This work aims to describe how developments in thinking on evolutionary biology require re-assessment of initial rejection of the relevance and applicability of neo-Darwinian evolution to the Gaia hypothesis.

That holobionts are units of selection squares poorly with the observation that microbes are often recruited from the environment, not passed down vertically from parent to offspring, as required for collective reproduction. The taxonomic makeup of a holobiont’s microbial community may vary over its lifetime and differ from that of conspecifics. In contrast, biochemical functions of the microbiota and contributions to host biology are more conserved, with taxonomically variable but functionally similar microbes recurring across generations and hosts. To save what (...) is of interest in holobiont thinking, we propose casting metabolic and developmental interaction patterns, rather than the taxa responsible for them, as units of selection. Such units need not directly reproduce or form parent-offspring lineages: their prior existence has created the conditions under which taxa with the genes necessary to carry out their steps have evolved in large numbers. These taxa or genes will reconstruct the original interaction patterns when favorable conditions occur. Interaction patterns will vary in ways that affect the likelihood of and circumstances under which such reconstruction occurs. Thus, they vary in fitness, and evolution by natural selection will occur at this level. It is on the persistence, reconstruction, and spread of such interaction patterns that students of holobiosis should concentrate, we suggest. This model also addresses other multi-species collectively beneficial interactions, such as biofilms or biogeochemical cycles maintaining all life. (shrink)

Biological science uses multiple species concepts. Order can be brought to this diversity if we recognize two key features. First, any given species concept is likely to have a patchwork structure, generated by repeated application of the concept to new domains. We illustrate this by showing how two species concepts (biological and ecological) have been modified from their initial eukaryotic applications to apply to prokaryotes. Second, both within and between patches, distinct species concepts may interact and hybridize. We thus defend (...) a semantic picture of the species concept as a collection of interacting patchwork structures. Thus, although not all uses of the term pick out the same kind of unit in nature, the diversity of uses reflects something more than mere polysemy. We suggest that the emphasis on the use of species to pick out natural units is itself problematic, because that is not the term’s sole function. In particular, species concepts are used to manage inquiry into processes of speciation, even when these processes do not produce clearly delimited species. (shrink)

Clade selection is unpopular with philosophers who otherwise accept multilevel selection theory. Clades cannot reproduce, and reproduction is widely thought necessary for evolution by natural selection, especially of complex adaptations. Using microbial evolutionary processes as heuristics, I argue contrariwise, that (1) clade growth (proliferation of contained species) substitutes for clade reproduction in the evolution of complex adaptation, (2) clade-level properties favoring persistence – species richness, dispersal, divergence, and possibly intraclade cooperation – are not collapsible into species-level traits, (3) such properties (...) can be maintained by selection on clades, and (4) clade selection extends the explanatory power of the theory of evolution. (shrink)

Here I advance two related evolutionary propositions. (1) Natural selection is most often considered to require competition between reproducing “individuals”, sometimes quite broadly conceived, as in cases of clonal, species or multispecies-community selection. But differential survival of non-competing and non-reproducing individuals will also result in increasing frequencies of survival-promoting “adaptations” among survivors, and thus is also a kind of natural selection. (2) Darwinists have challenged the view that the Earth’s biosphere is an evolved global homeostatic system. Since there is only (...) one biosphere, reproductive competition cannot have been involved in selection for such survival-promoting adaptations, they claim. But natural selection through survival could reconcile Gaia with evolutionary theory. (shrink)

This paper, like many before it, aims to solve the “species problem” by declaring it a non-problem. It borrows its title from an earlier article by Jeff Lawrence and its philosophical concepts from Marc Ereshefsky, John Dupré, Peter Godfrey-Smith, Ken Waters, and Jody Hey. The emphasis is on bacteria, but my pragmatic species anti-realist conclusion may be a general one.

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)

This paper investigates the complexity hypothesis in microbial evolutionary genetics from a philosophical vantage. This hypothesis, in its current version, states that genes with high connectivity are likely to be resistant to being horizontally transferred. We defend four claims. There is an important distinction between two different ways in which a gene family can persist: vertically and horizontally. There is a trade-off between these two modes of persistence, such that a gene better at achieving one will be worse at achieving (...) the other. At least some genes are likely to experience selection favoring increased transferability. One consequence of this can be encapsulated as the “simplicity hypothesis”: horizontally persisting genes will experience selection favoring reduced connectivity. In order to make sense of the simplicity hypothesis, we need to consider evolutionary populations that transcend species boundaries. Vertical and horizontal persistence are therefore not two competing ways of succeeding at the same game, but involve playing two different games altogether. The complexity hypothesis can be understood in terms of two related notions: entrenchment and Cuvierian functionalism. This framing reveals previously unrecognized and philosophically interesting connections between reasoning about deep conservation and horizontal transfer. (shrink)

