Preliminary remarks to an integrative theory of evolution

For nearly a century the main focus in biological disciplines such as molecular biology, biochemistry, genetics and evolutionary theory was cellular life as a machine like process in which mechanistic pathways regulate metabolism, genetic reading and translation into proteins and evolution by variations (random error replications) and selection. Modern biochemistry started with the cellular theory of life. Also the modern synthesis focused on cells at the starting event of life. The dominance of this paradigm lasted until ten years ago. Then the comeback of virology offered new empirical data and explanatory models of how viruses determine cellular life through an abundance of parasite host interactions that overrule cellular processes. The RNA world hypothesis demonstrated that prior to cellular life RNA group interactions were at the beginning of biological selection before cellular life emerged. Last but not least the central dogma of molecular biology collapsed when epigenetics demonstrated that history and developmental experiences of the past can be epigenetically imprinted and serve as identity markings that in every replication process of any cell in any organism on this planet the timely and locally coordinated replication is regulated and orchestrated by these programmings. In the light of this knowledge a better explanatory model than an extension of the modern synthesis will be more successful in the 21st century.

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.

What prevents mainstream evolutionists teaching the whole truth about how genomes evolve?

The common belief that the neo-Darwinian Modern Synthesis (MS) was buttressed by the discoveries of molecular biology is incorrect. On the contrary those discoveries have undermined the MS. This article discusses the many processes revealed by molecular studies and genome sequencing that contribute to evolution but nonetheless lie beyond the strict confines of the MS formulated in the 1940s. The core assumptions of the MS that molecular studies have discredited include the idea that DNA is intrinsically a faithful self-replicator, the one-way transfer of heritable information from nucleic acids to other cell molecules, the myth of "selfish DNA", and the existence of an impenetrable Weismann Barrier separating somatic and germ line cells. Processes fundamental to modern evolutionary theory include symbiogenesis, biosphere interactions between distant taxa (including viruses), horizontal DNA transfers, natural genetic engineering, organismal stress responses that activate intrinsic genome change operators, and macroevolution by genome restructuring (distinct from the gradual accumulation of local microevolutionary changes in the MS). These 21st Century concepts treat the evolving genome as a highly formatted and integrated Read-Write (RW) database rather than a Read-Only Memory (ROM) collection of independent gene units that change by random copying errors. Most of the discoverers of these macroevolutionary processes have been ignored in mainstream textbooks and popularizations of evolutionary biology, as we document in some detail. Ironically, we show that the active view of evolution that emerges from genomics and molecular biology is much closer to the 19th century ideas of both Darwin and Lamarck. The capacity of cells to activate evolutionary genome change under stress can account for some of the most negative clinical results in oncology, especially the sudden appearance of treatment-resistant and more aggressive tumors following therapies intended to eradicate all cancer cells. Knowing that extreme stress can be a trigger for punctuated macroevolutionary change suggests that less lethal therapies may result in longer survival times.

Invertebrate Paleontology and Evolutionary Thinking in the US and Britain, 1860-1940

The role of paleontology in evolutionary biology between the publication of The Origin of Species in 1859 and the Evolutionary Synthesis of the 1940s (the post-Darwin, pre-Synthesis [PDPS] period) is frequently described as mostly misguided failure. However, a significant number of American and British PDPS invertebrate paleontologists of this period did devote considerable attention to evolution, and their evolutionary theories and conclusions were a good deal more diverse and nuanced than previous histories have suggested. This paper brings into focus a number of important but underrecognized aspects of the history of paleontology within the history of biology, including that PDPS paleontologists were not all as theoretically backward as they have been portrayed; that the post-Synthesis narrative of the history of evolution should be continually reevaluated, in part to decouple historical understanding from the agendas of authors who have used history to advance particular views of evolution; and that there is a much richer story to be told about the history of evolutionary biology in both the pre- and post-Synthesis eras.

How the Modern Synthesis Came to Ecology

Ecology in principle is tied to evolution, since communities and ecosystems result from evolution and ecological conditions determine fitness values (and ultimately evolution by natural selection). Yet the two disciplines of evolution and ecology were not unified in the twentieth-century. The architects of the Modern Synthesis, and especially Julian Huxley, constantly pushed for such integration, but the major ideas of the Synthesis-namely, the privileged role of selection and the key role of gene frequencies in evolution-did not directly or immediately translate into ecological science. In this paper I consider five stages through which the Synthesis was integrated into ecology and distinguish between various ways in which a possible integration was gained. I start with Elton's animal ecology (1927), then consider successively Ford's ecological genetics in the 1940s, the major textbook Principles of animal ecology edited by Allee et al. (1949), and the debates over the role of competition in population regulation in the 1950s, ending with Hutchinson's niche concept (1959) and McArthur and Wilson's Principles of Island Biogeography (1967) viewed as a formal transposition of Modern Synthesis explanatory schemes. I will emphasize the key role of founders of the Synthesis at each stage of this very nonlinear history.

