Despite many years of discussion, the species problem has still not been adequately resolved. Why is this the case? Here I discuss two recent suggested answers to this question that place the blame on the species problem's empirical aspects or on its philosophical aspects. In contrast, I argue that neither of these two faces of the species problem constitute the principal cause of the species problem's persistence. Rather, they are merely symptoms of the real cause: the species problem has not (...) yet gone away because of a failure to recognize that not one but a number of distinct concepts are at the heart of the problem. To illustrate this point, a recently proposed solution to the problem is examined: the suggestion to understand the concept of species as a family resemblance concept. BioEssays 26:300–305, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

The correspondence between Edgar Anderson and Ernst Mayr leading into their 1941 Jesup Lectures on “Systematics and the Origin of Species” addressed population thinking, the nature of species, the relationship of microevolution to macroevolution, and the evolutionary dynamics of plants and animals, all central issues in what came to be known as the Evolutionary Synthesis. On some points, they found ready agreement; for others they forged only a short term consensus. They brought two different working styles to this project reflecting (...) their different appreciations of what was possible at this point in evolutionary studies. For Mayr, it was a focused project with definitive short term conclusions imminent while Anderson viewed it as an episode in an ongoing historical process that, while exciting and suggestive, remained openended. Thus, Mayr and Anderson represent two distinct perspectives on the Evolutionary Synthesis in formation; by understanding both of their points of view, we can grasp more fully the state of evolutionary theory at this key moment. (shrink)

I propose we abandon the unit concept of "the evolutionary synthesis". There was much more to evolutionary studies in the 1920s and 1930s than is suggested in our commonplace narratives of this object in history. Instead, four organising threads capture much of evolutionary studies at this time. First, the nature of species and the process of speciation were dominating, unifying subjects. Second, research into these subjects developed along four main lines, or problem complexes: variation, divergence, isolation, and selection. Some calls (...) for 'synthesis' focused on these problem complexes (sometimes on one of these; other times, all). In these calls, comprehensive and pluralist compendia of plausibly relevant elements were preferred over reaching consensus about the value of particular formulae. Third, increasing confidence in the study of common problems coincided with methodological and epistemic changes associated with experimental taxonomy. Finally, the surge of interest in species problems and speciation in the 1930s is intimately tied to larger trends, especially a shifting balance in the life sciences towards process-based biologies and away from object-based naturalist disciplines. Advocates of synthesis in evolution supported, and were adapting to, these larger trends. (shrink)

What does it look like when a group of scientists set out to re-envision an entire field of biology in symbolic and formal terms? I analyze the founding and articulation of Numerical Taxonomy between 1950 and 1970, the period when it set out a radical new approach to classification and founded a tradition of mathematics in systematic biology. I argue that introducing mathematics in a comprehensive way also requires re-organizing the daily work of scientists in the field. Numerical taxonomists sought (...) to establish a mathematical method for classification that was universal to every type of organism, and I argue this intrinsically implicated them in a qualitative re-organization of the work of all systematists. I also discuss how Numerical Taxonomy’s re-organization of practice became entrenched across systematic biology even as opposing schools produced their own competing mathematical methods. In this way, the structure of the work process became more fundamental than the methodological theories that motivated it. (shrink)

Genes are thought to have evolved from long-lived and multiply-interactive molecules in the early stages of the origins of life. However, at that stage there were no replicators, and the distinction between interactors and replicators did not yet apply. Nevertheless, the process of evolution that proceeded from initial autocatalytic hypercycles to full organisms was a Darwinian process of selection of favourable variants. We distinguish therefore between Neo-Darwinian evolution and the related Weismannian and Central Dogma divisions, on the one hand, and (...) the more generic category of Darwinian evolution on the other. We argue that Hull’s and Dawkins’ replicator/interactor distinction of entities is a sufficient, but not necessary, condition for Darwinian evolution to take place. We conceive the origin of genes as a separation between different types of molecules in a thermodynamic state space, and employ a notion of reproducers. (shrink)

This paper outlines an alternative perspective on species that avoids some of the underlying assumptions held by the BSC and other gene-centred species concepts. It begins with a characterisation of the species problem and some of the assumptions underpinning conceptions of species. In particular, the underlying bias of some conceptions (such as the BSC) to focus exclusively on the adult stage of the life cycle in articulating what a species is.

