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This chapter discusses the diversity of life, its classification into Eukarya, Eubacteria, and Archaea and their evolutionary relationships. It further investigates Halobacterium salinarum, which completely lacks chlorophyll but uses bacteriorhodopsin to perform photosynthesis and sunlight as a source of energy and information. The mechanism of photosynthesis is also analyzed. This chapter also discusses bacteriorhodopsin-based computers and the study of chemical dynamics of proteins. The sensory rhodopsins that are present in Halobacterium are also discussed.

Cells are life’s basic building blocks, and there is no more profound question than how they came to be. What made this murky subject accessible is the invention of methods to sequence nucleic acids and proteins, and to infer evolutionary relationships from those sequences. It seems that all living things share a common ancestry in LUCA (the Last Universal Common Ancestor), a shadowy entity thought to have lived nearly 4 billion years ago. LUCA’s nature has been much debated, but she appears to have been a cell of sorts endowed with membranes, metabolic networks, a usable energy source and the machinery to express and reproduce genetic information. The earliest known event in cell history was the divergence of Archaea from Bacteria, about 3.5 billion years ago. Eukaryotic cells, more closely allied with Archaea than with Bacteria, appear much later, some 2 billion years ago. Their origin remains one of life’s mysteries, but the evidence currently favors a fusion or merger of an early archaeon with a bacterium; the latter became the ancestor of mitochondria, and played a major role in cell evolution. Eukaryotic cells of the contemporary kind emerged over hundreds of million years. Prominent events included a second instance of intracellular symbiosis, this time with a cyanobacterium, that introduced photosynthesis into the eukaryotic universe and initiated the plant lineage. Eukaryotic cells are the building blocks of all higher organisms. Just what has given the eukaryotic order an edge is yet another of life’s stubborn mysteries.

The world seems to hold only three kinds of cells, three cellular designs: Eukarya, Bacteria and Archaea. This chapter attempts to define their essential characteristics. A central theme is the discovery, utterly unexpected at the time, that “prokaryotes” conflates two distinct modes of organization that become apparent only at the molecular level. The evidence that supports the separation of Archaea from Bacteria, and the affinity of the Archaea with the Eukarya, is considered in some detail. Attention is given to organisms that seem to straddle the border between domains, notably the planctomycetes, Bacteria whose internal organization is reminiscent of eukaryotic cells. The chapter concludes with viruses, which have no home on the universal tree but are clearly related to it. Viruses may represent an ancient line of molecular evolution, distinct from but intertwined with, that of cells.