This paper analyzes recent attempts to reject reproduction with lineage formation as a necessary condition for evolution by means of natural selection :560–570, 2008; Stud Hist Philos Sci Part C Stud Hist Philos Biol Biomed Sci 42:106–114, 2011; Bourrat in Biol Philos 29:517–538, 2014; Br J Philos Sci 66:883–903, 2015; Charbonneau in Philos Sci 81:727–740, 2014; Doolittle and Inkpen in Proc Natl Acad Sci 115:4006–4014, 2018). Building on the strengths of these attempts and avoiding their pitfalls, it is argued that (...) a robust formulation of evolution by natural selection without reproduction can be established. The main contribution of this paper is a reformulation of Lewontin’s three principles stating that minimal evolution by natural selection occurs when two conditions are met in a population: fitness-related variation and memory. Paradigmatic evolution by natural selection, which can generate adaptations, takes place when an additional condition is present, namely regeneration. (shrink)

Protistology, and evolutionary protistology in particular, is experiencing a golden research era. It is an extended one that can be dated back to the 1970s, which is when the molecular rebirth of microbial phylogeny began in earnest. John Archibald, a professor of evolutionary microbiology at Dalhousie University, focuses on the beautiful story of endosymbiosis in his book, John Archibald, One Plus One Equals One: Symbiosis and the Origin of Complex Life. However, this historical narrative could be treated as synecdochal of (...) how the molecular revolution has changed evolutionary biology forever, and that is how Archibald has structured his book. I will address the encompassing theme of molecular methods in detail, but also pay careful attention to the endosymbiosis thread in its own right. (shrink)

Kin selection and multilevel selection are alternative approaches for studying the evolution of social behaviour, the relation between which has long been a source of controversy. Many recent theorists regard the two approaches as ultimately equivalent, on the grounds that gene frequency change can be correctly expressed using either. However, this shows only that the two are formally equivalent, not that they offer equally good causal representations of the evolutionary process. This article articulates the notion of an ‘adequate causal representation’ (...) using causal graphs, and then seeks to identify circumstances under which kin and multilevel selection do and do not satisfy the test of causal adequacy. 1 Introduction2 The KS and MLS Approaches2.1 The MLS decomposition2.2 The KS decomposition3 Equivalence and Causality4 Two Problem Cases4.1 The non-social trait case4.2 Genotypic selection with meiotic drive5 Casual Adequacy: A Graphical Approach5.1 The basic idea5.2 Graphs with individual and group variables5.3 Cases where KS is causally adequate5.4 Cases where MLS is causally adequate6 Discussion6.1 Relation to previous work. (shrink)

Evolutionary biology is striking for its ability to explain a large and diverse range of empirical phenomena on the basis of a few general theoretical principles. This article offers a philosophical perspective on the way that evolutionary biology has come to achieve such impressive generality, by focusing on “the strategy of endogenization”. This strategy involves devising evolutionary explanations for biological features that were originally part of the background conditions, or scaffolding, against which such explanations take place. Where successful, the strategy (...) moves biology a step closer to the ideal of explaining as much as possible from evolutionary first principles. The strategy of endogenization is illustrated through a series of biological examples, historical and recent, and its philosophical implications are explored. (shrink)

John Harsanyi and John Rawls both used the veil of ignorance thought experiment to study the problem of choosing between alternative social arrangements. With his ‘impartial observer theorem’, Harsanyi tried to show that the veil of ignorance argument leads inevitably to utilitarianism, an argument criticized by Sen, Weymark and others. A quite different use of the veil-of-ignorance concept is found in evolutionary biology. In the cell-division process called meiosis, in which sexually reproducing organisms produce gametes, the chromosome number is halved; (...) when meiosis is fair, each gene has only a fifty percent chance of making it into any gamete. This creates a Mendelian veil of ignorance, which has the effect of aligning the interests of all the genes in an organism. This paper shows how Harsanyi's version of the veil-of-ignorance argument can shed light on Mendelian genetics. There turns out to be an intriguing biological analogue of the impartial observer theorem that is immune from the Sen/Weymark objections to Harsanyi's original. View HTML Send article to KindleTo send this article to your Kindle, first ensure [email protected] is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about sending to your Kindle. Find out more about sending to your Kindle. Note you can select to send to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be sent to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply. Find out more about the Kindle Personal Document Service.SOCIAL JUSTICE, GENOMIC JUSTICE AND THE VEIL OF IGNORANCE: HARSANYI MEETS MENDELVolume 28, Issue 1Samir Okasha DOI: https://doi.org/10.1017/S0266267112000119Your Kindle email address Please provide your Kindle [email protected]@kindle.com Available formats PDF Please select a format to send. By using this service, you agree that you will only keep articles for personal use, and will not openly distribute them via Dropbox, Google Drive or other file sharing services. Please confirm that you accept the terms of use. Cancel Send ×Send article to Dropbox To send this article to your Dropbox account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about sending content to Dropbox. SOCIAL JUSTICE, GENOMIC JUSTICE AND THE VEIL OF IGNORANCE: HARSANYI MEETS MENDELVolume 28, Issue 1Samir Okasha DOI: https://doi.org/10.1017/S0266267112000119Available formats PDF Please select a format to send. By using this service, you agree that you will only keep articles for personal use, and will not openly distribute them via Dropbox, Google Drive or other file sharing services. Please confirm that you accept the terms of use. Cancel Send ×Send article to Google Drive To send this article to your Google Drive account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about sending content to Google Drive. SOCIAL JUSTICE, GENOMIC JUSTICE AND THE VEIL OF IGNORANCE: HARSANYI MEETS MENDELVolume 28, Issue 1Samir Okasha DOI: https://doi.org/10.1017/S0266267112000119Available formats PDF Please select a format to send. By using this service, you agree that you will only keep articles for personal use, and will not openly distribute them via Dropbox, Google Drive or other file sharing services. Please confirm that you accept the terms of use. Cancel Send ×Export citation Request permission. (shrink)

