Structuralism and Adaptationism: Friends? Or foes?

Historically, the empirical study of phenotypic diversification has fallen into two rough camps; (1) "structuralist approaches" focusing on developmental constraint, bias, and innovation (with evo-devo at the core); and (2) "adaptationist approaches" focusing on adaptation, and natural selection. Whilst debates, such as that surrounding the proposed "Extended" Evolutionary Synthesis, often juxtapose these two positions, this review focuses on the grey space in between. Specifically, here I present a novel analysis of structuralism which enables us to take a more nuanced look at the motivations behind the structuralist and adaptationist positions. This makes clear how the two approaches can conflict, and points of potential commensurability. The review clarifies (a) the value of the evo-devo approach to phenotypic diversity, but also (b) how it properly relates to other predominant approaches to the same issues in evolutionary biology more broadly.

Theoretical plurality, the extended evolutionary synthesis, and archaeology.

The study of cultural evolution now includes multiple theoretical frameworks. Despite common influence from Darwinian evolutionary theory, there is considerable diversity. Thus, we recognize those most influenced by the tenets of the Modern Synthesis (evolutionary archaeology, cultural transmission theory, and human behavioral ecology) and those most aligned more closely with concepts emerging in the Extended Evolutionary Synthesis (cultural macroevolution and evolutionary cognitive archaeology). There has been substantial debate between adherents of these schools of thought as to their appropriateness and priority for addressing the fundamentals of cultural evolution. I argue that theoretical diversity is necessary to address research questions arising from a complex archaeological record. Concepts associated with the Extended Evolutionary Synthesis may offer unique insights into the cultural evolutionary process.

Learning from disability studies to introduce the role of the individual to naturalistic accounts of disease.

Disability studies have been successfully focusing on individuals' lived experiences, the personalization of goals, and the constitution of the individual in defining disease and restructuring public understandings of disability. Although they had a strong influence in the policy making and medical modeling of disease, their framework has not been translated to traditional naturalistic accounts of disease. I will argue that, using new developments in evolutionary biology (Extended Evolutionary Synthesis [EES] about questions of proper function) and behavioral ecology (Niche conformance and construction about the questions of reference classes in biostatistics accounts), the main elements of the framework of disability studies can be used to represent life histories at the conceptual level of the two main "non-normative" accounts of disease. I chose these accounts since they are related to medicine in a more descriptive way. The success of the practical aspects of disability studies this way will be communicated without causing injustice to the individual since they will represent the individuality of the patient in two main naturalistic accounts of disease: the biostatistical account and the evolutionary functional account. Although most accounts criticizing the concept of disease as value-laden do not supply a positive element, disability studies can supply a good point for descriptive extension of the concept through inclusion of epistemic agency.

Situating physiology within evolutionary theory.

Traditionally defined as the science of the living, or as the field that beyond anatomical structure and bodily form studies functional organization and behaviour, physiology has long been excluded from evolutionary research. The main reason for this exclusion is that physiology has a presential and futuristic outlook on life, while evolutionary theory is traditionally defined as the study of natural history. In this paper, I re-evaluate these classic science divisions and situate physiology within the history of the evolutionary sciences, as well as within debates on the Extended Evolutionary Synthesis and the need for a Third Way of Evolution. I then briefly point out how evolutionary physiology in particular contributes to research on function, causation, teleonomy, agency and cognition.

A non-adaptationist hypothesis of play behaviour.

Play is a suite of apparently non-functional, pleasurable behaviours observed in human and non-human animals. Although the phenomenon has been studied extensively, no adaptationist behavioural theory of how play evolved can be supported by the available evidence. However, the advancement of the extended evolutionary synthesis and developments in systems biology offer alternative avenues for non-adaptationist physiological hypotheses. I therefore propose a hypothesis of play, based upon a complex ACh activity that is under agential control of the organism, whereby play initiates ACh-mediated feedforward and feedback processes which act to: (i) regulate metabolic processes; (ii) form new ACh receptors via ACh mRNA activity; (iii) mediate attention, memory consolidation and learning; and (iv) mediate social behaviours, reproduction and embryonic development. However, play occurs across taxa, but does not occur across all taxonomic groups or within all species of a taxonomic group. Thus, to support the validity of the proposed hypothesis, I further propose potential explanations for this anomaly, which include sampling and observer biases, altricial versus precocial juvenile development, and the influence of habitat niche and environmental conditions on behaviour. The proposed hypothesis thus offers new avenues for study in both the biological and social sciences, in addition to having potential applications in applied sciences, such as animal welfare and biomedical research. Crucially, it is hoped that this hypothesis will promote further study of a valid and behaviourally significant, yet currently enigmatic, biological phenomenon.

