Week 1 HW: Principles and Practices

What

I would like developing a Microbial Oxytocin-Sensing Network，a decentralized, “invisible” biosensing system designed for non-invasive ecological monitoring. These “living sentinels” utilize chimeric GPCRs to detect mammalian oxytocin and record signals via CRISPR-genomic storage. To maintain ecological integrity, the data is expressed through near-infrared bioluminescence, creating an interface that is sensory yet non-intrusive to the local fauna.

Why

1. Upgrading from Survival Stats to Population Resilience Traditional monitoring methods (such as infrared cameras and satellite positioning) can only tell us that the animals “are alive” or “where they are”, but cannot answer the question “Are they doing well?”. Sometimes the increase in numbers can mask social breakdown or failure in raising offspring within the population. Therefore, this technology provides “leading indicators” for predicting the long-term survival ability of the population, rather than just being a lagging indicator of population statistics. This project attempts to conduct true zero-contact monitoring by distributing sensors at the microbial level. We capture biochemical signals in the animals’ most relaxed and natural social scenarios without interfering with their natural behaviors.

2. Challenging “Genomic Essentialism”: From Frozen DNA to Dynamic Associations (Beyond Genomic Essentialism) The mainstream conservation paradigm represented by the San Diego Frozen Zoo mainly focuses on storing the “sole and independent essence” of species, that is, the static DNA sequence. This “freezing logic” simplifies species into a set of digital codes. However, life is not just the accumulation of codes; it is a dynamic relationship. When a species is separated from its social context, it has already been fragmented ontologically. And the project refuses to view species as a “static asset”. It uses synthetic biology methods to capture the transient molecule oxytocin and attempts to preserve those “physiological moments” that cannot be recorded by DNA. It emphasizes: The essence of a species exists not only in its cell nucleus, but also in the “unstable” biochemical bond between individuals.

3. Eliminating “Technical Intrusion”: As a Hidden Infrastructure for Fail-Safe In current wildlife management, mechanical noise, reflection and physical presence can disturb sensitive species, trigger stress responses, and force them to alter their natural behaviors or even abandon their offspring. This project aims to establish an entirely invisible and decentralized biological network. It blends seamlessly with the environment and does not cause any physical disturbances.

Governance / Policy Goal

1 Ensure minimal impact on non-human life and ecosystems
MOSN must never introduce biological, ecological, or behavioral harm to animals, microbial ecologies, or habitats—even indirectly or over long temporal scales. AI Prompts：How do changes in soil microorganisms affect species and ecosystems?
Sub-goal 1.1: Microbial sensors must have strict ecological boundary control (such as environmental adaptability restrictions and self-limiting reproductive design), and the genetic editing operation must not have irreversible ecological spill-over risks. Sub-goal 1.2: The monitoring process neither triggers stress responses in the animals (eliminating physical or sensory disturbances) nor interferes with the species’ natural secretion of oxytocin, social interactions, and other biochemical processes.

2 Preventing the instrumental abuse of biochemical signals and safeguarding the dynamic essence of species’ lives
MOSN must not be reduced to a tool for secretly monitoring, extracting resources from, or commercializing animal intimate behaviors, reproduction, and sociability; it is necessary to reject simplifying species as “static genetic assets” and prohibiting the binding of biochemical signal data with digital and instrumentalized species management methods. AI Prompts：the potential risks of instrumental abuse of biochemical signals
Sub-goal 2.1: Anti-tooling monitoring protection Oxytocin signals cannot be correlated with location tracking, facial recognition, tagging systems, or behavioral profiling technologies. Data access must be restricted to ecological research, conservation ethics
Sub-goal 2.2: Establish a use-purpose firewall: data cannot be repurposed beyond the originally stated ethical and epistemic aims.

3 Ensure Ethical Human–Nonhuman Interface Design
The perception and interpretation of MOSN’s output data by humans require the cultivation of responsibility, restraint, and empathy towards non-human life (rather than the desire for control, possession, or prying); the core of interface design is to “capture biochemical bonds” rather than “monitoring life conditions”, emphasizing the understanding of species dynamic relationships rather than the control of individuals. Sub-goal 3.1:Design language should emphasize listening rather than seeing or controlling through.
Sub-goal 3.2:Require periodic ethical re-evaluation as ecosystems, technologies, and social contexts interaction evolve.

