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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.

Theoretical studies (philosophy, mathematical modelling, computer simulations, genomics and bioinformatics) have had a profound influence on our understanding of life’s origins. Replication-first and metabolism-first approaches have dominated the thinking, but for evolutionists one of the first hurdles to overcome was to explain how small replicators gave rise to larger ones. The issue, sometimes known as Eigen’s paradox, arose because the earliest replicators were unable to copy themselves with sufficient fidelity that could lead to sustainable populations of larger replicators from which life could take hold (the error catastrophe problem). The theories concerning quasispecies and hypercycles have to some degree addressed this issue, but significant problems remain. Compartmentalization and group selection, in one form or another, are presented as essential explanatory frameworks for overcoming this limitation. Gánti’s chemoton is an abstract protocell that brings together many of the philosophical, mathematical, and evolutionary questions regarding metabolism, hereditary, and replication issues, as well as compartmentalization into a self-sustaining chemical system. Evolutionary genomics complements the theoretical works and points to a fluid centroid of minimal gene sets, the proposed last universal common ancestor (LUCA) from which a tree of life emerged.

Chapter 7 is a culmination of the previous six chapters. A broad outline of the origin of life in eight steps is sketched out by integrating the information in the previous chapters. The key steps were likely not nearly as discrete as suggested here, but they help explain the major evolutionary innovations en route to the first proto-cells. Step 1 summarizes the emergence of biologically relevant molecules like ribonucleotides. Steps 2 and 3 capture the two important stages of the RNA world hypothesis – the emergence of small passively replicating RNA molecules and, subsequently, the evolution of larger, more complex ribozymes. Step 4 highlights the importance of compartmentalization, without which the emergence of a living system would not have been possible. The emergence of lower-level replicating units (step 5), the process that led to the functional and structural alignments of their evolutionary interests (step 6) and eventually the emergence of higher-level replicating units (step 7) were all key innovations. Step 8 summarizes the emergence of the first proto-cells or last universal common ancestors (LUCA), which incorporate the necessary components of hereditary information, compartmentalization, and metabolism. A parallel with Gánti’s chemoton is drawn.

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 origin of life is the most consequential problem in biology, possibly in all of science, and it remains unsolved. This chapter summarizes what has been learned and highlights questions that remain open, including How, Where, When, and especially Why. LUCA, some four billion years ago, already featured the basic capacities of contemporary cells. These must have evolved still earlier, at a nebulous proto-cellular stage. There is good reason to believe that enzymes, DNA, ribosomes, electron-transport chains, and the rotary ATP synthase all predate LUCA and were shaped by the standard process of variation and natural selection, but we know next to nothing about how cells ever got started. I favor the proposal that it began with a purely chemical dynamic network capable of reproducing itself, that may have originated by chance. Natural selection would have favored the incorporation of any ancillary factors that promoted its kinetic stability, especially ones that improved reproduction or gave access to energy. All the specifics are in dispute, including the role of a prebiotic broth of organic chemicals, the nature and origin of enclosure, the RNA world, and a venue in submarine hydrothermal vents. My sense is that critical pieces of the puzzle remain to be discovered.

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.

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.