Lateral gene transfer, the exchange of genetic information between lineages, not only makes construction of a universal Tree of Life 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)

The origin and prevalence of transposable elements may best be understood as resulting from “selfish” evolutionary processes at the within-genome level, with relevant populations being all members of the same TE family or all potentially mobile DNAs in a species. But the maintenance of families of TEs as evolutionary drivers, if taken as a consequence of selection, might be better understood as a consequence of selection at the level of species or higher, with the relevant populations being species or ecosystems (...) varying in their possession of TEs. In 2015, Brunet and Doolittle made the case for legitimizing claims for an evolutionary role for TEs by recasting such claims as being about species selection. Here I further develop this “how possibly” argument. I note that with a forgivingly broad construal of evolution by natural selection we might come to appreciate many aspects of Life on earth as its products, and TEs as—possibly—contributors to the success of Life by selection at several levels of a biological hierarchy. Thinking broadly makes this proposition a testable Darwinian one. (shrink)

In fact, nearly every scientist who has written on the general subject of evolution has felt compelled to show how deftly he can skate toward the abyss of teleology without falling in.J.H. Campbell, 163Molecular biology has as its primary objective the elucidation of the coupling between genotype and phenotype. This goal has so far been pursued within a neoDarwinian theoretical framework which is relatively limited. Within this framework we can indeed understand remarkably well the mechanisms of replication and expression of (...) genes and the means by which replication and expression are regulated in cells; we know how genotype determines phenotype at the molecular level, in single cells. We are also close to an understanding of the relationship between genes and development in muticellular animals and plants. (shrink)

To date, no definition of life has been unequivocally accepted by the scientific community. In frustration, some authors advocate alternatives to standard definitions. These include using a list of characteristic features, focusing on life’s effects, or categorizing biospheres rather than life itself; treating life as a fuzzy category, a process or a cluster of contingent properties; or advocating a ‘wait-and-see’ approach until other examples of life are created or discovered. But these skeptical, operational, and pluralistic approaches have intensified the debate, (...) rather than settled it. Given the failure of even these approaches, we advocate a new strategy. In this paper, we reverse the usual line of reasoning and argue that the “life problem” arises from thinking incorrectly about the nature of life. Scientists most often conceptualize life as a class or kind, with earthly life as a single instance of it. Instead, we advocate thinking about Earth’s Life as an individual, in the way that species are now thought to be. In this view, Life is a monophyletic clade that originated with a last universal common ancestor, and includes all its descendants. We can continue to use the category ‘life’ pragmatically to refer to similarities between various phenomena and Life. But the relevant similarities are a matter of interest and preference, not a matter of fact. The search for other life in the Universe, then, is merely a search for entities that resemble parts of Life in whatever sense astrobiologists find most appealing. This does not mean that the search for evolved complexity elsewhere in the universe or its creation in the lab are futile endeavors, but that debates over whether they count as ‘life’ are. Ironically, finally abandoning the concept ‘life’ may make our searches for evolved complexity more fruitful. We explain why. (shrink)

In fact, nearly every scientist who has written on the general subject of evolution has felt compelled to show how deftly he can skate toward the abyss of teleology without falling in.J.H. Campbell, 163Molecular biology has as its primary objective the elucidation of the coupling between genotype and phenotype. This goal has so far been pursued within a neoDarwinian theoretical framework which is relatively limited. Within this framework we can indeed understand remarkably well the mechanisms of replication and expression of (...) genes and the means by which replication and expression are regulated in cells; we know how genotype determines phenotype at the molecular level, in single cells. We are also close to an understanding of the relationship between genes and development in muticellular animals and plants. (shrink)

The genome contains elements which are most easily understood as the products of selection operating at the level of the genome, without regard to phenotypic effect. The properties of such elements, and more general implications of molecular biological data, are discussed.

