Biological theory demands a clear organism concept, but at present biologists cannot agree on one. They know that counting particular units, and not counting others, allows them to generate explanatory and predictive descriptions of evolutionary processes. Yet they lack a unified theory telling them which units to count. In this paper, I offer a novel account of biological individuality, which reconciles conflicting definitions of ‘organism’ by interpreting them as describing alternative realisers of a common functional role, and then defines individual (...) organisms as essentially possessing some mechanisms that play this role. (shrink)

Biologists studying complex causal systems typically identify some factors as causes and treat other factors as background conditions. For example, when geneticists explain biological phenomena, they often foreground genes and relegate the cellular milieu to the background. But factors in the milieu are as causally necessary as genes for the production of phenotypic traits, even traits at the molecular level such as amino acid sequences. Gene-centered biology has been criticized on the grounds that because there is parity among causes, the (...) “privileging” of genes reflects a reductionist bias, not an ontological difference. The idea that there is an ontological parity among causes is related to a philosophical puzzle identified by John Stuart Mill: what, other than our interests or biases, could possibly justify identifying some causes as the actual or operative ones, and other causes as mere background? The aim of this paper is to solve this conceptual puzzle and to explain why there is not an ontological parity among genes and the other factors. It turns out that solving this puzzle helps answer a seemingly unrelated philosophical question: what kind of causal generality matters in biology? (shrink)

Several authors have argued that causes differ in the degree to which they are ‘specific’ to their effects. Woodward has used this idea to enrich his influential interventionist theory of causal explanation. Here we propose a way to measure causal specificity using tools from information theory. We show that the specificity of a causal variable is not well-defined without a probability distribution over the states of that variable. We demonstrate the tractability and interest of our proposed measure by measuring the (...) specificity of coding DNA and other factors in a simple model of the production of mRNA. (shrink)

I defend a radical interpretation of biological populations—what I call population pluralism—which holds that there are many ways that a particular grouping of individuals can be related such that the grouping satisfies the conditions necessary for those individuals to evolve together. More constraining accounts of biological populations face empirical counter-examples and conceptual difficulties. One of the most intuitive and frequently employed conditions, causal connectivity—itself beset with numerous difficulties—is best construed by considering the relevant causal relations as ‘thick’ causal concepts. I (...) argue that the fine-grained causal relations that could constitute membership in a biological population are huge in number and many are manifested by degree, and thus we can construe population membership as being defined by massively multidimensional constructs, the differences between which are largely arbitrary. I end by showing that positions in two recent debates in theoretical biology depend on a view of biological populations at odds with the pluralism defended here. 1 Introduction2 Biological Population, Broad and Narrow3 Difficulties with Narrow Biological Population Conditions3.1 Against the genealogical condition3.2 Against the conspecificity condition3.3 Against the proximity condition3.4 Against the typology condition4 Causal Connectivity5 Massively Multidimensional Population Constructs6 Population Uniqueness and Natural Selection6.1 Statisticalism and its discontents6.2 Price at what price?7 Conclusion. (shrink)

Most philosophical accounts of emergence are incompatible with reduction. Most scientists regard a system property as emergent relative to properties of its parts if it depends upon their mode of organization-a view consistent with reduction. Emergence is a failure of aggregativity, in which ``the whole is nothing more than the sum of its parts''. Aggregativity requires four conditions, giving powerful tools for analyzing modes of organization. Differently met for different decompositions of the system, and in different degrees, the structural conditions (...) can provide evaluation criteria for choosing decompositions, ``natural kinds'', and detecting functional localization fallacies, approximations, and various biases of vulgar reductionisms. This analysis of emergence and use of these conditions as heuristics is consistent with a broader reductionistic methodology. (shrink)

This paper attempts to elucidate three characteristics of causal relationships that are important in biological contexts. Stability has to do with whether a causal relationship continues to hold under changes in background conditions. Proportionality has to do with whether changes in the state of the cause “line up” in the right way with changes in the state of the effect and with whether the cause and effect are characterized in a way that contains irrelevant detail. Specificity is connected both to (...) David Lewis’ notion of “influence” and also with the extent to which a causal relation approximates to the ideal of one cause–one effect. Interrelations among these notions and their possible biological significance are also discussed. (shrink)

