Bio Design & Bio Fabrication
The final week of HTGAA 2026 was curated by Suzanne Lee and Christina Agapakis — two figures who embody different traditions of the same question: what does it mean to design with living biology? Lee from material biofabrication (Biocouture, mycelium, kombucha leather), Agapakis from the interface between science, art, and scientific writing. The week functioned as a conceptual frame for what each student had built over the semester: not mastery of techniques, but the ability to articulate a project of one's own with rigor and with meaning.
The week's thesis — that bio-design and bio-fabrication are not stages that follow scientific discovery but independent forms of knowledge generation — describes exactly what Aim 1 of Füzi Poiesis attempts to demonstrate. The mathematical model is not a post-hoc validation of the design: it is the design. The three-strain ring topology is not proposed because it is known to work — it is proposed because the equations demonstrate that its containment properties are qualitatively distinct from any two-strain system. The computational design is the experiment.
Completing Füzi Poiesis — The Last Hours
Week 14 was not only a week of reading and reflection — it was the week that closed the cycle of work begun in January. In the hours before the May 13 presentation, following a late-night review session with Benjamín Arias (tutor of the SynBio USFQ Node), the final substantive revisions to the presentation were made. What follows is the log of that work.
Füzi Poiesis — Computational Proof of Concept
At the close of Week 14, Aim 1 of Füzi Poiesis is complete. The four computational and DNA design deliverables have been produced, internally validated, and documented with sufficient detail for independent reproduction.
The containment property of the three-strain ring does not improve the kinetic escape time relative to a two-strain system — the order of magnitude is the same (~decades with N=10⁸, μ_mut=10⁻⁸, f_escape=10⁻⁴). The advantage is topological: in a closed pair, a mutant that restores its auxotrophy can persist parasitically while its partner continues supplying metabolite. In the ring of three, restoring independence from one partner still leaves the mutant without the metabolite of the third strain, whose disappearance is a direct consequence of the cycle breaking. The ring fails closed; the pair fails open. This is the structural distinction the project demonstrates.
Committed Listeners — SynBio USFQ Node
On May 13, 2026, Füzi Poiesis was presented to the Committed Listeners of the SynBio USFQ Node. The presentation consisted of three slides, following the logic of the course: problem → computational evidence → progression toward the real world. Total duration was approximately five minutes, followed by audience questions.
The phrase "go ahead and upload them" — the final permission from a tutor who accompanied the project from the ODE models to the lake map — is not trivial in the context of a course where scientific validation and community validation are equally serious. Füzi Poiesis does not yet have permission from the Lafkenche community to enter the lake. It has, for now, its tutor's permission to upload the slides. Those two validations operate at entirely different scales — and the project recognizes them as such.
Aim 1 is complete. The lake is still waiting. I have given it everything I had.
What it means to design with biology
Week 14 of HTGAA does not close just a semester — it closes an argument that began in January with the question of what is possible with synthetic biology when you have access to the tools. Füzi Poiesis's answer is a specific proposal: design the mathematical conditions under which biogeochemical resilience can be encoded into the evolutionary architecture of a synthetic consortium.
The methodological contribution of Füzi Poiesis is not in any individual tool — Benchling, Python, SciPy, the RBS Calculator — but in using Lyapunov stability theory to establish a topological distinction as a rigorous mathematical result, not as an intuition. That is bio-design in the sense that Agapakis and Lee proposed this week: not applying biology to a problem, but letting the structure of the problem reveal which biological architecture belongs to it.
Lake Budi has three documented pathologies: fecal coliform contamination, hydrogen sulfide accumulation, and internal phosphorus eutrophication. The consortium has three strains, each targeting one pathology, coupled in a dependency cycle that replicates the cooperative structure of a healthy ecosystem. The solution is not proposed because it is known to work — it is proposed because the equations demonstrate that its properties are qualitatively distinct from any two-strain alternative. The design is the argument.
The model assumes a well-mixed environment and kinetic parameters from E. coli K-12 under amino acid restriction — a laboratory strain under controlled conditions, not a halotolerant strain in brackish water at 5–15 g/L NaCl with benthic anoxia. If the model is recalibrated with Halomonas elongata or native Budi strain parameters in Aim 2 and the interior fixed point loses stability, the three-strain ring requires redesign. The benthic metagenome of Lake Budi does not exist in the published literature: horizontal gene transfer risk cannot be quantified without it. That too is a result of Aim 1 — knowing precisely what is not yet known.
Füzi Poiesis — Final Project
Genetic design, mathematical modeling, Lyapunov stability analysis, and the ethical framework for deployment under Lafkenche governance. All of Aim 1 documented.
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