Week 1 HW: Principles and Practices

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

I am interested in developing a biological engineering approach that uses living organisms to help us understand and preserve archaeological materials and sites. Specifically, I want to explore how microorganisms could be used to study how materials such as stone, soil, or ceramics change over time, or how biological growth can be guided to protect fragile archaeological surfaces.

This idea is interesting to me because archaeological materials are shaped by long-term interactions between the environment and living systems. Instead of seeing biology only as a source of damage, I am curious about how biological processes could become a tool for analysis or conservation. For an HTGAA project, I want to explore how growth, decay, and environmental conditions can be treated as design variables to better understand the past and develop new, more sustainable conservation methods.

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.

One key governance and policy goal for this application is to ensure that biological tools used in archaeological contexts do not cause harm to people, sites, or cultural heritage. Because archaeological materials are fragile and often irreplaceable, it is important that biological interventions are carefully controlled and ethically guided.

A first sub-goal is non-malfeasance, meaning preventing physical or biological damage. This includes ensuring that any microorganisms used cannot spread uncontrollably, alter archaeological materials in irreversible ways, or disrupt surrounding ecosystems. Strict containment, reversibility, and testing protocols would be essential before any real-world application.

A second sub-goal is cultural and community respect. Archaeological sites are often connected to living communities and cultural identities. Governance frameworks should ensure that local stakeholders are informed, consulted, and involved in decisions about the use of biological technologies on heritage sites. This helps prevent extractive or colonial practices and supports ethical collaboration.

A third sub-goal is responsible knowledge use. Research outcomes, data, and tools should be shared transparently for conservation and educational purposes, while avoiding misuse, commercialization without consent, or applications that prioritize novelty over preservation. Together, these goals help ensure that biological engineering contributes to an ethical, respectful, and sustainable future for archaeology.

3. Next, describe at least three different potential governance “actions” by considering the four aspects below (Purpose, Design, Assumptions, Risks of Failure & “Success”)

Action 1 : Ethical Review Requirement for Biological Interventions in Archaeology

(New rule / requirement — actors: universities, museums, heritage authorities)

• Purpose Currently, ethical review processes mainly focus on research involving humans, while biological interventions on archaeological sites are often evaluated only for scientific merit. I propose creating a specific ethical review requirement for any use of living organisms in archaeological contexts, focused on protecting sites, materials, and surrounding ecosystems.

• Design This action would require interdisciplinary review committees including archaeologists, biologists, conservation experts, and ethicists. Universities, museums, and heritage authorities would require approval from these committees before allowing biological tools to be tested or deployed at archaeological sites. Researchers would opt in by agreeing to this process as a condition of site access.

• Assumptions This proposal assumes that such committees can be formed with sufficient expertise and that ethical review will meaningfully guide research rather than becoming a purely bureaucratic step. It also assumes researchers will accept additional oversight.

• Risks of Failure & “Success” This approach could fail if reviews become symbolic or overly slow, discouraging exploratory research. If highly successful, it could unintentionally favor large institutions with more resources, making it harder for smaller or community-based projects to participate.

Action 2: Incentives for Reversible and Low-Risk Biological Methods

(Incentive — actors: funding agencies, research sponsors)

• Purpose At present, research funding often prioritizes novelty and impact over safety, reversibility, or long-term risk. I propose creating funding incentives that prioritize biological methods which are reversible, low-risk, and environmentally contained when used in archaeological contexts.

• Design Funding agencies and foundations would include ethical and safety criteria in grant calls, explicitly rewarding projects that minimize ecological and cultural risk. Researchers would voluntarily design projects to meet these criteria, and reviewers would need guidance on how to evaluate risk and reversibility alongside scientific merit.

• Assumptions This proposal assumes that funding incentives can meaningfully influence research behavior and that risk can be reasonably assessed in advance. It also assumes that safer approaches will still allow for meaningful scientific insight.

