Week 1 HW: Principles and Practices

Week 1 assigment Valeria Quesada Ortega - Sj, Costa Rica.

Project.

Development of a bioengineered gastronomic powder designed to create a multisensory dining experience without modifying the original ingredients.

the powder will consist of edible microcapsules made from food grade biopolymers that will remain stable during plating but dissolve when exposed to the normal pH of human saliva. Upon dissolution, the microcapsules will release microbursts with encapsulated umami compounds, such as glutamate extracts from algae or fermented foods.

The goal of this gastronomic tech is not to correct poor cooking or override a chef’s creativity, but rather provide a precise finishing tool that amplifies the final sensory moment of a dish.

Governance

Primary governance goal

To ensure the bioengineered gastronomic experiences are safe, transparent and ethically deployed, while supporting creative culinary use.

Sub-goals Prevent physiological harm to consumers Ensure that the bioactive components do not accumulate or cause unwanted biological effects after consumption. Promote informed consumer Guarantee that consumers are aware they are consuming a bioengineered, interactive food component. Avoid unnecessary barriers to culinary innovation Ensure that governance measures do not disproportionately restrict chiefs and new culinary researchers.

Governance actions

Mandatory post consumptions biochemical deactivation.

	Purpose
	Currently, there is no standard requirement ensuring that bioactive food
	components deactivate after ingestion. This actions proposes requiring
	that the powder’s microcapsules re;iably deactivate once exposed to
	salivary pH.

	Design
	We must incorporate a validated biochemical off switch (pH sensitive 
	biopolymer dissolution). Regulatory agencies would require
	evidence of deactivations as part of food safety approval.

	Assumptions
	This assumes that salivary pH is likely consistent across individuals an 
	that deactivation mechanisms function reliably in diverse conditions.
	
	Risks of failure and “success”
	Failure would result in prolonged bioactivity or consumer harm, and even
	successful implementation could limit certain experimental designs or
	increase development costs.

Pre-market evaluation of sensory and metabolic safety.

	Purpose
	Gourmet food additives are not routinely assessed for individualized 
	biological interactions. This action proposes targeted safety testing
	for bioengineered sensory .
	
	Design
	Independent labs would conduct standardized tests assessing metabolic
	safety allergenicity, and sensory interaction. Approval would be required
	prior to commercial use.

	Assumptions
	This assumes labs testing accurately represents experiences and population
	diversity.
	
	Risks of failure and “success”
	Over-standarizations could reduce creative experimentation.

Transparent labeling and informed consent.
	
	Purpose.
	Consumers may not expect interactive bioeng components in their food.
	This action ensures transparency.

	Design.
	Restaurants and us, as producers, would disclose the presence of 
	bioengineered sensory additives through menus or verbal explanation.
	
	Assumptions
	This assumes consumers understand the information and that disclosure
	does not provoke unnecessary fear.
	
	Risk of failure and “success”
	Labeling could be ignored or misunderstood. Overemphasis could reduce
	adoption despite safety.

Conclusion.

Based on this evaluation, a combination of action 1 and action 2 should be prioritized, as they directly prevent harm and ensure consumer safety. Meanwhile, action 3 plays a complementary and important role by supporting transparency.

Week 1 Reflection.

During this first week, I thought a lot on the topics discussed, but particularly on the “dark side” of SynBiotech and Bioengineering. I also became more aware of how the limitation of these technologies significantly reduce progress, especially in Latin America, where structural and systemic barriers often restrict their reach.

Week 1 HW: Principles and Practices

Homework Questions from Professor Jacobson:

1.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?

-DNA polymerase has an error rate of aprox one mistake per 10^{8 nucleotides during DNA replication. This significant on the human genome which has around 3 x10}9 base pairs, so without correction, this woul result in a lot of mutations per replication. Biology addresses this discrepancy through multiple error correction mechanisms, such as post replication mismatch repair, to reduce the error rate to aprox one error per 10^9 nucleotides, maintaining th genomic stability.

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?

-Because the genetic code is degenerate, an average human protein of aprox 300 aminoacids can be encoded by a bunch of different DNA sequences creating a lot of different combinations, However, most of them do not function effectively. Factors such as codon bias, mRNA secondary strc, trasnlation spee, etc. limit which DNA sequences can successfully produce the desired protein. So, as a resultm only a small part of them are biologically viable.

Homework Questions from Dr. LeProust:

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

-The most commonly used method for oligonucleotide synthesis is solid-phase phosphoramidite chemistry

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

-Mainly due to error accumulation

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

-Because the cumulative error rate would be extremely high

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”? -histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine, and arginine -Due to the fact that animal do not produce Lysine, the abscence of it can function as a killer switch for engineered organisms. as a form of contingency