This dissertation concerns the active role of the organism in evolutionary theory. In particular, it concerns how our conception of the relationship between organism and environment, and the nature of natural selection, influences the causal and explanatory role of organismic activity and behavior in evolutionary explanations. The overarching aim is to argue that the behaviors and activities of organisms can serve both as the explananda (that which is explained) and the explanantia (that which explains) in evolutionary explanations. I attempt to (...) achieve this aim by offering three central arguments. First, that the organism-environment relation is the ontologically basic unit of biology. A common way of conceiving the relationship between organism and environment is as a duality—as two causally independent systems that overlap through interaction. I think this is a mistake. There cannot be organisms without environments and vice versa. They are codependent and codetermined. Second, that natural selection is an ecological process. By this I mean that natural selection acts primarily on organism-environment interactions. It is only in virtue of organisms interacting with their environments that there can be fitness differences amongst individual organisms in a population. The ecological approach to natural selection also entails that the nature of the system(s) of inheritance involved in the reoccurrence of favorable organism-environment interactions is, in principle, immaterial to the process of selection. It only matters for selection that organism-environment interactions actually do reoccur in subsequent generations. Third, that niche construction theory—the most well-developed theoretical and conceptual framework for studying how the activities of organisms influences evolutionary dynamics—can be seen as fully a compatible and integrated part of evolutionary theory. Together, these three arguments constitute an overarching argument. Namely that we both can, and should, take organismic activity and behavior to be crucial explanatory elements in evolutionary theory. Throughout the dissertation I also show how these three arguments have consequences for other debates in the philosophy of evolutionary theory, such as the nature of evolutionary processes, the structure of selection-based explanations, the validity and utility of the proximate-ultimate distinction, and the nature of teleology in evolutionary systems. (shrink)

This book is divided in two parts, the first of which shows how, beyond paleontology and systematics, macroevolutionary theories apply key insights from ecology and biogeography, developmental biology, biophysics, molecular phylogenetics, and even the sociocultural sciences to explain evolution in deep time. In the second part, the phenomenon of macroevolution is examined with the help of real life-history case studies on the evolution of eukaryotic sex, the formation of anatomical form and body-plans, extinction and speciation events of marine invertebrates, hominin (...) evolution and species conservation ethics. The book brings together leading experts, who explain pivotal concepts such as Punctuated Equilibria, Stasis, Developmental Constraints, Adaptive Radiations, Habitat Tracking, Turnovers, (Mass) Extinctions, Species Sorting, Major Transitions, Trends, and Hierarchies – key premises that allow macroevolutionary epistemic frameworks to transcend microevolutionary theories that focus on genetic variation, selection, migration and fitness. Along the way, the contributing authors review ongoing debates and current scientific challenges; detail new and fascinating scientific tools and techniques that allow us to cross the classic borders between disciplines; demonstrate how their theories make it possible to extend the Modern Synthesis; present guidelines on how the macroevolutionary field could be further developed; and provide a rich view of just how it was that life evolved across time and space. In short, this book is a must-read for active scholars and, because the technical aspects are fully explained, it is also accessible for non-specialists. Understanding evolution requires a solid grasp of above-population phenomena. Species are real biological individuals, and abiotic factors impact the future course of evolution. Beyond observation, when the explanation of macroevolution is the goal, we need both evidence and theory that enable us to explain and interpret how life evolves at the grand scale. (shrink)

With the advent of evolutionary developmental research, or EvoDevo, there is hope of discovering the roles that the genetic bases of development play in morphological evolution. Studies in EvoDevo span several levels of organismal organization. Low-level studies identify the ultimate genetic changes responsible for morphological variation and diversity. High-level studies of development focus on how genetic differences affect the dynamics of gene networks and epigenetic interactions to modify morphology. Whereas an increasing number of studies link independent acquisition of homoplastic or (...) convergent morphologies to similar changes in the genomes, homoplasies are not always found to have identical low-level genetic underpinnings. This suggests that a combination of low- and high-level approaches may be useful in understanding the relationship between genetic and morphological variation. Therefore, as an empirical and conceptual framework, we propose the causality horizon to signify the lowest level that allows linking homoplastic morphologies to similar changes in the development. A change in a system below the causality horizon cannot be generalized. In more concrete terms, homoplastic morphologies cannot be reduced to the same change in gene regulation when that change occurs below the causality horizon; rather, a higher-level mechanism should be identified. (shrink)

