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The process of inferring the set of proteins that was likely encoded in the genome of an extinct organism is called Ancestral Proteome Reconstruction. This process usually involves the comparison of proteomes of extant species and the reconstruction of their ancestors by using different methods that range from parsimonius reconstruction over a species-phylogeny to the reconstruction and analysis of complete phylomes. Although still in its infancy, Ancestral Proteome Reconstruction has proven to be a very useful tool to test hypotheses on extant organisms and past evolutionary events. This chapter provides an overview of the methodology involved and surveys recent studies that deal with the origin and evolution of the Last Universal Common Ancestor (LUCA), and eukaryotic organelles such as mitochondria and peroxisomes.

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.

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?

The hypothesis that all living things share a common ancestry was already part of Darwin's thinking. It crystallized in the 20th century and became solidly established with the recognition that basic molecular strategies are universal, including transcription, translation and especially the genetic code. LUCA, the Last Universal Common Ancestor, is represented on the universal tree by its deepest node, that which marks the divergence of Bacteria from Archaea/Eukarya. The nature of that entity has been much debated and remains controversial. It now appears that LUCA was a much more advanced organism than originally expected, endowed with genes, membranes, enzymes, metabolism and the basic mechanisms of gene expression, replication and energy transduction. LUCA was a cell of sorts, but probably represents a stage before discrete lineages, whose members swapped genes and evolved communally. The chapter concludes with a brief presentation of dissenting opinions, chiefly those of Thomas Cavalier-Smith, Radhey Gupta and James Lake.