Review of Peter Godfrey-Smith's Philosophy of Biology.

Rudolf Leuckart's 1851 pamphlet Ueber den Polymorphismus der Individuen (On the polymorphism of individuals) stood at the heart of naturalists' discussions on biological individuals, parts and wholes in mid-nineteenth-century Britain and Europe. Our analysis, which accompanies the first translation of this pamphlet into English, situates Leuckart's contribution to these discussions in two ways. First, we present it as part of a complex conceptual knot involving not only individuality and the understanding of compound organisms, but also the alternation of generations, the (...) division of labor in nature, and the possibility of finding general laws of the organic world. Leuckart's pamphlet is important as a novel attempt to give order to the strands of this knot. It also solved a set of key biological problems in a way that avoided some of the drawbacks of an earlier teleological tradition. Second, we situate the pamphlet within a longer trajectory of inquiry into part-whole relations in biology from the mid-eighteenth century to the present. We argue that biological individuality, along with the problem-complexes with which it engaged, was as central a problem to naturalists before 1859 as evolution, and that Leuckart's contributions to it left a long legacy that persisted well into the twentieth century. As biologists' interests in part-whole relations are once again on the upswing, the longue durée of this problem merits renewed consideration. (shrink)

Rudolf Leuckart’s 1851 pamphlet Ueber den Polymorphismus der Individuen stood at the heart of naturalists’ discussions on biological individuals, parts and wholes in mid-nineteenth-century Britain and Europe. Our analysis, which accompanies the first translation of this pamphlet into English, situates Leuckart’s contribution to these discussions in two ways. First, we present it as part of a complex conceptual knot involving not only individuality and the understanding of compound organisms, but also the alternation of generations, the division of labor in nature, (...) and the possibility of finding general laws of the organic world. Leuckart’s pamphlet is important as a novel attempt to give order to the strands of this knot. It also solved a set of key biological problems in a way that avoided some of the drawbacks of an earlier teleological tradition. Second, we situate the pamphlet within a longer trajectory of inquiry into part-whole relations in biology from the mid-eighteenth century to the present. We argue that biological individuality, along with the problem-complexes with which it engaged, was as central a problem to naturalists before 1859 as evolution, and that Leuckart’s contributions to it left a long legacy that persisted well into the twentieth century. As biologists’ interests in part-whole relations are once again on the upswing, the longue durée of this problem merits renewed consideration. (shrink)

Contrary to the common-sense view and positivist aspirations, scientific concepts are often imprecise. Many of these concepts are ambiguous, vague, or have an under-specified meaning. In this paper, I discuss how imprecise concepts promote integration in biology and thus benefit science. Previous discussions of this issue focus on the concepts of molecular gene and evolutionary novelty. The concept of molecular gene helps biologists integrate explanatory practices, while the notion of evolutionary novelty helps them integrate research questions into an interdisciplinary problem (...) New directions in the philosophy of science, Springer, Dordrecht, 2014). In what follows, I compare molecular gene and evolutionary novelty to another imprecise concept, namely biological lineage. This concept promotes two other types of scientific integration: it helps biologists integrate theoretical principles and methodologies into different areas of biology. The concept of biological lineage facilitates these types of integration because it is broad and under-specified in ways that the concepts of molecular gene and evolutionary novelty are not. Hence, I use the concept of biological lineage as a case study to reveal types of integration that have been overlooked by philosophers. This case study also shows that even very imprecise concepts can be beneficial to scientific practice. (shrink)

According to the species-as-individuals thesis(hereafter S-A-I), species are cohesive entities. Barker and Wilson recently pointed out that the type of cohesion exhibited by species is fundamentally different from that of organisms (paradigmatic individuals), suggesting that species are homeostatic property cluster kinds. In this article, I propose a shift in how to approach cohesion in the context of S-A-I: instead of analyzing the different types of cohesion and questioning whether species have them, I focus on the role played by cohesion in (...) the identity of individuals. This shift allows us to recognize why cohesion matters to S-A-I, as well as to reconceive the analogy between species and organisms (paradigmatic individuals), and also allows us to highlight the context sensitivity of both ‘‘cohesion’’ and ‘‘individuals.’’ From this perspective, I identify two problems in Barker and Wilson’s argumentation. Firstly, the authors fail to recognize that species are individuals even if they do not have the same type of cohesion that organisms have. Secondly, their argument relies on a misinterpretation of S-A-I. I conclude that species cohesion is still best framed as a feature of species individuality rather than a feature of species as homeostatic property cluster kinds. The arguments presented here contribute to the re-articulation and reevaluation of S-A-I in the face of contemporary discussions. (shrink)