Change is the fundamental idea of evolution. Explaining the extraordinary biological change we see written in the history of genomes and fossil beds is the primary occupation of the evolutionary biologist. Yet it is a surprising fact that for the majority of evolutionary research, we have rarely studied how evolution typically unfolds in nature, in changing ecological environments, over space and time. While ecology played a major role in the eventual acceptance of the population genetic viewpoint of evolution in the (...) synthetic era (circa 1918-1956), it held a lesser role in the development of evolutionary theory until the 1980s, when we began to systematically study the evolutionary dynamics of natural populations in space and time. As a result, early evolutionary theory was initially constructed in an abstract vacuum that was unrepresentative of evolution in nature. The subtle synthesis between ecology with evolutionary biology (eco-evo synthesis) over the past 40 years has progressed our knowledge of natural selection dynamics as they are found in nature, thus revealing how natural selection varies in strength, direction, form, and, more surprisingly, level of biological organization. Natural selection can no longer be reduced to lower levels of biological organization (i.e., individuals, selfish genes) over shorter timescales but should be expanded to include adaptation at higher levels and over longer timescales. Long-term and/or emergent evolutionary phenomena, such as multilevel selection or evolvability, have thus become tenable concepts within an evolutionary biology that embraces ecology and spatiotemporal change. Evolutionary biology is currently suspended at an intermediate stage of scientific progress that calls for the organization of all the recent knowledge revealed by the eco-evo synthesis into a coherent and unified theoretical framework. This is where philosophers of biology can be of particular use, acting as a bridge between the subdisciplines of biology and inventing new theoretical strategies to organize and accommodate the recent knowledge. Philosophers have recommended transitioning away from outdated philosophies that were originally derived from physics within the philosophical zeitgeist of logical positivism (i.e., monism, reductionism, and monocausation) and toward a distinct philosophy of biology that can capture the natural complexity of multifaceted biological systems within diverse ecosystems—one that embraces the emerging philosophies of pluralism, emergence, and multicausality. Therefore, I see recent advances in ecology, evolutionary biology, and the philosophy of biology as laying the groundwork for another major biological synthesis, what I refer to as the Second Synthesis because, in many respects, it is analogous to the aims and outcomes of the first major biological synthesis (but is notably distinct from the inorganic and contrived progressive movement known as the extended evolutionary synthesis). With the general development of a distinctive philosophy of science, biology has rightfully emerged as an autonomous science. Thus, while the first synthesis legitimized biology, the Second Synthesis autonomized biology and afforded biology its own philosophy, allowing biology to finally realize its full scientific potential. (shrink)

Current philosophical literature is saturated with the debate on biomedical enhancement, where bio-liberals and conservatives alike make compelling arguments for and against the enterprise. However, this literature is yet to consider the impact such enhancement would have on the individual’s actual lived experience. This article seeks to remedy that by situating the bioethics debate within the phenomenology of Maurice Merleau-Ponty, specifically theorising how biomedical enhancement of the physical kind would impact Merleau-Ponty’s notion of the body-subject. The central issue arises when (...) the reciprocal relationship between the physical body and phenomenal world (termed “body/world dynamic”) is shown to be off-balance because of the rapid rate at which human beings continue to “enhance” their environment. In this, we see that the development of the world has outweighed that of the body to the extent that we, as body-subjects, have become maladapted to the place we call home. This article will suggest that we can attempt to resolve this by restoring the balance of the body/world dynamic with “restrictive” enhancement, thereby providing an ethical justification for the pursuit of the enterprise. (shrink)

Niche construction theory concerns how organisms can change selection pressures by altering the feature–factor relationship between themselves and their environment. These alterations are standardly understood to be brought about through two kinds of organism–environment interaction: perturbative and relocational niche construction. We argue that a reconceptualization is needed on the grounds that if a niche is understood as the feature–factor relationship, then there are three fundamental ways in which organisms can engage in niche construction: constitutive, relational, and external niche construction. We (...) further motivate our reconceptualization by showing some examples of organismic activities that fall outside of the current categorization of niche construction, but nonetheless should be included. We end by discussing two objections to niche construction and show how our reconceptualization helps to undercut these objections. 1Introduction2Niche Construction Theory 2.1The standard account of niche construction2.2Two problems with the standard account of niche construction3Three Kinds of Niche Construction 3.1Constitutive niche construction3.2Relational niche construction3.3External niche construction4Conceptual Improvement on Niche Construction Theory 4.1Constitutive niche construction4.2Relational niche construction4.3External niche construction5The Status of Niche Construction Theory within Evolutionary Theory 5.1Is niche construction a helpful addition to evolutionary theory?5.2Is niche construction an evolutionary process?6Conclusion. (shrink)

