This study introduces a novel theoretical framework, the Stacked Autoencoder Evolution Hypothesis, which proposes that biological evolutionary systems operate through multi-layered self-encoding and decoding processes, analogous to stacked autoencoders in deep learning. Rather than viewing evolution solely as gradual changes driven by mutation and selection, this hypothesis suggests that self-replication inherently compresses and reconstructs genetic information across hierarchical layers of abstraction. This layered structure enables evolutionary systems to explore diverse possibilities not only at the sequence level but also across progressively more abstract layers of representation, making it possible for even simple mutations to navigate these higher-order spaces.Such a mechanism may explain punctuated evolutionary patterns and changes that can appear as if they are goal-directed in natural evolution, by allowing mutations at deeper latent layers to trigger sudden, large-scale phenotypic shifts. To illustrate the plausibility of this mechanism, artificial chemistry simulations were conducted, demonstrating the spontaneous emergence of hierarchical autoencoder structures. This framework offers a new perspective on the informational dynamics underlying both continuous and discontinuous evolutionary change.