While Darwin is commonly supposed to have demonstrated the inapplicability of the Aristotelian ontology of species to biological science, recent developments, especially in the wake of the Human Genome Project, have given rise to a new golden age of classification in which ontological ideas -- as for example in the Gene Ontology, the Cell Ontology, the Protein Ontology, and so forth -- are once again playing an important role. In regard to species, on the other hand, matters are more complex. (...) We provide a brief overview of recent proposals concerning the ontology of species, dealing with species as sets, classes and as collections, the views of Ernst Meyr, and mereological views. (shrink)

Many phylogenetic systematists have criticized the Biological Species Concept (BSC) because it distorts evolutionary history. While defenses against this particular criticism have been attempted, I argue that these responses are unsuccessful. In addition, I argue that the source of this problem leads to previously unappreciated, and deeper, fatal objections. These objections to the BSC also straightforwardly apply to other species concepts that are not defined by genealogical history. What is missing from many previous discussions is the fact that the Tree (...) of Life, which represents phylogenetic history, is independent of our choice of species concept. Some species concepts are consistent with species having unique positions on the Tree while others, including the BSC, are not. Since representing history is of primary importance in evolutionary biology, these problems lead to the conclusion that the BSC, along with many other species concepts, are unacceptable. If species are to be taxa used in phylogenetic inferences, we need a history-based species concept. (shrink)

The biological species (biospecies) concept applies only to sexually reproducing species, which means that until sexual reproduction evolved, there were no biospecies. On the universal tree of life, biospecies concepts therefore apply only to a relatively small number of clades, notably plants andanimals. I argue that it is useful to treat the various ways of being a species (species modes) as traits of clades. By extension from biospecies to the other concepts intended to capture the natural realities of what keeps (...) taxa distinct, we can treat other modes as traits also, and so come to understand that theplurality of species concepts reflects the biological realities of monophyletic groups.We should expect that specialists in different organisms will tend to favour those concepts that best represent the intrinsic mechanisms that keep taxa distinct in their clades. I will address the question whether modes ofreproduction such as asexual and sexual reproduction are natural classes, given that they are paraphyletic in most clades. (shrink)

This paper argues against the common, often implicit view that theories are some specific kind of thing. Instead, I argue for theory concept pluralism: There are multiple distinct theory concepts which we legitimately use in different domains and for different purposes, and we should not expect this to change. The argument goes by analogy with species concept pluralism, a familiar position in philosophy of biology. I conclude by considering some consequences for philosophy of science if theory concept pluralism is correct.

Recent discussion of mechanism has suggested new approaches to several issues in the philosophy of science, including theory structure, causal explanation, and reductionism. Here, I apply what I take to be the fruits of the 'new mechanical philosophy' to an analysis of a contemporary debate in evolutionary biology about the role of natural selection in speciation. Traditional accounts of that debate focus on the geographic context of genetic divergence--namely, whether divergence in the absence of geographic isolation is possible (or significant). (...) Those accounts are at best incomplete, I argue, because they ignore the mechanisms producing divergence and miss what is at stake in the biological debate. I argue that the biological debate instead concerns the scope of particular speciation mechanisms which assign different roles to natural selection at various stages of divergence. The upshot is a new interpretation of the crux of that debate--namely, whether divergence with gene flow is possible (or significant) and whether the isolating mechanisms producing it are adaptive. (shrink)

The year 2009 has been a year of numerous commemorations of both scientific and non-scientific achievements that contributed to the advancement of human kind. Protestants celebrated the 500th anniversary of the birth of Calvin; literary critics celebrated the 200th anniversary of the poet Edgar Allan Poe; and the musical genius Felix Mendelssohn-Bartholdy was also born 200 years ago. 2009 further marked the bicentennial of the birth of Louis Braille, the inventor of Braille; and Abraham Lincoln, the 16th president of the (...) United States, who founded the National Academy of Sciences. Pierre Curie, famous for his work on radioactivity that he conducted together with his wife Marie Curie, was born 150 ago; as was John Dewey, a philosopher and psychologist who is recognized as one of the founding fathers of both pragmatism as well as functional psychology. UNESCO and the International Astronomical Union dubbed 2009 the International Year of Astronomy. By doing so, astronomers celebrated the 400th anniversary of Galileo Galilei’s telescopic observations as well as the publication of Johannes Kepler’s Astronomia nova wherein he formulated the first two laws of planetary motion. 2009 also marked the last of a 3-year-long celebration of Planet Earth, another UNESCO-governed initiative. However, for evolutionary biologists and philosophers of science, 2009 will be largely remembered for its worldwide commemorations of the 200th anniversary of the birth of Charles Darwin, and the 150th anniversary of the publication of his magnum opus On the origin of species by means of natural selection. Footnote1 In order to pay tribute to Darwin’s major contribution to the advancement of evolutionary science, the International Union of Biological Sciences and the International Union of History and Philosophy of Science have called the year 2009 the Darwin Year. Given that so many scientific discoveries were commemorated, COPUS, the Coalition on the Public Understanding on Science, called out 2009 as the Year of Science, in the hope to pay equal tribute to both the field of biology as well as astronomy. 2009 was indeed a year of biology. Somewhat overshadowed by the big Darwin celebrations, smaller-scaled events were held to commemorate the 200th anniversary of the publication of Lamarck’s Philosophie Zoologique; and the 150th anniversary of the death of Alexander von Humboldt, the father of biogeography. In 1910, Constantin Mereschkowsky wrote his article on symbiogenesis entitled ‘The Theory of Two Plasmas as the Basis of Symbiogenesis, a New Study for the Origins of Organisms’. The article was published in the German Biologisches Zentralblatt, the journal that would later evolve into the current Theory in Biosciences. Somewhat forgotten, but equally important for the field of symbiogenesis, was the 200th anniversary of the birth of Pierre-Joseph Van Beneden, a Belgian paleontologist and zoologist famous for distinguishing parasitism from commensalism. Finally, Henry Bergson, known for inventing the currently rejected notion of élan vital, was born 150 years ago. In order to memorialize the important role these biologists played in the advancement of our understanding of the evolutionary process, a 2-day international conference was organized entitled: Evolution today and tomorrow, Darwin evaluated by contemporary evolutionary and philosophical theories. The conference was organized by The Centre for Philosophy of Science of the University of Lisbon (Portugal), in collaboration with the Centre for Environmental Biology of the same university, and the Lisbon Centre for Applied Psychology. The articles presented here are a spin-off of this conference. The current volumes contain the peer-reviewed articles of a selection of the plenary and invited speakers, as well as those of scholars who were additionally invited to contribute to the volumes. (shrink)