Eukaryogenesis is widely viewed as an improbable evolutionary transition uniquely affecting the evolution of life on this planet. However, scientific and popular rhetoric extolling this event as a singularity lacks rigorous evidential and statistical support. Here, we question several of the usual claims about the specialness of eukaryogenesis, focusing on both eukaryogenesis as a process and its outcome, the eukaryotic cell. We argue in favor of four ideas. First, the criteria by which we judge eukaryogenesis to have required a genuinely (...) unlikely series of events 2 billion years in the making are being eroded by discoveries that fill in the gaps of the prokaryote:eukaryote “discontinuity.” Second, eukaryogenesis confronts evolutionary theory in ways not different from other evolutionary transitions in individuality; parallel systems can be found at several hierarchical levels. Third, identifying which of several complex cellular features confer on eukaryotes a putative richer evolutionary potential remains an area of speculation: various keys to success have been proposed and rejected over the five-decade history of research in this area. Fourth, and perhaps most importantly, it is difficult and may be impossible to eliminate eukaryocentric bias from the measures by which eukaryotes as a whole are judged to have achieved greater success than prokaryotes as a whole. Overall, we question whether premises of existing theories about the uniqueness of eukaryogenesis and the greater evolutionary potential of eukaryotes have been objectively formulated and whether, despite widespread acceptance that eukaryogenesis was “special,” any such notion has more than rhetorical value. (shrink)

Understanding community-level selection using Lewontin’s criteria requires both community-level inheritance and community-level heritability, and in the discipline of community and ecosystem genetics, these are often conflated. While there are existing studies that show the possibility of both, these studies impose community-level inheritance as a product of the experimental design. For this reason, these experiments provide only weak support for the existence of community-level selection in nature. By contrast, treating communities as interactors (in line with Hull’s replicator-interactor framework or Dawkins’s idea (...) of the “extended phenotype”) provides a more plausible and empirically supportable model for the role of ecological communities in the evolutionary process. (shrink)

This paper investigates the complexity hypothesis in microbial evolutionary genetics from a philosophical vantage. This hypothesis, in its current version, states that genes with high connectivity are likely to be resistant to being horizontally transferred. We defend four claims. There is an important distinction between two different ways in which a gene family can persist: vertically and horizontally. There is a trade-off between these two modes of persistence, such that a gene better at achieving one will be worse at achieving (...) the other. At least some genes are likely to experience selection favoring increased transferability. One consequence of this can be encapsulated as the “simplicity hypothesis”: horizontally persisting genes will experience selection favoring reduced connectivity. In order to make sense of the simplicity hypothesis, we need to consider evolutionary populations that transcend species boundaries. Vertical and horizontal persistence are therefore not two competing ways of succeeding at the same game, but involve playing two different games altogether. The complexity hypothesis can be understood in terms of two related notions: entrenchment and Cuvierian functionalism. This framing reveals previously unrecognized and philosophically interesting connections between reasoning about deep conservation and horizontal transfer. (shrink)

Many contemporary biologists and philosophers of biology admit that selection occurs at any level of the biological hierarchy at which entities showing heritable variation in fitness are found, while insisting that fitness at any level entails differential reproduction, not differential persistence. Those who allow that persistence can be selected doubt that selection on nonreproducing entities can be reiterated, to produce “complex adaptations.” We present here a verbal model of subclones evolving in a simple idealized chemostat that calls into question these (...) suppositions and is usefully explanatory when taken as an analogy to selection for persistence of clades. (shrink)

The first complete sequence of an archaebacterial genome, that of Methanococcus jannaschii, has recently been published(1). Less than half of the open reading frames (ORFs) can be assigned a function based on similarity to known sequences in databases. These assignable ORFs fall into two general classes; those involved in transcription, translation and replication are more similar to eukaryotic homologs, while those determining metabolic processes are more similar to eubacterial versions. The immense but very rewarding task of making biological and evolutionary (...) sense of all this information has only just begun. (shrink)

This editorial introduces a series of review articles concerning the ways in which recent work on microbial evolution has both deepened and challenged the modern synthesis. The authors develop a framework for thinking about theory change in biology.

Here we endorse Hull’s replicator/interactor framework as providing the overarching understanding sought by MacCord and Maienschein. We suggest that difficulties in seeing the regeneration of limbs by salamanders and of forest ecosystems after fires as similar evolutionary processes can be overcome in this framework. In generalizing Dawkins’s “selfish gene” perspective, Hull defined natural selection as “a process in which the differential extinction and proliferation of interactors causes the differential perpetuation of the replicators that produced them”. Although genes and bacteria are (...) simultaneously both replicators and interactors, communities and ecosystems are generally only interactors. As reproducers, members of sexual species are intermediate. Within such species, organisms are indeed the interactors whose “differential extinction and proliferation” causes the “differential perpetuation” of replicators. But sexually-reproducing organisms do not individually replicate, persist, or recur as interactors, and in consequence it is only those genes causing an interactor differential that are specifically perpetuated in the long run. Higher-level interactors may seldom if ever reproduce, but their recurrence does enable the “differential perpetuation” of replicators specifically responsible for their “differential extinction and proliferation”. In offering answers to the question “What are the replicators specifically responsible for the differential extinction and proliferation of such higher-level entities?” we hope to unify adaptive regeneration across scales, from organisms to ecosystems. (shrink)

