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Ecology and exploration of the rare biosphere
Key Points
Microbial-community abundance distributions have a long 'tail' of low-abundance organisms, referred to as the rare biosphere, which often comprises the large majority of species.
Rare-biosphere microorganisms display specific and sometimes unique ecology and biogeography that can differ substantially from that of more abundant representatives.
The rare biosphere contributes to a persistent microbial seed bank, contrasting the influence of local microbial extinction and immigration.
Recruitment from the rare biosphere provides a broad reservoir of ecological function and resiliency (redundancy and flexibility).
Broad time-series studies with rich metadata will improve the study of rare-biosphere dynamics and conditionally rare taxa.
Study of the rare biosphere is prone to experimental artefacts (sequencing noise) and biological artefacts (dormancy and taphonomic gradients).
The majority of microbial diversity exists, at least transiently, in the rare biosphere.
Novel rare-biosphere members can be studied through cultivation, targeted phylogenetic mining and single-cell genomics.
The detection and subsequent analysis of low-abundance microbial populations — the 'rare biosphere' — have demonstrated the persistence, population dynamics, dispersion and predation of these microbial species. Lynch and Neufeld discuss the ecology of rare microbial populations and highlight molecular and computational methods for targeting taxonomic 'blind spots' in the rare biosphere of complex microbial communities.
The profound influence of microorganisms on human life and global biogeochemical cycles underlines the value of studying the biogeography of microorganisms, exploring microbial genomes and expanding our understanding of most microbial species on Earth: that is, those present at low relative abundance. The detection and subsequent analysis of low-abundance microbial populations — the 'rare biosphere' — have demonstrated the persistence, population dynamics, dispersion and predation of these microbial species. We discuss the ecology of rare microbial populations, and highlight molecular and computational methods for targeting taxonomic 'blind spots' within the rare biosphere of complex microbial communities.
Journal Article
Edward M. Almond and the US Army : from the 92nd Infantry Division to the X Corps
\"Edward Mallory \"Ned\" Almond belonged to the generation of US Army officers who came of age during World War I and then ascended to senior command positions during World War II and the Korean War. He displayed personal courage in combat, exercised strong leadership as a battalion and later a corps commander, demonstrated dedication and efficiency as a staff officer, and showed some capacity as an author and military innovator. Almond initially made his mark on history as the commander of the 92nd Infantry Division, one of only two African American divisions to see combat during World War II. Later he commanded the X Corps for the Inchon invasion that decisively changed the course of the Korean War. However, alongside these considerable achievements lurked the distasteful beliefs of a fervent racist and right- wing political zealot. Almond's vehement attitudes regarding African American soldiers serving in combat units overshadowed his accomplishments. In Edward M. Almond and the US Army, Michael E. Lynch takes a comprehensive look at the accomplishments and downfalls of US Army officer Edward Almond. While acknowledging Almond's faults, this book balances the historical ledger by arguing Almond played significant roles in the Army's history that are worthy of careful consideration. This critical examination of his life and career treats both the good and the bad, taking stock of a complex man who was so deeply flawed in some areas, yet supremely strong in many others.\"-- Provided by publisher.
Book
Mutation and Human Exceptionalism: Our Future Genetic Load
Although the human germline mutation rate is higher than that in any other well-studied species, the rate is not exceptional once the effective genome size and effective population size are taken into consideration. Human somatic mutation rates are substantially elevated above those in the germline, but this is also seen in other species. What is exceptional about humans is the recent detachment from the challenges of the natural environment and the ability to modify phenotypic traits in ways that mitigate the fitness effects of mutations, e.g., precision and personalized medicine. This results in a relaxation of selection against mildly deleterious mutations, including those magnifying the mutation rate itself. The long-term consequence of such effects is an expected genetic deterioration in the baseline human condition, potentially measurable on the timescale of a few generations in westernized societies, and because the brain is a particularly large mutational target, this is of particular concern. Ultimately, the price will have to be covered by further investment in various forms of medical intervention. Resolving the uncertainties of the magnitude and timescale of these effects will require the establishment of stable, standardized, multigenerational measurement procedures for various human traits.
