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This book describes the first molecular theory of the genotype-phenotype coupling (or cell language) based on two key concepts: (i) the conformon, the packet of free energy and genetic information stored in biopolymers; and (ii) the intracellular dissipative structures, the concentration gradients in the cell that drive all cell functions. Conformons provide the driving forces for all molecular machines in the cell including ATP-dependent chromatin remodeling proteins, and dissipative structures coordinate cell-wide processes such as gene expression and cell cycle.One prediction of the new theory is that there are two forms of genetic information - the Watson-Crick genes transmitting information in time (identified with DNA), and the Prigoginian genes transmitting information in space (identified with RNA expression profiles). The former is analogous to sheet music or written language, the latter is akin to audio music or spoken language, and conformons act as the pianist. The new theory of DNA structure and function can rationally account for most of the puzzling findings recently unearthed by the ENCODE (Encyclopedia of DNA Elements) project.The cell language theory described in this book, coupled with high-throughput experimental data and computational methods, is expected to facilitate the practical applications of cell biological knowledge to biomedical sciences, including diagnosis, therapeutics, and drug discovery.