Potential Governance “Actions”

1 Establish “cross-species sensory avoidance” review criteria
Executor: Environmental Regulatory Agency / Ethical Committee
Purpose: To prevent near-infrared (NIR) bioluminescence from causing behavioral disturbances in animals with specific visual ranges.
Design: Similar to the allocation of radio frequency spectrum. All MOSN deployments must pass the “redshift compliance test” before implementation. Developers must adjust the expression frequency of luciferase (Luciferase) based on the visual curves of the target species (such as rodents, reptiles, etc.) at the deployment site, ensuring that the light-emitting points are within the “visual blind zone” of that ecological niche species. AI Prompts：What design and research methods are there to prevent bioluminescence from interfering with animals?
Assumptions: We assume that we have sufficient scientific data to support the retinal sensory anatomy of all protected species in this area.
Risks/Failure: Certain insects or organisms in the deep soil may be extremely sensitive to heat or weak photons, causing changes in their migration or feeding behaviors.
The side effect of “success”: To completely avoid being detected by animal vision, it may result in extremely long signal wavelengths, which increases the technical difficulty and equipment cost for human receivers to process the data.

2 Establish a Global Stewardship Regime
Purpose：Establish a MOSN Global Stewardship Regime—a unified framework of mandatory rules, technical standards, and incentive mechanisms
Executor: Federal Regulators (e.g., EPA, EU EBA, national biotech regulatory bodies)
Design：Enact a Specialized MOSN Biotech Mandate (analogous to drone flight restriction zones) that classifies MOSN microbial sensors as “non-instrumental conservation biotech”—mandating technical compliance with signal irreducibility standards (no individual-level data capture) and banning any integration with wildlife tracking/genomic extraction technologies; approve only MOSN deployments with a certified “dynamic life purpose plan
Assumptions: Federal regulators across jurisdictions will harmonize the MOSN biotech mandate (no cross-country regulatory arbitrage for non-compliant deployments).AI Prompts：If you were part of the federal regulator, how would you assess the Risks of Failure and “Success” of MOSN?
Risks/Failure:1.Regulatory inconsistencyDifferent countries or agencies set different rules, creating loopholes where unethical MOSN projects can operate. 2.Regulators lack technical expertiseThey cannot verify whether the technology actually avoids individual-level data or tracking, so rules exist only on paper.
Risk of success：1.Standards have become uniform.The rules ignore the local ecological needs and the viewpoints of the indigenous people, resulting in the Environmental Protection Agency being compliant in form but having no effect in terms of ecology.2.Excessive standard uniformity leads to the suppression of technological innovation: The regulation “succeeded” in achieving global uniformity of MOSN technical standards and standardization of the approval process. However, in order to avoid the risk of tooling up, overly conservative technical restriction clauses were formulated.

3 Ethical Human–Nonhuman Interface Design
Purpose:Current conservation data and interfaces often reinforce human-centrism, framing non-human life as resources, subjects, or study objects. Use MOSN’s output and interface as a form of anti-anthropocentric education in the Anthropocene — to cultivate public empathy for the dynamic, relational vitality of non-human species, rather than treating them as measurable assets or controllable systems.
Executor:Interface designers + artists + ethicists + conservation biologists
Design:Co-design interfaces that prioritize listening over surveillance, using near‑infrared bioluminescence patterns and ambient expressions rather than individual tracking or control-style dashboards and by using remote information transmission and visualization tools.
Assumptions:That people can understand and connect with abstract, non‑instrumental “relational signals” without demanding clearer, more intrusive, or more “useful” data.That ethical review panels will meaningfully update standards as ecosystems, technologies, and social values change.
Risks of Failure: The interface becomes just another “monitoring tool”; ethical reviews become symbolic; data is interpreted as a way to predict or manage animals rather than respect their autonomy.
Risks of “Success”: The interface is so abstract it fails to educate; “ethical listening” becomes a branding label for projects that still treat non‑human life as a source of information or spectacle.