• Risks of Failure & “Success” The action may fail if incentives are too weak or applied superficially. If overly successful, it could discourage more experimental or unconventional approaches, potentially slowing innovation in the field.

Action 3: Community Co-Governance of Bio-Archaeological Applications

(Governance strategy — actors: local communities, researchers, heritage organizations)

• Purpose Decisions about technological interventions at archaeological sites are often made by researchers or institutions, with limited involvement from local or descendant communities. I propose a co-governance approach in which communities connected to archaeological sites participate directly in decisions about the use of biological tools.

• Design This would involve early consultation processes, accessible communication (non-technical language), and shared decision-making authority. Researchers and institutions would need to allocate time and resources to support meaningful participation and be willing to adapt or halt projects based on community input.

• Assumptions This approach assumes that communities wish to participate, that diverse perspectives can be reconciled, and that scientific and local knowledge can productively inform each other.

• Risks of Failure & “Success” Co-governance could fail if participation is symbolic rather than meaningful or if internal conflicts arise. If highly successful, it may slow down research or limit certain projects, but this may be an acceptable trade-off in contexts involving irreversible cultural heritage.

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. The following is one framework but feel free to make your own:

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.

Based on the scoring, I would prioritize a combination of Option 1 (Ethical Review Requirement) and Option 2 (Incentives for Reversible and Low-Risk Methods). This recommendation is directed to international organizations such as UNESCO and the United Nations, which play a key role in setting global norms for cultural heritage protection and emerging technologies.

Option 1 should function as a global baseline. It scores highest in preventing biosecurity, lab safety, and environmental harm, which is especially important for archaeological sites that are fragile and irreversible. An international ethical review framework, supported by UNESCO and the UN, could guide national and local authorities while allowing for contextual adaptation. The main trade-off is the potential increase in administrative complexity and slower research approval processes.

Option 2 should complement this baseline by encouraging safer and reversible biological methods through funding priorities and international research programs. This incentive-based approach preserves flexibility and innovation while reinforcing ethical behavior.

Option 3 (Community Co-Governance) should be promoted by UNESCO and the UN as a guiding principle, particularly in culturally sensitive contexts. While it may reduce speed and scalability, it strengthens legitimacy, equity, and long-term trust in the governance of biological tools applied to archaeology.

This approach assumes that UNESCO and the UN can influence national policies through standards, funding, and guidance, but there is uncertainty around consistent adoption and enforcement across different regions.

                       - ASSIGNMENT(Week 2 Lecture Prep) -

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 is the enzyme that copies DNA. It is very accurate, but not perfect:

• It makes about 1 mistake in every 10 million DNA letters.

• With correction systems, the final error rate is about 1 mistake in 1 billion letters.

The human genome has about 3 billion DNA letters, so without correction there would be many mistakes every time DNA is copied. How does biology fix this?

• DNA polymerase checks its own work (proofreading).

• Cells have repair systems that fix mistakes.

• Harmful mutations are reduced over time by natural selection.

3. 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 made of three-letter codons and there are 64 possible codons but only 20 amino acids, most amino acids can be encoded by more than one codon. This means that the same protein can be written in many different DNA sequences. For an average human protein, the number of possible DNA sequences that could code for it is extremely large.

However, in practice, not all of these DNA sequences work equally well. Some codons are translated more efficiently in human cells, while others slow down protein production. Certain DNA sequences can form mRNA structures that interfere with translation or make the mRNA unstable. In addition, some sequences can disrupt regulatory signals or affect how the protein folds during synthesis. As a result, only a subset of possible DNA codes is actually effective for producing the desired protein in cells.

Homework Questions from Dr. LeProust:

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

Oligos are made using a chemical method where DNA is built one letter at a time on a solid surface. This method is called phosphoramidite synthesis, and it is the standard method used today.

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

Each time a new DNA letter is added, there is a small chance of error.When the oligo gets longer, these small errors add up. Because of this:

• Many DNA strands end up incomplete
• Many have mistakes
• Very few are perfect full-length oligos

After about 200 nucleotides, the number of correct oligos becomes very low.