The field of the philosophy of biology is flourishing in its aim to evaluate and rethink the view inherited from the previous century ---the Modern Synthesis. Different research areas and theories have come to the fore in the last decades in order to account for different biological phenomena that, in the first instance, fall beyond the explanatory scope of the Modern Synthesis. This thesis is anchored and motivated by this revolt in the philosophy of biology. -/- The central target in (...) this context is the possibility of naturalizing teleology, a classical nightmare for the history of biology itself. This requires, principally, understanding the causes of teleological explanations without assuming an unfashioned backward causation of sorts. As the riddles of teleological explanations are about their temporal dimension, I analyze different temporal scales of biological processes: evolutionary, developmental, and physiological. -/- The first one is the one defended in the context of the Modern Synthesis. As expected, one of the aims of this thesis is to evaluate the adequacy of an evolutionary account of teleological explanation. The scrutiny is negative. Evolutionary explanations in the context of the Modern Synthesis lack the necessary causal roots to naturalize teleology. Concerning the physiological scale, a long tradition pushed up by Kant and the organicist movement in the 20th century allows us to better understand how teleological explanations can be naturalized in physiological process. The key notions in this temporal scale are self-organization and the recursive, looped character of physiological process. While the physiological scale may be suitably accounted by contemporaries views, such as Autonomous Systems Theory, different central teleological phenomena remain unexplained from a purely physiological perspective. In particular, different issues concerning the (adaptive) construction of organism ---such as plasticity, robustness, variation, novelty, inheritance--- deserve an ontogenetic analysis. -/- The principal aim of this thesis is to provide a theory of teleological development that falls beyond the Modern Synthesis' framework and is prompted by different insights from the history of biology. I call it Agential Teleosemantics. It rests on two central pillars. First, that developmental processes, beyond any gene-centered stance, can be understood in informational terms; i.e. developmental processes are about the interaction of developmental resources conveying biological information. The second ingredient is agentivity, namely the idea that development is regulated by an agentive system according to the adaptiveness of the phenotypic outcomes produced. The role of agency in Agential Teleosemantic is equivalent to the role of genes in the Modern Synthesis: it is responsible for explaining the order and the adaptive complexity in the living realm. -/- The second target of this thesis regards the possibility of naturalizing intentional explanations in cognitive science. The central project involved in such an aim is known as teleosemantics. Classical teleosemantics however is etiological: it explains the teleofunctions of representational systems in terms of evolutionary processes. The different disputes in the contemporary philosophy of biology provide two insights to analyze teleosemantics in cognitive science. First, the challenges against the Modern Synthesis must be extended to the evolutionary approach of etiological teleosemantics. Second, as Agential Teleosemantics suggests an alternative source for teleofunctions ---ontogeny, I offer an attempt to integrate Agential Teleosemantics into cognitive science in order to provide an alternative teleosemantic project to understand intentional explanations in cognitive science. (shrink)

In this paper, I critically assess Mark Richard’s interesting and important development of the claim that linguistic meanings can be fruitfully analogized with biological species. I argue that linguistic meanings qua cluster of interpretative presuppositions need not and often do not display the population-level independence and reproductive isolation that is characteristic of the biological species concept. After developing these problems in some detail, I close with a discussion of their implications for the picture that Richard paints concerning the dangers of (...) conceptual engineering and the prospects for dynamic notions of semantic stability. (shrink)

