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This chapter starts with a vivid description of the Crafoord prize 2003 ceremony in Stockholm when Carl Woese was honoured. The experiments that led to his discovery of archaea are described, with emphasis on the ribosomal RNA, the Rosetta stone of evolutionists. The bases of molecular phylogeny and the construction of the first rooted universal tree are explained. The hypothesis of direct link between a hot origin of life and a hyperthermophilic Last Universal Common Ancestor (LUCA) is criticized, based on the fragility of RNA and the RNA world theory. The author discusses his thermoreduction scenario in which Archaea and Bacteria originated from a cold LUCA by adaptation to high temperature. This scenario is supported by ancestral sequences reconstruction from Manolo Gouy, a “La recherche” prize winner, suggesting a cold LUCA and hot ancestors for Archaea and Bacteria and by comparative genomic suggesting that LUCA had a RNA genome. A visit to virologist Dennis Bamford in Helsinki allows discussing arguments revealing that viruses were already present at the time of LUCA and played a major role in the RNA to DNA transition. The chapter ends on challenging questions; are viruses living and where are there in the tree of life?

This chapter starts summarizing how our conception of the living world classification evolved. The concepts of microbes, cells, prokaryotes, eukaryotes, and viruses are briefly presented and the reasons why life was not expected to be present in hell are explained. The history of hyperthermophile unexpected discovery is then described, starting from the first observations of “vegetation” in hot springs of Yellowstone national park in the nineteen century to the first isolation in 1972 of an actual hyperthermophile in this park, Sulfolobus. Amazingly, this bug turned out to be member of a new domain of life described in 1977 by Carl Woese and George Fox, the archaebacteria (later on called archaea). The concept of archaebacteria led to the rapid discovery new families of hyperthermophiles growing at temperatures up to 110°C by German microbiologists Wolfram Zillig and Karl Stetter during their expeditions in Iceland and Italy. This was followed by the discovery of unique viruses infecting these microbes. The chapter ends with a first description of the origin of life problem and how the discovery of hyperthermophiles suggested new hypotheses favouring at first a hot origin.

The idea that all living things arose from their progenitors by descent with modification, and that this history can be depicted as a great tree, goes back to Darwin and beyond. Construction of a universal tree became possible after Carl Woese introduced ribosomal RNA sequences as a molecular chronometer. The tree consists of three great stems, or domains, designated Bacteria, Archaea and Eukarya, and this tripartite division is now generally accepted. But soon a serious complication arose: lateral transfer of genes between species, genera and even domains is common, particularly among prokaryotes. Lateral gene transfer erodes the phylogenetic trace, and has led some to question the very principle of a tree of life, but the division of all living things into three domains has held up. It is not easy to assign absolute dates to their emergence. The prokaryotes, Bacteria and Archaea, clearly go back more than 3 billion years. Modern Eukarya are much more recent, a billion years or so, but the eukaryotic lineage appears to be very ancient, possibly comparable to the prokaryotic ones.

History is a genre consisting historically of different kinds with different functions. Instead of just writing “a history” of system, we need to recover the changing relationship between these two genres—starting with Bacon’s emphasis on the need for new histories and Galileo’s focus on system. This chapter follows their interrelations into the eighteenth century using a new computational resource I call Tectonics. It maps spatially over time the coming together of system and history at the century’s end as they share more and more title pages, modifying each other and forming a new platform for knowledge: the narrow-but-deep disciplines of modernity. The chapter confirms this finding using Encyclopedia Britannica and then—with turns to William Jones and the novel--shows how history itself became one of those narrowed disciplines by foregrounding “ideas” and the modern subject that embodies them. The chapter shows how these interrelations of system and history shaped the efforts of system theory, including Immanuel Wallerstein and Niklas Luhmann, and recovers for this book a different kind of history: Bacon’s notion of a capacious literary history that would tell the “story of learning” from age to age. The chapter concludes with Carl Woese’s efforts to transform biology through a newly capacious history, and with explanations of the scope and kinds of history featured in this book: the histories of “mediation,” “blame,” and the “real.”.

Chapter 8 recalled John Platt’s recommendation that testing alternative hypotheses is a preferred way to perform research rather than focusing on a single hypothesis. Karl Popper proposed an additional way to evaluate research approaches, which is that a strong hypothesis is one that can be falsified by one or more crucial experiments. This chapter proposes that life can begin with chance ensembles of encapsulated polymers, some of which happen to store genetic information in the linear sequences of their monomers while others catalyze polymerization reactions. These interact in cycles in which genetic polymers guide the synthesis of catalytic polymers, which in turn catalyze the synthesis of the genetic polymers. At first, the cycle occurs in the absence of metabolism, driven solely by the existing chemical energy available in the environment. At a later stage, other polymers incorporated in the encapsulated systems begin to function as catalysts of primitive metabolic reactions described in Chapter 7. The emergence of protocells with metabolic processes that support polymerization of self-reproducing systems of interacting catalytic and genetic polymers marks the final step in the origin of life. The above scenario can be turned into a hypothesis if it can be experimentally tested— or falsified, as described in the epigraph. The goal of falsification tends to be uncomfortable for active researchers. It’s a very human tendency to be delighted with a creative new idea and want to prove it correct. This can be such a strong emotion that some fall in love with their idea and actually hesitate to test it. They begin to dislike colleagues who are critical and skeptical. However, my experience after 50 years of active research is that we need to think of our ideas as mental maps and expect that most of them will not match the real world very well. And so, I say to my students, “When you have a new idea it’s OK to enjoy it and share it with others, but then you must come up with an experiment that lets you discard it.