Okasha, in Evolution and the Levels of Selection, convincingly argues that two rival statistical decompositions of covariance, namely contextual analysis and the neighbour approach, are better causal decompositions than the hierarchical Price approach. However, he claims that this result cannot be generalized in the special case of soft selection and argues that the Price approach represents in this case a better option. He provides several arguments to substantiate this claim. In this paper, I demonstrate that these arguments are flawed and (...) argue that neither the Price equation nor the contextual and neighbour partitionings sensu Okasha are adequate causal decompositions in cases of soft selection. The Price partitioning is generally unable to detect cross-level by-products and this naturally also applies to soft selection. Both contextual and neighbour partitionings violate the fundamental principle of determinism that the same cause always produces the same effect. I argue that a fourth partitioning widely used in the contemporary social sciences, under the generic term of ‘hierarchical linear model’ and related to contextual analysis understood broadly, addresses the shortcomings of the three other partitionings and thus represents a better causal decomposition. I then defend this model against the argument that because it predicts that there is some organismal selection in some specific cases of segregation distortion then it should be rejected. I show that cases of segregation distortion that intuitively seem to contradict the conclusion drawn from the hierarchical linear model are in fact cases of multilevel selection 2 while the assessment of the different partitionings are restricted to multilevel selection 1. (shrink)

I defend a radical interpretation of biological populations—what I call population pluralism—which holds that there are many ways that a particular grouping of individuals can be related such that the grouping satisfies the conditions necessary for those individuals to evolve together. More constraining accounts of biological populations face empirical counter-examples and conceptual difficulties. One of the most intuitive and frequently employed conditions, causal connectivity—itself beset with numerous difficulties—is best construed by considering the relevant causal relations as ‘thick’ causal concepts. I (...) argue that the fine-grained causal relations that could constitute membership in a biological population are huge in number and many are manifested by degree, and thus we can construe population membership as being defined by massively multidimensional constructs, the differences between which are largely arbitrary. I end by showing that positions in two recent debates in theoretical biology depend on a view of biological populations at odds with the pluralism defended here. (shrink)

Microbes are generally thought of as unicellular organisms, but we know that many microbes live as parts of biofilms—complex, surface-attached microbial communities numbering millions of cells. Some authors have recently argued in favour of reconceiving biofilms as biological entities in their own right. In particular, some have claimed that multispecies biofilms are evolutionary individuals : 10126–10132 2015). Against this view, I defend the conservative consensus that selection acts primarily upon microbial cells.

This paper provides a philosophical analysis of the ongoing controversy surrounding R.A. Fisher's famous ‘fundamental theorem’ of natural selection. The difference between the ‘traditional’ and ‘modern’ interpretations of the theorem is explained. I argue that proponents of the modern interpretation have captured Fisher's intended meaning correctly and shown that the theorem is mathematically correct, pace the traditional consensus. However, whether the theorem has any real biological significance remains an unresolved issue. I argue that the answer depends on whether we accept (...) Fisher's non-standard notion of environmental change, on which the theorem rests; arguments for and against this notion are explored. I suggest that there is a close link between Fisher's fundamental theorem and the modern ‘gene's eye’ view of evolution. Introduction What Does the Fundamental Theorem Say? Key Concepts Explained Alleged Significance of the FTNS Traditional versus Modern Interpretations of the FTNS The Modern Interpretation Illustrated Fisher's Concept of ‘Environmental Change’ Causality and the Modern Interpretation The Significance of the FTNS Re-considered Appendix CiteULike Connotea Del.icio.us What's this? (shrink)

Group-structured populations, of the kind prominent in discussions of multilevel selection, are contrasted with ‘neighbor-structured’ populations. I argue that it is a necessary condition on multilevel description of a selection process that there should be a nonarbitrary division of the population into equivalence classes (or an approximation to this situation). The discussion is focused via comparisons between two famous problem cases involving group structure (altruism and heterozygote advantage) and two neighbor-structured cases that resemble them. Conclusions are also drawn about the (...) role of correlated interaction in the evolution of altruism. 1 Introduction 2 Two Kinds of Population Structure 3 Objections and Replies 4 Particles on a Line 5 Conclusion Appendix: Neighborhoods and Selection CiteULike Connotea Del.icio.us What's this? (shrink)

The evolutionary problem of the units of selection has elicited a good deal of conceptual work from philosophers. We review this work to determine where the issues now stand.

