Podcast with Yaki Setty on synthetic biology and agent-based modeling

Can you grow an organ inside a computer , and would it teach you something biology alone cannot? Computational biologist Yaki Setty describes how agent-based models of stem cell development can reconstruct the pancreas, the C. elegans gonad, and even parts of the brain from first principles, revealing emergent properties that no single experiment could predict. Subscribe for more from the Convergent Science Network podcast series. Yaki Setty joins Paul Verschure and Tony Prescott at the BCBT summer school to present his approach to synthetic organ development using autonomous agent-based modeling. Each cell in the simulation is defined by biologically justified state diagrams , covering differentiation, proliferation, movement, and environmental sensing , with every parameter traceable to published experimental data. The environment is modeled as a three-dimensional grid of voxels containing chemical gradients governed by differential equations, and cells interact with this environment and with each other to produce emergent organ structures. The discussion walks through three applications of increasing complexity. The pancreas model, with over 150 cell states, reproduces the characteristic cauliflower-like morphology of pancreatic tissue and demonstrates how blood vessel scaffolding guides cell aggregation. The C. elegans gonad model achieves quantitative predictions about cell numbers, zone lengths, and cell cycle ratios with far fewer states, validated against experimental measurements within weeks rather than years. The conversation also touches on extending these methods to neural development, where the same platform and principles apply but the complexity of cell types and connectivity presents new challenges. Key topics include how autonomous agent models differ from conventional computational approaches, why all available biological data should be incorporated rather than held back for testing, how mutations serve as the primary validation strategy for these models, what the relationship is between stem cell stemness and differentiation potential, why morphological benchmarks like cauliflower structure are difficult to quantify rigorously, and how these simulations could eventually model disease processes by tracing developmental history back to its origins. Part of the Convergent Science Network podcast series from the BCBT Summer School.