Diverse living systems possess the capacity for regeneration; that is, they can under some circumstances repair, re-produce, and maintain themselves in the face of disturbance or damage. Think of systems as diverse as forests, microbial biofilms, corals, salamanders, hydra, and human skin cells. This capacity is fundamental to life—without it, many biological systems would be too fragile to cope with stress and would frequently collapse—but because it is multiply realized in wildly different living systems at many scales, finding a common (...) understanding may seem futile, and in fact research has proceeded along independent lines. For example, the sciences of organismal regeneration and ecological regeneration appear to have little more than a nominal relationship. Progress towards unification can be made, we think, by turning to evolutionary theory, specifically by synthesizing recent discussions of the evolution of individuals versus collectives with older literature about replicators versus interactors. This allows us to provide a partial answer in response to MacCord and Maienschein’s call for “basic units and mechanisms” of regeneration, relevant when that process is “adaptive.” We argue that the basics of adaptive regeneration can be understood and generalized through a modification of David Hull’s replicator-interactor framework. (shrink)

In the half century since the formulation of the prokaryote : eukaryote dichotomy, many authors have proposed that the former evolved from something resembling the latter, in defiance of common (and possibly common sense) views. In such ‘eukaryotes first’ (EF) scenarios, the last universal common ancestor is imagined to have possessed significantly many of the complex characteristics of contemporary eukaryotes, as relics of an earlier ‘progenotic’ period or RNAworld. Bacteria and Archaea thus must have lost these complex features secondarily, through (...) ‘streamlining’. If the canonical three-domain tree in which Archaea and Eukarya are sisters is accepted, EF entails that Bacteria and Archaea are convergently prokaryotic.We ask what this means and how it might be tested. (shrink)

Constructive Neutral Evolution is an evolutionary mechanism that can explain much molecular inter-dependence and organismal complexity without assuming positive selection favoring such dependency or complexity, either directly or as a byproduct of adaptation. It differs from but complements other non-selective explanations for complexity, such as genetic drift and the Zero Force Evolutionary Law, by being ratchet-like in character. With CNE, purifying selection maintains dependencies or complexities that were neutrally evolved. Preliminary treatments use it to explain specific genetic and molecular structures (...) or processes, such as retained gene duplications, the spliceosome, and RNA editing. Here we aim to expand the scope of such explanation beyond the molecular level, integrating CNE with Multi-Level Selection theory, and arguing that several popular higher-level selection scenarios are in fact instances of CNE. Suitably contextualized, CNE occurs at any level in the biological hierarchy at which natural selection as normally construed occurs. As examples, we focus on modularity in protein–protein interaction networks or “interactomes,” the origin of eukaryotic cells and the evolution of co-dependence in microbial communities—a variant of the “Black Queen Hypothesis” which we call the “Gray Queen Hypothesis”. (shrink)

Koonin, in an article in this issue, claims that CRISPR–Cas systems are mechanisms for the inheritance of acquired adaptive characteristics, and that the operation of such systems comprises a “Lamarckian mode of evolution.” We argue that viewing the CRISPR–Cas mechanism as facilitating a form of “directed mutation” more accurately represents how the system behaves and the history of neoDarwinian thinking, and is to be preferred.

Microbiologists are transitioning from the study and characterization of individual strains or species to the profiling of whole microbiomes and microbial ecology. Equipped with high-throughput methods for studying the taxonomic and functional characteristics of diverse samples, they are just beginning to encounter the conceptual, theoretical, and experimental problems of comparing taxonomy to function, and extracting useful measures from such comparisons. Although still unresolved, these problems are well studied in macro-ecology and are reiterated here as an historical precautionary for microbial ecologists. (...) Beyond expected and unresolved terminological vagueness, we argue that assessments and comparisons of taxonomic and functional profiles in micro-ecology suffer from theoretically unresolvable arbitrariness and ambiguities. We divide these into problems of scale, individuation, and commensurability. We argue that there is no technically/theoretically “correct” scale, individuation, or comparison of taxonomy and function, but there are nonetheless better and worse methodologies for profiling. (shrink)