Science is about conceptualizing the natural world in a way that can be understood by human beings while at the same time reflecting as much as possible what we can empirically infer about how the world actually is. Among the crucial tools that allow scientists to formulate hypotheses and to contribute to a progressive understanding of nature are the use of imagery and metaphors, on the one hand, and the ability to assume certain starting points on which to build new (...) avenues of inquiry on the other hand. The premise of this work is that, in the words of philosopher of science Daniel Dennett, "There is no such thing as philosophy-free science; there is only science whose philosophical baggage is taken on board without examination." The purpose here is precisely to examine some of this philosophical baggage, and to see where such analysis may lead us. Obviously, it is not possible for a single project to take on science as a whole, or even an entire discipline such as physics, or ecology. Therefore, the core of this work is constituted by a series of eight case studies drawn from the field of evolutionary biology, with which I am particularly familiar as a practicing biologist. The hope is that combining expertise in both philosophy and science in one person, the resulting insights might be useful for the practicing scientist as well as because of their value as philosophical inquires. The dissertation is a combination of conceptual analysis and science criticism applied to specific questions in organismal biology, largely of an evolutionary nature, with the eight case studies grouped into three broad categories: Unexamined Baggage, Bad Habits, and Good and bad metaphors. (shrink)

This essay reviews the long tradition of experimental genetics of the Drosophila indirect flight muscles (IFM). It discusses how genetics can operate in tandem with multidisciplinary approaches to provide a description, in molecular terms, of the functional properties of the muscle myofibril. In particular, studies at the interface of genetics and proteomics address protein function at the cellular scale and offer an outstanding platform with which to elucidate how the myofibril works. Two generalizations can be enunciated from the studies reviewed. (...) First, the study of mutant IFM proteomes provides insight into how proteins are functionally organized in the myofibril. Second, IFM mutants can give rise to structural and contractile defects that are unrelated, a reflection of the dual function that myofibrillar proteins play as fundamental components of the sarcomeric framework and biochemical “parts” of the contractile “engine”. BioEssays 23:1047–1063, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

A foundational idea of evo‐devo is that morphological variation is not isotropic, that is, it does not occur in all directions. Instead, some directions of morphological variation are more likely than others from DNA‐level variation and these largely depend on development. We argue that this evo‐devo perspective should apply not only to morphology but to evolution at all phenotypic levels. At other phenotypic levels there is no development, but there are processes that can be seen, in analogy to development, as (...) constructing the phenotype (e.g., protein folding, learning for behavior, etc.). We argue that to explain the direction of evolution two types of arguments need to be combined: generative arguments about which phenotypic variation arises in each generation and selective arguments about which of it passes to the next generation. We explain how a full consideration of the two types of arguments improves the explanatory power of evolutionary theory. Also see the video abstract here: https://youtu.be/Egbvma_uaKc. (shrink)

The two authors of this paper have diametrically opposed views of the prevalence and strength of adaptation in nature. Hendry believes that adaptation can be seen almost everywhere and that evidence for it is overwhelming and ubiquitous. Gonzalez believes that adaptation is uncommon and that evidence for it is ambiguous at best. Neither author is certifiable to the knowledge of the other, leaving each to wonder where the other has his head buried. Extensive argument has revealed that each author thinks (...) his own view is amply supported by both theory and empirical evidence. Further reflection has revealed that the differences in opinion may start with the different disciplines in which we work: evolutionary ecology for Hendry and community ecology for Gonzalez. In the present paper, we each present devastating evidence supporting our own position and thus refuting that of the other. We then identify the critical differences that led to such opposing views. We close by combining our two perspectives into a common framework based on the adaptive landscape, and thereby suggest means by which to assess the prevalence and strength of adaptation. (shrink)