Molecular methods have revolutionised virtually every area of biology, and metazoan phylogenetics is no exception: molecular phylogenies, molecular clocks, comparative phylogenomics, and developmental genetics have generated a plethora of molecular data spanning numerous taxa and collectively transformed our understanding of the evolutionary history of animals, often corroborating but at times opposing results of more traditional approaches. Moreover, the diversity of methods and models within molecular phylogenetics has resulted in significant disagreement among molecular phylogenies as well as between these and earlier (...) phylogenies. How should this broad and multifaceted problem be tackled? I argue that the answer lies in integrating evidence to infer the best evolutionary scenario. I begin with an overview of recent development in early metazoan phylogenetics, followed by a discussion of key conceptual issues in phylogenetics revolving around phylogenetic evidence, theory, methodology, and interrelations thereof. I then argue that the integration of different kinds of evidence is necessary for arriving at the best evolutionary scenario rather than merely the best-fitting cladogram. Finally, I discuss the prospects of this view in stimulating interdisciplinary cross-talk in early metazoan research and beyond, and challenges that need to be overcome. (shrink)

The concept of population thinking was introduced by Ernst Mayr as the right way of thinking about the biological domain, but it is difficult to find an interpretation of this notion that is both unproblematic and does the theoretical work it was intended to do. I argue that, properly conceived, Mayr’s population thinking is a version of trope nominalism: the view that biological property-types do not exist or at least they play no explanatory role. Further, although population thinking has been (...) traditionally used to argue against essentialism about biological kinds, recently it has been suggested that it may be consistent with at least some forms of essentialism—ones that construe essential properties as relational. I argue that if population thinking is a version of trope nominalism, then, as Mayr originally claimed, it rules out any version of essentialism about biological kinds. (shrink)

According to a once influential view of selection, it consists of repeated cycles of replication and interaction. It has been argued that this view is wrong: replication is not necessary for evolution by natural selection. I analyze the nine most influential arguments for this claim and defend the replication–interaction conception of selection against these objections. In order to do so, however, the replication–interaction conception of selection needs to be modified significantly. My proposal is that replication is not the copying of (...) an entity, the replicator, but the copying of a property. Thus, we can have a replication process without there being a replicator that is being copied. (shrink)

Since Darwin it is widely accepted that natural selection (NS) is the most important mechanism to explain how biological organisms—in their amazing variety—evolve and, therefore, also how the complexity of certain natural systems can increase over time, creating ever new functions or functional structures/relationships. Nevertheless, the way in which NS is conceived within Darwinian Theory already requires an open, wide enough, functional domain where selective forces may act. And, as the present paper will try to show, this becomes even more (...) evident if one looks into the problem of origins. If there was a time when NS was not operating (as it is quite reasonable to assume), where did that initial functional diversity, necessary to trigger off the process, come from? Self-organization processes may be part of the answer, as many authors have claimed in recent years, but surely not the complete one. We will argue here that a special type of self-maintaining organization, arising from the interplay among a set of different endogenously produced constraints (pre-enzymatic catalysts and primitive compartments included), is required for the appearance of functional diversity in the first place. Starting from that point, NS can progressively lead to new (and, at times, also more complex) organizations that, in turn, provide wider functional variety to be selected for, enlarging in this way the range of action and consequences of the mechanism of NS, in a kind of mutually enhancing effect. (shrink)

The transition from chemistry to biology is an extremely complex issue because of the huge phenomenological differences between the two domains and because this transition has many different aspects and dimensions. In this paper, I will try to analyze how chemical systems have developed a cohesive, self-maintaining and functionally differentiated system that recruits its organization to stay far from equilibrium. This organization cannot exist but in an individualized form, and yet, it unfolds both a diachronic-historical and a synchronic collective dimension. (...) I will argue that, far from being a problem, these different dimensions of the phenomenon of life, appear as a consequence of the nature of this individualized organization. (shrink)

This paper is an application of the principles of individuality found in Guay and Pradeu to illuminate biological individuality in mushrooms. I begin with the distinction between logico-cognitive individuals and ontological individuals, and then I argue for genidentity plus material continuity, as a minimum conception of ontological individuality in biology. Of the many materially-continuous genidenticals found in fungi, only those with functional roles in biological theory, either evolutionary or physiological, warrant consideration. Given numerous ways that theory picks out materially-continuous genidenticals (...) in fungi, I argue for a pluralistic account of mushroom individuality. (shrink)