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

To make a 2000 bp gene, you would need to add 2000 DNA letters in a row. With so many steps, almost every DNA molecule will contain errors. So, direct synthesis does not work for long genes. Instead, scientists make short oligos and then join them together to build long genes.

Homework Question from George Church:

1. What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency”?

Animals need 20 amino acids to make proteins, but they cannot make all of them. The 10 essential amino acids (they must come from the diet) are: Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine, and Arginine (Arginine is essential especially during growth.)

Because animals cannot make these amino acids themselves, they depend on their food to get them.

The “Lysine Contingency” refers to the idea that lysine availability strongly limits animal growth, especially because lysine is often low in plant-based foods. Since lysine is essential and cannot be synthesized by animals, a lack of lysine can directly restrict protein synthesis and growth. This highlights how animal biology is dependent on plants and microbes, which can make lysine. It supports the idea that animal evolution and nutrition are constrained by the availability of lysine in the environment.

Week 2 HW: DNA Read, Write, & Edit

Part 1: Benchling & In-silico Gel Art

Create a pattern/image in the style of Paul Vanouse’s Latent Figure Protocol artworks.

Part 2: Gel Art - Restriction Digests and Gel Electrophoresis

Optional for Committed Listeners

Part 3: DNA Design Challenge

3.1 Choose your protein

For this assignment, I chose Collagen Type I (alpha 1 chain). I selected this protein because collagen is the main structural protein found in bone, teeth, and connective tissues. In archaeology, collagen is extremely important because it can survive for thousands of years in skeletal remains and artifacts made from bone or leather. It is widely used in radiocarbon dating and paleoproteomics to identify species and study ancient diets. Since I am interested in archaeology, this protein connects molecular biology with archaeological research.

Using UniProt, I obtained the protein sequence for human Collagen Type I alpha 1 chain (COL7A1).

