This book deals with the missing link in the domain of functional genomics viz. genomic architecture. It begins with a deconstruction of the Darwinian paradigm using the proposed model of modified involuted manifolds. It recasts the process of natural selection as a process of information transfer. Using a topological model, this book outlines a new genomic architecture. The key argument for this proposed model is that some such structuralism has always been implicit in genomics. The proposed model fits very well with the known genomic characteristics and allows to separate the regulatory genome from the transcriptive genomes. The model is capable of discerning modular architecture of genomes with different genomic functionalities existing in hierarchical relationships and demonstrates that genomes act as units of selection and as the environment for the individual genes which act as competing species. Towards the end, the book also examines the role of genomic evolution in cancer and the principles of natural selection and evolution of the genotype. The regulatory genome is also discussed, with an emphasis on its evolution and natural selection. It is a valuable source for researchers working in functional genomics, mathematical modeling in biology and evolutionary genomics.