Hist. Phil. Life Sci., 34 (2012), 391-406 The Place of Viruses in Biology in Light of the Metabolism- versus-replication-first Debate Purificación López-García Unité d’Ecologie, Systématique et Evolution CNRS UMR8079, Université Paris-Sud 91405 Orsay, France ABSTRACT - The last decade has seen a revival of old virocentric ideas. These concepts are heterogeneous, extending from proposals that consider viruses functionally as living beings and/or as descendants of viral lineages that preceded cell evolution to other claims that consider viruses and/or some viral families a fourth domain of life. While the debates about whether viruses are alive or not and whether some virus-like replicators preceded the first cells fall under the long-lasting dichotomous view on the nature and origin of life (metabolism- versus replication-first), the claim that some giant viruses form a fourth domain in an organismal tree of life is not consistent with current evidence and can be falsified. KEYWORDS - Tree of life, metabolism, self-replication, origin of life, definition of life, giant viruses, horizontal gene transfer, evolution Introduction At the beginning of the twentieth century, the conditions for a scientific investigation into the origin of life on Earth were established. The rebuttal of continuous spontaneous generation by Louis Pasteur in the 1860s and the publication of On the Origin of Species in 1859 by Charles Darwin, led inevitably to the question of how the first life forms emerged. At the same time, immense progress in organic chemistry, biochemistry, cytology, and, among other advances, the discovery of the crucial importance of the cell nucleus, made it possible to approach a question that had remained until then too complex and intractable (Fry 2006). From very early on, however, two clear ideological currents emerged. One current gave primacy to self-replication (making copies of itself) as the crucial starting point for life and the other gave primacy to metabolism or self-maintenance. This persistent chicken-and-egg dichotomy corresponded, in the terminology of the time, to a nucleus © 2012 Stazione Zoologica Anton Dohrn 392 PURIFICACIÓN LÓPEZ-GARCÍA versus cytoplasm debate. Accordingly, hypotheses on the origin of life subscribed either to nucleocentric or cytoplasmic views of life. Among the important discoveries due to microscopy and other tech- nological advances at the onset of the twentieth century was the discov- ery of viruses. Viruses were first discovered at the end of the nineteenth century when the Russian botanist Dmitri Ivanovsky (1892) observed that suspensions of plant tissues afflicted with mosaic tobacco disease were still infectious after passage through ceramic filters that retained bacteria. This observation was confirmed in 1898 by one of the spiri- tual founders of the so-called Delft school of microbiology, Martinus Beijerinck, who popularized the term “virus” to refer to the filterable infectious agents (reviewed in Podolsky 1996). A few years later, Freder- ick Twort (1915) and Felix D’Hérelle (1917) discovered viruses infect- ing bacteria, which were subsequently called bacteriophages. It is not surprising that at the time many researchers considered the mysterious viruses, with their infective capacities and their small sizes, the simplest living entities. As such, they were intermingled in the debate on the ori- gin of life for several decades with different connotations: the virus as a metaphor for the simplest form of life, the virus as a functional model (an independent existing gene) and, collectively, the viruses as a phylo- genetic lineage with historical continuity that could be placed between the chemical world and the first cells (Podolsky 1996). The importance of viruses for models on the origin of life and on the concept of what is life has vacillated over time. As reviewed in Podolsky (1996), until the mid-1930s the idea of a virus-centered origin-of-life was gaining credence. As early as 1914, the American psycho-physiologist Leonard Troland had envisaged that the first life form might have been an “enzyme or organic catalyst” (Troland 1914), although he later spoke of a “genetic enzyme,” and identified it with nucleic acids and proteins in the nucleus (Troland 1917). Subsequently, Herman Muller adopted and simplified Troland’s ideas, replacing “genetic enzyme” with “gene” (Fry 2006). In 1922, Muller made a clear conceptual link between virus and gene, saying that “there is no distinction between genes and them [viruses]” (Muller 1922) and, in 1929, he openly proposed that the first living organism was a primitive gene (Muller 1929). The same year, John B.S. Haldane, in his essay on the origin of life, extended that opera- tional view to a more phylogenetic