This episode of "Matters Microbial" features Dr. Mark Martin interviewing Sebastian Kochoa, a self-funded citizen scientist dedicated to making science accessible and affordable. Kochoa shares his journey outside traditional academia, emphasizing curiosity-driven research and community building. The discussion highlights several of his innovative, open-source scientific tools, including a safe, blue-light LED transilluminator for DNA visualization and a custom palette of chromoprotein-expressing E. coli strains for engaging microbiology education. Kochoa also presents a simplified turbidostat for measuring microbial growth. He elaborates on his philosophy of creating "good enough" tools that significantly undercut commercial prices, fostering self-sufficiency among biologists. Looking to the future, Kochoa expresses a desire to blend science with art, focusing on bio-artistic flower design, while continuing to champion the vast, underexplored potential of microbiology and interdisciplinary scientific inquiry.
Exploring Citizen Science and Open-Source Tools with Sebastian Kochoa
0:00 Introduction to "Matters Microbial": Host Dr. Mark Martin introduces the ninth episode, celebrating microbiology, microbiologists, and microbial centrism. He pays tribute to microbial pioneer Carl Woese and shares personal inspirational pins promoting authenticity and curiosity.
2:18 Microbiology Class Update: Martin describes his students' current projects, involving single-colony PCR and sequencing of microbes from water bottles and marine samples (including agar degraders, unusual colony morphologies, and filamentous microbes) to identify isolates.
3:34 Introducing Sebastian Kochoa: Kochoa is presented as a citizen scientist with boundless energy and diverse interests, known for making scientific tools accessible to others.
4:33 The Blue-Light Transilluminator: Kochoa designed and built an open-source, LED-driven transilluminator that safely visualizes DNA on agarose gels using blue light, in contrast to expensive and potentially harmful UV alternatives. This device costs approximately $64, significantly less than commercial units priced around $600.
6:13 Philosophy of Tool Development: As a self-funded biologist, Kochoa's motivation for building tools stems from "necessity and borderline desperation," aiming to make basic research accessible by creating affordable, "good enough" instruments that challenge the high markups of commercial apparatuses.
10:10 Chromoprotein-Expressing E. coli Strains: Kochoa developed a diverse set of E. coli strains expressing various chromoproteins (red, orange, yellow, green, blue, purple) that are visible in daylight, making them ideal for engaging students in microbial handling. He utilized open-source genetic sequences and traditional cloning techniques.
12:54 Open-Source and Community Focus: Kochoa's work is rooted in open-source principles, using public domain genetic sequences and sharing his creations for educational and academic use. He envisions a future where students contribute to creating new color variations.
15:20 Fostering Curiosity in Students: Martin notes that Kochoa's colorful strains prompted students to observe unusual mixed colonies, underscoring the value of student observation and inquiry.
16:34 Simplified Turbidostat: Kochoa also developed a simplified turbidostat for measuring bacterial growth rates, making complex instrumentation more user-friendly.
18:02 Sebastian's Citizen Science Journey: Kochoa, who dropped out of university for financial reasons, pursued his passion for science independently, eventually co-founding Binomica Labs. He advocates for curiosity-driven research outside academic funding pressures, emphasizing the vast, unexplored microbial world and the affordability of modern scientific exploration.
24:26 Tool Building as a Life Focus: Having gained expertise in building infrastructure due to early limitations, Kochoa's current life's focus is on creating tools to empower others in scientific exploration.
25:06 Interdisciplinary Approach: Martin highlights Kochoa's unique blend of electronic engineering and molecular biology skills, which enables him to bridge the gap between tool creation and biological research.
30:44 Future Aspirations: Bio-Art and Flower Design: Kochoa's ultimate goal is to become a "flower designer," creating novel plant morphologies and integrating students into bio-art projects, defining his career path as an "uncareer" driven by passion rather than conventional employment.
36:17 Interconnectedness of Biology: Kochoa explains that plant engineering fundamentally relies on understanding and manipulating microbes like Agrobacterium, highlighting the interdisciplinary nature of scientific endeavors.
39:29 Advice for Listeners: Kochoa encourages listeners to "explore their nature" and the microbes around them, emphasizing that current tools make Homebrew microbiology more accessible than ever. He mentions the ongoing discoveries in archaea and the historical impact of undergraduate discoveries like Thermus aquaticus (found by Hudson Freeze with Tom Brock), essential for PCR technology.