The longstanding species problem in biology has a history that suggests a solution, and that history is not the received history found in many texts written by biologists or philosophers. The notion of species as the division into subordinate groups of any generic predicate was the staple of logic from Aristotle through the middle ages until quite recently. However, the biological species concept during the same period was at first subtly and then overtly different. Unlike the logic sense, which relied (...) on definitions of the essence of both genus and species, biological species from the time of Epicurus were consistently considered to involve a reproductive element: in short, living species relied not on essential definitions, but on the generative cause, which might not be definable. I term this the generative conception of species: species were the generation by reproduction of form. This undercuts the claim that species before Darwin were essentialist, and divorces the notion of a type from that of essence. In fact, as late as the end of the nineteenth century, logicians explicitly treated biological “species” as a homonym only of logical essentialist species, and permitted considerable deviation from the type or form. At every point, species in logic were thought to be a subset, in effect, of some more general notion. I sketch a history of both philosophical and biological traditions of the species concept, before turning to the current conceptions. These are reconsidered in the light of this history, and in particular Mayr’s changing views are shown to be somewhat Whiggish, historiographically. Of the many touted biological species concepts, only one of which (Mayr’s) is called _the_ Biological Species Concept, none appears to capture all the relevant facts, intuitions, and operational requirements of biology. Cladistic conceptions, however, have much in common with the older philosophical literature, in that the natural group of cladism is the clade, or monophyletic group. After considering the Individuality Thesis, and the metaphysics of species, we see that species are the most particular terminal taxa in a clade, and that they are “defined” in terms of the particular synapomorphies, or evolved characters, that are causally responsible for keeping the lineages that organisms form distinct from one another. In this way, we can remain within the generative conception of species that has been in play for over two millennia, and yet avoid the pitfalls of prior attempts to find a universal conception of species. (shrink)

This paper isolates a hard, long-standing species problem: developing a comprehensive and exacting theory about the constitutive conditions of the species category, one that is accurate for most of the living world, and which vindicates the widespread view that the species category is of more theoretical import than categories such as genus, sub-species, paradivision, and stirp. The paper then uncovers flaws in several views that imply we have either already solved that hard species problem or dissolved it altogether – so-called (...) We Are Done views. In doing so the paper offers new criticisms of the general lineage species concept (GLSC), evolutionary species concept (EvSC), biological species concept (BSC), other similar concepts, Ereshefsky’s eliminative pluralism about the species category, and both Mishler’s pessimism and Wilkins’ phenomenalism about that category. Opposed to We Are Done views, the paper argues for a Revving Up view, on which we are nearly ready to begin the hard species problem in earnest. To help work towards these conclusions, the paper begins with an outline of a new kind of view of species (Barker 2019a), which proposes they are feedback systems of a mathematically specifiable and empirically testable sort. (shrink)

In their landmark 2010 paper, “The weirdest people in the world?”, Henrich, Heine, and Norenzayan outlined a serious methodological problem for the psychological and behavioural sciences. Most of the studies produced in the field use people from Western, Educated, Industrialised, Rich and Democratic (WEIRD) societies, yet inferences are often drawn to the species as a whole. In drawing such inferences, researchers implicitly assume that either there is little variation across human populations, or that WEIRD populations are generally representative of the (...) species. Yet neither of these assumptions is justified. In many psychological and behavioural domains, cultural variation begets cognitive variation, and WEIRD samples are recurrently shown to be outliers. In the years since the article was published, attention has focused on the implications this has for research on extant human populations. Here we extend those implications to the study of ancient _H. sapiens_, their hominin forebears, and cousin lineages. We assess a range of characteristic arguments and key studies in the cognitive archaeology literature, identifying issues stemming from the problem of sample diversity. We then look at how worrying the problem is, and consider some conditions under which inferences to ancient populations via cognitive models might be provisionally justified. (shrink)

Mismatch is a prominent concept in evolutionary medicine and a number of philosophers have published analyses of this concept. The word ‘mismatch’ has been used in a diversity of ways across a range of sciences, leading these authors to regard it as a vague concept in need of philosophical clarification. Here, in contrast, we concentrate on the use of mismatch in modelling and experimentation in evolutionary medicine. This reveals a rigorous theory of mismatch within which the term ‘mismatch’ is indeed (...) used in several ways, not because it is ill-defined but because different forms of mismatch are.distinguished within the theory. Contemporary evolutionary medicine has unified the idea of ‘evolutionary mismatch’, derived from the older idea of ‘adaptive lag’ in evolution, with ideas about mismatch in development and physiology derived from the Developmental Origins of Health and Disease (DOHaD) paradigm. A number of publications in evolutionary medicine have tried to make this theoretical framework explicit. We build on these to present the theory in as simple and general a form as possible. We introduce terminology, largely drawn from the existing literature, to distinguish the different forms of mismatch. This integrative theory of mismatch captures how organisms track environments across space and time on multiple scales in order to maintain an adaptive match to the environment, and how failures of adaptive tracking lead to disease. Mismatch is a productive organising concept within this theory which helps researchers articulate how physiology, development and evolution interact with one another and with environmental change to explain health outcomes. (shrink)

