Physiology, phylogeny, and the energetic roots of life

Before the days of molecular phylogenies, the standard way of viewing microbial evolution was as process of physiological evolution: the ordering of the sequence of events in which different pathways that microbes use to harness carbon and energy arose. The physiological view of microbial evolution was, of course, replaced in the 1980s by a gene centered view of microbial evolution that was built around the ribosomal RNA tree of life, also called the universal tree or the three domain tree. The universal tree installed long sought order into microbial systematics, but left physiological evolution out in the cold, because physiology never mapped properly onto the rRNA tree. That was not because the universal tree had an incorrect branching pattern. Rather it was because physiological characters have never mapped neatly onto any phylogenetic tree for prokaryotes, regardless of its topology. The reason is that prokaryotes, though they have an undeniable tendency to vertically inherit their ribosome, distribute the physiological traits that enable synthesis of ribosomes via lateral gene transfer (LGT). Geochemical isotope evidence harbors evidence for the existence of physiological processes, not for phylogeny, because LGT decouples physiology from phylogeny in prokaryotes. If we want a fuller picture of microbial evolution, we will have to incorporate aspects of physiology, phylogeny, and the geological record. The issue of how physiology got started has always been interesting. Non-fermentative substrate level phosphorylations as they occur in some acetogens and methanogens now look like good candidate reactions for that starting point, helping to put chemical roots on life\u27s tree.</p

Early evolution without a tree of life

Life is a chemical reaction. Three major transitions in early evolution are considered without recourse to a tree of life. The origin of prokaryotes required a steady supply of energy and electrons, probably in the form of molecular hydrogen stemming from serpentinization. Microbial genome evolution is not a treelike process because of lateral gene transfer and the endosymbiotic origins of organelles. The lack of true intermediates in the prokaryote-to-eukaryote transition has a bioenergetic cause

Do Childhood Vaccines Have Non-Specific Effects on Mortality

A recent article by Kristensen et al. suggested that measles vaccine and bacille Calmette–Guérin (BCG) vaccine might\ud reduce mortality beyond what is expected simply from protection against measles and tuberculosis. Previous reviews of the potential effects of childhood vaccines on mortality have not considered methodological features of reviewed studies. Methodological considerations play an especially important role in observational assessments, in which selection factors for vaccination may be difficult to ascertain. We reviewed 782 English language articles on vaccines and childhood mortality and found only a few whose design met the criteria for methodological rigor. The data reviewed suggest that measles vaccine delivers its promised reduction in mortality, but there is insufficient evidence to suggest a mortality benefit above that caused by its effect on measles disease and its sequelae. Our review of the available data in the literature reinforces how difficult answering these considerations has been and how important study design will be in determining the effect of specific vaccines on all-cause mortality.\u

Hydrogen, metals, bifurcating electrons, and proton gradients: The early evolution of biological energy conservation

AbstractLife is a persistent, self-specified set of far from equilibrium chemical reactions. In modern microbes, core carbon and energy metabolism are what keep cells alive. In very early chemical evolution, the forerunners of carbon and energy metabolism were the processes of generating reduced carbon compounds from CO2 and the mechanisms of harnessing energy as compounds capable of doing some chemical work. The process of serpentinization at alkaline hydrothermal vents holds promise as a model for the origin of early reducing power, because Fe2+ in the Earth’s crust reduces water to H2 and inorganic carbon to methane. The overall geochemical process of serpentinization is similar to the biochemical process of methanogenesis, and methanogenesis is similar to acetogenesis in that both physiologies allow energy conservation from the reduction of CO2 with electrons from H2. Electron bifurcation is a newly recognized cytosolic process that anaerobes use generate low potential electrons, it plays an important role in some forms of methanogenesis and, via speculation, possibly in acetogenesis. Electron bifurcation likely figures into the early evolution of biological energy conservation

Cow, farm, and herd management factors in the dry period associated with raised somatic cell counts in early lactation

This study investigated cow characteristics, farm facilities, and herd management strategies during the dry period to examine their joint influence on somatic cell counts (SCC) in early lactation. Data from 52 commercial dairy farms throughout England and Wales were collected over a 2-yr period. For the purpose of analysis, cows were separated into those housed for the dry period (6,419 cow-dry periods) and those at pasture (7,425 cow-dry periods). Bayesian multilevel models were specified with 2 response variables: ln SCC (continuous) and SCC >199,000 cells/mL (binary), both within 30 d of calving. Cow factors associated with an increased SCC after calving were parity, an SCC >199,000 cells/mL in the 60 d before drying off, increasing milk yield 0 to 30 d before drying off, and reduced DIM after calving at the time of SCC estimation. Herd management factors associated with an increased SCC after calving included procedures at drying off, aspects of bedding management, stocking density, and method of pasture grazing. Posterior predictions were used for model assessment, and these indicated that model fit was generally good. The research demonstrated that specific dry-period management strategies have an important influence on SCC in early lactation

GTP before ATP: The energy currency at the origin of genes

Life is an exergonic chemical reaction. Many individual reactions in metabolism entail slightly endergonic processes that are coupled to free energy release, typically as ATP hydrolysis, in order to go forward. ATP is almost always supplied by the rotor-stator ATP synthetase (the ATPase), which harnesses chemiosmotic ion gradients. Because the ATPase is a protein, it arose after the ribosome did. Here we address two questions using comparative physiology: What was the energy currency of metabolism before the origin of the ATPase? How (and why) did ATP come to be the universal energy currency? About 27 percent of a cell's energy budget is consumed as GTP during translation. The universality of GTP-dependence in ribosome function indicates that GTP was the ancestral energy currency of protein synthesis. The use of GTP in translation and ATP in small molecule synthesis are conserved across all lineages, representing energetic compartments that arose in the last universal common ancestor, LUCA.Comment: 27 pages, 5 figures, 2 table