Online research in philosophy

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)

Andrew Bourke’s Principles of Social Evolution identifies three stages that characterize an evolutionary transition in individuality and deploys inclusive fitness theory to explain each stage. The third stage, social group transformation, has hitherto received relatively little attention from inclusive fitness theorists. In this review, I first discuss Bourke’s “virtual dominance” hypothesis for the evolution of the germ line. I then contrast Bourke’s inclusive fitness approach to the major transitions with the multi-level approach developed by Richard Michod, Samir Okasha and others. (...) I suggest that, rather than choosing between these approaches, we should exploit the strengths of both. Finally, I stress the need for a firmer conceptual grasp of the nature of social group transformation. (shrink)

Inclusive fitness theory was not originally designed to explain the major transitions in evolution, but there is a growing consensus that it has the resources to do so. My aim in this paper is to highlight, in a constructive spirit, the puzzles and challenges that remain. I first consider the distinctive aspects of the cooperative interactions we see within the most complex social groups in nature: multicellular organisms and eusocial insect colonies. I then focus on one aspect in particular: the (...) extreme redundancy these societies exhibit. I argue that extreme redundancy poses a distinctive explanatory puzzle for inclusive fitness theory, and I offer a potential solution which casts coercion as the key enabler. I suggest that the general moral to draw from the case is one of guarded optimism: while inclusive fitness is a powerful tool for understanding evolutionary transitions, it must be integrated within a broader framework that recognizes the distinctive problems such transitions present and the distinctive mechanisms by which these problems may be overcome. (shrink)

According to vitalism, living organisms differ from machines and all other inanimate objects by being endowed with an indwelling immaterial directive agency, ‘vital force,’ or entelechy . While support for vitalism fell away in the late nineteenth century many biologists in the early twentieth century embraced a non vitalist philosophy variously termed organicism/holism/emergentism which aimed at replacing the actions of an immaterial spirit with what was seen as an equivalent but perfectly natural agency—the emergent autonomous activity of the whole organism. (...) Organicists hold that organisms unlike machines are ‘more than the sum of their parts’ and predict that the vital properties of living things can never be explained in terms of mechanical analogies and that the reductionist agenda is doomed to failure. Here we review the current status of the mechanist and organicist conceptions of life particularly as they apply to the cell. We argue that despite the advances in biological knowledge over the past six decades since the molecular biological revolution, especially in the fields of genetics and cell biology the unique properties of living cells have still not been simulated in mechanical systems nor yielded to reductionist—analytical explanations. And we conclude that despite the dominance of the mechanistic–reductionist paradigm through most of the past century the possibility of a twentyfirst century organicist revival cannot be easily discounted. (shrink)

Gers (Biol Philos, 2011) provides a positive and constructive view of the project to generalise Darwinian principles in Geoffrey Hodgson and Thorbjørn Knudsen’s Darwin’s Conjecture. We note considerable overlap with his work and ours, and also with important recent work of Godfrey-Smith ( 2009 ), which Gers cites extensively. But we also note that there are differences in research objectives between Gers and Godfrey-Smith, on the one hand, and ourselves, on the other. Gers and Godfrey-Smith focus on the elucidation of (...) the most general principles possible. Our aim is to derive principles that are sufficiently abstract to span the natural and human social worlds, and then add additional principles to help understand the Darwinian evolution of human society. Furthermore, Gers and Godfrey-Smith critique a replicator concept that is different from ours. Once these points are made apparent, the criticisms are essentially disabled, and we end up in a position with different but complementary and overlapping research projects. (shrink)

A deflationary perspective on theories of cultural evolution, in particular dual-inheritance theory, has recently been proposed by Lewens. On this ‘pop-culture’ analysis, dual-inheritance theorists apply population thinking to cultural phenomena, without claiming that cultural items evolve by natural selection. This paper argues against this pop-culture analysis of dual-inheritance theory. First, it focuses on recent dual-inheritance models of specific patterns of cultural change. These models exemplify population thinking without a commitment to natural selection of cultural items. There are grounds, however, for (...) doubting the added explanatory value of the models in their disciplinary context—and thus grounds for engaging in other potentially explanatory projects based on dual-inheritance theory. One such project is suggested by advocates of the theory. Some of the motivational narratives that they offer can be interpreted as setting up an adaptationist project with regard to cumulative change in cultural items. We develop this interpretation here. On it, dual-inheritance theory features two interrelated selection processes, one on the level of genetically inherited learning mechanisms, another on the level of the cultural items transmitted through these mechanisms. This interpretation identifies a need for further modelling efforts, but also offers scope for enhancing the explanatory power of dual-inheritance theory. (shrink)