Recommendation and Priority

I prioritize a strategic integration of Option 1 (Cross-species Sensory Avoidance) and Option 3 (Ethical Human–Nonhuman Interface Design). My recommendation is directed toward the International Union for Conservation of Nature (IUCN) and National Environmental Regulatory Agencies (such as the EPA).
The reason why is while Option 2 (Global Stewardship) offers a necessary regulatory shell, it risks becoming a bureaucratic bottleneck that could stifle the very innovation needed for urgent conservation. By combining Options 1 and 3, we address the core ethical tension of MOSN: the paradox of observing without “intruding.”
Option 1 Cross-species Sensory Avoidance: Ensures the technology respects the “sensory sovereignty” of the fauna. It moves biosafety from “preventing human infection” to “preventing ecological disruption.”
Option 3 Ethical Human–Nonhuman Interface Design: Ensures that the data produced does not become a tool for “digital colonialism.” It forces us to engage with the wild through empathy and “listening” rather than through the lens of a control-oriented dashboard.

Trade-offs Considered

1. Innovation vs. Bureaucratic Control Option 2 (Global Stewardship) focuses on strong international regulation. This can provide legal authority and global coordination. However, it may also create slow decision-making processes and administrative delays.In urgent conservation contexts, technology needs to adapt quickly to local ecological conditions. If every development must go through heavy global approval systems, innovation may slow down. By choosing Option 1 and 3, we allow governance to happen through design principles rather than only through top-down control. This keeps flexibility while still setting ethical boundaries. Trade-off: We sacrifice some global regulatory consistency in order to maintain speed and adaptability.

2. External Oversight vs. Built-in Ethical Design Option 2 relies mainly on external monitoring and enforcement. It assumes that rules and compliance systems can prevent misuse.However, once a technology is widely distributed, enforcement becomes difficult. In some regions, regulations may be weak or politically influenced. Option 1 and 3 instead build ethical limits directly into the technology:Option 1 limits sensory disturbance biologically.Option 3 limits how much and what type of data can be accessed.This reduces the need to rely only on legal systems.

Trade-off: We accept less centralized authority in exchange for stronger built-in ethical safeguards.

In conclusion, prioritizing Option 1 and Option 3 shifts governance from external control to internal ethical design. Instead of relying mainly on international regulatory systems, ethical responsibility is embedded directly into the technology itself.
This approach reduces pressure on geopolitical systems and minimizes conflicts caused by uneven regulatory capacity between countries. When ethical limits are built into the design — such as sensory protection and restricted data access — the technology becomes less dependent on political stability or advanced enforcement infrastructure.
In this way, internal monitoring through design ethics can help bridge global inequalities in environmental governance and information technology. It creates a more resilient and adaptable framework, especially in regions where formal regulation may be slow, inconsistent, or politically sensitive.

Assumptions and Uncertainties

Assumption: I assume that “relational vitality” (social bonding) is a universally accepted indicator of ecological health that can bridge the gap between Western science and indigenous knowledge.

Uncertainty: There is a significant knowledge gap regarding the retinal anatomy of soil micro-fauna. While we can protect mammals from light pollution, we do not fully know how NIR-emitting bacteria might disrupt the behaviors of deep-soil invertebrates or fungi.

Week-02-hw-dna-read-write-and-edit

Part 1 Benchling & In-silico Gel Art

Limbda Sequence Import

Part 2 Gel Art - Restriction Digests and Gel Electrophoresis

Limbda gel electrophoresis

The style of Paul Vanouse’s Latent Figure Protocol artworks

Part 3 DNA Design Challenge

Protein choose: Oxytocin-neurophysin 1 (Prairie Vole)
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Why: I chose this protein from the prairie vole (Microtus ochrogaster) because these rodents are famous models in neuroscience for studying monogamy and social bonding. Oxytocin is the key molecular driver of their lifelong pair-bonding behavior. Sequence (FASTA):
sp|E0V840|OXYT_MICOC Oxytocin-neurophysin 1 OS=Microtus ochrogaster OX=10031 GN=Oxt PE=3 SV=1
MACPSLACCLLGLLALTSACYIQNCPLGGKRAALDLDTRKCLPCGPGGKGRCFGPNICCADELGCFVGTAEALRCQEENYLPSPCQSGQKPCGSGGRCAAAGVCCSPDGCRMDPACDPESAFSER