At least below the level of species, biological populations are not mind‐independent objects that scientists discover. Rather, biological populations are pragmatically constructed as objects of investigation according to the aims, interests, and values that inform particular research contexts. The relations among organisms that are constitutive of population‐level phenomena (e.g., mating propensity, genealogy, and competition) occur as matters of degree and so give rise to statistically defined open‐ended biological systems. These systems are rendered discrete units to satisfy practical needs and theoretical (...) preferences associated with specific contexts of investigation. While it may be possible to defend a realist position regarding biological relations among organisms, biological populations are “made” when contextual features determine which kinds and degrees of relations to privilege over others, and so how to bound genes in space and time. Consequently, the objectivity of population‐based approaches to species genome diversity cannot rest in the mind‐independence of populations themselves. (shrink)

The most consistent definition of fitness makes it a static property of organisms. However, this is not how fitness is used in many evolutionary models. In those models, fitness is permitted to vary with an organism’s circumstances. According to this second conception, fitness is dynamic. There is consequently tension between these two conceptions of fitness. One recently proposed solution suggests resorting to conditional properties. We argue, however, that this solution is unsatisfactory. Using a very simple model, we show that it (...) can lead to incompatible fitness values and indecision about whether selection actually occurs. (shrink)

In this article I explore some statistical difficulties confronting going conceptions of ‘group’ as understood in accounts of group selection. Most such theories require real groups but define the reality of groups in ways that make it impossible to test for their reality. There are alternatives, but they either require or invite a nominalism about groups that many theorists abjure.

We argue for a new conventionalism about many kinds of evolutionary groups, including clades, cohesive units, and populations. This rejects a consensus, which says that given any one of the many legitimate grouping concepts, only objective biological facts determine whether a collection is such a group. Surprisingly, being any one kind of evolutionary group typically depends on which of many incompatible values are taken by suppressed variables. This is a novel pluralism underlying most any one group concept, rather than a (...) familiar pluralism claiming many concepts are legitimate. Consequently, we must help biological facts determine grouphood, even when given a single grouping concept. (shrink)

There is a tension between, on the one hand, the view that natural selection refers to individual-level causes, and on the other hand, the view that it refers to a population-level cause. In this article, I make the case for the individual-level cause view. I respond to recent claims made by McLoone that the individual-level cause view is inconsistent. I show that if one were to follow his arguments, any causal claim in any context would have to be regarded as (...) vindicating a form of population-level cause view. I show why this is implausible and how a consistent individual-level cause position can be held within the interventionist account of causation. Finally, I argue that there is one sense in which natural selection might be said to refer to population-level causes of evolutionary change. The upshot is that, as noted by others, natural selection can be regarded as referring to a population-level cause in the context of frequency-dependent selection and other situations of fitness-altering interactions between the individuals of a population. But whether this statement is true will depend on the empirical case investigated, not some a priori conceptual distinction. Thus, even though situations of frequency dependence might be ubiquitous, it is orthogonal to the conceptual question of whether frequency-independent natural selection—McLoone’s target—refers to individual- or population-level causes. (shrink)

What changes when an evolutionary transition in individuality takes place? Many different answers have been given, in respect of different cases of actual transition, but some have suggested a general answer: that a major transition is a change in the extent to which selection acts at one hierarchical level rather than another. The current paper evaluates some different ways to develop this general answer as a way to characterise the property ‘evolutionary individuality’; and offers a justification of the option taken (...) in Clarke :413–435, 2013)—to define evolutionary individuality in terms of an object’s capacity to undergo selection at its own level. In addition, I suggest a method by which the property can be measured and argue that a problem which is often considered to be fatal to that method—the problem of ‘cross-level by-products’—can be avoided. (shrink)

This paper examines David Hull’s and Peter Godfrey-Smith’s accounts of biological individuality using the case of biofilms. Biofilms fail standard criteria for individuality, such as having reproductive bottlenecks and forming parent-offspring lineages. Nevertheless, biofilms are good candidates for individuals. The nature of biofilms shows that Godfrey-Smith’s account of individuality, with its reliance on reproduction, is too restrictive. Hull’s interactor notion of individuality better captures biofilms, and we argue that it offers a better account of biological individuality. However, Hull’s notion of (...) interactor needs more precision. We suggest some ways to make Hull’s notion of interactor and his account of individuality more precise. Generally, we maintain that biofilms are a good test case for theories of individuality, and a careful examination of biofilms furthers our understanding of biological individuality. (shrink)

This paper aims to illustrate one of the primary goals of the philosophy of biology⎯namely, the examination of central concepts in biological theory and practice⎯through an analysis of the concepts of population and metapopulation in evolutionary biology and ecology. I will first provide a brief background for my analysis, followed by a characterization of my proposed concepts: the causal interactionist concepts of population and metapopulation. I will then illustrate how the concepts apply to six cases that differ in their population (...) structure; this analysis will also serve to flesh out and defend the concepts a bit more. Finally, I will respond to some possible questions that my analysis may have raised and then conclude briefly. (shrink)

