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This chapter deals with the traditional objections to the Modern Synthesis to decide whether the genome perusal forces us to update (or change) this synthesis. After a journey from Darwin's ideas to the Modern Synthesis, the origin of genetic variability and its gradual crafting by natural selection are analysed under the present knowledge. Several functional analyses, ranging from bacteria to vertebrates, are described to discover that highly integrated systems can evolve stepwise, validating Darwinian gradualism. Phenotypic plasticity, a missing point in the Modern Synthesis, is also discussed from the pioneer works of genetic assimilation till the molecular buffering systems that, like heat shock proteins, encrypt lots of variability ready to be assimilated. It is concluded that genome studies favour the reconstruction of Darwinism rather than its deconstruction. The ‘finale’ launches natural selection like a tinkerer amidst all the ‘music of the biosphere’ as the only way to understand evolution.

This book reviews the directions that contribute to an Extended Synthesis. It deals with the significant advances in the understanding of the tightly linked ideas (in the Modern Synthesis [MS]) of natural selection and adaptation. The book addresses the new information from molecular genetics and genomics that brings significant new issues to evolutionary theory, and describes the kinds of hereditary and replicatory mechanisms which are not considered within the framework of the MS. Additionally, it analyzes the ongoing revisions of the MS that come from the new field of evolutionary developmental biology (EvoDevo). The principles of macroevolution and evolvability that are outside the scope of the traditional MS are explained. An overview of the chapters included in the book is finally given.

This chapter discusses the Modern Synthesis of evolution that emerged between the 1920s and 1950s and persisted in the 1960s. The Modern Synthesis refers to the fusion of ideas among biologists about the nature and dynamics of evolutionary change. This chapter considers why the notion of soft inheritance and inheritance of acquired characters were rejected with the establishment of the Modern Synthesis in the 1960s. It also explains why Mendelian genetics dominated evolutionary thinking during that period.

This chapter begins with a brief history of pre-Darwinian, evolutionary studies concerning genetic exchange. It then discusses various organismal systems to exemplify some ways in which post-Modern Synthesis research has been pursued to test the evolutionary role of genetic exchange. It considers examples of well-developed evolutionary model systems including plants, animals, bacteria, and viruses. These were chosen because they reflect broadly based, in-depth studies of the possible evolutionary consequences from natural hybridization and/or lateral gene transfer. Some cases (e.g. viral lineages) also afford the opportunity to point to the uncertainty in categorizing them as either natural hybridization or lateral gene transfer.

A number of prominent modern evolutionists embraced ‘human nature’, signalling their commitment to the Modern Synthesis. Their claim is that for most of our evolutionary history, culture was of little importance, and that genes, not culture, controlled early development. More recently, cultural evolutionists have argued that culture and reason were present deep in the Homo lineage, and that the ability to learn socially develops in the first year of life. Thus, it is reasonable to think that genes and culture coevolved in the evolutionary past, and that they codevelop in infancy and childhood. Human nature theorists seek to deny this claim, while at the same time trying in various ways to make room for human culture and reason. I argue here that they are unsuccessful in their attempts.

This chapter reviews the debate on group selection, a concept that has experienced vertiginous ups and downs since the 1960s, and brings it up to modern standards within the broader context of multilevel selection (MLS) theory. It specifically offers a brief overview of MLS theory, major evolutionary transitions, and human evolution as a major transition, so that these subjects can become part of an extended evolutionary synthesis. The chapter also describes how MLS theory relates to the Modern Synthesis. A comment on all aspects of human behavior and culture from an evolutionary perspective is then presented.

This chapter characterizes the consequences of a shift of focus from individual genes to gene networks. It describes some of the opportunities and challenges that the genomic era brings to evolutionary biology, and some of the ways current research into genome evolution is extending the Modern Synthesis. The chapter also discusses three extensions to the Modern Synthesis that are emerging out of the tumult and excitement of evolutionary genomics. It suggests that applying the traditional approaches of population genetics, evolutionary genetics, and molecular evolution to genomic data sets presents nontrivial challenges.

This chapter presents three important reasons why evolutionary biologists dismissed Lamarckism or soft inheritance from the Modern Synthesis. The first is the legacy of adhering to August Weismann's ideas of the separation of germ line and soma. The second is the absence, from the 1920s through the 1940s, of convincing for strong evidence for the inheritance of acquired characteristics. The third reason came from the assumptions of population and quantitative genetics, which were developing at the time.

This chapter discusses important issues concerning the Modern Synthesis. First, it describes the neglected ideas and overlooked theories of Cyril Darlington. It then discusses the decline of the plasmon and several plasmagene theories developed by geneticists after the Second World War. The chapter also examines the role of institutional and political factors in biological research in the United States. Finally, the chapter discusses some of the experimental studies that supported the Modern Synthesis view. These include the Luria-Delbrück experiments on bacterial mutations, H.B.D. Kettlewell's studies of melanism in the peppered moth, and Scott Gilbert's work on hemoglobin and sickle-cell anemia.