sp|Q02388-1|CO7A1_HUMAN Isoform 1 of Collagen alpha-1(VII) chain OS=Homo sapiens OX=9606 GN=COL7A1 MTLRLLVAALCAGILAEAPRVRAQHRERVTCTRLYAADIVFLLDGSSSIGRSNFREVRSF LEGLVLPFSGAASAQGVRFATVQYSDDPRTEFGLDALGSGGDVIRAIRELSYKGGNTRTG AAILHVADHVFLPQLARPGVPKVCILITDGKSQDLVDTAAQRLKGQGVKLFAVGIKNADP EELKRVASQPTSDFFFFVNDFSILRTLLPLVSRRVCTTAGGVPVTRPPDDSTSAPRDLVL SEPSSQSLRVQWTAASGPVTGYKVQYTPLTGLGQPLPSERQEVNVPAGETSVRLRGLRPL TEYQVTVIALYANSIGEAVSGTARTTALEGPELTIQNTTAHSLLVAWRSVPGATGYRVTW RVLSGGPTQQQELGPGQGSVLLRDLEPGTDYEVTVSTLFGRSVGPATSLMARTDASVEQT LRPVILGPTSILLSWNLVPEARGYRLEWRRETGLEPPQKVVLPSDVTRYQLDGLQPGTEY RLTLYTLLEGHEVATPATVVPTGPELPVSPVTDLQATELPGQRVRVSWSPVPGATQYRII VRSTQGVERTLVLPGSQTAFDLDDVQAGLSYTVRVSARVGPREGSASVLTVRREPETPLA VPGLRVVVSDATRVRVAWGPVPGASGFRISWSTGSGPESSQTLPPDSTATDITGLQPGTT YQVAVSVLRGREEGPAAVIVARTDPLGPVRTVHVTQASSSSVTITWTRVPGATGYRVSWH SAHGPEKSQLVSGEATVAELDGLEPDTEYTVHVRAHVAGVDGPPASVVVRTAPEPVGRVS RLQILNASSDVLRITWVGVTGATAYRLAWGRSEGGPMRHQILPGNTDSAEIRGLEGGVSY SVRVTALVGDREGTPVSIVVTTPPEAPPALGTLHVVQRGEHSLRLRWEPVPRAQGFLLHW QPEGGQEQSRVLGPELSSYHLDGLEPATQYRVRLSVLGPAGEGPSAEVTARTESPRVPSI ELRVVDTSIDSVTLAWTPVSRASSYILSWRPLRGPGQEVPGSPQTLPGISSSQRVTGLEP GVSYIFSLTPVLDGVRGPEASVTQTPVCPRGLADVVFLPHATQDNAHRAEATRRVLERLV LALGPLGPQAVQVGLLSYSHRPSPLFPLNGSHDLGIILQRIRDMPYMDPSGNNLGTAVVT AHRYMLAPDAPGRRQHVPGVMVLLVDEPLRGDIFSPIREAQASGLNVVMLGMAGADPEQL RRLAPGMDSVQTFFAVDDGPSLDQAVSGLATALCQASFTTQPRPEPCPVYCPKGQKGEPG EMGLRGQVGPPGDPGLPGRTGAPGPQGPPGSATAKGERGFPGADGRPGSPGRAGNPGTPG APGLKGSPGLPGPRGDPGERGPRGPKGEPGAPGQVIGGEGPGLPGRKGDPGPSGPPGPRG PLGDPGPRGPPGLPGTAMKGDKGDRGERGPPGPGEGGIAPGEPGLPGLPGSPGPQGPVGP PGKKGEKGDSEDGAPGLPGQPGSPGEQGPRGPPGAIGPKGDRGFPGPLGEAGEKGERGPP GPAGSRGLPGVAGRPGAKGPEGPPGPTGRQGEKGEPGRPGDPAVVGPAVAGPKGEKGDVG PAGPRGATGVQGERGPPGLVLPGDPGPKGDPGDRGPIGLTGRAGPPGDSGPPGEKGDPGR PGPPGPVGPRGRDGEVGEKGDEGPPGDPGLPGKAGERGLRGAPGVRGPVGEKGDQGDPGE DGRNGSPGSSGPKGDRGEPGPPGPPGRLVDTGPGAREKGEPGDRGQEGPRGPKGDPGLPG APGERGIEGFRGPPGPQGDPGVRGPAGEKGDRGPPGLDGRSGLDGKPGAAGPSGPNGAAG KAGDPGRDGLPGLRGEQGLPGPSGPPGLPGKPGEDGKPGLNGKNGEPGDPGEDGRKGEKG DSGASGREGRDGPKGERGAPGILGPQGPPGLPGPVGPPGQGFPGVPGGTGPKGDRGETGS KGEQGLPGERGLRGEPGSVPNVDRLLETAGIKASALREIVETWDESSGSFLPVPERRRGP KGDSGEQGPPGKEGPIGFPGERGLKGDRGDPGPQGPPGLALGERGPPGPSGLAGEPGKPG IPGLPGRAGGVGEAGRPGERGERGEKGERGEQGRDGPPGLPGTPGPPGPPGPKVSVDEPG PGLSGEQGPPGLKGAKGEPGSNGDQGPKGDRGVPGIKGDRGEPGPRGQDGNPGLPGERGM AGPEGKPGLQGPRGPPGPVGGHGDPGPPGAPGLAGPAGPQGPSGLKGEPGETGPPGRGLT GPTGAVGLPGPPGPSGLVGPQGSPGLPGQVGETGKPGAPGRDGASGKDGDRGSPGVPGSP GLPGPVGPKGEPGPTGAPGQAVVGLPGAKGEKGAPGGLAGDLVGEPGAKGDRGLPGPRGE KGEAGRAGEPGDPGEDGQKGAPGPKGFKGDPGVGVPGSPGPPGPPGVKGDLGLPGLPGAP GVVGFPGQTGPRGEMGQPGPSGERGLAGPPGREGIPGPLGPPGPPGSVGPPGASGLKGDK GDPGVGLPGPRGERGEPGIRGEDGRPGQEGPRGLTGPPGSRGERGEKGDVGSAGLKGDKG DSAVILGPPGPRGAKGDMGERGPRGLDGDKGPRGDNGDPGDKGSKGEPGDKGSAGLPGLR GLLGPQGQPGAAGIPGDPGSPGKDGVPGIRGEKGDVGFMGPRGLKGERGVKGACGLDGEK GDKGEAGPPGRPGLAGHKGEMGEPGVPGQSGAPGKEGLIGPKGDRGFDGQPGPKGDQGEK GERGTPGIGGFPGPSGNDGSAGPPGPPGSVGPRGPEGLQGQKGERGPPGERVVGAPGVPG APGERGEQGRPGPAGPRGEKGEAALTEDDIRGFVRQEMSQHCACQGQFIASGSRPLPSYA ADTAGSQLHAVPVLRVSHAEEEERVPPEDDEYSEYSEYSVEEYQDPEAPWDSDDPCSLPL DEGSCTAYTLRWYHRAVTGSTEACHPFVYGGCGGNANRFGTREACERRCPPRVVQSQGTG TAQD