This paper argues that a plant together with the symbiotic fungus attached to its roots, a mycorrhizal collective, is an evolutionary individual, and further, that mycorrhizal individuality has important implications for evolutionary theory. Theoretical individuation is defended and then employed to show that mycorrhizal collectives function as interactors according to David Hull’s replicator-interactor model of evolution by natural selection, and because they have the potential to engage in pseudo-vertical transmission, mycorrhizal collectives also function as Darwinian individuals, according to Peter Godfrey-Smith’s (...) Darwinian Populations model of evolution by natural selection. Mycorrhizae in nature usually connect the roots of multiple plants, so mycorrhizal individuality entails the existence of overlapping evolutionary individuals, and because the potential to engage in pseudo-vertical transmission comes in degrees, it follows that these overlapping evolutionary individuals also come in degrees. I suggest here that the degree of evolutionary individuality in a symbiotic collective corresponds to its probability of reproducing with vertical or pseudo-vertical transmission. This probability constitutes a fourth parameter of graded Darwinian individuality in collective reproducers and warrants an update to Godfrey-Smith’s 3D model. (shrink)

Elsewhere, I defend the “causal interactionist population concept” (CIPC). Here I further defend the CIPC by showing how it clarifies another concept that biologists grapple with, namely, environment. Should we understand selection as ranging only over homogeneous environments or, alternatively, as ranging over any habitat area we choose to study? I argue instead that the boundaries of the population dictate the range of the environment, whether homogeneous or heterogeneous, over which selection operates. Thus, understanding the concept of population helps us (...) to understand concepts of selective environment, exemplifying the importance of the CIPC to other concepts and debates. (shrink)

The current tendency to moderate expectations that DNA barcode can be a method of discovering new species is due to the essentialist interpretation of this scientific analogy that is conceptually unsustainable. Something similar has happened in the philosophical field with the weakening of the initial versions of intrinsic biological essentialism. To examine the nature of this transition, I propose two principles that define a moderate EBI: one that assumes that the history of the taxon is metaphysically dependent on the evolution (...) of its intrinsic properties and another that assumes the necessary coextensivity between the intrinsic properties that explain the phenotype of the species and the bearers of identity conditions of a species. I argue that both principles are conceptually and empirically unsatisfactory. (shrink)

Causalism is the thesis that natural selection can cause evolution. A standard argument for causalism involves showing that a hypothetical intervention on some population-level property that is identified with natural selection will result in evolution. In a pair of articles, one of which recently appeared in the pages of this journal, Jun Otsuka has put forward a quite different argument for causalism. Otsuka attempts to show that natural selection can cause evolution by considering a hypothetical intervention on an individual-level property. (...) Specifically, Otsuka identifies natural selection with the causal relationship between a trait and fitness, claims an intervention on the strength of this relationship can cause evolution, then concludes that natural selection can cause evolution. Below I describe why Otsuka’s argument for causalism is unconvincing. Central to my criticism is that Otsuka’s argument works only if one adopts an indefensible account of natural selection, according to which natural selection can occur in the absence of trait or fitness variation. I go on to explain why any attempt to demonstrate the truth of causalism via a hypothetical intervention on an individual-level property would appear to require one to adopt an account of natural selection that is inadequate for the same reason. This in turn means the plausibility of causalism does indeed depend on the plausibility of the claim that population-level properties, which supervene on the properties of the individuals in the population, can be causally efficacious. (shrink)

‘Gouldian arguments’ appeal to the contingency of a scientific domain to establish that domain’s autonomy from some body of theory. For instance, pointing to evolutionary contingency, Stephen Jay Gould suggested that natural selection alone is insufficient to explain life on the macroevolutionary scale. In analysing contingency, philosophers have provided source-independent accounts, understanding how events and processes structure history without attending to the nature of those events and processes. But Gouldian Arguments require source-dependent notions of contingency. An account of contingency is (...) source-dependent when it is indexed to some pattern and some process. Positions like Gould’s do not turn on the mere fact of life’s contingency—that life’s shape could have been different due to its sensitivity to initial conditions, path-dependence or stochasticity. Rather, Gouldian arguments require that the contingency is due to particular kinds of processes: in this case, those which microevolutionary theory cannot account for. This source-dependent perspective clarifies both debates about the nature and importance of contingency, and empirical routes for testing Gould’s thesis. (shrink)

Functional localization is a central aim of cognitive neuroscience. But the nature and extent of functional localization in the human brain have been subjects of fierce theoretical debate since the 19th Century. In this essay, I first examine how concepts of functional localization have changed over time. I then analyze contemporary challenges to functional localization drawing from research on neural reuse, neural degeneracy, and the context-dependence of neural functions. I explore the consequences of these challenges for topics in philosophy of (...) science and philosophy of mind including localizationist versus anti-localizationist approaches to cognitive neuroscience, multiple realizability, reverse inference in functional neuroimaging, and the modularity of mind. (shrink)

Natural selection comes in degrees. Some biological traits are subjected to stronger selective force than others, selection on particular traits waxes and wanes over time, and some groups can only undergo an attenuated kind of selective process. This has downstream consequences for any notions that are standardly treated as binary but depend on natural selection. For instance, the proper function of a biological structure can be defined as what caused that structure to be retained by natural selection in the past. (...) We usually think of proper functions in binary terms: storing bile is a function of the gall bladder, but making stones is not. However, if functions arise through natural selection, and natural selection comes in degrees, then a binary approach to proper functions is in tension with the biological facts. In order to resolve this tension, we need to revise our standard accounts of proper function. In particular, we may have to seriously consider the possibility that functions themselves come in degrees, in spite of the ramifications this will have for the way we speak about functions and related concepts such as dysfunction, disease, and teleosemantic content. (shrink)