Why we don't want another "Synthesis"

High-level debates in evolutionary biology often treat the Modern Synthesis as a framework of population genetics, or as an intellectual lineage with a changing distribution of beliefs. Unfortunately, these flexible notions, used to negotiate decades of innovations, are now thoroughly detached from their historical roots in the original Modern Synthesis (OMS), a falsifiable scientific theory. The OMS held that evolution can be adequately understood as a process of smooth adaptive change by shifting the frequencies of small-effect alleles at many loci simultaneously, without the direct involvement of new mutations. This shifting gene frequencies theory was designed to support a Darwinian view in which the course of evolution is governed by selection, and to exclude a mutation-driven view in which the timing and character of evolutionary change may reflect the timing and character of events of mutation. The OMS is not the foundation of current thinking, but a special case of a broader conception that includes (among other things) a mutation-driven view introduced by biochemists in the 1960s, and now widely invoked. This innovation is evident in mathematical models relating the rate of evolution directly to the rate of mutation, which emerged in 1969, and now represent a major branch of theory with many applications. In evo-devo, mutationist thinking is reflected by a concern for the "arrival of the fittest". Though evolutionary biology is not governed by any master theory, and incorporates views excluded from the OMS, the recognition of these changes has been hindered by woolly conceptions of theories, and by historical accounts, common in the evolutionary literature, that misrepresent the disputes that defined the OMS.

REVIEWERS

This article was reviewed by W. Ford Doolittle, Eugene Koonin and J. Peter Gogarten.

The evolutionary implications of epigenetic inheritance

The Modern Evolutionary Synthesis (MS) forged in the mid-twentieth century was built on a notion of heredity that excluded soft inheritance, the inheritance of the effects of developmental modifications. However, the discovery of molecular mechanisms that generate random and developmentally induced epigenetic variations is leading to a broadening of the notion of biological heredity that has consequences for ideas about evolution. After presenting some old challenges to the MS that were raised, among others, by Karl Popper, I discuss recent research on epigenetic inheritance, which provides experimental and theoretical support for these challenges. There is now good evidence that epigenetic inheritance is ubiquitous and is involved in adaptive evolution and macroevolution. I argue that the many evolutionary consequences of epigenetic inheritance open up new research areas and require the extension of the evolutionary synthesis beyond the current neo-Darwinian model.

Dobzhansky and Montagu's Debate on Race: The Aftermath

Dobzhansky and Montagu debated the use and validity of the term "race" over a period of decades. They failed to reach an agreement, and the "debate" has continued to the present. The ms contains an account of the debate to the present. This essay is part of a Special Issue, Revisiting Garland Allen's Views on the History of the Life Sciences in the Twentieth Century.

"A temporary oversimplification": Mayr, Simpson, Dobzhansky, and the origins of the typology/population dichotomy (part 2 of 2)

The dichotomy between 'typological thinking' and 'population thinking' features in a range of debates in contemporary and historical biology. The origins of this dichotomy are often traced to Ernst Mayr, who is said to have coined it in the 1950s as a rhetorical device that could be used to shield the Modern Synthesis from attacks by the opponents of population biology. In this two-part essay, I argue that the origins of the typology/population dichotomy are considerably more complicated and more interesting than is commonly thought. In the first part, I argued that Mayr's dichotomy was based on two distinct type/population contrasts that had been articulated much earlier by George Gaylord Simpson and Theodosius Dobzhansky. Their distinctions made eminent sense in their own, isolated contexts. In this second part, I will show how Mayr conflated these type/population distinctions and blended in some of his own, unrelated concerns with 'types' of a rather different sort. Although Mayr told his early critics that he was merely making "a temporary oversimplification," he ended up burdening the history and philosophy of biology with a troubled dichotomy.

"A temporary oversimplification": Mayr, Simpson, Dobzhansky, and the origins of the typology/population dichotomy (part 1 of 2)

The dichotomy between 'typological thinking' and 'population thinking' features in a range of debates in contemporary and historical biology. The origins of this dichotomy are often traced to Ernst Mayr, who is said to have coined it in the 1950s as a rhetorical device that could be used to shield the Modern Synthesis from attacks by the opponents of population biology. In this two-part essay I argue that the origins of the typology/population dichotomy are considerably more complicated and more interesting than is commonly thought. In this first part, I will argue that Mayr's dichotomy was based on two distinct type/population contrasts that had been articulated much earlier by George Gaylord Simpson and Theodosius Dobzhansky. Their distinctions made eminent sense in their own, isolated contexts. In the second part, I will show how Mayr conflated these type/population distinctions and blended in some of his own, unrelated concerns with 'types' of a rather different sort. Although Mayr told his early critics that he was merely making "a temporary oversimplification," he ended up burdening the history and philosophy of biology with a troubled dichotomy.

Paleontology at the "high table"? Popularization and disciplinary status in recent paleontology

This paper examines the way in which paleontologists used "popular books" to call for a broader "expanded synthesis" of evolutionary biology. Beginning in the 1970s, a group of influential paleontologists, including Stephen Jay Gould, Niles Eldredge, David Raup, Steven Stanley, and others, aggressively promoted a new theoretical, evolutionary approach to the fossil record as an important revision of the existing synthetic view of Darwinism. This work had a transformative effect within the discipline of paleontology. However, by the 1980s, paleontologists began making their case to a wider audience, both within evolutionary biology, and to the general public. Many of their books-for example, Eldredge's provocatively-titled Unfinished Synthesis-explicitly argued that the received synthetic view of Darwinian evolution was incomplete, and that paleontological contributions such as punctuated equilibria, the hierarchical model of macroevolution, and the study of mass extinction dynamics offered a substantial corrective to evolutionary theory. This paper argues that books-far from being "mere popularizations" of scientific ideas-played an important role in disciplinary debates surrounding evolutionary theory during the 1980s, and in particular that paleontologists like Gould and Eldredge self-consciously adopted the book format because of the importance of that genre in the history of evolutionary biology.