In the late 1940s, the discipline of paleontology took major steps towards becoming more fully integrated into the community of evolutionary biology. Key to this process was the development of quantitative ways of documenting and analyzing morphological variation in fossils, which allowed paleontologists to integrate paleontology into the Modern Evolutionary Synthesis. Paleontologists, however, wrestled with accommodating fossil data to the populational understanding of species promoted by geneticists in the Synthesis. In so doing, these paleontologists posed a solution to the problem of incorporating “population thinking” into paleontology; introduced greater analytical and quantitative rigor into paleontology; and introduced new theoretical possibilities for interpreting the evolutionary significance of the fossil record, which greatly contributed to the further growth of evolutionary paleobiology.

This chapter analyzes the revolutionary impact of genomic science on the study of evolution, and addresses the issues that modern evolutionary biology has either learned or needs to grapple with in the age of genomics. It suggests that transposable elements are genomic constituents which can result in novel genes or gene functions. The chapter proposes that although epigenetic changes remain compatible with the Modern Synthesis, dissecting the details could possibly result in new insights into the dynamics of the evolutionary process which are not currently considered. It shows that the nature of epistasis is increasingly gaining prominence, and offers new avenues of research into the genetic architecture of evolutionary change.

This chapter addresses the possible role of phenotypic plasticity in macroevolution. It analyzes how evolutionary biologists are now using the concept of plasticity to expand the horizons of the Modern Synthesis of the 1930s and 1940s, and what role plasticity may play in the shaping of an Extended Evolutionary Synthesis. The chapter considers the issues linked to the mechanics of plasticity in terms of molecular basis (genes, proteins, and hormones involved), as well as of epigenetic effects and development. It presents a discussion of the modern sense of phenotypic and genotypic accommodation, and suggests that the phenotypic plasticity will significantly elaborate the way organic evolution takes place.

Throughout his life Darwin collected and investigated a host of creatures from a wide range of relatively simple species—zoophytes, sea pens, corals, worms, insects, and a diversity of plants. These studies aimed to answer fundamental questions about the characteristics of life, the nature of individuality, reproduction, and the implications of agency. Central amongst these implications were interdependencies between organisms, with their conspecifics, with different species, and with their conditions of life. In this way Darwin built up a picture of the living world as a theatre of agency. The derivation of evolution from this living theatre—which he called ‘the struggle for existence’—gave Darwin’s vision of nature its distinctiveness. While twentieth-century biology sidelined the agency of organisms in favour of the gene, the twenty-first century has returned to Darwin’s view that evolution is led by organisms (or ‘phenotypes’)—with implications for psychology differing considerably from contemporary evolutionary psychologies.

This chapter reports the case of transgenerational epigenetic inheritance. It concentrates on developmental biology, in particular on molecular studies of epigenetics, and on one specific challenge: That of “soft inheritance.” The chapter reviews the assumptions about heredity and development that were built into the late twentieth-century version of the Modern Synthesis, and shows that the transgenerational transmission of epigenetic variations through cellular inheritance and through routes which bypass the germ line is not a rarity. It explains how incorporating epigenetic inheritance affects adaptation, genetic assimilation, reproductive isolation, evolution of development, and macroevolutionary change.

This chapter examines the important morphological tradition in German paleontology. It suggests that the pluralistic and biologically oriented German paleontology both predated and anticipated many of the concerns of the paleobiology movement in the United States. This chapter explains that German paleontology developed its own paleobiology independently of both the Anglo-American tradition and the Modern Evolutionary Synthesis. Thus, it can be considered a perfect topic for a cultural history of science that places the development of scientific theories and concepts clearly within the framework of cultural references, values, and transformations.

This chapter analyzes the relative roles of contingency and chance variation in evolutionary theory. It describes the tradition and line of reasoning, from Charles Darwin throughout the Modern Synthesis, which completely subordinate the importance of chance variation to that of natural selection. The chapter demonstrates the very real role which chance variation and the order of variation play in directing the course of evolution, arguing that chance variation was initially conceived for the purpose of being subordinated. It also shows that chance variation need not be predictably directed in order to impact the direction of evolutionary change.

The hierarchy theory at its onset was primarily committed to vindicate the distinctness of macro-evolutionary phenomena from micro-evolutionary processes, minimizing the explanatory relevance of levels and entities below the organism and above the gene. The current focus on phenotypic evolution, however, suggests a refinement and revision of the role of the so-called “somatic” or “phenotypic hierarchy”, and the evolutionary bearing of its structured variability at different levels. The paper reviews some theoretical reasons and implications of such reassessment.

Since the 1970s, frequent attempts were made to bridge the gap between ecology and evolution. Ecology was divided into community ecology, that studies the composition and assembly of populations, communities, and metacommunities, and ecosystem science, that studies organisms and their environment as parts of interactive systems characterized by various “functions” (e.g., productivity, decomposition) and efficiency measures (e.g., food chain efficiency). Following the Modern Synthesis, evolutionary biology, on the other hand, was focused on genealogical processes (natural selection, drift, speciation) and came to consider ecological assemblies as aggregations characterized by secondary, derived patterns, or even to imagine them as a rather uninteractive 'stage' for the evolutionary play. Paleobiological macroevolutionary studies, models of niche construction and evolutionary ecology are attempts towards greater integration between ecological and genealogical patterns. The hierarchy theory of evolution is suggested to provide the most appropriate theoretical framework for the multiscale integration between the two disciplines.