Using as case studies two early diagrams that represent mechanisms of the cell division cycle, we aim to extend prior philosophical analyses of the roles of diagrams in scientific reasoning, and specifically their role in biological reasoning. The diagrams we discuss are, in practice, integral and indispensible elements of reasoning from experimental data about the cell division cycle to mathematical models of the cycle’s molecular mechanisms. In accordance with prior analyses, the diagrams provide functional explanations of the cell cycle and (...) facilitate the construction of mathematical models of the cell cycle. But, extending beyond those analyses, we show how diagrams facilitate the construction of mathematical models, and we argue that the diagrams permit nomological explanations of the cell cycle. We further argue that what makes diagrams integral and indispensible for explanation and model construction is their nature as locality aids: they group together information that is to be used together in a way that sentential representations do not. (shrink)

Alex Mesoudi’s book shows cultural evolution to be a mature field, which has already illuminated many instances of cultural change. Mesoudi’s presentation of the discipline nonetheless invites three objections. First, the culture concept it makes use of is not clearly defined; second, Mesoudi’s historical argument which looks back to the modern synthesis in order to predict an analogous synthesis in the social sciences is flawed; third, Mesoudi’s understanding of the positions held by leading figures within social science is shaky.

Voles are attracting attention because genetic variation at a single locus appears to have a profound impact on a complex social behavior, namely monogamy. After briefly reviewing the state of the most relevant scientific literature, I examine the way that this research gets taken up by the popular media, by scientists, and by the notable philosopher of neuroscience Patricia Churchland and interpreted as having deeply revisionary implications for how we ordinarily understand ourselves as persons. We have all these big questions (...) we would like to resolve about free will, consciousness, our understanding of persons, and the nature of morality and there is a tendency to ask more of neuroscience than it can yet answer. I do not deny that advances in neuroscience may eventually bear on important philosophical issues. However, it is not at all clear that this research has many of the sweeping implications being claimed for it and, in communicating science responsibly to the public, there is reason to be cautious about suggesting that it does. (shrink)

In 1966, island biogeographer Sherwin Carlquist published a list of 24 principles governing long-distance dispersal and evolution on islands. The 24 principles describe many aspects of island biology, from long-distance dispersal and establishment to community change and assemblage. Although this was an active period for island biogeography, other models and research garnered much more attention than did Carlquist’s. In this review, over 40 years of support for or against Carlquist’s principles is presented. Recent work has supported most of the 24 (...) principles, and improved methodologies have generally substantiated his initial claims. However, Carlquist’s original work and ideas remain relatively under-represented in the biogeographic literature. Use of philosophical model domains provides one explanation as to why Carlquist’s work has received little attention. Carlquist’s principles are largely natural history tests, and don’t translate well into the theoretical, design of preserves, or the experimental domains—whereas other competing models do well in such domains. (shrink)

What’s Darwin got to do with it? The role of evolutionary theory in psychiatry Content Type Journal Article Category Review Essay Pages 1-12 DOI 10.1007/s10539-011-9301-3 Authors Ian Ravenscroft, Philosophy Department, Flinders University, Adelaide, SA, Australia Journal Biology and Philosophy Online ISSN 1572-8404 Print ISSN 0169-3867.