• I take the Oxytocin（Prairie Vole）sequence from the Uniprot

• I use bioinformatic to reverse translate the protein by bioinformatic

Reverse Translate: Protein (amino acid) sequence to DNA (nucleotide) sequence

gcgtgcgatgaatttggccatattaaactgatgaacccgcagcgcagcaccgtgtggtat taaatggcgggcccgagcctggcgtgctgctttctgggcctgctggcgctgaccagcgcg tgctatattcagaactgcccgctgggcggcaaacgcgtgctggatctggatgtgcgcacc tgcccgccgtgcggcccgggcggccgcggccgctgctttggcccgagcatttgctgcgcg gatgaactgggctgctttgtgggcaccgcggaagcgctgcgctgccaggaagaaaactat ctgccgagcccgtgccagagcggccagaaagcgtgcggcagcggcggccgctgcgcggcg ctgggcctgtgctgcagcccggatggctgccatgcggatccggcgtgcgatgcggaagcg acctttagccagcgc

Codon Optimization I have chosen Escherichia coli (E. coli) as the host organism for optimization.

Reason: E. coli is the gold standard “workhorse” in synthetic biology and biotechnology. It has a very rapid growth rate, its genetics are thoroughly understood, and it is highly cost-effective for large-scale recombinant protein production. By optimizing the Prairie Vole oxytocin sequence for E. coli, we ensure that the bacteria can efficiently “read” the instructions and produce high concentrations of the hormone for research or industrial use

Sequence：

gcgtgcgatgaatttggccatatcaagctgatgaacccgcagcgttccaccgtgtggtat taaatggcgggtccgagcctggcgtgctgcttcctgggcctgctggcgctgaccagcgcg tgctacatccagaactgcccgctgggcggcaaacgtgtgctggatctggatgtgcgcacc tgcccgccgtgcggtccgggcggtcgtggccgttgctttggcccgagcatctgctgcgcg gatgaactgggctgctttgtgggcaccgcggaagcgctgcgttgccaggaagaaaactac ctgccgagcccgtgccagagcggccagaaagcgtgcggtagcggcggtcgttgcgcggcg ctgggcctgtgctgcagcccggatggctgccatgcggatccggcgtgcgatgcggaagcg accttcagccagcgt

https://benchling.com/s/seq-8tGivOKSZJUUVEjLY7cE?m=slm-y1fK0BVnbJ3uF2UYnwf2

Part 4: Prepare a Twist DNA Synthesis Order

Build MY DNA Insert Sequence

• I imported Oxytocin-neurophysin 1 (Prairie Vole) using Benchling and created an annotation to describe each piece.

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• And then, in the Twsit, the DNA sequence was virtually combined with the vector and exported as a Genbank document.

• This is the plasmid i just built with my expression cassette included. Congratulations on building my first plasmid!

Part 5: DNA Read/Write/Edit

DNA Read
What DNA would you want to sequence (e.g., read) and why? This could be DNA related to human health (e.g. genes related to disease research), environmental monitoring (e.g., sewage waste water, biodiversity analysis), and beyond (e.g. DNA data storage, biobank).

Target DNA: The frozen cell DNA of endangered or extinct species (such as the Bucardo Pyrenean goat or the mammoth) stored in biological repositories like the San Diego Zoo’s “Frozen Zoo”. +2 Reason: These DNA molecules are not merely chemical entities; they are carriers of “Salvage Genomics”. By reading these DNA sequences, we can transform the organism into a “biological information unit”, which is the first step towards achieving “functional de-extinction”, that is, identifying the key genetic characteristics (Functional Traits) that define the species.