Category-specific impairments of object recognition and naming are among the most intriguing disorders in neuropsychology, affecting the retrieval of knowledge about either living or nonliving things. They can give us insight into the nature of our representations of objects: Have we evolved different neural systems for recognizing different categories of object? What kinds of knowledge are important for recognizing particular objects? How does visual similarity within a category influence object recognition and representation? What is the nature of our semantic knowledge (...) about different objects? We review the evidence on category-specific impairments, arguing that deficits even for one class of object cannot be accounted for in terms of a single information processing disorder across all patients; problems arise at contrasting loci in different patients. The same apparent pattern of impairment can be produced by damage to different loci. According to a new processing framework for object recognition and naming, the hierarchical interactive theory, we have a hierarchy of highly interactive stored representations. HIT explains the variety of patients in terms of lesions at different levels of processing and different forms of stored knowledge used both for particular tasks and for particular categories of object. Key Words: category-specific deficits; functional imaging; hierarchical models; interactive activation models; neuropsychology; object recognition; perceptual and functional knowledge. (shrink)

We summarise and respond to the main points made by the commentators on our target article, which concern: whether structural similarity can play a causal role in normal object identification and in neuropsychological deficits for living things, the nature of our structural knowledge of the world, the relations between sensory and functional knowledge of objects, and the nature of our functional knowledge about living things, whether we need to posit a “core” semantic system, arguments that can be marshalled from evidence (...) on functional imaging, the causal mechanisms by which category differences can emerge in object representations, and the nature of our knowledge about categories other than living and nonliving things. We also highlight points raised in our article that seem to be accepted. (shrink)

Objective: To determine the views of people with multiple sclerosis (MS) and professionals in relation to confidentiality, consent and access to data within a proposed MS register in the UK. Design: Qualitative study using focus groups (10) and interviews (13). Setting: England and Northern Ireland. Participants: 68 people with MS, neurologists, MS nurses, health services management professionals, researchers, representatives from pharmaceutical companies and social care professionals. Results: People with MS expressed open and altruistic views towards the use of their personal (...) information to facilitate service provision and research, placing trust in responsible guardianship and legitimate use of their information. Participant’s proposed that people with MS should be able to select their individual level of involvement in a register using levels of consent. It was agreed that access to the register should be governed by a guardianship committee composed of a range of stakeholders. People with MS did not wish their details to be used by marketing agencies and did not consider this a legitimate use of their data. Whilst participants were positive of the role a register could play in promoting research, participants felt that access to data by pharmaceutical industries should be administered by the guardianship committee. People with MS are concerned should their employers be able to access their personal information. Professionals were more cautious than people with MS in their approach to the use of patient personal data within a register. Conclusions: Whilst all stakeholders were positive of the benefits of an MS register, development of such a resource must incorporate robust data security and guardianship measures in order to ensure that, whilst opportunities are maximised, risks to the privacy of individuals and legal challenges to professionals are avoided. (shrink)

The chapters in this book have evolved from talks originally presented at The First International Workshop on Human and Machine Cognition.

© 2014 Taylor Francis. The Centers for Disease Control and Prevention recommends routine human immunodeficiency virus testing of every client presenting for services in venues where HIV prevalence is high. Because older adults have particularly poor prognosis if they receive their diagnosis late in the course of HIV disease, any screening provided to younger adults in these venues should also be provided to older adults. We examined aging-related disparities in recent and ever HIV testing in a probability sample of at-risk (...) adults seeking services in needle exchange sites, sexually transmitted disease clinics, and Latino community clinics that provide HIV testing. Using multiple logistic regression with generalized estimating equations, we estimated associations between age category and each HIV testing outcome. Even after controlling for covariates such as recent injection drug use, older adults had 40% lower odds than younger adults did of having tested in the past 12 months or ever. Aging-related disparities in HIV testing exist among clients of these high HIV prevalence venues and may contribute to known aging-related disparities in late diagnosis of HIV infection and poor long-term prognosis. (shrink)

The chapters in this book have evolved from talks originally presented at The First International Workshop on Human and Machine Cognition.

This collection of essays, offered in honor of the distinguished career of prominent political philosophy professor Clifford Orwin, brings together internationally renowned scholars to provide a wide context and discuss various aspects of the virtue of “humanity” through the history of political philosophy.

This collection of essays, offered in honor of the distinguished career of prominent political philosophy professor Clifford Orwin, brings together internationally renowned scholars to provide a wide context and discuss various aspects of the virtue of “humanity” through the history of political philosophy.