Week 1 HW: Principles and Practices

Here are some ideas that I brainstormed:

🩹 Regenerative Medicine

• Autologous skin grafts to replace necrotic, cancerous, scarred, or miscoloured tissue etc
• Synthetic skin models for surgeons or tattoo artists to practice on
• Self regenerating organs (for people with damaged organs, cancer, people who need transplants i.e. bioink)
• Cure for frostbite → regenerating cell tissue or even whole digits or limbs!
• Growing teeth in a lab to replace damaged or missing teeth!
• Regeneration of spinal column

🧪 Cures

• Targeting misfolded proteins (prions) in the brain
• Making malarial mosquitos infertile (* ethical considerations)
• Synthesising biofuel
• AIDS cure
• Cancer detection mechanism to cause cellular death/induce apoptosis in abnormal cells
• Cure for sickle cell
• Cure for cataracts by growing autologous lenses
• Cure for blindness or eyesight degeneration
• Making VADs → (HKU hydrogel transistors, electrical interaction with living cells)
• Helping diabetics to endogenously produce effective insulin

🛡️ Prophylaxis

• Predicting/modelling viruses and vaccines (* ethics/dangers must be taken into consideration)

🏭 Biomaterial/Industrial applications

• Manufacturing leather without the need for mass animal slaughter
• Bioplastic on industrial scale (mitigation of microplastic crisis)
• Industrially producing natural inks
• Bioremediation:
  • Landfills
  • Radioactive sites
  • Sewage systems

🎭 Fun ideas

• Tabulating or transcribing music on plants (patterns on leaves → gene expression)
• Bioluminescent lamps for:
  • industrial applications
  • architectural applications (can be used practically in hospitals, clubs as exit signs etc)
  • design/decor!
  • bioluminescent paint
  • hair dye/cosmetics
• Printing the taste of a meal! for art/deisgn installation involving the coding of Hana programme/Hana AI to detect what is in an image and “print out” certain proteins? that correspond to flavours etc
  • edible
• Print out QR codes on biomaterial to be scanned and play music for art/design installations
  • or if not QR codes then fun characters or shapes (presets) that can be scanned by Hana programme/Hana AI which then play certain songs?
  • stills from films even?
  • covers of albums?
• Mushroom testing kit which prints out species name on flesh of mushroom or testing strip once pricked or sample collected (kind of like pregnancy test but not, more like DNA sequencing mushrooms to determine what species that are)
• Sustainable nail polish
• Generating music from colony of bacteria for art/design/science installation

. . . In the end I decided that I would like to pursue further the idea of printing an image as well as the taste of a food/meal using edible media. I would like to call it “Tastemaker” or “Yum Dot Com.” This project highlights the sensory potential of biological engineering, whilst sitting at the intersection of biology, technology, design, the culinary, and the quotidian human experience.

🔐 Data Protection and Consent

• This application will be handilng datasets in the form of photos that are submitted by users, therefore it is important that they know what their images are being used for, where they will be held, how they will be held, and who will have access to them → Images submitted by users constitute personal data under GDPR and related frameworks
• Explicit consent must be given by participants to enable the use of their photographs/images
• Participants may withdraw their consent at any moment

🔎 Promoting transparency

• Ensure consumers understand what biological materials are being used, how the food is produced, and what they are ingesting
• Clearly distinguish between artistic/experimental food products and nutritionally complete or medically relevant foods
• Prevent deceptive use in advertising, novelty food products, or commercial settings

🧯 Preventing Malfeasance

• Ensure that edible biological media used to print images and taste profiles is safe to consume, ethically produced, and not misleading or harmful, while still allowing creative and experimental uses:
• Ensure all edible media and biological components are non-toxic, allergen-aware, and safe for repeated consumption
• Prevent accidental or intentional contamination during production, printing, or distribution
• Avoid misleading representations of nutritional value or ingredients (e.g. printing “healthy” foods that are not)
• Avoid applications that could be used to manipulate consumers, i.e. by falsely replicating branded foods, culturally significant dishes, or nutritionally complete meals
• Ensuring the technology is not repurposed for coercive or exploitative contexts, such as pressuring individuals to consume unfamiliar or unsafe substances i.e. spiking or biowarfare

🧩 Non-malificence

• Prevent misuse of biosensing infrastructure for coercive surveillance or targeting specific communities
• Make sure that biomaterial is sourced as ethically as possible

📝 Mandatory Explicit Consent & Transparency Requirements

Purpose:

