Evolutionary Processes in Cancer

Cancer develops through the evolution of somatic cells in multicellular bodies. The familiar dynamics of organismal evolution, including mutations, natural selection, genetic drift, and migration, also occur among the cells of multicellular organisms. In some cases, but not all, these evolutionary processes lead to cancer. This has profound implications for both our understanding of cancer and our treatment of the disease, as well as its prevention. All of our medical interventions impose selective pressures on the heterogeneous populations of billions of cells in tumors, and tend to select for mutant cells that are resistant to the intervention, regardless of whether the intervention is a drug, radiation, the immune system, or anything else that has been tried. We will likely need evolutionary and ecological approaches to cancer to manage its evolution in response to our interventions. The field of the evolutionary biology and ecology of cancer is still young and relatively small. We are in the early stages of translating ideas and tools from evolutionary biology and ecology to study and manage cancers. There is a desperate need for more researchers with expertise in evolutionary biology and ecology to apply their skills and ideas to cancer. Currently, there are far more important questions that need to be addressed than there are people to address them.

Evolutionary Ecology of Natural Comammox Nitrospira Populations

Microbial species interact with each other and their environment (ecological processes) and undergo changes in their genomic repertoire over time (evolutionary processes). How these two classes of processes interact is largely unknown, especially for complex communities, as most studies of microbial evolutionary dynamics consider single species in isolation or a few interacting species in simplified experimental systems.

Evolutionary and Ideation Concepts for Cybersecurity Education

Evolution is a well-established biological theory, but some basic concepts can be abstracted and applied to non-biological domains such as the education domain for the purposes of knowledge sharing. There is a gap in the literature regarding how evolutionary processes can be applied to cyber security education. This article presents the general evolutionary algorithm and pairs it with an ideation technique (SCAMPER) to illustrate how certain evolutionary processes can be applied to cyber security education and learning. This paper does not attempt to close the gap, but rather offer a theoretical approach to address the gap.

Water as a thermodynamic parameter of biosphere evolution

Water has a profound influence on the evolution of the biosphere and can be regarded as a thermodynamic parameter. The priorities and objectives in this research include determining the hydrological features of rivers and lakes in the region as indicators of the thermodynamic activity of water in the evolutionary processes; hydrology and ecology of the cryptobiosphere; the effects of water on the evolutionary adaptations and strategies in living organisms in biogeochemical systems of different origins; and the hydrology of possible alternative stable states of biogeochemical systems.

The transition of insurgent-guerrilla movements to radical terrorist methods of struggle: retrospective features

The realities of modern reality indicate that there are a significant number of unjustified attempts to resolve controversial issues based on the use of force. The article shows the evolutionary processes of the transition of insurgent-guerrilla movements to radical terrorist methods of struggle in the period of 1991-2001 and reveals the reasons for this process. The article analyzes the definition of "international terrorism" in the modern sense, analyzes the characteristic features of international terrorism of the 1990s, the reasons for its spread, new forms of terrorist activity. The following methods were used in the study of the chosen topic: historical-genetic, comparative-historical; problem-chronological, the method of historical modeling. Authors conclude, there is no doubt that all the insurgent-guerilla movements, without exception, pursued their own goals. The most effective way to achieve them at the turn of the century turned out to be precisely terrorist attacks, which, with all the strength of state structures, were not possible to fend off. Thus, terrorism has become a strong weapon in the hands of weak players in the international arena.

Polymorphism-aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes

The availability of population genomic data through new sequencing technologies gives unprecedented opportunities for estimating important evolutionary forces such as genetic drift, selection, and mutation biases across organisms. Yet, analytical methods that can handle polymorphisms jointly with sequence divergence across species are rare and not easily accessible to empiricists. We implemented polymorphism-aware phylogenetic models (PoMos), an alternative approach for species tree estimation, in the Bayesian phylogenetic software RevBayes. PoMos naturally account for incomplete lineage sorting, which is known to cause difficulties for phylogenetic inference in species radiations, and scale well with genome-wide data. Simultaneously, PoMos can estimate mutation and selection biases. We have applied our methods to resolve the complex phylogenetic relationships of a young radiation of Chorthippus grasshoppers, based on coding sequences. In addition to establishing a well-supported species tree, we found a mutation bias favoring AT alleles and selection bias promoting the fixation of GC alleles, the latter consistent with GC-biased gene conversion. The selection bias is two orders of magnitude lower than genetic drift, validating the critical role of nearly neutral evolutionary processes in species radiation. PoMos offer a wide range of models to reconstruct phylogenies and can be easily combined with existing models in RevBayes - e.g., relaxed clock and divergence time estimation - offering new insights into the evolutionary processes underlying molecular evolution and, ultimately, species diversification.

Evolutionary Processes Driving the Rise and Fall of Staphylococcus aureus ST239, a Dominant Hybrid Pathogen

The rise of antibiotic resistance in most pathogenic bacteria has been driven by the spread of a small number of epidemically successful resistant strains. However, the processes that drive the rise and fall of these “superbugs” remain poorly understood.

Ecology drives the degree of convergence in the gene expression of extremophile fishes

Convergent evolution, where independent lineages evolve similar traits when adapting to similar habitats, is a common phenomenon and testament to the repeatability of evolutionary processes. Still, non-convergence is also common, and a major question is whether apparently idiosyncratic, lineage-specific evolutionary changes are reflective of chance events inherent to evolutionary processes, or whether they are also influenced by deterministic genetic or ecological factors. To address this question, we quantified the degree of convergence in genome-wide patterns of gene expression across lineages of livebearing fishes (family Poeciliidae) that span 40 million years of evolution and have colonized extreme environments in the form of toxic, hydrogen-sulfide-rich springs. We specifically asked whether the degree of convergence across lineage pairs was related to their phylogenetic relatedness or the ecological similarity of the habitats they inhabit. Using phylogenetic comparative analyses, we showed that the degree of convergence was highly variable across lineage pairs residing in sulfide springs. While closely related lineages did not exhibit higher degrees of convergence than distantly related ones, we uncovered a strong relationship between degree of convergence and ecological similarity. Our results indicate that variation in the degree of convergence is not merely noise associated with evolutionary contingency. Rather, cryptic environmental variation that is frequently ignored when we employ reductionist approaches can significantly contribute to adaptive evolution. This study highlights the importance of multivariate approaches that capture the complexities of both selective regimes and organismal design when assessing the roles of determinism and contingency in evolution.

Culturing Belief

What kind of being are we? This of course is one of the oldest questions in philosophy. In earlier eras, answers were often non-naturalistic (we are animals with souls, for instance). Today, one of the oldest answers is also one of the most popular: with Aristotle, we often think we are distinguished from other animals by our rationality. This chapter suggests that another answer is at least as defensible: we are epistemically social animals. In making the case for this answer, it provides some of the background for the account of belief formation developed in the book. It highlights evidence from cultural evolution for our epistemic dependence on one another. Cultural evolution shows how human flourishing is due to cultural knowledge that escapes the grasp of individuals and that is the product of evolutionary processes. The chapter then turns to our central paradigm of a successful epistemic enterprise: modern science. It argues that science, too, owes its success to the way in which cognition is distributed across agents, groups, and even artifacts.