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Inherent limitations of contemporary machine learning systems in crucial areas—importantly in continual learning, information reuse, comprehensibility, and integration with deliberate behavior—are receiving increasing attention. To address these challenges, we introduce a system design, fueled by a novel learning approach conceptually grounded in principles of evolutionary developmental biology, that overcomes key limitations of current methods. Our design comprises three core components: The Modeller, a gradient-free learning mechanism inherently capable of continual learning and structural adaptation; a planner for goal-directed action over learned models; and a behavior encapsulation mechanism that can decompose complex behaviors into a hierarchical structure. We demonstrate proof-of-principle operation in a simple test environment. Additionally, we extend our modeling framework to higher-dimensional network-structured spaces, using MNIST for a shape detection task. Our framework shows promise in overcoming multiple major limitations of contemporary machine learning systems simultaneously and in an organic manner.