Traditionally, Thomas S. Kuhn’s The Structure of Scientific Revolutions (1962) is largely identified with his analysis of the structure of scientific revolutions. Here, we contribute to a minority tradition in the Kuhn literature by interpreting the history of evolutionary biology through the prism of the entire historical developmental model of sciences that he elaborates in The Structure. This research not only reveals a certain match between this model and the history of evolutionary biology but, more importantly, also sheds new light (...) on several episodes in that history, and particularly on the publication of Charles Darwin’s On the Origin of Species (1859), the construction of the modern evolutionary synthesis, the chronic discontent with it, and the latest expression of that discontent, called the extended evolutionary synthesis. Lastly, we also explain why this kind of analysis hasn’t been done before. (shrink)

The theory of concepts advanced in the dissertation aims at accounting for a) how a concept makes successful practice possible, and b) how a scientific concept can be subject to rational change in the course of history. Traditional accounts in the philosophy of science have usually studied concepts in terms only of their reference; their concern is to establish a stability of reference in order to address the incommensurability problem. My discussion, in contrast, suggests that each scientific concept consists of (...) three components of content: 1) reference, 2) inferential role, and 3) the epistemic goal pursued with the concept's use. I argue that in the course of history a concept can change in any of these three components, and that change in one component—including change of reference—can be accounted for as being rational relative to other components, in particular a concept's epistemic goal.This semantic framework is applied to two cases from the history of biology: the homology concept as used in 19th and 20th century biology, and the gene concept as used in different parts of the 20th century. The homology case study argues that the advent of Darwinian evolutionary theory, despite introducing a new definition of homology, did not bring about a new homology concept (distinct from the pre-Darwinian concept) in the 19th century. Nowadays, however, distinct homology concepts are used in systematics/evolutionary biology, in evolutionary developmental biology, and in molecular biology. The emergence of these different homology concepts is explained as occurring in a rational fashion. The gene case study argues that conceptual progress occurred with the transition from the classical to the molecular gene concept, despite a change in reference. In the last two decades, change occurred internal to the molecular gene concept, so that nowadays this concept's usage and reference varies from context to context. I argue that this situation emerged rationally and that the current variation in usage and reference is conducive to biological practice.The dissertation uses ideas and methodological tools from the philosophy of mind and language, the philosophy of science, the history of science, and the psychology of concepts. (shrink)

This paper surveys questions about the nature of the Modern Synthesis as a historical event : was it rather theoretical than institutional? When and where did it actually happen? Who was involved? It argues that all answers to these questions are interrelated, and that systematic sets of answers define specific perspectives on the Modern Synthesis that are all complementary.

Le texte suivant s'appuie assez largement sur des informations scientifiques de la biologie végétale. Ce choix de philosopher à partir de la technicité et de l'historicité des objets botaniques correspond à un parti pris. La proximité de l’humain à ses objets d’étude, sa tendance à anthropomorphiser, voire anthropocentrer, les observations ou les problèmes qui se présentent à lui, a fait l’objet de multiples réflexions philosophiques et épistémologiques. Kant, pour qui « tout intérêt est finalement pratique [...] même celui de la (...) raison spéculative n’est que conditionné et n’est complet que dans l’usage pratique » 1 , Bachelard, qui appelle à « substituer à la notion anthropomorphe de cause la notion scientifique de fonction » 2 , ou Canguilhem pour qui « l’anthropocentrisme est plus aisé à rejeter que l’anthropomorphisme [...] Peut-on être biologistes sans se sentir du côté des vivants ? » 3 . Ces réflexions ne sont-elles pas toujours centrées sur les modes de connaissance ou de pensée de l’humain, alors que les « objets d’étude » en question demeurent souvent dans un certain flou, voire une large indétermination ? La démarche suivie ici tente d’aller dans une autre direction. Elle interroge les effets de l’anthropocentrisation d’objets spécifiques à la biologie végétale, envisagée aussi bien dans sa profondeur historique que dans ses développements techniques récents. Nous tentons ici un pari : une analyse précise de nos connaissances botaniques, actuelles et passées, peut nourrir la réflexion philosophique sur notre rapport aux plantes et, à travers elles, sur nous-mêmes. (shrink)