Biologists studying ecology and evolution use the term “population” in many different ways. Yet little philosophical analysis of the concept has been done, either by biologists or philosophers, in contrast to the voluminous literature on the concept of “species.” This is in spite of the fact that “population” is arguably a far more central concept in ecological and evolutionary studies than “species” is. The fact that such a central concept has been employed in so many different ways is potentially problematic (...) for the reason that inconsistent usages (especially when the usage has not been made explicit) might lead to false controversies in which disputants are simply talking past one another. However, the inconsistent usages are not the only, or even the most important reason to examine the concept. If any set of organisms is legitimately called a “population,” selection and drift processes become purely arbitrary, too. Moreover, key ecological variables, such as abundance and distribution, depend on a nonarbitrary way of identifying populations. I sketch the beginnings of a population concept, drawing inspiration from the Ghiselin-Hull individuality thesis, and show why some alternative approaches are nonstarters. (shrink)

It is now widely accepted that microorganisms play many important roles in the lives of plants and animals. Every macroorganism has been shaped in some way by microorganisms. The recognition of the ubiquity and importance of microorganisms has led some to argue for a revolution in how we understand biological individuality and the primary units of natural selection. The term “holobiont” was introduced as a name for the biological unit made up by a host and all of its associated microorganisms, (...) and much of this new debate about biological individuality has focused on whether holobionts are integrated individuals or communities. In this paper, I show how parts of the holobiont can span both characterizations. I argue that most holobionts share more affinities with communities than they do with organisms, and that, except for maybe in rare cases, holobionts do not meet the criteria for being organisms, evolutionary individuals, or units of selection. (shrink)

We assess the arguments for recognising functionally integrated multispecies consortia as genuine biological individuals, including cases of so-called ‘holobionts’. We provide two examples in which the same core biochemical processes that sustain life are distributed across a consortium of individuals of different species. Although the same chemistry features in both examples, proponents of the holobiont as unit of evolution would recognize one of the two cases as a multispecies individual whilst they would consider the other as a compelling case of (...) ecological dependence between separate individuals. Some widely used arguments in support of the ‘holobiont’ concept apply equally to both cases, suggesting that those arguments have misidentified what is at stake when seeking to identify a new level of biological individuality. One important aspect of biological individuality is evolutionary individuality. In line with other work on the evolution of individuality, we show that our cases can be distinguished by focusing on the fitness alignment between the partners of the consortia. We conclude that much of the evidence currently presented for the ubiquity and importance of multi-species individuals is simply not to the point, at least unless the issue of biological individuality is firmly divorced from the question of evolutionary individuality. (shrink)

The contextual approach is a prominent framework for thinking about group selection. Here, I highlight ambiguity about what the contextual approach is. Then, I discuss problematic entailments the contextual approach has for what processes count as group selection—entailments more troublesome than typically noted. However, Sober and Wilson’s version of the Price approach, which is the main alternative to the contextual approach, is problematic too: it leads to an underappreciated paradox called the vanishing selection problem and thereby generates the wrong qualitative (...) account of whether group selection is occurring in a certain family of cases. In response, I develop an account of group selection that can deal with the counterexamples to both the contextual approach and the Price approach. I then discuss the role that contextual analysis can continue to play in the discussion of individual fitness and metapopulation evolution. (shrink)

Evolutionary transitions in individuality (ETIs) are events during which individuals at a given level of organization (particles) interact to form higher-level entities (collectives) which are then recognized as new individuals at that level. ETIs are intimately related to levels of selection, which, following Okasha, can be approached from two different perspectives. One, referred to as ‘synchronic’, asks whether selection occurs at the collective level while the partitioning of particles into collectives is taken for granted. The other, referred to as ‘diachronic’, (...) asks about the origins of the partitioning of particles into collectives. After having presented the two perspectives and a classical formalism used to deal with the levels-of-selection question in the literature, namely the multilevel version of the Price equation, I show that because this formalism treats the levels-of-selection question from a synchronic perspective, it is inadequate to explain ETIs. This is because a fundamental aspect of ETIs is the origin of collectives. From there, I develop a framework for levels of selection compatible with the diachronic perspective. This framework relies on the distinction between what I call, on the one hand, a ‘functional aggregative collective trait’, and on the other hand, a ‘functional non-aggregative collective trait’. After having presented this distinction, I implement it in the Price equation, leading to a new statistical partitioning of this equation which, I argue, represents a causal decomposition more relevant for ETIs. Finally, I exploit this partitioning to explain the critical stages of an ETI. In addition to its explanatory power, a measure of the degree of functional non-aggregativity could be used as a proxy for the degree of individuality of a collective. (shrink)

