Evolutionary conceptions of species place special weight on each species having dynamic independence as a unit of evolution. However, the idea that species have their own historical fates, tendencies, or roles has resisted systematic analysis. Growing evidence from population genomics shows that many paradigm species regularly engage in hybridization. How can species be defined in terms of independent evolutionary identities if their genomes are dynamically coupled through lateral exchange? I introduce the concept of a “composite lineage” to distinguish species and (...) subspecies on the basis of the proportion of a group’s heritable traits that are uncoupled from reproductive exchange. (shrink)

Ernst Mayr’s influence on philosophy of biology has given the field a particular perspective on evolution, phylogeny and life in general. Using debates about the tree of life as a guide, I show how Mayrian evolutionary biology excludes numerous forms of life and many important evolutionary processes. Hybridization and lateral gene transfer are two of these processes, and they occur frequently, with important outcomes in all domains of life. Eukaryotes appear to have a more tree-like history because successful lateral events (...) tend to occur among more closely related species, or at a lower frequency, than in prokaryotes, but this is a difference of degree rather than kind. Although the tree of life is especially problematic as a representation of the evolutionary history of prokaryotes, it can function more generally as an illustration of the limitations of a standard evolutionary perspective. Moreover, for philosophers, questions about the tree of life can be applied to the Mayrian inheritance in philosophy of biology. These questions make clear that the dichotomy of life Mayr suggested is based on too narrow a perspective. An alternative to this dichotomy is a multidimensional continuum in which different strategies of genetic exchange bestow greater adaptiveness and evolvability on prokaryotes and eukaryotes. (shrink)

Recently the functional model of reduction has become something like the standard model of reduction in philosophy of mind. In this paper, I argue that the functional model fails as an account of reduction due to problems related to three key concepts: functionalization, realization and causation. I further argue that if we try to revise the model in order to make it more coherent and scientifically plausible, the result is merely a simplified version of what in philosophy of science is (...) known as mechanistic explanation. Hence, instead of analyzing reduction in philosophy of mind in terms of functional reduction, it should be analyzed in terms of mechanistic explanation. (shrink)

Our understanding of what microbes are and how they evolve has undergone many radical shifts since the late nineteenth century, when many still believed that bacteria could be spontaneously generated and most thought microbial “species” (if any) to be unstable and interchangeable in form and function (pleomorphic). By the late twentieth century, an ontology based on single cells and definable species with predictable properties, evolving like species of animals or plants, was widely accepted. Now, however, genomic and metagenomic data show (...) that lateral gene transfer compromises this picture of stability and predictability, and refocuses our attention on multilineage communities. Treating such communities as unstable but identifiable evolving “individuals” makes us again pleomorphists, of a sort. (shrink)

The word “gene” means different things to different people, and can even be used in multiple ways by the same individual. In this review, I follow a particular thread running through Griffith and Stotz’s “Genetics and Philosophy: an introduction”, which is the way that methods of investigation influence the way we define the concept of “gene”, from nineteen century breeding experiments to twenty-first century big data bioinformatics. These different views lead to a set of gene concepts, which only partially overlap (...) each other, each of which picks up on a different part of gene behaviour, function or scientific utility. This plurality of concepts carries over to the use of the concept of “information” in biology, where the non-overlapping concepts can be connected to whether you view the genome as a blueprint for development, a response to environmental triggers, an engine of heritability, or a document of history. (shrink)

Recently improved understanding of evolutionary processes suggests that tree-based phylogenetic analyses of evolutionary change cannot adequately explain the divergent evolutionary histories of a great many genes and gene complexes. In particular, genetic diversity in the genomes of prokaryotes, phages, and plasmids cannot be fit into classic tree-like models of evolution. These findings entail the need for fundamental reform of our understanding of molecular evolution and the need to devise alternative apparatus for integrated analysis of these genomes. We advocate the development (...) of integrative phylogenomics for analyzing these genomes and their histories, with tools suited to analyzing the importance of lateral gene transfer (LGT) and of DNA evolution in extra-cellular mobile genetic elements (e.g., viruses, plasmids). These phenomena greatly increase the complexity of relationships among interacting genetic partners, as they exchange functional genetic units. We examine the ontology of functional genetic units, interacting genetic partners, and emergent genetic associations, argue that these three categories of entities are required for a successful integrated phylogenomics. We conclude with arguments to suggest that the proposed new perspective and associated tools are suitable, and perhaps required, as a replacement for the bifurcating trees that have dominated evolutionary thinking for the last 150 years. (shrink)

This afterword to Species and Beyond provides some reflections on species, with special attention to what I think the most significant developments have been in the thinking of biologists and philosophers working on species over the past 25 years, as well as some bad jokes.