[A Second Look at the Origins of the Concept of Epigenetics']

Even today, 'epigenetics' is a rather difficult field to define. The explosive growth of epigenetics over the last twenty years is sometimes seen as a revolutionary event in the life sciences, a paradigm shift that would devalue genetics or the standard view of the evolutionary synthesis. The aim of this paper is to place this controversial issue in its historical context. Building on the excellent work of David Haig, I will show that in the late 1950s, the modern concept of epigenetics emerged as an extension of the nascent theory of molecular biology. Given that genetic information was assimilated to the DNA sequence, and that each cell of an organism was supposed to possess a complete genome, it was thought that certain as yet undiscovered molecular mechanisms were necessary to regulate gene expression. These hypothetical "epigenetic systems", which would not modify the DNA sequence, should also have heritable effect on gene expression, which would explain the stability of cell differentiation during embryogenesis.

"The Logic of Monsters:" Pere Alberch and the Evolutionary Significance of Experimental Teratology

This paper offers an historical introduction to Pere Alberch's evolutionary thought and his contributions to Evo-Devo, based on his unique approach to experimental teratology. We will take as our point of reference the teratogenic experiments developed by Alberch and Emily A. Gale during the 1980s, aimed at producing monstrous variants of frogs and salamanders. We will analyze his interpretation of the results of these experiments within the framework of the emergence of evolutionary developmental biology (or "Evo-Devo"). The aim is understand how Alberch interpreted teratological anomalies as highly revealing objects of study for understanding the development of organic form, not only in an ontogenetic sense-throughout embryonic development-but also phylogenetically-throughout the evolution of species. Alberch's interpretation of monsters reflects the influence of a long tradition of non-Darwinian evolutionary thought, which began in the nineteenth century and was continued in the twentieth century by people such as Richard Goldschmidt, Conrad H. Waddington, and Stephen Jay Gould. They all proposed various non-gradualist models of evolution, in which embryonic development played a central role. Following this tradition, Alberch argued that, in order to attain a correct understanding of the role of embryological development in evolution, it was necessary to renounce the gradualist paradigm associated with the Darwinian interpretation of evolution, which understood nature as a continuum. According to Alberch, the study of monstrous abnormalities was of great value in understanding how certain epigenetic restrictions in development could give rise to discontinuities and directionality in morphological transformations throughout evolution.

A framework for the integration of development and evolution: The forgotten legacy of James Meadows Rendel

The historical challenges to bridge the gaps between developmental biology and population or statistical genetics under the explanatory dominance of the Modern Evolutionary Synthesis during the 20th century have been thoroughly documented. However, although several attempts to integrate these fields have been made, most have been deemed unsuccessful. As an example of those efforts, in this paper I discuss the work of James Meadows Rendel, a student of J. B. S. Haldane and disciple of Conrad Hal Waddington. I present his largely forgotten or unrecognized, but innovative, ideas about canalization and the role of development in phylogeny as a valuable piece to connect these fields that could still have important ramifications for today's evolutionary biology. In fact, it is expected that the legacy of J. M. Rendel will be rediscovered, and more importantly, incorporated and extended by future researchers, in light of the growth of evolutionary developmental biology in the last decades. What is more, this case offers a chance to critically revisit standard historiographies about the dichotomy between developmental and population genetics research frameworks in 20th century biology.

Sex diversity in the 21st century: Concepts, frameworks, and approaches for the future of neuroendocrinology

Sex is ubiquitous and variable throughout the animal kingdom. Historically, scientists have used reductionist methodologies that rely on a priori sex categorizations, in which two discrete sexes are inextricably linked with gamete type. However, this binarized operationalization does not adequately reflect the diversity of sex observed in nature. This is due, in part, to the fact that sex exists across many levels of biological analysis, including genetic, molecular, cellular, morphological, behavioral, and population levels. Furthermore, the biological mechanisms governing sex are embedded in complex networks that dynamically interact with other systems. To produce the most accurate and scientifically rigorous work examining sex in neuroendocrinology and to capture the full range of sex variability and diversity present in animal systems, we must critically assess the frameworks, experimental designs, and analytical methods used in our research. In this perspective piece, we first propose a new conceptual framework to guide the integrative study of sex. Then, we provide practical guidance on research approaches for studying sex-associated variables, including factors to consider in study design, selection of model organisms, experimental methodologies, and statistical analyses. We invite fellow scientists to conscientiously apply these modernized approaches to advance our biological understanding of sex and to encourage academically and socially responsible outcomes of our work. By expanding our conceptual frameworks and methodological approaches to the study of sex, we will gain insight into the unique ways that sex exists across levels of biological organization to produce the vast array of variability and diversity observed in nature.

