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

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)

After an initial discussion of the character of interdisciplinary linkages between complex disciplines, I consider an area with confluences of many diverse disciplines—the study of cultural evolution. This must embrace not only the traditional biological sciences, but also the multiple often warring disciplines of the human sciences. This interdisciplinary articulation is in its early stages compared, e.g., to that of evolutionary biology or evolutionary developmental biology, and I try to lay out major axes along which its articulation should plausibly occur, (...) given the relevant causal processes acting at different levels. One cannot have an adequate account of cultural evolution without recognizing a central role for cognitive and social development and the social and cultural organizations and institutions and artifactual tools and infrastructure that support and structure these developmental processes. These induce a population structure that mediates the transmission, expression, and elaboration of culture, and in particular the different ways in which they scaffold learning and the development and articulation of complex skills. I consider how these elements should articulate the disciplines that tend to focus separately on them. Intentions and the market are not explicitly included in this account, and I consider ways in which these perspectives might enter. (shrink)

Richard Levins’ distinction between aggregate, composed and evolved systems acquires new significance as we recognize the importance of mechanistic explanation. Criteria for aggregativity provide limiting cases for absence of organization, so through their failure, can provide rich detectors for organizational properties. I explore the use of failures of aggregativity for the analysis of mechanistic systems in diverse contexts. Aggregativity appears theoretically desireable, but we are easily fooled. It may be exaggerated through approximation, conditions of derivation, and extrapolating from some conditions (...) of decomposition illegtimately to others. Evolved systems particularly may require analyses under alternative complementary decompositions. Exploring these conditions helps us to better understand the strengths and limits of reductionistic methods. (shrink)

The vision of natural kinds that is most common in the modern philosophy of biology, particularly with respect to the question whether species and other taxa are natural kinds, is based on a revision of the notion by Mill in A System of Logic. However, there was another conception that Whewell had previously captured well, which taxonomists have always employed, of kinds as being types that need not have necessary and sufficient characters and properties, or essences. These competing views employ (...) different approaches to scientific methodologies: Mill’s class-kinds are not formed by induction but by deduction, while Whewell’s type-kinds are inductive. More recently, phylogenetic kinds (clades, or monophyletic-kinds) are inductively projectible, and escape Mill’s strictures. Mill’s version represents a shift in the notions of kinds from the biological to the physical sciences. (shrink)

The Darwinian concept of natural selection was conceived within a set of Newtonian background assumptions about systems dynamics. Mendelian genetics at first did not sit well with the gradualist assumptions of the Darwinian theory. Eventually, however, Mendelism and Darwinism were fused by reformulating natural selection in statistical terms. This reflected a shift to a more probabilistic set of background assumptions based upon Boltzmannian systems dynamics. Recent developments in molecular genetics and paleontology have put pressure on Darwinism once again. Current work (...) on self-organizing systems may provide a stimulus not only for increased problem solving within the Darwinian tradition, especially with respect to origins of life, developmental genetics, phylogenetic pattern, and energy-flow ecology, but for deeper understanding of the very phenomenon of natural selection itself. Since self-organizational phenomena depend deeply on stochastic processes, self-organizational systems dynamics advance the probability revolution. In our view, natural selection is an emergent phenomenon of physical and chemical selection. These developments suggest that natural selection may be grounded in physical law more deeply than is allowed by advocates of the autonomy of biology, while still making it possible to deny, with autonomists, that evolutionary explanations can be modeled in terms of a deductive relationship between laws and cases. We explore the relationship between, chance, self-organization, and selection as sources of order in biological systems in order to make these points. (shrink)

The genomes of vertebrates, flies, and nematodes contain highly conserved noncoding elements (CNEs). CNEs cluster around genes that regulate development, and where tested, they can act as transcriptional enhancers. Within an animal group CNEs are the most conserved sequences but between groups they are normally diverged beyond recognition. Alternative CNEs are, however, associated with an overlapping set of genes that control development in all animals. Here, we discuss the evidence that CNEs are part of the core gene regulatory networks (GRNs) (...) that specify alternative animal body plans. The major animal groups arose >550 million years ago. We propose that the cis‐regulatory inputs identified by CNEs arose during the “re‐wiring” of regulatory interactions that occurred during early animal evolution. Consequently, different animal groups, with different core GRNs, contain alternative sets of CNEs. Due to the subsequent stability of animal body plans, these core regulatory sequences have been evolving in parallel under strong purifying selection in different animal groups. (shrink)