In the first part of the paper, I present a framework for the description and evaluation of teleosemantic theories of intentionality, and use it to argue that several different objections to these theories (the various indeterminacy and adequacy problems) are, in a certain precise sense, manifestations of the same underlying issue. I then use the framework to show that Millikan's biosemantics, her own recent declarations to the contrary notwithtanding, presents indeterminacy. In the second part, I develop a novel teleosemantic proposal (...) which makes progress in the treatment of this family of problems. I describe a procedure to derive a (unique) homeostatic property cluster [HPC] from facts having to do with the properties that a certain indicator relied on, in the events leading to its fixation in a certain population. This HPC is the one that should figure in the content attribution to the indicator in question. (shrink)

Thinking about organisms as if they were rational agents which could choose their own phenotypic traits according to their fitness values is a common heuristic in the field of evolutionary theory. In a 1998 paper, however, Elliott Sober has emphasized several alleged shortcomings of this kind of analogical reasoning when applied to the analysis of social behaviors. According to him, the main flaw of this heuristic is that it proves to be a misleading tool when it is used for predicting (...) the evolution of cooperation. Here, I show that these charges raised against the heuristic use of this analogy are misguided. I argue, contra Sober, that such a heuristic turns out to be a perfect predictive tool in all relevant contexts where cooperation can at least evolve. Moreover, I argue that it constitutes a powerful and sufficient methodological framework for the analysis of social evolution. (shrink)

In this paper, using a multilevel approach, we defend the positive role of natural selection in the generation of organismal form. Despite the currently widespread opinion that natural selection only plays a negative role in the evolution of form, we argue, in contrast, that the Darwinian factor is a crucial (but not exclusive) factor in morphological organization. Analyzing some classic arguments, we propose incorporating the notion of ‘downward causation’ into the concept of ‘natural selection.’ In our opinion, this kind of (...) causation is fundamental to the operation of selection as a creative evolutionary process. (shrink)

The concept of “life” certainly is of some use to distinguish birds and beavers from water and stones. This pragmatic usefulness has led to its construal as a categorical predicate that can sift out living entities from non-living ones depending on their possessing specific properties—reproduction, metabolism, evolvability etc. In this paper, we argue against this binary construal of life. Using text-mining methods across over 30,000 scientific articles, we defend instead a degrees-of-life view and show how these methods can contribute to (...) experimental philosophy of science and concept explication. We apply topic-modeling algorithms to identify which specific properties are attributed to a target set of entities (bacteria, archaea, viruses, prions, plasmids, phages and the molecule of adenine). Eight major clusters of properties were identified together with their relative relevance for each target entity (two that relate to metabolism and catalysis, one to genetics, one to evolvability, one to structure, and—rather unexpectedly—three that concern interactions with the environment broadly construed). While aligning with intuitions—for instance about viruses being less alive than bacteria—these quantitative results also reveal differential degrees of performance that have so far remained elusive or overlooked. Taken together, these analyses provide a conceptual “lifeness space” that makes it possible to move away from a categorical construal of life by empirically assessing the relative lifeness of more-or-less alive entities. (shrink)

Due to its high degree of complexity and its historical nature, evolutionary biology has been traditionally portrayed as a messy science. According to the supporters of such a view, evolutionary biology would be unable to formulate laws and robust theories, instead just delivering coherent narratives and local models. In this article, our aim is to challenge this view by showing how the Price equation can work as the core of a general theoretical framework for evolutionary phenomena. To support this claim, (...) we outline some unnoticed structural similarities between physical theories and evolutionary biology. More specifically, we shall argue that the Price equation, in the same way as fundamental formalisms in physics, can serve as a heuristic principle to formulate and systematise different theories and models in evolutionary biology. (shrink)

Reichenbach’s early solution to the scientific problem of how abstract mathematical representations can successfully express real phenomena is rooted in his view of coordination. In this paper, I claim that a Reichenbach-inspired, ‘layered’ view of coordination provides us with an effective tool to systematically analyse some epistemic and conceptual intricacies resulting from a widespread theorising strategy in evolutionary biology, recently discussed by Okasha (2018) as ‘endogenization’. First, I argue that endogenization is a form of extension of natural selection theory that (...) comprises three stages: quasi-axiomatisation, functional extension, and semantic extension. Then, I argue that the functional extension of one core principle of natural selection theory, namely, the principle of heritability, requires the semantic extension of the concept of inheritance. This is because the semantic extension of ‘inheritance’ is necessary to establish a novel form of coordination between the principle of heritability and the extended domain of phenomena that it is supposed to represent. Finally, I suggest that – despite the current lack of consensus on the right semantic extension of ‘inheritance’ – we can fruitfully understand the reconceptualization of ‘inheritance’ provided by niche construction theorists as the result of a novel form of coordination. (shrink)