3.2 Reverse Translation

According to the Central Dogma, DNA is transcribed into RNA and then translated into protein. Since each amino acid is encoded by a three-nucleotide codon, we can work backwards from a protein sequence to determine a possible DNA sequence.

For the partial collagen sequence shown previously:

• Protein sequence (partial): MTLRLLVAALCAGILAEAPRVRAQHRERVTCTRLYAADIVFLLDGSSSIGRSNFREVRSF

Using NCBI, one possible nucleotide sequence that encodes this amino acid sequence is:

• DNA sequence (one possible version):

    1 aattcccaca aaccctgctg acttgacccc attggcccag acccctgttc cctgccactg
   61 gatgagggct cctgcactgc ctacaccctg cgctggtacc atcgggctgt gacaggcagc
  121 acagaggcct gtcacccttt tgtctatggt ggctgtggag ggaatgccaa ccgttttggg
  181 acccgtgagc ctgcgagcgc cgctgcccac cccgggtgtc cagagccagg ggacaggtac
  241 tgcccaggac tgaggcccag ataatgagct gagattcagc atcccctgga ggacgtcggg
  301 gtctcagcag aaccccactg tccctcccct tggtgctaga ggcttgtgtg cacgtgagcg
  361 tcggttgtgc agttcccgtt atttcagtga cttggtcccg tgggtctaac cttcccccct
  421 gtggacaaac ccccattgtg gctccn
  

Explanation:

ATG → Methionine (M)

GGT → Glycine (G)

CCT → Proline (P)

CGT → Arginine (R)

Because the genetic code is degenerate (multiple codons can encode the same amino acid), this is only one possible DNA sequence. Many other nucleotide sequences could produce the exact same collagen protein segment.

3.3 Codon Optimization

After obtaining a possible DNA sequence from reverse translation, the next step is codon optimization. Although multiple DNA sequences can encode the same protein, different organisms prefer certain codons over others. This is known as codon bias. If a gene contains many codons that are rarely used in the host organism, protein production may be slow or inefficient. For this assignment, I chose to optimize the collagen sequence for Escherichia coli because it is widely used in biotechnology. E. coli grows quickly, is inexpensive to culture, and is commonly used for recombinant protein production. Using an online codon optimization tool, the DNA sequence was adjusted to:

• Use codons that are frequently used in E. coli
• Improve translation efficiency
• Avoid problematic sequences (such as strong secondary structures or unwanted restriction sites)

Importantly, codon optimization does not change the amino acid sequence of the protein. It only changes the nucleotide sequence to improve expression in the chosen organism. By optimizing the codons for E. coli, the collagen gene would be more efficiently transcribed and translated, leading to higher protein yield.