The intersection of ELSI and science forms a complicated nexus yet their integration is an important goal both for society and for the successful advancement of science. In what follows, I present a heuristic that makes boundary identification and crossing an important tool in the discovery of potential areas of ethical, legal, and social concern in science. A dynamic and iterative application of the heuristic can lead towards a fuller integration and appreciation of the concerns of ELSI and of science (...) from both sides of the divide. (shrink)

Around 540 million years ago there was a sudden, dramatic adaptive radiation known as the Cambrian Explosion. This event marked the origin of almost all of the phyla (major lineages characterized by fundamental body plans) of animals that would ever live on earth, as well the appearance of many notable features such as rigid skeletons and other hard parts, complex jointed appendages, eyes, and brains. This radical evolutionary event has been a major puzzle for evolutionary biologists since Darwin, and while (...) our understanding of it has recently improved with new fossil finds, richer molecular phylogenies, and better grasp of ecological, evolutionary, and developmental processes generally, unanswered questions remain. In this paper I argue that a basic cognitive toolkit for embodied, object-oriented, spatial cognition (what I call Basic Cognitive Embodiment) is a practical necessity for control of a large, mobile, complexly articulated body in space. This hypothesis allows us to relate the complexification of animal bodies to the complexification of perception, cognition and behavior in a way that can help to fill in gaps in our emerging picture of the Cambrian Explosion, as well as shed light on the deep evolutionary origins of the mind. (shrink)

The cross-disciplinary framework of Material Engagement Theory (MET) has emerged as a novel research program that flexibly spans archeology, anthropology, philosophy, and cognitive science. True to its slogan to ‘take material culture seriously’, “MET wants to change our understanding of what minds are and what they are made of by changing what we know about what things are and what they do for the mind” (Malafouris 2013, 141). By tracing out more clearly the conceptual contours of ‘material engagement,’ and firming (...) up its ontological commitments, the main goal of this article is to help refine Malafouris’ fertile approach. In particular, we argue for a rapprochement between MET and the tradition of Cultural-Historical Activity Theory, based on the ‘Vygotskian’ hypothesis of scaffolded and/or distributed cognition. (shrink)

In this paper we argue that ecological evolutionary developmental biology accounts of cognitive modernity are compatible with cultural evolution theories of language built upon iterated learning models. Cultural evolution models show that the emergence of near universal properties of language do not require the preexistence of strong specific constraints. Instead, the development of general abilities, unrelated to informational specificity, like the copying of complex signals and sharing of communicative intentions is required for cultural evolution to yield specific properties, such as (...) language structure. We argue that eco-evo-devo provides the appropriate conceptual background to ground an account for the many interconnected genetic, environmental and developmental factors that facilitated the emergence of an organic system able to develop language through the iterated transmission of information. We use the concept of niche construction to connect evolutionary developmental accounts for sensory guided motor capacities and cultural evolution guided by iterated learning models. This integrated theoretical model aims to build bridges between biological and cultural approaches. (shrink)

One of the classic debates in cognitive science is between nativism and empiricism about the development of psychological capacities. In principle, the debate is empirical. However, in practice nativist hypotheses have also been challenged for relying on an ill-defined, or even unscientific, notion of innateness as that which is “not learned”. Here this minimal conception of innateness is defended on four fronts. First, it is argued that the minimal conception is crucial to understanding the nativism-empiricism debate, when properly construed; Second, (...) various objections to the minimal conception—that it risks overgeneralization, lacks an account of learning, frustrates genuine explanations of psychological development, and fails to unify different notions of innateness across the sciences—are rebutted. Third, it is argued that the minimal conception avoids the shortcomings of primitivism, the prominent view that innate capacities are those that are not acquired via a psychological process in development. And fourth, the minimal conception undermines some attempts to identify innateness with a natural kind. So in short, we have little reason to reject, and good reason to accept, the minimal conception of innateness in cognitive science. (shrink)

The theory and practice of contemporary comparative biology and phylogeny reconstruction (systematics) emphasizes algorithmic aspects but neglects a concern for the evidence. The character data used in systematics to formulate hypotheses of relationships in many ways constitute a black box, subject to uncritical assessment and social influence. Concerned that such a state of affairs leaves systematics and the phylogenetic theories it generates severely underdetermined, we investigate the nature of the criteria of homology and their application to character conceptualization in the (...) context of transformationist and generative paradigms. Noting the potential for indeterminacy in character conceptualization, we conclude that character congruence (the coherence of character statements) relative to a hierarchy is a necessary, but not a sufficient, condition for phylogeny reconstruction. Specifically, it is insufficient due to the lack of causal grounding of character hypotheses. Conceptualizing characters as homeostatic property cluster natural kinds is in accordance with the empirical practice of systematists. It also accounts for the lack of sharpness in character conceptualization, yet requires character identification and re-identification to be tied to causal processes. (shrink)

