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While the origin of genes and proteins is still unknown, it has been traditionally assumed that a genome containing primitive, intronless, contiguous genes coding for simple proteins arose pre-biotically in a bacterial-like life form. Following its inception, this putative ancestor has been assumed to have evolved, in a tree-like linear branching pattern, into all of the complex genomes of the biota by random genetic mutation (1-7). This Linear Branching Evolution (LBE) model has been the prevailing paradigm of modern biology. In contrast, recent comparative genomics and proteomics studies have led to unexpected discoveries that challenge these assumptions. For example, studies examining the nature of domains, proteins, and protein fold superfamilies across phyla have shown that the earliest life-forms must have had sophisticated, eukaryote-like, proteins (8-24). In accordance, numerous complex proteins and domains that are widely distributed in nature have been found at the base of the evolutionary tree (8-24). Phylogenomic studies have also demonstrated the presence of a eukaryote, rather than a prokaryote, at the base of the evolutionary tree (25-37). Contrary to prior beliefs that primitive split genes must have been present in the eukaryotic ancestor that became increasingly complex through evolution, interkingdom analyses have shown that the eukaryotic ancestor had a highly complex intron-rich genome akin to that of the modern eukaryotes (38-39). Furthermore, the genes of basal eukaryotes (e.g., trichoplax and sea anemone) were found to be as complex and intron-rich as those of higher animals (e.g., human) (40-43). Also, contrary to the earlier idea that the splicing process and the spliceosome must have been very simple in the eukaryotic ancestor, increasing in complexity through evolution, current evidence shows that the spliceosome of the earliest eukaryote must have been extremely complex and fully developed, with the same structure, function, and the >200 proteins and five non-coding RNAs present in modern higher eukaryotes (44-47). These discoveries demonstrate that the genomes and proteomes of the very first life forms may have been much more complex than originally hypothesized, and moreover may have been eukaryotic. Consistent with these findings, emerging evidence concerning the character of several cellular components indicates that a eukaryote did not evolve from a prokaryote. Recent findings show that the RNA processing machinery within the eukaryotic cell nucleus, for example, is far too complex to have arisen by any endosymbiotic event from any prokaryote (44-47). Furthermore, the eukaryotic nucleus itself, with a unique membrane structure, integrated with the nuclear pore and the endoplasmic reticulum, lacks a clear homologue or precursor among prokaryotes (48-52). Several eukaryotic protein families Origin of biological information 1

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Origin of biological information: Inherent occurrence of intron-rich split genes, coding for complex extant proteins, within pre-biotic random genetic sequences