Cells use many codes, which operate through abstract symbolism and formal rules. To instantiate the logic, dedicated decoding processors—hardware molecular machines—must interpret each kind of variable and the associated values. Decoders include ribosomes, DNA polymerases, RNA polymerases, spliceosomes, Hsp70 and Hsp60 chaperones, proteasomes, RNA degradasomes, protein translocases, reverse transcriptases, aminoacyl-tRNA synthetases, and error-correcting machines. Many codes are mutually dependent in order to function, and cells could not have evolved each decoder sequentially. Ribosomes require the mRNAs from DNA-dependent RNA polymerases, but these polymerases are composed of protein products from ribosomes. Both decoders require the energetic ATP molecules from ATP synthases, which themselves cannot exist until ribosomes and RNA polymerases already work. Being coded information systems, additional guidance is provided in cells through engineered components such as the cytoskeleton, lipid rafts, membranes, pores, chemical gradients, correct placements of synapses, correct binding strengths, and nuclear subcompartments. Computer architectures structure long-term storage capacity hierarchically to process data at different levels of granularity: data centers and distributed file systems; hard discs; disk partitions; files and extents; tracks; sectors and data blocks; and bits. In cells the same kinds of hardware principles are observed: ecologies of cooperating bacteria and multiple cells in eukaryote organisms; genomes; chromosomes, plasmids, mitochondria, and chloroplasts; euchromatin/heterochromatin and DNA looping; DNA regions defining primary RNA transcripts; exons/introns; and nucleotides. Cells must be interpreted as holistic systems whose origin cannot be explained by neoDarwinian theory.