A long-standing debate has dominated systematic biology and the ontological commitments made by its theories. The debate has contrasted individuals and the part – whole relationship with classes and the membership relation. This essay proposes to conceptualize the hierarchy of higher taxa is terms of a hierarchy of homeostatic property cluster natural kinds (biological species remain largely excluded from the present discussion). The reference of natural kind terms that apply to supraspecific taxa is initially fixed descriptively; the extension of those (...) natural kind terms is subsequently established by empirical investigation. In that sense, classification precedes generalization, and description provides guidance to empirical investigation. The reconstruction of a hierarchy of (homeostatic property cluster) natural kinds is discussed in the light of cladistic methods of phylogeny reconstruction. (shrink)

In recent decades it has become increasingly clear that a substantial amount of cognitive work goes on independent of consciousness. The research has been carried out largely under two rubrics, implicit learning and implicit memory. The former has been concerned primarily with the acquisition of knowledge independent of awareness and the latter with the manner in which memories not readily available to conscious recall or recognition play a role in behavior; collectively these operations comprise the essential functions of the cognitive (...) unconscious. This paper reviews the recent history of work on these issues, identifies some of the problems confronting researchers, and introduces a theoretical framework based on principles of evolutionary biology within which to view them. The argument is that the cognitive unconscious, despite its apparent sophistication, is of considerable evolutionary antiquity and antedates conscious cognitive systems by a considerable amount of time. Various entailments of this evolutionary perspective are explored including such issues as phylogeny and ontogeny of implicit processes, the robustness of the implicit functions as displayed by the capacity to resist disruptions from psychological and neurological disorders, the relationship between implicit cognition and intelligence, and individual differences in implicit cognitive abilities. (shrink)

This paper is an attempt to put the work of the past several decades on the problems of implicit learning and unconscious cognition into an evolutionary context. Implicit learning is an inductive process whereby knowledge of a complex environment is acquired and used largely independently of awareness of either the process of acquisition or the nature of that which has been learned. Characterized this way, implicit learning theory can be viewed as an attempt to come to grips with the classic (...) epistemological issues of knowledge acquisition, representation and use. The argument is made that the process, despite its seeming cognitive sophistication, is of considerable evolutionary antiquity and that it antedates awareness and the capacity for conscious control of mentation. Various classic heuristics from evolutionary biology are used to substantiate this claim and several specific entailments of this line of argument are outlined. (shrink)

The theory of Punctuated Equilibria challenges the neo‐Darwinian tenet that evolution is a uniform process. Recently, an article by Hunt1 has found that directional change during the evolution of a lineage is relatively small (occurring only in 5% of 250 analyzed traits). Of those traits that were shown to follow a trend, size was more likely to show gradual changes, whereas shape changes were more random. Here, we provide a short view of the nature of evolutionary trends, showing that directional (...) change within lineages and among clades provides valuable evolutionary information about the processes involved in their generation. BioEssays 30:521–525, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

I object to eliminativism about innateness and André Ariew’s identification of innateness with canalization, and I propose a new treatment of innateness. I first argue that the concept of innateness is serving a valuable function in a diverse set of research contexts, and in these contexts, claims about innateness are best understood as claims about the insensitivity of the appearance of a trait to certain variations in the environment. I then argue that innateness claims, like claims about canalization, should be (...) explicitly relativized to the specific range of environmental variations of interest to the scientist. My account characterizes an important way in which scientists are employing the concept and offers a way for scientists to carry on using the concept in their research while minimizing confusion and miscommunication. There is a fruitful research program, I claim, in which scientists employ the concept of innateness to help distinguish environmental factors of interest that have a causal influence on the appearance of a trait from those that do not. (shrink)

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

We suggest that human culture exhibits key Darwinian evolutionary properties, and argue that the structure of a science of cultural evolution should share fundamental features with the structure of the science of biological evolution. This latter claim is tested by outlining the methods and approaches employed by the principal subdisciplines of evolutionary biology and assessing whether there is an existing or potential corresponding approach to the study of cultural evolution. Existing approaches within anthropology and archaeology demonstrate a good match with (...) the macroevolutionary methods of systematics, paleobiology, and biogeography, whereas mathematical models derived from population genetics have been successfully developed to study cultural microevolution. Much potential exists for experimental simulations and field studies of cultural microevolution, where there are opportunities to borrow further methods and hypotheses from biology. Potential also exists for the cultural equivalent of molecular genetics in “social cognitive neuroscience,” although many fundamental issues have yet to be resolved. It is argued that studying culture within a unifying evolutionary framework has the potential to integrate a number of separate disciplines within the social sciences. (shrink)