This paper presents an account of the biological populations that can undergo paradigmatic natural selection. I argue for, and develop Peter Godfrey-Smith’s claim that reproductive competition is a core attribute of such populations. However, as Godfrey-Smith notes, it is not the only important attribute. I suggest what the missing element is, co-opting elements of Alan Templeton’s notion of exchangeability. The final framework is then compared to two recent discussions regarding biological populations proposed by Roberta Millstein and Jacob Stegenga.

Evolutionary transitions in individuality (ETIs) involve the formation of Darwinian collectives from Darwinian particles. The transition from cells to multicellular life is a prime example. During an ETI, collectives become units of selection in their own right. However, the underlying processes are poorly understood. One observation used to identify the completion of an ETI is an increase in collective-level performance accompanied by a decrease in particle-level performance, for example measured by growth rate. This seemingly counterintuitive dynamic has been referred to (...) as fitness decoupling and has been used to interpret both models and experimental data. Extending and unifying results from the literature, we show that fitness of particles and collectives can never decouple because calculations of fitness performed over appropriate and equivalent time intervals are necessarily the same provided the population reaches a stable collective size distribution. By way of solution, we draw attention to the value of mechanistic approaches that emphasise traits, and tradeoffs among traits, as opposed to fitness. This trait-based approach is sufficient to capture dynamics that underpin evolutionary transitions. In addition, drawing upon both experimental and theoretical studies, we show that while early stages of transitions might often involve tradeoffs among particle traits, later—and critical—stages are likely to involve the rupture of such tradeoffs. Thus, when observed in the context of ETIs, tradeoff-breaking events stand as a useful marker of these transitions. (shrink)

This paper argues that the contextual approach to natural selection does not offer an estimation of the contributions of individual and group selection to evolutionary change in multi-level selection scenarios, and that this is so because the term “group selection”, as defined by the contextual approach, does not refer to a process taking place at the group level. In the contextual analysis framework, this term simply denotes an evolutionary change that takes place due to the fact that, overall, individual types (...) do not share similar contexts or environments, and the only way to claim that such an evolutionary change is a result of selection is by admitting that “group selection” is in fact a kind of frequency-dependent selection, i.e. a selection process taking place at the individual level. Therefore, under the names “individual selection” and “group selection”, the contextual approach actually isolates two aspects of the relation between individual types and their environment, and not two distinct levels of selection. (shrink)

Multi-level selection can be understood via the Price equation or contextual analysis, which offer incompatible statistical decompositions of evolutionary change into components of group and individual selection. Okasha argued that each approach suffers from problem cases. I introduce further problem cases for the Price approach, arguing that it is appropriate for MLS 2 group selection but not MLS 1. I also show that the problem cases Okasha raises for contextual analysis can be resolved. For some such cases, however, it emerges (...) that there is no determinate answer to the question of how much of the total selective effect was due to group selection compared to individual selection. This suggests that when there is interaction between the effect of group character and individual character, one cannot separate selection into distinct ‘levels’ at all. (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)

Drift is often characterized in statistical terms. Yet such a purely statistical characterization is ambiguous for it can accept multiple physical interpretations. Because of this ambiguity it is important to distinguish what sorts of processes can lead to this statistical phenomenon. After presenting a physical interpretation of drift originating from the most popular interpretation of fitness, namely the propensity interpretation, I propose a different one starting from an analysis of the concept of drift made by Godfrey-Smith. Further on, I show (...) how my interpretation relates to previous attempts to make sense of the notion of expected value in deterministic setups. The upshot of my analysis is a physical conception of drift that is compatible with both a deterministic and indeterministic world. (shrink)

Altruism is one of the most studied topics in theoretical evolutionary biology. The debate surrounding the evolution of altruism has generally focused on the conditions under which altruism can evolve and whether it is better explained by kin selection or multilevel selection. This debate has occupied the forefront of the stage and left behind a number of equally important questions. One of them, which is the subject of this article, is whether the word “selection” in “kin selection” and “multilevel selection” (...) necessarily refers to “evolution by natural selection.” I show, using a simple individual-centered model, that once clear conditions for natural selection and altruism are specified, one can distinguish two kinds of evolution of altruism, only one of which corresponds to the evolution of altruism by natural selection, the other resulting from other evolutionary processes. (shrink)