(ii) In lecture, a variety of sequencing technologies were mentioned. What technology or technologies would you use to perform sequencing on your DNA and why?
Is your method first-, second- or third-generation or other? How so?
What is your input? How do you prepare your input (e.g. fragmentation, adapter ligation, PCR)? List the essential steps.
What are the essential steps of your chosen sequencing technology, how does it decode the bases of your DNA sample (base calling)?
What is the output of your chosen sequencing technology?

Technology: Illumina short-read sequencing (NGS) combined with PacBio or Oxford Nanopore (long-read sequencing). Reason: Biological sample libraries (such as cells frozen for several decades) may be subject to degradation. Illumina offers high-precision base coverage, and long-read sequencing is helpful in reconstructing the complete genomic map of extinct species without a reference genome, through De Novo Assembly.

Input and Preparation Steps (Library Preparation):

The genomic DNA extracted from the Frozen Zoo samples, which have been frozen for several decades. Key steps:

Fragmentation: Break down the extracted long-chain DNA. Adapter Ligation: This process connects the specific primers required for sequencing with the sample labels. Library enrichment: The target fragment is amplified through PCR (if it is a second-generation method).

Core steps of sequencing and base identification (Base Calling):

Step: Synthesize fluorescently labeled bases on the flow cell (for sequencing by synthesis method). Base Calling: The machine captures the color of the fluorescence signal produced by each cycle, and converts it into an A, T, C, G sequence through an algorithm.

What is the output?

Output: FASTQ format file containing sequence information and quality scores

DNA Write (i) What DNA would you want to synthesize (e.g., write) and why?

Objective: To synthesize DNA fragments encoding specific functional traits of mammoths (such as cold-resistant hemoglobin genes or thick fur genes). Reason: During the process of extinction, we cannot directly “revive” the old life forms. Instead, by writing these specific sequences, we use them as “designable materials” to create a new organism capable of performing ecological functions (as Novak described it as an ecological substitute). +1

（ii) What technology or technologies would you use to perform this DNA synthesis and why?

Technology: Inkjet-based (inkjet-based) high-throughput DNA synthesis or enzymatic synthesis. Reason: The enzymatic synthesis method is more environmentally friendly and can synthesize longer DNA fragments, making it suitable for synthesizing complex and large-scale genetic circuits like that of a mammoth.

DNA Edit (i) What DNA would you want to edit and why?

Objective: Use the genome of Asian elephant stem cells as a template to remove the specific sites that do not match those of the mammoth. +2

Reason: This editing behavior exemplifies the “deconstruction of species essentialism” as mentioned in RP - species are no longer fixed boundaries, but rather a set of “programmable function libraries” that can be modified, stored, and recombined.

(ii) What technology or technologies would you use to perform these DNA edits and why?
How does your technology of choice edit DNA? What are the essential steps?
What preparation do you need to do (e.g. design steps) and what is the input (e.g. DNA template, enzymes, plasmids, primers, guides, cells) for the editing?
What are the limitations of your editing methods (if any) in terms of efficiency or precision?

What technology is being used?

Technology: CRISPR-Cas9 gene editing technology. Reason: It can precisely and efficiently perform multi-site editing within the vast elephant genome, which is the core technology currently adopted by companies like Colossal.

How to conduct editing? Key steps

Design: Design sgRNAs that specifically recognize the genetic loci of mammoth animals. Cutting: The Cas9 protein cuts the double-stranded DNA under the guidance of the gRNA. Repair: Introduce synthetic mammoth DNA template and use homologous recombination repair (HDR) to insert the new sequence into the genome.

Preparation and Input

Input: Asian elephant fibroblast cells, Cas9 protein, designed guide RNA (gRNA), and donor DNA template containing the mammoth sequence.

Limitations of Technology

Off-target effects: May accidentally damage the key survival genes in the Asian elephant genome. Efficiency issue: It is extremely difficult to carry out thousands of gene edits simultaneously within a living cell. Ethical challenges: As you stated in your report, this kind of editing blurs the boundaries between “nature” and “design”, and may give rise to entirely new and difficult-to-define “new life (Neolife)”.

