Size Doesn't Matter: Towards a More Inclusive Philosophy of Biology

notes: As the primary author, O’Malley drafted the paper, and gathered and analysed data (scientific papers and talks). Conceptual analysis was conducted by both authors.publication-status: Publishedtypes: ArticlePhilosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations

The Physics of Star Cluster Formation and Evolution

© 2020 Springer-Verlag. The final publication is available at Springer via https://doi.org/10.1007/s11214-020-00689-4.Star clusters form in dense, hierarchically collapsing gas clouds. Bulk kinetic energy is transformed to turbulence with stars forming from cores fed by filaments. In the most compact regions, stellar feedback is least effective in removing the gas and stars may form very efficiently. These are also the regions where, in high-mass clusters, ejecta from some kind of high-mass stars are effectively captured during the formation phase of some of the low mass stars and effectively channeled into the latter to form multiple populations. Star formation epochs in star clusters are generally set by gas flows that determine the abundance of gas in the cluster. We argue that there is likely only one star formation epoch after which clusters remain essentially clear of gas by cluster winds. Collisional dynamics is important in this phase leading to core collapse, expansion and eventual dispersion of every cluster. We review recent developments in the field with a focus on theoretical work.Peer reviewe

Ecology and molecular targets of hypermutation in the global microbiome

Changes in the sequence of an organism’s genome, i.e., mutations, are the raw material of evolution. The frequency and location of mutations can be constrained by specific molecular mechanisms, such as diversity-generating retroelements (DGRs). DGRs have been characterized from cultivated bacteria and bacteriophages, and perform error-prone reverse transcription leading to mutations being introduced in specific target genes. DGR loci were also identified in several metagenomes, but the ecological roles and evolutionary drivers of these DGRs remain poorly understood. Here, we analyze a dataset of >30,000 DGRs from public metagenomes, establish six major lineages of DGRs including three primarily encoded by phages and seemingly used to diversify host attachment proteins, and demonstrate that DGRs are broadly active and responsible for >10% of all amino acid changes in some organisms. Overall, these results highlight the constraints under which DGRs evolve, and elucidate several distinct roles these elements play in natural communities. © 2021, The Author(s).Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Pines

Pinus is the most important genus within the Family Pinaceae and also within the gymnosperms by the number of species (109 species recognized by Farjon 2001) and by its contribution to forest ecosystems. All pine species are evergreen trees or shrubs. They are widely distributed in the northern hemisphere, from tropical areas to northern areas in America and Eurasia. Their natural range reaches the equator only in Southeast Asia. In Africa, natural occurrences are confined to the Mediterranean basin. Pines grow at various elevations from sea level (not usual in tropical areas) to highlands. Two main regions of diversity are recorded, the most important one in Central America (43 species found in Mexico) and a secondary one in China. Some species have a very wide natural range (e.g., P. ponderosa, P. sylvestris). Pines are adapted to a wide range of ecological conditions: from tropical (e.g., P. merkusii, P. kesiya, P. tropicalis), temperate (e.g., P. pungens, P. thunbergii), and subalpine (e.g., P. albicaulis, P. cembra) to boreal (e.g., P. pumila) climates (Richardson and Rundel 1998, Burdon 2002). They can grow in quite pure stands or in mixed forest with other conifers or broadleaved trees. Some species are especially adapted to forest fires, e.g., P. banksiana, in which fire is virtually essential for cone opening and seed dispersal. They can grow in arid conditions, on alluvial plain soils, on sandy soils, on rocky soils, or on marsh soils. Trees of some species can have a very long life as in P. longaeva (more than 3,000 years)