• Improved ADN: GCCGCAACCACCTGCTGCTGCGCCTGCGCCGCGGCCTGCTGTTGCACCGGCTGCACCGGCGCGTGTACCACCGGCGCATGCTGCTGCTGCGCGACCACCGGTGGTTGCTGTTGTGCGGGTGCCTGCTGCTGTTGCACCGGCACCACCTGTTGCTGCACCGGCTGCTGCGCATGTACCGGCGGAGCCACCGGCGCGGGCGGTGGCTGCACCTGTTGCACCGGCTGCGCATGTACCGGCTGCTGCACCGCGTGCGCCTGCTGCTGCACCGGCTGCGGCTGCACTGGCGGTACTGCATGCTGCGCGACCTGCGGCGGCGGCTGCACCGGCACCGGTGCCTGTGCCGGCGGCTGCGCGGGCTGCGCGTGCGCGGGCGCCGGTGGCTGCTGCACCGGCACCTGCGCCTGTTGCTGCACCACCACCACCGGCACCTGTACAGCGACCGGCGGCACCGGCGGCTGCACCGGCACCGGCGGTGCGGGTGGCGGCGCGGCGACCGGTTGTTGTGCAGCGTGCTGCGGCACCACCACCACAGGTGGTGGTGCGTGTTGCTGCGGCACCGGCGCGGGCTGCTGCACCGGCTGTGGTGCGGGCTGCGGCTGTTGCGGCTGTACCGGCTGTTGCTGCGCGTGTTGCTGTTGTGGCGGTGGCACCGGTACCTGCTGCGCGGGCGCGGGTTGCTGTGCCGGCGGCGGCGGCGCCTGTGCGGGTGGCACCGCGTGCACCGGCTGCTGCTGCGCCGGAGGCGCGTGCACCGGCGCCGGTGGTTGCTGTTGCGCGGGTGCCACCGCGGCAACCGGCGCGGGCTGTACCGGCGCAGGCGCAACCACCTGCGCAGGTTGTGCGACGTGCTGCTGTTGTACAGGTGGCGCGGGCGGCGCCTGTGGCACGTGTGGCGGCGGCGGTACCTGCACCTGTGCCGGCTGCGCGGGCGCAGCGTGTTGTTGCTGCGCGTGCACGGGCACCTGCTGTTGCACCTGCTGTTGCTGTACCACCGGGGGCACCGGCTGCACCGCAGGTGCCGGCGGTTGTACCACCGGTACCGGTACCGGTTGTGCGTGCGGCACCGGCGCGGGCTGCGGCACCTGCGGCGGTACCACCGGTACCGGCTGCGCGGGTACCACCTGCTGCTGCGGCACCACCGCGACGACCACCTGCGCAGGTACCGGTGCGTGCACCACCGGTGGCACCTGCTGCTGTGGCACCGGCGGTGGTACCTGCACAGCGGCCTGCTGCACCACCTGCTGTTGCTGCTGTTGCACCGGCACCGGTGGTGCGTGTGCGGCGGCCTGCTGCTGCTGTTGCGCGACGACCGGCACCGGCGGATGTACCTGCTGCAATTAA

3.4 You have a sequence! Now what?

Now that I have a codon-optimized DNA sequence for collagen, the next step is to produce the protein. One common method is a cell-dependent system. In this approach, the optimized DNA sequence is inserted into a plasmid (a small circular DNA molecule). The plasmid is then introduced into Escherichia coli cells through transformation. Once inside the cell:

• The DNA is transcribed into mRNA.
• The mRNA is translated by ribosomes into the collagen protein.
• The bacterial cell essentially acts as a biological factory, producing the protein as it grows.