Abstract In order to illuminate the role of information in biology, Bergstrom and Rosvall (Biol Philos 26:159–176, 2011a ; Biol Philos 26:195–200, 2011b ) propose a ‘transmission sense of information’ which builds on Shannon’s theory. At the core of the transmission sense is an appeal to the reduction in uncertainty in receivers and to etiological function. I explore several ways of cashing out uncertainty reduction as well as the consequences of appealing to function. Content Type Journal Article Pages 1-4 DOI (...) 10.1007/s10539-012-9310-x Authors Ulrich E. Stegmann, School of Divinity, History and Philosophy, University of Aberdeen, Old Brewery, High Street, Aberdeen, AB24 3UB UK Journal Biology and Philosophy Online ISSN 1572-8404 Print ISSN 0169-3867. (shrink)

Robin Nunn has argued that we should stop using the terms ‘placebo’ and ‘placebo effect’. I argue in support of Nunn’s position by considering the logic of why we perform placebo comparisons. Like all comparisons, placebo comparison is just a case of comparing one thing with another, but it is a mistake, I argue, to think of placebo comparison as a case where something is compared to ‘a placebo’. Rather, placebo comparison should be understood as a situation which sets-up the (...) treatment and control groups in a particular way; not as a case involving objects or procedures called ‘placebos’ employed in order to control for ‘placebo effects’. (shrink)

We discuss the impact of horizontal gene transfer (HGT) on phylogenetic reconstruction and taxonomy. We review the power of HGT as a creative force in assembling new metabolic pathways, and we discuss the impact that HGT has on phylogenetic reconstruction. On one hand, shared derived characters are created through transferred genes that persist in the recipient lineage, either because they were adaptive in the recipient lineage or because they resulted in a functional replacement. On the other hand, taxonomic patterns in (...) microbial phylogenies might also be created through biased gene transfer. The agreement between different molecular phylogenies has encouraged interpretation of the consensus signal as reflecting organismal history or as the tree of cell divisions; however, to date the extent to which the consensus reflects shared organismal ancestry and to which it reflects highways of gene sharing and biased gene transfer remains an open question. Preferential patterns of gene exchange act as a homogenizing force in creating and maintaining microbial groups, generating taxonomic patterns that are indistinguishable to those created by shared ancestry. To understand the evolution of higher bacterial taxonomic units, concepts usually applied in population genetics need to be applied. (shrink)

Abstract Emergent antireductionism in biological sciences states that even though all living cells and organisms are composed of molecules, molecular wholes are characterized by emergent properties that can only be understood from the perspective of cellular and organismal levels of composition. Thus, an emergence claim (molecular wholes are characterized by emergent properties) is thought to support a form of antireductionism (properties of higher-level molecular wholes can only be understood by taking into account concepts, theories and explanations dealing with higher-level entities). (...) I argue that this argument is flawed: even if molecular wholes are characterized by emergent properties and even if many successful explanations in biology are not molecular, there is no entailment between the two claims. Content Type Journal Article Pages 1-16 DOI 10.1007/s10539-011-9290-2 Authors Tudor M. Baetu, Department of Philosophy, University of Maryland, 1107D Skinner Building, College Park, MD 20742, USA Journal Biology and Philosophy Online ISSN 1572-8404 Print ISSN 0169-3867. (shrink)

Frequent lateral genetic transfer undermines the existence of a unique “tree of life” that relates all organisms. Vertical inheritance is nonetheless of vital interest in the study of microbial evolution, and knowing the “tree of cells” can yield insights into ecological continuity, the rates of change of different cellular characters, and the evolutionary plasticity of genomes. Notwithstanding within-species recombination, the relationships most frequently recovered from genomic data at shallow to moderate taxonomic depths are likely to reflect cellular inheritance. At the (...) same time, it is clear that several types of ‘average signals’ from whole genomes can be highly misleading, and the existence of a central tendency must not be taken as prima facie evidence of vertical descent. Phylogenetic networks offer an attractive solution, since they can be formulated in ways that mitigate the misleading aspects of hybrid evolutionary signals in genomes. But the connections in a network typically show genetic relatedness without distinguishing between vertical and lateral inheritance of genetic material. The solution may lie in a compromise between strict tree-thinking and network paradigms: build a phylogenetic network, but identify the set of connections in the network that are potentially due to vertical descent. Even if a single tree cannot be unambiguously identified, choosing a subnetwork of putative vertical connections can still lead to drastic reductions in the set of candidate vertical hypotheses. (shrink)

