Week 11 HW — Building Genomes
Part A: The 1,536 Pixel Artwork Canvas | Collective Artwork
Reflection on Collective Contribution
Interestingly, the pixels I initially contributed are no longer individually identifiable in the final composition.
Rather than seeing this as a loss, I interpret it as a key feature of the system. The artwork demonstrates how individual inputs dissolve into a collective output, similar to biological systems where single components rarely remain distinguishable but still contribute to the overall structure.
This reflects an important shift in thinking: from authorship to participation, from control to emergence.
From a design perspective, this is highly relevant to my broader research, where I am interested in systems that produce spatial and material outcomes through distributed, local interactions rather than centralized control. The system does not preserve individuality — it amplifies collectivity.
Cell-Free Systems & Fluorescent Proteins
Part B — Cell-Free System as a Designed Platform
A cell-free system can be understood as a modular biological toolkit composed of:
- E. coli lysate → provides transcription and translation machinery
- Salts and buffers → stabilize biochemical conditions
- Energy system → drives protein synthesis
- Amino acids → building blocks
- Additives → enhance performance
What makes this system powerful is not just its biological function, but its tunability.
Two energy strategies illustrate this:
- PEP system → rapid, high-output expression
- NMP + glucose system → slower, sustained production
This demonstrates that biological output can be shaped not only by genetic design, but also by system composition.
Part C — Fluorescent Proteins as Outputs
Different fluorescent proteins behave differently in cell-free systems due to variations in:
- folding speed
- maturation time
- environmental sensitivity
Proteins such as sfGFP perform reliably due to fast folding, while others like mRFP1 require longer time to mature, resulting in delayed signal.
This highlights that biological outputs are not only determined by sequence, but also by temporal dynamics.
Hypothesis — System Optimization
I hypothesize that adjusting magnesium concentration and optimizing the energy system will improve fluorescence output for slower-maturing proteins such as mRFP1.
Magnesium ions support ribosome activity and protein folding, while sustained energy availability improves translation efficiency over time. Together, these factors are expected to enhance total protein production and allow sufficient time for maturation.
Design Reflection
This experiment shifts the role of biology from something that is observed to something that is actively designed and tuned.
For my research, this is particularly important. It suggests that biological systems can be treated similarly to materials — where performance is shaped not only by composition, but also by conditions, timing, and environment.
In this sense, cell-free systems are not just experimental tools, but a framework for designing responsive systems, where biological processes can be integrated into spatial and material contexts.