view, asserting that “life may have remained in the virus stage for many millions of years before a suitable assemblage of elementary units was brought together in the first cell” (Haldane 1929). Along the same line of thought, Alexander and Bridges conceived of self-copying entities such as genes and viruses as the sim- plest components necessary to life, even dividing living beings into two THE PLACE OF VIRUSES IN BIOLOGY 393 taxonomic categories, “Cytobiontia” (cellular organisms) and “Ultrabi- ontia” (viruses) (Alexander and Bridges 1928). The syllogism, “smallest = virus, smallest = first, so that virus = first” (Beutner 1938), was readily accepted during those early years; the nucleocentric view of the origin of life was also virocentric. This view, however, soon fell out of favor largely due to the cytoplas- mist Alexander I. Oparin’s extensive work on the origin of life. Oparin conceived the origin of life from a biochemical or “colloidal chemistry” perspective, placing the emphasis on metabolism (Oparin 1938). For Oparin, life was a self-regulating system of catalytic reactions. In addi- tion to Oparin’s influential model for the origin of life, several investi- gators called into question the progressivist view of viruses. Robert G. Green perceived viruses as products of the most extensive retrograda- tion and parasitization (Green 1932). This regressive view of viral evolu- tion, shared by André Lwoff (Lwoff 1943; 1957), was increasingly ac- cepted. Furthermore, Haldane affirmed that “most evolutionary change has been degenerative” (Haldane 1932). Haldane’s position became, however, increasingly conciliatory to Oparin’s views. Although Haldane identified life with molecular self-reproduction, he pointed out that in a true living system the function of any part, including genes, depended on the cooperation of all other parts (Fry 2006). Nucleocentric views of life regained credence after the discovery that DNA was the genetic material (Avery et al. 1944) and, most importantly, after determination of the DNA structure, which suggested an elegant self-copying mechanism (Watson and Crick 1953). It was also shown that the nucleic acid component of viruses was the infectious component (Hershey and Chase 1952). Consequently, the association of virus - nu- cleic acid - gene was easy to make. Even so, the initial notion that viruses were phylogenetically the most primitive organisms on Earth was aban- doned in the 1950s in favor of an operational view according to which viruses were seen as metaphors for “living genes” (Podolsky 1996). Virocentric ideas on the origin of life were largely abandoned in the 1960s and throughout the remainder of the twentieth century. This was due to two major factors. First, advances in biochemistry and molecular biology led to the recognition that viruses were strict molecular para- sites. Since then, viruses have been considered biological entities able, like genes, to evolve but unable to self-replicate and to self-sustain, a position still held by the International Committee on Taxonomy of Vi- ruses (van Regenmortel 2000; 2008). Second, the discovery was made that some RNAs have catalytic activity and, thus, display dual functions as informative polymers and catalysts. This and the discovery that the highly conserved ribosome is a ribozyme, led to the development of the 394 PURIFICACIÓN LÓPEZ-GARCÍA “RNA world” as a powerful model of early life evolution (for a review, see Orgel 2004; Robertson and Joyce 2010). RNA replaced viruses in origin-of-life thinking: nucleocentric views on the origin of life were no longer virocentric. Renaissance of old virocentric ideas: what’s new in the viral world? At the beginning of the twenty-first century, a renaissance of old virocentric ideas has taken place. Interestingly, this revival is taking place at both an operational level, with viruses seen functionally as living beings (Raoult and Forterre 2008), and at a phylogenetic level, with viruses viewed as descendants of viral lineages that preceded cell evolution (Bamford et al. 2005; Koonin et al. 2006). Additional claims assert more strongly that viruses and/or some viral families form a fourth domain of life (Raoult et al. 2004; Raoult and Forterre 2008). Some authors even consider viruses as “capsid-encoding organisms,” a renovated version of the Ultrabiontia, as opposed to “ribosome- encoding organisms” (cells) (Raoult and Forterre 2008). Collectively, these proposals are heterogeneous and, as we will see in the following, while some of these ideas fall under the two rival views on the nature and origin of life (metabolism versus genetic information), others are not consistent with current evidence and can be falsified (López-García and Moreira 2009; Moreira and López-García 2009). Why have