Racial constructionists, anti-naturalists, and anti-realists have challenged users of the biological race concept to provide and defend, from the perspective of biology, biological philosophy, and ethics, a biologically informed concept of race. In this paper, an ontoepistemology of biology is developed. What it is, by this, to be "biological real" and "biologically meaningful" and to represent a "biological natural division" is explained. Early 18th century race concepts are discussed in detail and are shown to be both sensible and not greatly (...) dissimilar to modern concepts. A general biological race concept (GBRC) is developed. It is explained what the GBRC does and does not entail and how this concept unifies the plethora of specific ones, past and present. Other race concepts as developed in the philosophical literature are discussed in relation to the GBRC. The sense in which races are both real and natural is explained. Racial essentialism of the relational sort is shown to be coherent. Next, the GBRC is discussed in relation to anthropological discourse. Traditional human racial classifications are defended from common criticisms: historical incoherence, arbitrariness, cluster discordance, etc. Whether or not these traditional human races could qualify as taxa subspecies – or even species – is considered. It is argued that they could qualify as taxa subspecies by liberal readings of conventional standards. Further, it is pointed out that some species concepts potentially allow certain human populations to be designated as species. It is explained why, by conventional population genetic and statistical standards, genetic differences between major human racial groups are at least moderate. Behavioral genetic differences associated with human races are discussed in general and in specific. The matter of race differences in cognitive ability is briefly considered. Finally, the race concept is defended from various criticisms. First, logical and empirical critiques are dissected. These include: biological scientific, sociological, ontological, onto-epistemological, semantic, and teleological arguments. None are found to have any merit. Second, moral-based arguments are investigated in context to a general ethical frame and are counter-critiqued. Racial inequality, racial nepotism, and the “Racial Worldview" are discussed. What is dubbed the Anti-Racial Worldview is rejected on both empirical and moral grounds. Finally, an area of future investigation – the politics of the destruction of the race concept – is pointed to. (shrink)

Speciation—the origin of new species—has been one of the most active areas of research in evolutionary biology, both during, and since the Modern Synthesis. While the Modern Synthesis certainly shaped research on speciation in significant ways, providing a core framework, and set of categories and methods to work with, the history of work on speciation since the mid-twentieth century is a history of divergence and diversification. This piece traces this divergence, through both theoretical advances, and empirical insights into how different (...) lineages, with different genetics and ecological conditions, are shaped by very different modes of diversification. (shrink)

It is time to escape the constraints of the Systematics Wars narrative and pursue new questions that are better positioned to establish the relevance of the field in this time period to broader issues in the history of biology and history of science. To date, the underlying assumptions of the Systematics Wars narrative have led historians to prioritize theory over practice and the conflicts of a few leading theorists over the less-polarized interactions of systematists at large. We show how shifting (...) to a practice-oriented view of methodology, centered on the trajectory of mathematization in systematics, demonstrates problems with the common view that one camp straightforwardly “won” over the other. In particular, we critique David Hull’s historical account in Science as a Process by demonstrating exactly the sort of intermediate level of positive sharing between phenetic and cladistic theories that undermines their mutually exclusive individuality as conceptual systems over time. It is misleading, or at least inadequate, to treat them simply as holistically opposed theories that can only interact by competition to the death. Looking to the future, we suggest that the concept of workflow provides an important new perspective on the history of mathematization and computerization in biology after World War II. (shrink)

The species problem is often described as the abundance of conflicting definitions of _species_, such as the biological species concept and phylogenetic species concepts. But biologists understand the notion of species in a non-definitional as well as a definitional way. In this article I argue that when they understand _species_ without a definition in their mind, their understanding is often mediated by the notion of _good species_, or prototypical species, as the idea of ``prototype'' is explicated in cognitive psychology. This (...) distinction helps us make sense of several puzzling phenomena regarding biologists' dealing with species, such as the fact that in everyday research biologists often behave as if the species problem is solved, while they should be fully aware that it is not. I also briefly discuss implications of this finding, including that some extant attempts to answer what the nature of species is have an inadequate assumption about how the notion of species is represented in biologists' minds. (shrink)

This paper maps the landscape for a range of views concerning the metaphysics of natural kinds. I consider a range of increasingly ontologically committed views concerning natural kinds and the possible arguments for them. I then ask how these relate to natural kind essentialism, arguing that essentialism requires commitment to kinds as entities. I conclude by examining the homeostatic property cluster view of kinds in the light of the general understanding of kinds developed.

Many attempts have been made at supporting either one of the allegedly complementary divergence models Phyletic Gradualism and Punctuated Equilibria by patterns found in specific fossil sequences. However, assessing each model's connection with reality via such “individual case histories” appears not to constitute a relevant approach. Instead, in order to correctly establish the possible merits of both concepts, the claims of each have to be verified against general evolutionary theory. This is being pointed out herein by analyzing cladogenesis at the (...) specific level as an example. [Phyletic Gradualism; Punctuated Equilibria; evolutionary theory; divergence models; case histories; additive speciation.]. (shrink)

Speciation is an aspect of evolutionary biology that has received little philosophical attention apart from articles mainly by biologists such as Mayr (1988). The role of speciation as a terminus a quo for the individuality of species or in the context of punctuated equilibrium theory has been discussed, but not the nature of speciation events themselves. It is the task of this paper to attempt to bring speciation events into some kind of general scheme, based primarily upon the work of (...) Sergey Gavrilets on adaptive landscapes, using migration rate, or gene flow, as the primary scale, and concluding that adaptive and drift explanations are complementary rather than competing. I propose a distinction between intrinsic and extrinsic selection, and the notion of reproductive reach and argue that speciation modes should be discriminated in terms of gene flow, the nature of selection maintaining reproductive reach, and whether the predominant cause is selective or stochastic. I also suggest that the notion of an adaptive “quasispecies” for asexual species is the primitive notion of species, and that members of reproductively coherent sexual species are additionally coadapted to their mating partners. (shrink)

