a certification system (like “Organic” or “Fair Trade” labels) for 3D-printed biomaterials to ensure they are safe, biodegradable, and produced sustainably.
   • Design: Requires regulatory agencies (e.g. the EPA or an industry consortium) to define standards and testing protocols.
   • Assumptions: Companies will comply if incentives (e.g. tax breaks or marketing benefits) exist.
   • Risks: Over-regulation might slow down innovation or create high costs for small businesses.

   Action 2: Government & Institutional Funding for Research

   • Purpose: Provide grants or subsidies to encourage research into scalable, affordable biomaterial-based textile printing.
   • Design: Funding from agencies like the NSF, with partnerships between academia, startups, and fashion brands.
   • Assumptions: More funding will accelerate breakthroughs and industry adoption.
   • Risks: If poorly allocated, funds might not lead to viable, scalable solutions.

   Action 3: Incentives for Industry Adoption

   • Purpose: Implement tax breaks or sustainability credits for companies adopting 3D-printed biomaterials in their products.
   • Design: Requires legislative approval and collaboration with sustainability-focused fashion organizations.
   • Assumptions: Brands will transition if there is financial motivation.
   • Risks: Some companies might greenwash their efforts without making meaningful changes.

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.

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. For this, you can choose one or more relevant audiences for your recommendation, which could range from the very local (e.g. to MIT leadership or Cambridge Mayoral Office) to the national (e.g. to President Biden or the head of a Federal Agency) to the international (e.g. to the United Nations Office of the Secretary-General, or the leadership of a multinational firm or industry consortia). These could also be one of the “actor” groups in your matrix.

Based on scoring, a combination of Research Funding and Industry Incentives would be the best approach. Certification and regulation are necessary but could slow down early-stage adoption, so they should be introduced later when the industry matures. The recommendation could be addressed to national funding agencies (e.g., NSF), sustainability leaders in fashion, or policymakers focused on textile industry regulations.

Week 2 Lecture Prep

Homework Questions from Professor Jacobson:

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?

A: Polymerase error rate appprox. 1 in 10^6 base pairs, vs. human genome approx. 3.2 billion base pairs. This leads to thousands of errors per replication. Biology deals with that discrepancy by proofreading polyerases, and through post-replication mismatch repair systems and evolutionary selection.

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?

A: There are approximately 10^165 different DNA sequences in which a human protein can be encoded. In practice, most of these sequecees are not functional because DNA and RNA are physical molecules subject to physical constraints such as translation-dependent protein folding. As a result, only a small subset of possible sequences can produce functional proteine expressions.

Homework Questions from Dr. LeProust:

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

A: solid-phase phosphoramidite chemical synthesis.

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

A: Chemical DNA is stepwise and imperfect, and small inefficiencies at each nucleotidic addition accumulae exponentially with length. Therefore, beyond 200nt, the yield of full-length error-free molecules becomes extremely unlikely due to errors.

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

A: Genes are built by assembling short oligos because direct chemical synthesis does not scale. therefore a 2000bp gene would require thousands of sequential chemical coupling steps, causing error rates. So genes are therefore not directly synthesized, but assembled hierarchically from any shorter oligos using enzymatic processes such as PCR.

Homework 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”?

A: The 10 essential amino-acids are: Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine, Arginine.

The “lysine Contingency” presents lysine as a point of dependency since it is not synthesizable by animals, and must obtain it externally. This concept is already deeply embedded in biological environments such as with microbes, and in food chains