Driving forces in the origins of life

What were the physico-chemical forces that drove the origins of life? We discuss four major prebiotic ‘discoveries’: persistent sampling of chemical reaction space; sequence-encodable foldable catalysts; assembly of functional pathways; and encapsulation and heritability. We describe how a ‘proteins-first’ world gives plausible mechanisms. We note the importance of hydrophobic and polar compositions of matter in these advances.     

DNA and the origins of life in micaceous clay

Reproducible imaging of DNA by atomic force microscopy was a useful predecessor to Ned Seeman’s DNA nanotechnology. Many of the products of DNA nanotechnology were imaged in the atomic force microscope. The mica substrate used in this atomic force microscopy research formed the inspiration for the hypothesis that micaceous clay was a likely habitat for the origins of life. Montmorillonite clay has been a successful substrate for the polymerization of amino acids and nucleotides into peptides and DNA oligomers in research on life’s origins. Mica and montmorillonite have the same anionic lattice, with a hexagonal spacing of 0.5 nm. Micas are nonswelling clays, with potassium ions (K⁺) holding the crystal sheets together, providing a stable environment for the processes and molecular complexes needed for the emergence of living cells. Montmorillonite crystal sheets are held together by smaller sodium ions (Na⁺), which results in swelling and shrinking during wet-dry cycles, providing a less stable environment. Also, the cells in all types of living systems have high intracellular K⁺ concentrations, which makes mica a more likely habitat for the origins of life than montmorillonite. Finally, moving mica sheets provides mechanical energy at the split edges of the sheets in mica “books.” This mechanical energy of mica sheets, moving open and shut, in response to fluid flow, may have preceded chemical energy at life’s origins, powering early prebiotic processes, such as the formation of covalent bonds, the interactions of molecular complexes, and the budding off of protocells before the molecular mechanism of cell division had developed.     

On the independent gene trees assumption in phylogenomic studies

Multilocus coalescent methods for inferring species trees or historical demographic parameters typically require the assumption that gene trees for sampled SNPs or DNA sequence loci are conditionally independent given their species tree. In practice, researchers have used different criteria to delimit “independent loci.” One criterion identifies sampled loci as being independent of each other if they undergo Mendelian independent assortment (IA criterion). O'Neill et al. (2013, Molecular Ecology, 22, 111–129) used this approach in their phylogeographic study of North American tiger salamander species complex. In two other studies, researchers developed a pair of related methods that employ an independent genealogies criterion (IG criterion), which considers the effects of population‐level recombination on correlations between the gene trees of intrachromosomal loci. Here, I explain these three methods, illustrate their use with example data, and evaluate their efficacies. I show that the IA approach is more conservative, is simpler to use and requires fewer assumptions than the IG approaches. However, IG approaches can identify much larger numbers of independent loci than the IA method, which, in turn, allows researchers to obtain more precise and accurate estimates of species trees and historical demographic parameters. A disadvantage of the IG methods is that they require an estimate of the population recombination rate. Despite their drawbacks, IA and IG approaches provide molecular ecologists with promising a priori methods for selecting SNPs or DNA sequence loci that likely meet the independence assumption in coalescent‐based phylogenomic studies.     

The origins of cellular life

All life on earth can be naturally classified into cellular life forms and virus-like selfish elements, the latter being fully dependent on the former for their reproduction. Cells are reproducers that not only replicate their genome but also reproduce the cellular organization that depends on semipermeable, energy-transforming membranes and cannot be recovered from the genome alone, under the famous dictum of Rudolf Virchow, Omnis cellula e cellula. In contrast, simple selfish elements are replicators that can complete their life cycles within the host cell starting from genomic RNA or DNA alone. The origin of the cellular organization is the central and perhaps the hardest problem of evolutionary biology. I argue that the origin of cells can be understood only in conjunction with the origin and evolution of selfish genetic elements. A scenario of precellular evolution is presented that involves cohesion of the genomes of the emerging cellular life forms from primordial pools of small genetic elements that eventually segregated into hosts and parasites. I further present a model of the coevolution of primordial membranes and membrane proteins, discuss protocellular and non-cellular models of early evolution, and examine the habitats on the primordial earth that could have been conducive to precellular evolution and the origin of cells.     