We address the controversy in the literature concerning the definition of holobionts and the apparent constraints on their evolution using concepts from community population genetics. The genetics of holobionts, consisting of a host and diverse microbial symbionts, has been neglected in many discussions of the topic, and, where it has been discussed, a gene-centric, species-centric view, based in genomic conflict, has been predominant. Because coevolution takes place between traits or genes in two or more species and not, strictly speaking, between (...) species, it may affect some traits but not others in either host or symbiont. Moreover, when interacting species pairs are embedded in a larger community, indirect ecological effects can alter the expected pairwise dynamics. Mode of symbiont transmission and the degree of host inbreeding both affect the extent of microbial mixing across host lineages and thereby the degree to which selection on one trait of either partner affects other aspects of a holobiont phenotype. We discuss several potential defining criteria for holobionts using community genetics and population genetics models, suggesting their application and limitations. Using community genetics models, we show how conflict between genomes can be self-limiting, while cooperation and mutualism tend to be self-accelerating. It is likely that this bias in the evolutionary dynamics of interaction between hosts and symbionts is an important feature of holobionts. This bias in the evolutionary dynamic could contribute to explaining the absence of cheaters from natural mutualisms, although cheaters are predicted by gene-centered conflict theory to cause the evolutionary instability of mutualisms. Additionally, it may help explain the more frequent origin of mutualisms from parasitic than from free-living systems, an evolutionary trajectory opposite to that predicted by genome conflict theory. (shrink)

Political science is divided between methodological individualists, who seek to explain political phenomena by reference to individuals and their interactions, and holists (or nonreductionists), who consider some higher-level social entities or properties such as states, institutions, or cultures ontologically or causally significant. We propose a reconciliation between these two perspectives, building on related work in philosophy. After laying out a taxonomy of different variants of each view, we observe that (i) although political phenomena result from underlying individual attitudes and behavior, (...) individual-level descriptions do not always capture all explanatorily salient properties, and (ii) nonreductionistic explanations are mandated when social regularities are robust to changes in their individual-level realization. We characterize the dividing line between phenomena requiring nonreductionistic explanation and phenomena permitting individualistic explanation and give examples from the study of ethnic conflicts, social-network theory, and international-relations theory. (shrink)

Peter Godfrey-Smith’s introduction to the philosophy of biology is excellent. This review questions one implication of his book, namely that Darwin’s case for the efficacy of natural selection was hampered by his ignorance of the particulate nature of inheritance. I suggest, instead, that Darwin was handicapped by an inability to effectively engage in quantitative population thinking. I also question Godfrey-Smith’s understanding of the role that Malthusian struggle plays in linking natural selection to the origination of new adaptive traits, and I (...) raise problems for his defence of apparently unproblematic conceptions of human nature. Finally, I highlight the welcome conception of a ‘philosophy of nature’ developed by Godfrey-Smith. (shrink)

All epistemic agents physically consist of parts that must somehow comprise an integrated cognitive self. Biological individuals consist of subunits (organs, cells, molecular networks) that are themselves complex and competent in their own context. How do coherent biological Individuals result from the activity of smaller sub-agents? To understand the evolution and function of metazoan bodies and minds, it is essential to conceptually explore the origin of multicellularity and the scaling of the basal cognition of individual cells into a coherent larger (...) organism. In this paper I synthesize ideas in cognitive science, evolutionary biology, and developmental physiology toward a hypothesis about the origin of Individuality: “Scale-Free Cognition”. I propose a fundamental definition of an Individual based on the ability to pursue goals at an appropriate level of scale and organization, and suggest a formalism for defining and comparing the cognitive capacities of highly diverse types of agents. Any Self is demarcated by a computational surface – the spatio-temporal boundary of events that it can measure, model, and try to affect. This surface sets a functional boundary - a cognitive “light cone” which defines the scale and limits of its cognition. I hypothesize that higher-level goal-directed activity and agency, resulting in larger cognitive boundaries, evolve from the primal homeostatic drive of living things to reduce stress – the difference between current conditions and life-optimal conditions. The mechanisms of developmental bioelectricity - the ability of all cells to form electrical networks that process information - suggests a plausible set of gradual evolutionary steps that naturally lead from physiological homeostasis in single cells to memory, prediction, and ultimately complex cognitive agents, via scale-up of the drive of infotaxis. Recent data on the molecular mechanisms of pre-neural bioelectricity suggest a model of how increasingly sophisticated cognitive functions emerge smoothly from cell-cell communication used to guide embryogenesis and regeneration. This set of hypotheses provides a novel perspective on numerous phenomena, such as cancer, and makes several unique, testable predictions for interdisciplinary research that have implications not only for evolutionary developmental biology but also for biomedicine and perhaps artificial intelligence and exobiology. (shrink)

One of the major developments in cancer research in recent years has been the construction of models that treat cancer as a cellular population subject to natural selection. We expand on this idea, drawing upon multilevel selection theory. Cancer is best understood in our view from a multilevel perspective, as both a by-product of selection at other levels of organization, and as subject to selection at several levels of organization. Cancer is a by-product in two senses. First, cancer cells co-opt (...) signaling pathways that are otherwise adaptive at the organismic level. Second, cancer is also a by-product of features distinctive to the metazoan lineage: cellular plasticity and modularity. Applying the multilevel perspective in this way permits one to explain transitions in complexity and individuality in cancer progression. Our argument is a reply to Germain’s scepticism towards the explanatory relevance of natural selection for cancer. The extent to which cancer fulfills the conditions for being a paradigmatic Darwinian population depends on the scale of analysis, and the details of the purported selective scenario. Taking a multilevel perspective clarifies some of the complexities surrounding how to best understand the relevance of evolutionary thinking in cancer progression. (shrink)