Design:

Assumptions:

Risks of Failure & “Success:”

• Success: Overly strict consent enforcement may slow down research or creative experimentation

🧰 Technical data safeguards

Purpose:

Design:

Assumptions:

Risks of Failure & “Success:”  Failure: - Hacking or accidental leaks - Users abuse terms of upload

Success:

• Minimal data retention may limit research/creativity

🥽 Safety standards for edible media

Purpose:

Design:

Assumptions:

Risks of Failure & “Success:”

• Success: excessive regulation could slow innovation or increase costs

📊 4. Scoring Policy Goals

Option 1: Mandatory consent & transparency
Option 2: Technical data safeguards
Option 3: Regulatory oversight for edible media

⚠️ 5. Ethical concerns highlighted above

📚 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?

• Naturual error rate: 1:10⁶ or 1 in a million
• Human error rate: 1:10² or 1 in a hundred
• Biological mechanisms are x10⁴ or 10,000 better than human ones The length of the human genome is roughly 3.2 billion base pairs.

Biology deals with this discrepancy through built in error correction mechanisms; 3’-5’ exonuclease activity which is an intrinsic “proofreading” function is an example of this. Exonucleases are specialist enzymes which catalyse the removal of incorrectly incorporated nucleotides by breaking phosphodiester bonds via hydrolysis.

Furthermore, the genetic code is particularly robust due to its degeneracy meaning that multiple codons can code for the same amino acid i.e. all of the codons for alanine start with GC, all of the codons for leucine start with CU etc. In this way, the effect of mutations can be mitigated. Moreover in the case of a conservative substitution (or replacement), which is a missense mutation (whereby a nucleotide change results in a different amino acid being incorporated into a protein), the incorrect amino acid has similar physicochemical properties to the original one and therefore does not affect the protein’s tertiary or 3D structure. Physicochemical properties in this instance refer mostly to hydrophobicity and size.

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?

Theoretically a lot. 😹 This is due to the degenerate nature of the genetic code. Practically speaking, not all of these different codes work to code the protein of interest as Cells engaged in translation prefer certain codons Rare codons correspond to rare tRNA molecules The number of actually functional proteins is smaller than the theoretical possibilities

🧪 Homework Questions from Dr. LeProust

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

Currently, the most commonly used method for oligo synthesis is through phosphoramidite chemistry via the phosphodiester method pioneered by Har-Gobind Khorana in the 1950s.

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

It is difficult to make oligos longer than 200nt long through direct synthesis as full length product synthesis drops exponentially as length increases. The more chemical reactions that must be done, the greater the rate of error and contamination.

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

Error accumulation as mentioned in previous answer.

🧬 Homework Question from Dr. George Church

Choose ONE of the following three questions to answer; and please cite AI prompts or paper citations used, if any. What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency”?

The ten essential amino acids in all animals are

• Arginine
• Histidine
• Isoleucine
• Lucine
• Lysine
• Methionine
• Phenylalanine
• Threonine
• Tryptophan
• Valine

The Lysine Contingency is codswallop because even if dinosaurs were not able to naturally produce endogenous lysine, they could get it from food sources! Humans can’t even produce it and must get it from their diet.

Week 3 HW: Lab automation

Week 2 HW: DNA Reading

I was thinking of choosing between two proteins

1. Titin (also known as connectin) which is the largest known protein encoded by the TTN gene. In humans it accounts for 0.5kg of body weight! Titin is important in muscle cells, acting as a molecular spring. It is the third most abundant protein in muscles, giving them their elasticity, structural integrity, and stability.

1. Green fluorescent protein or GFP which is found in the crystal jelly or hydromedusa (Aequorea Victoria), as well as various species of coral, sea anemones, and crustaceans. GFP is often used as a reporter gene in cell as well as molecular biology.

Scientists have created many organisms which can express GFP which is thusly a proof of concept that a gene can be expressed by a given organism. This protein has been introduced and expressed by many species, maintained in their genome, and even passed on to their offspring; such organisms include bacteria, yeast, fungi, fish, and mammalian cells, including those of humans.

Interestingly, the winners of the 2008 Nobel Prize in Chemistry: Roger Y. Tsien, Osamu Shimomura, and Martin Chalfie, were awarded such due to their discovery and development of GFP.

I decided to choose GFP as it is extremely abundant and familiar to scientists due to its in vivo and in vitro applications, but also because of my interest in creating a bioluminescent biosensor.