Journal Article
frailty of adaptive hypotheses for the origins of organismal complexity
The vast majority of biologists engaged in evolutionary studies interpret virtually every aspect of biodiversity in adaptive terms. This narrow view of evolution has become untenable in light of recent observations from genomic sequencing and population-genetic theory. Numerous aspects of genomic architecture, gene structure, and developmental pathways are difficult to explain without invoking the nonadaptive forces of genetic drift and mutation. In addition, emergent biological features such as complexity, modularity, and evolvability, all of which are current targets of considerable speculation, may be nothing more than indirect by-products of processes operating at lower levels of organization. These issues are examined in the context of the view that the origins of many aspects of biological diversity, from gene-structural embellishments to novelties at the phenotypic level, have roots in nonadaptive processes, with the population-genetic environment imposing strong directionality on the paths that are open to evolutionary exploitation.
Journal Article
Know-it-all society : truth and arrogance in political culture
Examines how a growing culture of narcissism is behind the fragmented political landscapes of today, drawing on the works of classic philosophers to explain the essential role of truth and humility in democracy.
Book
The evolutionary scaling of cellular traits imposed by the drift barrier
Owing to internal homeostatic mechanisms, cellular traits may experience long periods of stable selective pressures, during which the stochastic forces of drift and mutation conspire to generate variation. However, even in the face of invariant selection, the drift barrier defined by the genetic effective population size, which is negatively associated with organism size, can have a substantial influence on the location and dispersion of the long-term steady-state distribution of mean phenotypes. In addition, for multilocus traits, the multiplicity of alternative, functionally equivalent states can draw mean phenotypes away from selective optima, even in the absence of mutation bias. Using a framework for traits with an additive genetic basis, it is shown that 1) optimal phenotypic states may be only rarely achieved; 2) gradients of mean phenotypes with respect to organism size (i.e., allometric relationships) are likely to be molded by differences in the power of random genetic drift across the tree of life; and 3) for any particular set of population-genetic conditions, significant variation in mean phenotypes may exist among lineages exposed to identical selection pressures. These results provide a potentially useful framework for understanding numerous aspects of cellular diversification and illustrate the risks of interpreting such variation in a purely adaptive framework.
Journal Article
Defining crime : a critique of the concept and its implication
\"Defining Crime explores the limitations of the legal definition of crime, how that politically based definition has shaped criminological research, and why criminologists must redefine crime to include scientific objectivity. Lynch, Stretesky, and Long argue that a scientific definition of crime must be detached from criminal law and the variation the political construction imposes. The authors propose an alternative definition of crime, explore its limitations, and how it can reshape criminological research. \"-- Provided by publisher.
Book
Rate, molecular spectrum, and consequences of human mutation
Although mutation provides the fuel for phenotypic evolution, it also imposes a substantial burden on fitness through the production of predominantly deleterious alleles, a matter of concern from a human-health perspective. Here, recently established databases on de novo mutations for monogenic disorders are used to estimate the rate and molecular spectrum of spontaneously arising mutations and to derive a number of inferences with respect to eukaryotic genome evolution. Although the human per-generation mutation rate is exceptionally high, on a per-cell division basis, the human germline mutation rate is lower than that recorded for any other species. Comparison with data from other species demonstrates a universal mutational bias toward A/T composition, and leads to the hypothesis that genome-wide nucleotide composition generally evolves to the point at which the power of selection in favor of G/C is approximately balanced by the power of random genetic drift, such that variation in equilibrium genome-wide nucleotide composition is largely defined by variation in mutation biases. Quantification of the hazards associated with introns reveals that mutations at key splice-site residues are a major source of human mortality. Finally, a consideration of the long-term consequences of current human behavior for deleterious-mutation accumulation leads to the conclusion that a substantial reduction in human fitness can be expected over the next few centuries in industrialized societies unless novel means of genetic intervention are developed.
Journal Article