Lateral gene transfer (LGT), the exchange of genetic information between (primarily prokaryotic) lineages, not only makes construction of a universal Tree of Life (TOL) difficult to achieve, but calls into question the utility and meaning of any result. Here I review the science of prokaryotic LGT, the philosophy of the TOL as it figured in Darwin’s formulation of the Theory of Evolution, and the politics of the current debate within the discipline over how threats to the TOL should be represented (...) outside it. We could encourage a more realistic and supportive public understanding of evolution by admitting that what we believe in is not a unified meta-theory but a versatile and well-stocked explanatory toolkit. (shrink)

This paper examines the species problem in microbiology and its implications for the species problem more generally. Given the different meanings of ‘species’ in microbiology, the use of ‘species’ in biology is more multifarious and problematic than commonly recognized. So much so, that recent work in microbial systematics casts doubt on the existence of a prokaryote species category in nature. It also casts doubt on the existence of a general species category for all of life (one that includes both prokaryotes (...) and eukaryotes). Prokaryote biology also undermines recent attempts to save the species category, such as the suggestion that species are metapopulation lineages and the idea that ‘species’ is a family resemblance concept. (shrink)

Darwin’s Conjecture is a bold attempt to bring evolutionary explanation to the social sciences, particularly economics. The book outlines the history of Darwinian explanation in social science then puts forward a generalized replicator account of social evolution by natural selection. The authors identify habits and routines as examples of the generative replicators necessary in order that social evolution is Darwinian. This reviewer notes that the replicator approach limits the generality of this account and suggests that habits and routines might better (...) be seen as members of a Darwinian population in the tradition of Godfrey-Smith’s (2009) generalized account of natural selection instead. Furthermore, the existence of levels of social evolution will constrain what evolution can occur low in the hierarchy. (shrink)

The Tree of Life hypothesis frames the evolutionary process as a series of events whereby lineages diverge from one another, thus creating the diversity of life as descendent lineages modify properties from their ancestors. This hypothesis is under scrutiny due to the strong evidence for lateral gene transfer between distantly related bacterial taxa, thereby providing extant taxa with more than one parent. As a result, one argues, the Tree of Life becomes confounded as the original branching structure is gradually superseded (...) by reticulation, ultimately losing its ability to serve as a model for bacterial evolution. Here we address a more fundamental issue: is there a Tree of Life that results from bacterial evolution without considering such lateral gene transfers? Unlike eukaryotic speciation events, lineage separation in bacteria is a gradual process that occurs over tens of millions of years, whereby genetic isolation is established on a gene-by-gene basis. As a result, groups of closely related bacteria, while showing robust genetic isolation as extant lineages, were not created by an unambiguous series of lineage-splitting events. Rather, a temporal fragmentation of the speciation process results in cognate genes showing different genetic relationships. We argue that lineage divergence in bacteria does not produce a tree-like framework, and inferences drawn from such a framework have the potential to be incorrect and misleading. Therefore, the Tree of Life is an inappropriate paradigm for bacterial evolution regardless of the extent of gene transfer between distantly related taxa. (shrink)

Historians and philosophers of science agree that Darwin had an understanding of species which led to a workable theory of their origins. To Darwin species did not differ essentially from ‘varieties’ within species, but were distinguishable in that they had developed gaps in formerly continuous morphological variation. Similar ideas can be defended today after updating them with modern population genetics. Why then, in the 1930s and 1940s, did Dobzhansky, Mayr and others argue that Darwin failed to understand species and speciation? (...) Mayr and Dobzhansky argued that reproductively isolated species were more distinct and ‘real’ than Darwin had proposed. Believing species to be inherently cohesive, Mayr inferred that speciation normally required geographic isolation, an argument that he believed, incorrectly, Darwin had failed to appreciate. Also, before the sociobiology revolution of the 1960s and 1970s, biologists often argued that traits beneficial to whole populations would spread. Reproductive isolation was thus seen as an adaptive trait to prevent disintegration of species. Finally, molecular genetic markers did not exist, and so a presumed biological function of species, reproductive isolation, seemed to delimit cryptic species better than character-based criteria like Darwin’s. Today, abundant genetic markers are available and widely used to delimit species, for example using assignment tests: genetics has replaced a Darwinian reliance on morphology for detecting gaps between species. In the 150th anniversary of The Origin of Species , we appear to be returning to more Darwinian views on species, and to a fuller appreciation of what Darwin meant. (shrink)