If ecological systems are functionally organised, they can possess functions or malfunctions. Natural function would provide justification for conservationists to act for the protection of current ecological arrangements and control the presence of populations that create ecosystem malfunctions. Invasive species are often thought to be malfunctional for ecosystems, so functional arrangement would provide an objective reason for their control. Unfortunately for this prospect, I argue no theory of function, which can support such normative conclusions, can be applied to large scale (...) ecosystems. Instead ecological systems have causal structure, with small clusters of populations achieving functional arrangement. This, however, does not leave us without reason to control invasive species. We can look at the causal arrangement of ecological systems for populations that support ecological features that we should preserve. Populations that play a causal role in reducing biodiversity should be controlled, because biodiversity is a good all prudent agents should want to preserve. (shrink)

In this article I examine “Ontology Matters!” (OM!) arguments. OM! arguments conclude that ontology can contribute to empirical success in social science. First, I capture the common form between different OM! arguments. Second, I describe quantifier variance as discussed in metaontology. Third, I apply quantifier variance to the common form of OM! arguments. I then present two ways in which ontology is prior to social science methodology, one realist and one pragmatic. I argue that a pragmatic interpretation of ontology’s priority (...) gives proponents of realist OM! arguments a special burden that they must meet to render their argument successful. (shrink)

The clonal evolution model and the cancer stem cell model are two independent models of cancers, yet recent data shows intersections between the two models. This article explores the impacts of the CSC model on the CE model. I show that CSC restriction, which depends on CSC frequency in cancer cell populations and on the probability of dedifferentiation of cancer non-stem cells into CSCs, can favor or impede some patterns of evolution and some processes of evolution. Taking CSC restriction into (...) account for the CE model thus has implications for the way in which we understand the patterns and processes of evolution, and can also provide new leads for therapeutic interventions. (shrink)

This article argues that evolutionary models based on selection validate, under appropriate conditions, the relevance of optimality as an explanatory mechanism in rational choice theory. The reason is that these frameworks share the mechanism that drives the results, namely, optimization, even if they situate it at different levels. The consequences of our argument are twofold. First, it resolves the tension between those predictions of rational choice theory that are accurate and the evidence showing that individuals seldom optimize. Second, it relativizes (...) the explanatory import of rationality without diminishing the role of optimization as a mechanism. (shrink)

While the struggle for life played an important role in the process of natural selection as it was conceived by Darwin, natural selection is commonly characterized today as a process which does not necessarily involve struggle. Nevertheless, there have been some attempts to show the importance of struggle to the process of natural selection. The present paper aims to continue these attempts and clarify the precise evolutionary role of struggle. The paper focuses on a recent dispute regarding the role of (...) struggle between Peter Godfrey-Smith and Tim Lewens. Godfrey-Smith argues that struggle makes populations into "paradigm cases of Darwinian populations", meaning that struggle leads natural selection to produce adaptations. Lewens, in contrast, argues that Godfrey-Smith's argument fails to show that struggle plays such a role. I argue that Godfrey-Smith's argument that struggle leads selection to produce adaptations can be understood in two different ways. Lewens interprets Godfrey-Smith's argument in one of these ways, and rightly argues that thus understood, this argument fails to show that struggle leads selection to produce adaptations. However, I show that understood in a second way, Godfrey-Smith's argument does show that struggle plays such a role. Still, I show that there is an additional problem with Godfrey-Smith's argument that struggle makes populations into "paradigm cases of Darwinian populations". It does not capture the precise role played by struggle in the relation between selection and adaptation. Thus, the present paper clarifies the unique role that struggle plays in the relation between selection and adaptation in evolutionary theory. (shrink)

The so-called “dark room problem” makes vivd the challenges that purely predictive models face in accounting for motivation. I argue that the problem is a serious one. Proposals for solving the dark room problem via predictive coding architectures are either empirically inadequate or computationally intractable. The Free Energy principle might avoid the problem, but only at the cost of setting itself up as a highly idealized model, which is then literally false to the world. I draw at least one optimistic (...) conclusion, however. Real-world, real-time systems may embody motivational states in a variety of ways consistent with idealized principles like FEP, including ways that are intuitively embodied and extended. This may allow predictive coding theorists to reconcile their account with embodied principles, even if it ultimately undermines loftier ambitions. (shrink)

Exactly what makes an interaction between two organisms a case of communication is contentious. Historically, debate has taken place between definitions of communication invoking information transmission vs definitions invoking causal influence. More recently, there has been some convergence on a hybrid definition: invoking causal influence mediated via the transmission of information. After proposing an understanding of what it means to say that a receiver is causally influenced by the transmission of information, I argue that an information-mediated influence definition overextends to (...) include most, indeed maybe all, co-adapted interactions. This is because the transmission of correlational information is actually a feature of most, if not all, co-adapted interactions. I end by considering whether adding an arbitrariness criterion to an information-mediated influence definition helps. After giving an account of what arbitrariness amounts to, I argue that it swings things too far in the opposite direction: we go from a definition of communication that is too liberal to one that is too restrictive. This is because many signal kinds are not arbitrary. It turns out to be extremely difficult to capture what makes communication unique. (shrink)