Another option is a cell-free system. In this method, instead of using living cells, the DNA is added to a solution containing the necessary molecular machinery (ribosomes, enzymes, nucleotides, amino acids). The transcription and translation processes occur in a test tube, producing the protein directly. This method is faster and more controlled, but usually more expensive. In both cases, the DNA sequence follows the Central Dogma: DNA → RNA → Protein, resulting in the production of the collagen protein.

Part 4: Prepare a Twist DNA Synthesis Order

This project uses E. coli and collagen to create reproducible patterns that simulate organic components of ancient artifacts, such as textiles or adhesives. Collagen acts as a structural scaffold to hold proteins in place, while engineered E. coli produce proteins that form visible patterns. Automation ensures precision and repeatability, allowing us to study how these materials might degrade or be preserved over time, providing insights into experimental archaeology and conservation.

Week 3 HW: Lab Automation

Assignment: Python Script for Opentrons Artwork

This design is inspired by traditional Inca geometric art, particularly the tocapu textile patterns of the Inca Empire. The composition features a symmetrical stepped cross motif enclosed within a square, referencing the Andean worldview and the symbolic structure of the Chakana (Andean cross). The use of straight lines and geometric repetition reflects the mathematical precision and cosmological symbolism characteristic of Inca visual culture. (https://opentrons-art.rcdonovan.com/?id=6ef1d0494o5n1p7)

Post-Lab Questions

1. Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications.

A relevant example is the paper “An open-source automated platform for high-throughput RT-qPCR testing” developed during the COVID-19 pandemic. In this work, researchers used the Opentrons OT-2 liquid handling robot to automate RNA extraction and RT-qPCR setup.

The system enabled scalable, low-cost diagnostic testing by reducing manual pipetting steps, minimizing human error, and increasing reproducibility. This study demonstrated how open-source automation tools can expand access to molecular diagnostics, especially in resource-limited settings.

The novelty of this application lies in democratizing laboratory automation—allowing smaller labs to perform high-throughput testing without expensive proprietary systems.

LINK: https://pubmed.ncbi.nlm.nih.gov/34260637/

2. Write a description about what you intend to do with automation tools for your final project. You may include example pseudocode, Python scripts, 3D printed holders, a plan for how to use Ginkgo Nebula, and more.

For my final project, I plan to use laboratory automation tools to develop controlled collagen-based biomaterials inspired by ancient Andean techniques. Collagen will serve as a structural matrix that mimics organic components found in archaeological artifacts such as textiles, adhesives, or composite materials. By using automated liquid handling, I aim to precisely control mixing ratios and spatial deposition of biological components within the collagen scaffold. This will allow the creation of reproducible material samples that can be used to study degradation processes, conservation strategies, or experimental archaeology models.

Automation ensures precision and repeatability, which are essential when comparing material behavior under different environmental conditions.

For my final project, I plan to use two main pieces of equipment to create collagen-based materials inspired by archaeological patterns. First, I will use the Opentrons OT-2 liquid handling robot. This robot allows precise mixing of liquids and can deposit the mixture in exact locations with consistent volumes. In my project, I will prepare different mixtures of collagen and pigments that mimic the colors and textures of ancient textiles or other organic components found in archaeological artifacts. The robot will then deposit these mixtures according to a predetermined pattern, such as geometric motifs inspired by Inca textiles. Using the robot ensures that each replica is precise and reproducible, allowing me to create multiple samples under the same conditions without human error.

Second, I will use 3D-printed holders or molds to support the materials during deposition. These molds will be designed to match the shape of specific archaeological patterns, such as squares or other geometric compartments. The robot will deposit the collagen mixtures into these molds, and once the collagen sets, the molds can be removed to reveal a precise replica of the intended pattern. This combination of automation and custom molds allows me to accurately reproduce complex designs and study how these materials behave, degrade, or can be conserved, providing a controlled and repeatable approach to experimental archaeology.

Final Project Ideas

Week 1 Lab: Pipetting

Individual Final Project

Group Final Project