The partial stream sampling assumption in intestinal perfusion studies

During the past several years, the technique ofin vivo intestinal perfusion with partial stream sampling has been increasingly widely used to gather information on intestinal absorptive processes in man. The basic technique involves infusion of test solution through a proximal opening; and aspiration of samples through one or more distal openings a fixed distance apart. Samples are analyzed for test solute concentrations; from such sample data, conclusions are drawn concerning alterations in stream concentrations between the sampling sites. An underlying assumption for the validity of such a method is: that sample concentrations are the same as average stream concentrations. This assumption has not previously been precisely stated. A precise statement of it is given here, together with an analytic proof of conditions necessary and sufficient for its validity. A brief verbal comment is included to clarify the practical meaning of the analytic statement.     

L-form bacteria,cell walls and the origins of life

The peptidoglycan wall is a defining feature of bacterial cells and was probably already present in their last common ancestor. L-forms are bacterial variants that lack a cell wall and divide by a variety of processes involving membrane blebbing, tubulation, vesiculation and fission. Their unusual mode of proliferation provides a model for primitive cells and is reminiscent of recently developed in vitro vesicle reproduction processes. Invention of the cell wall may have underpinned the explosion of bacterial life on the Earth. Later innovations in cell envelope structure, particularly the emergence of the outer membrane of Gram-negative bacteria, possibly in an early endospore former, seem to have spurned further major evolutionary radiations. Comparative studies of bacterial cell envelope structure may help to resolve the early key steps in evolutionary development of the bacterial domain of life.     

Evolutionary oscillation in prebiology: Igneous activity and the origins of life

The processes of chemical evolution are responsible for the origin of life. Three such processes have special importance: oscillation, creation, and competition.An oscillation from one kind of environment to another provides a mechanism for instituting processes that can only take place under conditions far removed from equilibrium. Oscillating evolutionary processes are likely to have played an important part in the origin of life. It is a mistake to assume that life originated in any one environment. It did not arrive in a moment of time. It was the result of a long period of chemical evolution during which it passed through a variety of environments. Biopoesis took place in an environment in which a variety of different kinds of protolife were assembled and concentrated.One essential form of protolife involved in these processes is the protocell. The experiments of Fox suggest that the creation of protocells involves violent oscillations of temperature and hydration. Igneous activity is especially characterised by oscillating conditions. Volcanic eruptions consist of violent changes from one extreme condition to another. Temperature, pressure, phase, concentration and hydration all oscillate violently, and are subject to shock pulses of many kinds. Protolife may well have passed through extremes of environment far wider than those that life itself can sustain.The most probable environment for the assembly of the various forms of protolife would be on mudbanks forming either at the mouth of streams draining regions of active vulcanicity, or round the edge of hot volcanic pools. In this situation one could find concentrated not only the various strands of protolife necessary for the final act of biopoesis, but also prebiologically formed nutrients necessary as food for the first eobionts. As soon as the first protocells start to grow, they start to compete with each other, and so initiate a new and additional evolutionary process, that of natural selection. Only after such competition has been initiated is life itself likely to be established.Given at the International Seminar Origin of Life, 2–7 August 1974, Moscow, U.S.S.R.     

Lagoa Santa's contribution to the origins and life of early Americans

The region of Lagoa Santa, Central‐Eastern Brazil, provides an exceptional archeological record about Late Pleistocene/Early Holocene occupation of the Americas. Since the first interventions made by the Danish naturalist Peter Lund in the 19th century, hundreds of human skeletons have been exhumed in the region. These skeletons are complemented by a rich botanic, faunal, technological, and geomorphological archeological record. We explore here the contributions of Lagoa Santa material to the origins and lifestyle of early Americans, providing an historic background. Cranial morphology of Lagoa Santa skeletons allowed the proposition of a model of two biological components for the occupation of the Americas, in which early Americans are morphologically similar to people of African and Australo‐Melanesian origin. Furthermore, the archeological record in the region has revealed an intense use of plant resources, a restricted spatial distribution, and the symbolic elaboration of local hunter‐gatherers, unveiling a distinct lifestyle compared to early North American populations.