In philosophy of science, the literature on abduction and the literature on styles of thinking have existed almost totally in parallel. Here, for the first time, we bring them together and explore their mutual relevance. What is the consequence of the existence of several styles of scientific thinking for abduction? Can abduction, as a general creative mode of inference, have distinct characteristic forms within each style? To investigate this, firstly, we present the concept of abduction; secondly we analyze what is (...) understood by styles of thinking; thirdly, we give some comments on abduction and styles of thinking by analyzing examples of scientific discovery or innovation within each style. We develop a case-based comparative investigation of creative aspects of abductive reasoning with examples drawn from different styles of scientific thinking and doing as understood by the Crombie/hacking tradition. We argue that abduction, as a general mode of reasoning, can have a variety of specific expressions enabled and constrained by the styles of scientific thinking. Finally, we draw some conclusions on the relationship between abduction and styles of thinking suggesting that scientific discovery is a dynamical goal-directed activity within the scientific community that benefits from distinct styles of thinking and doing research. (shrink)

Welch :263–279, 2017) has recently proposed two possible explanations for why the field of evolutionary biology is plagued by a steady stream of claims that it needs urgent reform. It is either seriously deficient and incapable of incorporating ideas that are new, relevant and plausible or it is not seriously deficient at all but is prone to attracting discontent and to the championing of ideas that are not very relevant, plausible and/or not really new. He argues for the second explanation. (...) This paper presents a twofold critique of his analysis: firstly, the main calls for reform do not concern the field of evolutionary biology in general but rather, or more specifically, the modern evolutionary synthesis. Secondly, and most importantly, these calls are not only inspired by the factors, enumerated by Welch, but are also, and even primarily, motivated by four problematic characteristics of the modern synthesis. This point is illustrated through a short analysis of the latest reform challenge to the modern synthesis, the so-called extended evolutionary synthesis. We conclude with the suggestion that the modern synthesis should be amended, rather than replaced. (shrink)

The traditional practice of establishing morphological types and investigating morphological organization has found new support from evolutionary developmental biology (evo-devo), especially with respect to the notion of body plans. Despite recurring claims that typology is at odds with evolutionary thinking, evo-devo offers mechanistic explanations of the evolutionary origin, transformation, and evolvability of morphological organization. In parallel, philosophers have developed non-essentialist conceptions of natural kinds that permit kinds to exhibit variation and undergo change. This not only facilitates a construal of species (...) and higher taxa as natural kinds, but also broadens our perspective on the diversity of kinds found in biology. There are many different natural kinds relevant to the investigative and explanatory aims of evo-devo, including homologues and developmental modules. (shrink)

Can we be realists about a general category but pluralists about concepts relating to that category? I argue that paleobiological methods of delineating species are not affected by differing species concepts, and that this underwrites an argument that species concept pluralists should be species category realists. First, the criteria by which paleobiologists delineate species are ‘indifferent’ to the species category. That is, their method for identifying species applies equally to any species concept. To identify a new species, paleobiologists show that (...) interspecies processes, such as phenotypic plasticity, sexual dimorphism, or ontogenetic diversity, are a worse explanation of the variance between specimens than intraspecies processes. As opposed to operating under a single or plurality of species concepts, then, paleobiologists use abductive inferences, which would be required regardless of any particular species concept. Second, paleobiologists are frequently interested in large-scale, long-term morphological patterns in the fossil record, and resolving the fine-grained differences which result from different species concepts is irrelevant at those scales. I argue that this claim about paleobiological practice supports what I call ‘indifference realism’ about the species category. The indifference realist argues that when legitimate investigation is indifferent to a plurality of concepts, we should be realists about the category those concepts pertain to. (shrink)

Building upon a non-standard understanding of evolutionary process focusing on variation and persistence, I will argue that communities and ecosystems can evolve by natural selection as emergent individuals. Evolutionary biology has relied ever increasingly on the modeling of population dynamics. Most have taken for granted that we all agree on what is a population. Recent work has reexamined this perceived consensus. I will argue that there are good reasons to restrict the term “population” to collections of monophyletically related replicators and (...) interactors, which explains why many existing models in population biology exclude by definition many genuine evolving biological individuals such as communities and ecosystems. By studying a case of community evolution (a symbiotic termite–fungus community), we will see that it is variation that is important to evolutionary processes, not populations. Variation within a population is only one of many types of variation that can lead to evolution by natural selection. The upshot of focusing on variation is that cases of community and ecosystem adaptive change become tractable in evolutionary terms. I will show that complex emergent individuals such as communities and ecosystems cannot be fully accommodated by conventional population/reproduction models but can be accommodated by variation/persistence models. (shrink)

Studying cartoons about the economic crisis and focusing on a pair of scissors as a symbol, I prove how they first turn into unambiguous metaphor for the economic crisis and then experience an evolution in order to adapt to new communication contexts. Along these processes, they undergo more complex changes such as coadaptation and speciation. This has allowed for the scissors meme as a symbol of economic cutbacks to permeate society, and for its metaphorical use to occupy many disparate communication (...) scenarios, unlike other symbolic elements that were also used, but turned out to be less cognitively efficient and therefore offered fewer evolutionary possibilities. (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.