Inferring cultural reproduction from lithic data: A critical review.

The cultural reproduction of lithic technology, long an implicit assumption of archaeological theories, has garnered increasing attention over the past decades. Major debates ranging from the origins of the human culture capacity to the interpretation of spatiotemporal patterning now make explicit reference to social learning mechanisms and cultural evolutionary dynamics. This burgeoning literature has produced important insights and methodological innovations. However, this rapid growth has sometimes led to confusion and controversy due to an under-examination of underlying theoretical and methodological assumptions. The time is thus ripe for a critical assessment of progress in the study of the cultural reproduction of lithic technology. Here we review recent work addressing the evolutionary origins of human culture and the meaning of artifact variation at both intrasite and intersite levels. We propose that further progress will require a more extended and context-specific evolutionary approach to address the complexity of real-world cultural reproduction.

Random with Respect to Fitness or External Selection? An Important but Often Overlooked Distinction.

Mutations are often described as being "random with respect to fitness." Here we show that the experiments used to establish randomness with respect to fitness are only capable of showing that mutations are random with respect to current external selection. Current debates about whether or not mutations are directed may be at least partially resolved by making use of this distinction. Additionally, this distinction has important mathematical, experimental, and inferential implications.

The extended evolutionary synthesis and human origins: Archaeological perspectives.

Recent developments in evolutionary biology have led to a call for an extension of standard evolutionary theory, with its emphasis on processes such as selection and drift, into a much larger theoretical framework that includes processes such as niche construction, developmental plasticity, inclusive inheritance, and developmental bias. Skeptics argue that these processes are already subsumed within the standard theory and thus an extension is not required. Here, we outline what this evolutionary "rethink" might mean for the study of human origins. Specifically, can paleoanthropologists benefit from an extended theoretical toolkit? The papers in this special issue suggest it can be useful but may not be necessary, depending on the kinds of questions that are being asked.

Human behavioral ecology and niche construction.

We examine the relationship between niche construction theory (NCT) and human behavioral ecology (HBE), two branches of evolutionary science that are important sources of theory in archeology. We distinguish between formal models of niche construction as an evolutionary process, and uses of niche construction to refer to a kind of human behavior. Formal models from NCT examine how environmental modification can change the selection pressures that organisms face. In contrast, formal models from HBE predict behavior assuming people behave adaptively in their local setting, and can be used to predict when and why people engage in niche construction. We emphasize that HBE as a field is much broader than foraging theory and can incorporate social and cultural influences on decision-making. We demonstrate how these approaches can be formally incorporated in a multi-inheritance framework for evolutionary research, and argue that archeologists can best contribute to evolutionary theory by building and testing models that flexibly incorporate HBE and NCT elements.

The ripples of modernity: How we can extend paleoanthropology with the extended evolutionary synthesis.

Contemporary understandings of paleoanthropological data illustrate that the search for a line defining, or a specific point designating, "modern human" is problematic. Here we lend support to the argument for the need to look for patterns in the paleoanthropological record that indicate how multiple evolutionary processes intersected to form the human niche, a concept critical to assessing the development and processes involved in the emergence of a contemporary human phenotype. We suggest that incorporating key elements of the Extended Evolutionary Synthesis (EES) into our endeavors offers a better and more integrative toolkit for modeling and assessing the evolution of the genus Homo. To illustrate our points, we highlight how aspects of the genetic exchanges, morphology, and material culture of the later Pleistocene complicate the concept of "modern" human behavior and suggest that multiple evolutionary patterns, processes, and pathways intersected to form the human niche.