In this paper, I identify two general positions with respect to the relationship between environment and natural selection. These positions consist in claiming that selective claims need and, respectively, need not be relativized to homogenous environments. I then show that adopting one or the other position makes a difference with respect to the way in which the effects of selection are to be measured in certain cases in which the focal population is distributed over heterogeneous environments. Moreover, I show that (...) these two positions lead to two different interpretations—the Pricean and contextualist ones—of a type of selection scenarios in which multiple groups varying in properties affect the change in the metapopulation mean of individual-level traits. Showing that these two interpretations stem from different attitudes towards environmental homogeneity allows me to argue: that, unlike the Pricean interpretation, the contextualist interpretation can only claim that drift or selection is responsible for the change in frequency of the focal trait in a given metapopulation if details about whether or not group formation is random are specified; that the traditional main objection against the Pricean interpretation—consisting in arguing that the latter takes certain side-effects of individual selection to be effects of group selection—is unconvincing. This leads me to suggest that the ongoing debate about which of the two interpretations is preferable should concentrate on different issues than previously thought. (shrink)

In this short paper, I argue against what I call the “belonging to” interpretation of group selection in scenarios in which a group’s fitness is defined as the per capita reproductive output of the individuals of the group. According to this interpretation, group selection acts on “belonging to” properties of individuals, i.e. on relational or contextual properties that all the individuals of a group share simply by belonging to that group; thus, if differences in the individuals’ “belonging to” properties cause (...) differences in their fitness, group selection sensu the “belonging to” interpretation is said to be at work. I argue that the main problem with the “belonging to” interpretation is that it confuses evolutionary changes due to differences in environmental quality with evolutionary changes due to selection. In other words, I argue that, in the majority of cases, this interpretation actually takes the “selection” out of the “group selection” notion it aims to interpret: by adopting this perspective, one implicitly commits to explaining the evolutionary change under consideration not by a kind of selection, but by differences in the environmental quality experienced by individual types. (shrink)

Most attempts to answer the question of whether populations of groups can undergo natural selection focus on properties of the groups themselves rather than the dynamics of the population of groups. Those approaches to group selection that do emphasize dynamics lack an account of the relevant notion of equivalent dynamics. I show that the theory of ‘dynamical kinds’ I proposed in Jantzen :3617–3646, 2014) can be used as a framework for assessing dynamical equivalence. That theory is based upon the notion (...) of a dynamical symmetry, a transformation of a system that commutes with its evolution through time. In the proposed framework, structured sets of dynamical symmetries are used to pick out equivalence classes of systems. These classes are large enough to encompass the range of phenomena we associate with natural selection, yet restrictive enough to guarantee a sort of causal homogeneity. By characterizing dynamical kinds via symmetry structures in this way, the question of levels of selection becomes a precise question about which populations respect the dynamical symmetries of Darwinian evolution. Standard population genetic models suggest that populations undergoing evolution by natural selection are partially characterized by a group of fitness-scaling symmetries. I demonstrate conditions under which these symmetries may be satisfied by populations of individuals, populations of groups of individuals, or both simultaneously. (shrink)

In this paper, we compare the mechanisms of protein synthesis and natural selection. We identify three core elements of mechanistic explanation: functional individuation, hierarchical nestedness or decomposition, and organization. These are now well understood elements of mechanistic explanation in fields such as protein synthesis, and widely accepted in the mechanisms literature. But Skipper and Millstein have argued that natural selection is neither decomposable nor organized. This would mean that much of the current mechanisms literature does not apply to the mechanism (...) of natural selection.We take each element of mechanistic explanation in turn. Having appreciated the importance of functional individuation, we show how decomposition and organization should be better understood in these terms. We thereby show that mechanistic explanation by protein synthesis and natural selection are more closely analogous than they appear—both possess all three of these core elements of a mechanism widely recognized in the mechanisms literature. (shrink)

Evolution by natural selection has been extended to several supraorganismic levels, but whether it can apply to ecosystems remains controversial on two main counts. First, local ecosystems are loosely individuated, so that it is unclear how they manifest heredity and fitness. Second, even if they did, the meta-ecosystem formed by this population of local ecosystems will also suffer from a very low degree of cohesion, which will jeopardize any ENS. We suggest a way to overcome both issues, focusing on ecosystem (...) properties rather than on ecosystemic individuals. First, we follow recent theoretical developments which deny the centrality of reproduction in ENS. This leads us to merge heredity and fitness in a single process, in which a local ecosystem causally influences its neighbors, in a way responsible for their phenotypic similarity. Second, we suggest that the resulting meta-ecosystem need not meet the criteria of individuality. Instead, the evolving meta-ecosystem is best understood as a homeostatic property cluster, i.e., a set of phenotypes that together evolve by ENS at the ecosystem level. We illustrate this conceptual framework with a hypothetical example of local ecosystems that vary in terms of stability, productivity, diversity, and complementarity between species. Finally, we stress that our property-based account of ecosystemic ENS can help understand evolution at other biological levels, such as early life evolution and holobionts. (shrink)