Biologists and philosophers have offered differing concepts of biological race. That is, they have offered different candidates for what a biological correlate of race might be; for example, races might be subspecies, clades, lineages, ecotypes, or genetic clusters. One thing that is striking about each of these proposals is that they all depend on a concept of population. Indeed, some authors have explicitly characterized races in terms of populations. However, including the concept of population into concepts of race raises three (...) puzzles, all having to do with time. In this paper, I extend the causal interactionist population concept (CIPC) by introducing some simple assumptions about how to understand populations through time. These assumptions help to shed light on the three puzzles, and in the process show that if we want to understand races in terms of populations, we will need to revise our concept(s) of race. (shrink)

The allegedly alternative theories of Phyletic Gradualism and Punctuated Equilibria are examined as regards the nature of their differences. The explanatory value of both models is determined by establishing their actual connection with reality. It is concluded that they are to be considered complementary rather than mutually exclusive at all levels of infraspecific, specific, and supraspecific evolution. So, in order to be described comprehensively, the pathways of evolution require at least two distinct models, each based on a discrete range of (...) real phenomena. [Phyletic Gradualism; Punctuated Equilibria; evolutionary theories; divergence models; additive speciation; microevolution; macroevolution; anagenesis.]. (shrink)

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

A common worry about the genetic engineering of human beings is that it will reduce human genetic diversity, creating a biological monoculture that could not only increase our susceptibility to disease but also hasten the extinction of our species. Thus far, however, the evolutionary implications of human genetic modification remain largely unexplored. In this paper, I consider whether the widespread use of genetic engineering technology is likely to narrow the present range of genetic variation, and if so, whether this would (...) in fact lead to the evolutionary harms that some authors envision. By examining the nature of biological variation and its relation to population immunity and evolvability, I show that not only will genetic engineering have a negligible impact on human genetic diversity, but also that it will be more likely to ensure rather than undermine the health and longevity of the human species. (shrink)

There is a growing appreciation of the extent of transcriptome variation across individual cells of the same cell type. While expression variation may be a byproduct of, for example, dynamic or homeostatic processes, here we consider whether single‐cell molecular variation per se might be crucial for population‐level function. Under this hypothesis, molecular variation indicates a diversity of hidden functional capacities within an ensemble of “identical” cells, and this functional diversity facilitates collective behavior that would be inaccessible to a homogenous population. (...) In reviewing this topic, we explore possible functions that might be carried by a heterogeneous ensemble of cells; however, this question has proven difficult to test, both because methods to manipulate molecular variation are limited and because it is complicated to define, and measure, population‐level function. We consider several possible methods to further pursue the hypothesis that “variation is function” through the use of comparative analysis and novel experimental techniques. (shrink)

Species pluralism allows for multiple species concepts. Given the overwhelming number of such concepts, this seems like an obvious interpretation of how `species' is used in contemporary biology. But why has it taken so long for this approach to be considered? I argue that part of the reason pluralism was overlooked due to the widespread use of a particular rhetorical strategy developed by Ernst Mayr. This strategy provided a framework for debates about the correct conception of species. That is, the (...) strategy offered a means of comparing modern concepts with a monistic-essentialist understanding of species. I ask what would happen if we replaced this concept with Aristotle's own pluralist-essentialist understanding of species. As recent scholarship shows, Aristotle's philosophy of biology allows for an approach to classification that is in practice highly pluralistic. From this new framework we can understand what sort of assumptions are at stake between modern forms of species pluralism. My analysis shows that the essentialist story told by Mayr and others left us asking the wrong questions about how to conceive of species in an evolutionary world. Having a deeper understanding of Aristotle's approach to the classification of animals allows us to shift focus from the so-called species problem in order to raise four issues that are relevant to current debates. These are questions about: the explanatory power of taxonomic ranks, the importance of the species category problem, whether species are constituted by intrinsic or extrinsic properties, and how to interpret the ``cross-cutting'' metaphor endemic to the pluralist literature. In order to get to these questions I will first explain what sort of claim species pluralism is at the most general level, and a gloss on the standard interpretation of the historical shift from species monism to species pluralism. (shrink)

Many have argued that unified theories ought to be pursued wherever possible. We deny this on the basis of social-epistemological and decision-theoretic considerations. Consequently, those seeking a more ubiquitous role for unification must either attend to the scientific community’s social structure in greater detail than has been the case, and/or radically revise their conception of unification.