Week-03-hw-Lab-Automation

Python Script for Opentrons Artwork

My Inspiration

In taxonomy, Bucardo belongs to the genus Capra (goats). In my Opentrons practice, I discovered that the mosaic pattern formed by fluorescent bacteria blurred the boundaries between specific species and macroscopic classification. I am not depicting an exact sheep, but rather using the universality of the “Capra” attribute to reconstruct an image of “Resurrection for 7 Minutes”. This mosaic-like visual language is not only a numerical metaphor for Bucardo’s shattered life, but also a vague expression about ’existence and disappearance’ that transcends species classification.

Process

Firstly, I initially used the Automatic Art Interface to generate the image I desired. However, due to the color restrictions mentioned in the Colab document, I had to limit the use of the design sheep’s colors.

Since I had no coding experience, at the beginning I simply copied the coordinates and fed them to the AI along with the reference seven, in order to generate the code.

However, during the process, several errors occurred, including confusion between instructions and spaces, a situation where the machine pipette’s printing exceeded the capacity, and undefined terms such as: mko2_points and mrfp1_points.

After resolving these minor errors, when I copied the code given by the AI, there were still several errors in the generated code. I did not achieve the pattern I wanted.

After reflection, taking into account the previous mistakes, I realized that I had not clearly stated where to draw specifically. Therefore, I shifted my focus to how to make the coordinates and colors I obtained clearly expressed in the coding. After correcting the overflow error, I continued to give instructions to the AI.

Promote：Based on the code you provided, the image I generated is the first one. Please refer to the coordinates I set in the generator and help me modify the code further.

This time, the instruction, combined with the errors I had already fixed before, enabled me to generate my target image. The coding is divided into two parts. 1.Define the coordinate list 2.The drawing process.

Coding

Outcome

Post-Lab Questions

I have found two papers that I am particularly interested in.

Automation of protein crystallization scaleup via Opentrons-2 liquid handling

Description: This paper demonstrates how to scale up and automate the sitting drop protein crystallization process using the Opentrons-2 (OT-2) robot. The research focuses on using Python scripts to precisely control microliter-level liquid handling to optimize crystallization conditions for proteins such as lysozyme. Technical Highlights: The authors developed a flexible automated workflow, including: Serial Dilution: The robot can automatically configure gradients of different precipitant concentrations. Custom Hardware: To accommodate non-standard crystallization plates, the authors used 3D printing to create dedicated adapters. High Throughput and Accuracy: The system can automatically set up 24-well crystallization plates, ensuring highly consistent component proportions in each tiny droplet (approximately 4 μL).

What I intented to do

I plan to use the OT-2 automation platform to create a project titled “Crystal Architecture: Programming Microscopic Landscapes”. This project aims to leverage the self-organizing nature of protein crystallization, under artificial intervention (code), to “grow” microscopic artworks with complex geometric structures on specific biological substrates.

Automation of protein crystallization scaleup via Opentrons-2 liquid handling

Description: This paper introduces a highly integrated automated system called Piccolo, which is specifically designed to address the bottlenecks in protein production. The core innovation of this system lies in its ability to automate the entire process from cell culture, growth monitoring (OD value), induction of expression, to protein purification. Technical highlights: Unlike traditional timed operations, the Piccolo system can dynamically adjust (Reschedule) the induction time based on the real-time growth curve of cells in each 24-well bioreactor. This means that the robot can “sense” the rhythm of life and add the inducer at the most appropriate moment.

What I intented to do

This system not only supports the cultivation of Escherichia coli, but also that of insect cells (animal-derived cells). In my exploration of biological art, this provides an opportunity to view the “molecular purification” process as “artistic transformation of matter”. It demonstrates how, through precise automated control, pure biological art media with specific colors (such as fluorescent proteins) can be extracted from turbid biomass.

Final Idea

Week 1 Lab: Pipetting

Individual Final Project

Group Final Project