I present and apply some powerful tools for studying human evolution and the impact of cultural resources on it. The tools in question are a theory of niche construction and a theory about the evolutionary significance of extragenetic (and, in particular, of psychological and social) inheritance. These tools are used to show how culturally transmitted resources can be recruited by development and become generatively entrenched. The case study is constituted by those culturally transmitted items that social psychologists call ‘expectancies’. Expectancy (...) effects are mindshaping effects of our mindreading dispositions. I show how expectancies may have been recruited by important human developmental processes (like those involved in language acquisition and those responsible for gender differences) and how they may have become entrenched. If the hypothesis is correct, the relation between mindreading and human evolution is more intricate than usually thought. (shrink)

The concept of innateness is a part of folk wisdom but is also used by biologists and cognitive scientists. This concept has a legitimate role to play in science only if the colloquial usage relates to a coherent body of evidence. We examine many different candidates for the post of scientific successor of the folk concept of innateness. We argue that none of these candidates is entirely satisfactory. Some of the candidates are more interesting and useful than others, but the (...) interesting candidates are not equivalent to each other and the empirical and evidential relations between them are far from clear. Researchers have treated the various scientific notions that capture some aspect of the folk concept of innateness as equivalent to each other or at least as tracking properties that are strongly correlated with each other. But whether these correlations exist is an empirical issue. This empirical issue has not been thoroughly investigated because in the attempt to create a bridge between the folk view and their theories, researchers have often assumed that the properties must somehow cluster. Rather than making further attempts to import the folk concept of innateness into the sciences, efforts should now be made to focus on the empirical questions raised by the debates and pave the way to a better way of studying the development of living organisms. Such empirical questions must be answered before it can be decided whether a good scientific successor – in the form of a concept that refers to a collection of biologically significant properties that tend to co-occur – can be identified or whether the concept of innateness deserves no place in science. (shrink)

This article illustrates in which sense genetic determinism is still part of the contemporary interactionist consensus in medicine. Three dimensions of this consensus are discussed: kinds of causes, a continuum of traits ranging from monogenetic diseases to car accidents, and different kinds of determination due to different norms of reaction. On this basis, this article explicates in which sense the interactionist consensus presupposes the innate?acquired distinction. After a descriptive Part 1, Part 2 reviews why the innate?acquired distinction is under attack (...) in contemporary philosophy of biology. Three arguments are then presented to provide a limited and pragmatic defense of the distinction: an epistemic, a conceptual, and a historical argument. If interpreted in a certain manner, and if the pragmatic goals of prevention and treatment are taken into account, then the innate?acquired distinction can be a useful epistemic tool. It can help, first, to understand that genetic determination does not mean fatalism, and, second, to maintain a system of checks and balances in the continuing nature?nurture debates. (shrink)

This article illustrates in which sense genetic determinism is still part of the contemporary interactionist consensus in medicine. Three dimensions of this consensus are discussed: kinds of causes, a continuum of traits ranging from monogenetic diseases to car accidents, and different kinds of determination due to different norms of reaction. On this basis, this article explicates in which sense the interactionist consensus presupposes the innate?acquired distinction. After a descriptive Part 1, Part 2 reviews why the innate?acquired distinction is under attack (...) in contemporary philosophy of biology. Three arguments are then presented to provide a limited and pragmatic defense of the distinction: an epistemic, a conceptual, and a historical argument. If interpreted in a certain manner, and if the pragmatic goals of prevention and treatment (ideally specifying what medicine and health care is all about) are taken into account, then the innate?acquired distinction can be a useful epistemic tool. It can help, first, to understand that genetic determination does not mean fatalism, and, second, to maintain a system of checks and balances in the continuing nature?nurture debates. (shrink)

Despite growing interest in evolutionary economics since the 1980s, a unified theoretical approach has so far been lacking. Methodological and ontological discussions within evolutionary economics have attempted to understand and help rectify this failure, but have revealed in turn further differences of perspective. One aim of this article is to show how different approaches relate to different levels of abstraction. A second purpose is to show that generalized Darwinism is some way from the most abstract level, and illustrates how it (...) may be used to move towards more specific theoretical applications. Nevertheless, there is a long way to go before these become more evident. (shrink)