Using niche construction theory to generate testable foraging hypotheses at Liang Bua.

Niche construction theory (NCT) has emerged as a promising theoretical tool for interpreting zooarchaeological material. However, its juxtaposition against more established frameworks like optimal foraging theory (OFT) has raised important criticism around the testability of NCT for interpreting hominin foraging behavior. Here, we present an optimization foraging model with NCT features designed to consider the destructive realities of the archaeological record after providing a brief review of OFT and NCT. Our model was designed to consider a foragers decision to exploit an environment given predation risk, mortality, and payoff ratios between different ecologies, like more-open or more-forested environments. We then discuss how the model can be used with zooarchaeological data for inferring environmental exploitation by a primitive hominin, Homo floresiensis, from the island of Flores in Southeast Asia. Our example demonstrates that NCT can be used in combination with OFT principles to generate testable foraging hypotheses suitable for zooarchaeological research.

Unmodern Synthesis: Developmental Hierarchies and the Origin of Phenotypes.

The question of whether the modern evolutionary synthesis requires an extension has recently become a topic of discussion, and a source of controversy. We suggest that this debate is, for the most part, not about the modern synthesis at all. Rather, it is about the extent to which genetic mechanisms can be regarded as the primary determinants of phenotypic characters. The modern synthesis has been associated with the idea that phenotypes are the result of gene products, while supporters of the extended synthesis have suggested that environmental factors, along with processes such as epigenetic inheritance, and niche construction play an important role in character formation. We argue that the methodology of the modern evolutionary synthesis has been enormously successful, but does not provide an accurate characterization of the origin of phenotypes. For its part, the extended synthesis has yet to be transformed into a testable theory, and accordingly, has yielded few results. We conclude by suggesting that the origin of phenotypes can only be understood by integrating findings from all levels of the organismal hierarchy. In most cases, parts and processes from a single level fail to accurately explain the presence of a given phenotypic trait.

Assessing elements of an extended evolutionary synthesis for plant domestication and agricultural origin research.

The development of agricultural societies, one of the most transformative events in human and ecological history, was made possible by plant and animal domestication. Plant domestication began 12,000-10,000 y ago in a number of major world areas, including the New World tropics, Southwest Asia, and China, during a period of profound global environmental perturbations as the Pleistocene epoch ended and transitioned into the Holocene. Domestication is at its heart an evolutionary process, and for many prehistorians evolutionary theory has been foundational in investigating agricultural origins. Similarly, geneticists working largely with modern crops and their living wild progenitors have documented some of the mechanisms that underwrote phenotypic transformations from wild to domesticated species. Ever-improving analytic methods for retrieval of empirical data from archaeological sites, together with advances in genetic, genomic, epigenetic, and experimental research on living crop plants and wild progenitors, suggest that three fields of study currently little applied to plant domestication processes may be necessary to understand these transformations across a range of species important in early prehistoric agriculture. These fields are phenotypic (developmental) plasticity, niche construction theory, and epigenetics with transgenerational epigenetic inheritance. All are central in a controversy about whether an Extended Evolutionary Synthesis is needed to reconceptualize how evolutionary change occurs. An exploration of their present and potential utility in domestication study shows that all three fields have considerable promise in elucidating important issues in plant domestication and in agricultural origin and dispersal research and should be increasingly applied to these issues.

Holobionts, Multispecies Ecologies, and the Biopolitics of Care: Emerging Landscapes of Praxis in a Medical Anthropology of the Anthropocene.

Medical anthropology, given its diversity of practical and historical entanglements with (and outside of) numerous threads of anthropology, is a key site for productive theoretical and methodological confluences in the Anthropocene. Multispecies approaches, ethnographically, theoretically and methodologically, are developing as central locations for the hybridization and mingling of diverse and innovative research questions, particularly those engaging the processes, patterns, and constructs of health.

O Organism, Where Art Thou? Old and New Challenges for Organism-Centered Biology.