The recent conception of biodiversity proposed by James Maclaurin and Sterelny was developed mostly with macrobiological life in mind. They suggest that we measure biodiversity by dividing life into natural units (typically species) and quantifying the differences among units using phenetic rather than phylogenetic measures of distance. They identify problems in implementing quantitative phylogenetic notions of difference for non-prokaryotic species. I suggest that if we focus on microbiological life forms that engage in frequent, promiscuous lateral gene transfer (LGT), and their (...) associated reticulated phylogenies, we need to rethink the notion of species as the natural unit, and we discover additional problems with phylogenetic notions of distance. These problems suggest that a phenetic approach based on morphospaces has just as much appeal, if not more, for microbes as they do for multi-cellular life. Facts about LGT, however, offer no new insight into the additional challenge of reconciling units and differences into a single measure of biodiversity. (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)

The ‘Tree of Life’ is intended to represent the pattern of evolutionary processes that result in bifurcating species lineages. Often justified in reference to Darwin’s discussions of trees, the Tree of Life has run up against numerous challenges especially in regard to prokaryote evolution. This special issue examines scientific, historical and philosophical aspects of debates about the Tree of Life, with the aim of turning these criticisms towards a reconstruction of prokaryote phylogeny and even some aspects of the standard evolutionary (...) understanding of eukaryotes. These discussions have arisen out of a multidisciplinary collaboration of people with an interest in the Tree of Life, and we suggest that this sort of focused engagement enables a practical understanding of the relationships between biology, philosophy and history. (shrink)

The history of biological systematics documents a continuing tension between classifications in terms of nested hierarchies congruent with branching diagrams (the ‘Tree of Life’) versus reticulated relations. The recognition of conflicting character distribution led to the dissolution of the scala naturae into reticulated systems, which were then transformed into phylogenetic trees by the addition of a vertical axis. The cladistic revolution in systematics resulted in a representation of phylogeny as a strictly bifurcating pattern (cladogram). Due to the ubiquity of character (...) conflict—at the genetic or morphological level, or at any level in between—some characters will necessarily have to be discarded ( qua noise) in favor of others in support of a strictly bifurcating phylogenetic tree. Pattern analysts will seek maximal congruence in the distribution of characters (ultimately of any kind) relative to a branching tree-topology; process explainers will call such tree-topologies into question by reference to incompatible evolutionary processes. Pattern analysts will argue that process explanations must not be brought to bear on pattern reconstruction; process explainers will insist that the reconstructed pattern requires a process explanation to become scientifically relevant, i.e., relevant to evolutionary theory. The core question driving the current debate about the adequacy of the ‘Tree of Life’ metaphor seems to be whether the systematic dichotomization of the living world is an adequate representation of the complex evolutionary history of global biodiversity. In ‘Questioning the Tree of Life’, it seems beneficial to draw at least four conceptual distinctions: pattern reconstruction versus process explanation as different epistemological approaches to the study of phylogeny; open versus closed systems as expressions of different kinds of population (species) structures; phylogenetic trees versus cladograms as representations of evolutionary processes versus patterns of relationships; and genes versus species as expressions of different levels of causal integration and evolutionary transformation. (shrink)

Researchers typically define animal signaling as morphology or behavior specialized for transmitting encoded information from a signaler to a perceiver. Although intuitively appealing, this conception is inherently metaphorical and leaves concepts of both information and encoding undefined. To justify relying on the information construct, theorists often appeal to Shannon and Weaver’s quantitative definition. The two approaches are, however, fundamentally at odds. The predominant definition of animal signaling is thus untenable, which has a number of undesirable consequences for both theory and (...) practice in the field. Theoretical problems include conceptual circularity and running afoul of fundamental evolutionary principles. Problems in empirical work include that research is often grounded in abstractions such as signal honesty and semanticity, and thereby distracted from more basic and concrete factors shaping communication. A revised definition is therefore proposed, making influence rather than transmission of encoded information the central function of animal signaling. This definition is conceptually sound, empirically testable, and inclusive, yet bounded. Implications are considered in both theoretical and empirical domains. (shrink)