This paper addresses theoretical challenges, still relevant today, that arose in the first decades of the twentieth century related to the concept of the organism. During this period, new insights into the plasticity and robustness of organisms as well as their complex interactions fueled calls, especially in the UK and in the German-speaking world, for grounding biological theory on the concept of the organism. This new organism-centered biology (OCB) understood organisms as the most important explanatory and methodological unit in biological investigations. At least three theoretical strands can be distinguished in this movement: Organicism, dialectical materialism, and (German) holistic biology. This paper shows that a major challenge of OCB was to describe the individual organism as a causally autonomous and discrete unit with consistent boundaries and, at the same time, as inextricably interwoven with its environment. In other words, OCB had to conciliate individualistic with anti-individualistic perspectives. This challenge was addressed by developing a concept of life that included functionalist and metabolic elements, as well as biochemical and physical ones. It allowed for specifying organisms as life forms that actively delimit themselves from the environment. Finally, this paper shows that the recent return to the concept of the organism, especially in the so-called "Extended Evolutionary Synthesis," is challenged by similar anti-individualistic tendencies. However, in contrast to its early-twentieth-century forerunner, today's organism-centered approaches have not yet offered a solution to this problem.

The sources of adaptive variation.

The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed.

The extended evolutionary synthesis: its structure, assumptions and predictions.

Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways­one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the 'extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism-environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology.

Mechanisms of adaptation and evolution in Toxoplasma gondii.

Toxoplasma has high host flexibility, infecting all nucleated cells of mammals and birds. This implies that during its infective process the parasite must constantly adapt to different environmental situations, which in turn leads to modifications in its metabolism, regulation of gene transcription, translation of mRNAs and stage specific factors. There are conserved pathways that support these adaptations, which we aim to elucidate in this review. We begin by exploring the widespread epigenetic mechanisms and transcription regulators, continue with the supportive role of Heat Shock Proteins (Hsp), the translation regulation, stress granules, and finish with the emergence of contingency genes in highly variable genomic domains, such as subtelomeres. Within epigenetics, the discovery of a new histone variant of the H2B family (H2B.Z), contributing to T. gondii virulence and differentiation, but also gene expression regulation and its association with the metabolic state of the parasite, is highlighted. Associated with the regulation of gene expression are transcription factors (TFs). An overview of the main findings on TF and development is presented. We also emphasize the role of Hsp90 and Tgj1 in T. gondii metabolic fitness and the regulation of protein translation. Translation regulation is also highlighted as a mechanism for adaptation to conditions encountered by the parasite as well as stress granules containing mRNA and proteins generated in the extracellular tachyzoite. Another important aspect in evolution and adaptability are the subtelomeres because of their high variability and gene duplication rate. Toxoplasma possess multigene families of membrane proteins and contingency genes that are associated with different metabolic stresses. Among them parasite differentiation and environmental stresses stand out, including those that lead tachyzoite to bradyzoite conversion. Finally, we are interested in positioning protozoa as valuable evolution models, focusing on research related to the Extended Evolutionary Synthesis, based on models recently generated, such as extracellular adaptation and ex vivo cyst recrudescence.

Thomas S. Kuhn: key to a better understanding of the extended evolutionary synthesis.

In recent years, some scholars have explicitly questioned the desirability or utility of applying the classical and "old-fashioned" theories of scientific change by the likes of Karl Popper and Thomas S. Kuhn to the question of the precise nature and significance of the extended evolutionary synthesis (EES). Supposedly, these twentieth-century philosophers are completely irrelevant for a better understanding of this new theoretical framework for the study of evolution. Here, it will be argued that the EES can be fruitfully interpreted in terms of, as yet, insufficiently considered or even overlooked elements from Kuhn's theory. First, in his original, historical philosophy of science, Kuhn not only distinguished between small and big scientific revolutions, he also pointed out that paradigms can be extended and reformulated. In contrast with what its name suggests, the mainstream EES can be interpreted as a Kuhnian reformulation of modern evolutionary theory. Second, it has, as yet, also been overlooked that the EES can be interpreted in terms of Kuhn's later, tentative evolutionary philosophy of science. With the EES, an old dichotomy in evolutionary biology is maybe being formalized and institutionalized.

Exploring the patterns of evolution: Core thoughts and focus on the saltational model.

The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.