Phenotype-first hypotheses, spandrels and early metazoan evolution

Against the neo-Darwinian assumption that genetic factors are the principal source of variation upon which natural selection operates, a phenotype-first hypothesis strikes us as revolutionary because development would seem to constitute an independent source of variability. Richard Watson and his co-authors have argued that developmental memory constitutes one such variety of phenotypic variability. While this version of the phenotype-first hypothesis is especially well-suited for the late metazoan context, where animals have a sufficient history of selection from which to draw, appeals to developmental memory seem less plausible in the evolutionary context of the early metazoans. I provide an interpretation of Stuart Newman's account of deep metazoan phylogenesis that suggests that spandrels are, in addition to developmental memory, an important reservoir of phenotypic variability. I conclude by arguing that Gerd Müller's "side-effect hypothesis" is an illuminating generalization of the proposed non-Watsonian version of the phenotype-first hypothesis.

The environment: An ambiguous concept in Waddington's biology

Waddington is usually acknowledged as a biologist who proposed a more subtle concept of environment than the one generally in currency during the rise of the Modern Synthesis. As such, he was among the few scientists in the mid-twentieth century to develop an elaborated concept of the environment that would fully embrace its constructive role both in development and evolution. Yet, on close inspection, there is an inconsistency in Waddington's theoretical positioning. On the one hand, as a critic of population genetics, Waddington never stopped claiming that natural selection acts on phenotypes and that the phenotype is the outcome of both the genome and the environment. On the other, however, the topology of his famous epigenetic landscape was anchored only in the genome, and the variation of the environment was treated as an external perturbation. In other words, the genes and the environment were sometimes considered as symmetric agents in the epigenetic system, and sometimes not. My aim is to shed light on the significance of this tension in Waddington's theoretical framework. I show that Waddington's biology is best characterized as an asymmetric understanding of the causal role of genes and environment both in development and evolution. His model of genetic assimilation was based on the idea of differential levels of hereditary responsiveness to environmental variations, giving the genome a leading role and paving the way for critics of his conceptions. In the final section, I argue that eventually Waddington was trapped by his diagram of the epigenetic landscape, which might also have been an obstacle to achieving a proper conception of the creativity of embryogenesis.

Epigenetic inheritance and evolution: a historian's perspective

The aim of this article is to put the growing interest in epigenetics in the field of evolutionary theory into a historical context. First, I assess the view that epigenetic inheritance could be seen as vindicating a revival of (neo)Lamarckism. Drawing on Jablonka's and Lamb's considerable output, I identify several differences between modern epigenetics and what Lamarckism was in the history of science. Even if Lamarckism is not back, epigenetic inheritance might be appealing for evolutionary biologists because it could potentiate two neglected mechanisms: the Baldwin effect and genetic assimilation. Second, I go back to the first ideas about the Baldwin effect developed in the late nineteenth century to show that the efficiency of this mechanism was already linked with a form of non-genetic inheritance. The opposition to all forms of non-genetic inheritance that prevailed at the time of the rise of the Modern Synthesis helps to explain why the Baldwin effect was understood as an insignificant mechanism during the second half of the twentieth century. Based on this historical reconstruction, in §4, I examine what modern epigenetics can bring to the picture and under what conditions epigenetic inheritance might be seen as strengthening the causal relationship between adaptability and adaptation. Throughout I support the view that the Baldwin effect and genetic assimilation, even if they are quite close, should not be conflated, and that drawing a line between these concepts is helpful in order to better understand where epigenetic inheritance might endorse a new causal role. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'

Environmental Carcinogenesis and Transgenerational Transmission of Carcinogenic Risk: From Genetics to Epigenetics

The dominant pathogenic model, somatic mutation theory (SMT), considers carcinogenesis as a ‘genetic accident’ due to the accumulation of ‘stochastic’ DNA mutations. This model was proposed and accepted by the scientific community when cancer mainly affected the elderly, but it does not explain the epidemiological observation of the continuous increase in cancer incidence among children and young adults. Somatic mutation theory has been proposed for a revision based on the emerging experimental evidence, as it does not fully address some issues that have proven to be crucial for carcinogenesis, namely: the inflammatory context of cancer; the key role played by the stroma, microenvironment, endothelial cells, activated macrophages, and surrounding tissues; and the distorted developmental course followed by the neoplastic tissue. Furthermore, SMT is often not able to consider either the existence of specific mutations resulting in a well-defined cancer type, or a clear relationship between mutations and tumor progression. Moreover, it does not explain the mechanism of action of the non-mutagenic and environmental carcinogens. In the last decade, cancer research has highlighted the prominent role of an altered regulation of gene expression, suggesting that cancer should be considered as a result of a polyclonal epigenetic disruption of stem/progenitor cells, mediated by tumour-inducing genes. The maternal and fetal exposure to a wide range of chemicals and environmental contaminants is raising the attention of the scientific community. Indeed, the most powerful procarcinogenic mechanisms of endocrine disruptors and other pollutants is linked to their potential to interfere epigenetically with the embryo-fetal programming of tissues and organs, altering the regulation of the genes involved in the cell cycle, cell proliferation, apoptosis, and other key signaling pathways. The embryo-fetal exposure to environmental, stressful, and proinflammatory triggers (first hit), seems to act as a ‘disease primer’, making fetal cells and tissues more susceptible to the subsequent environmental exposures (second hit), triggering the carcinogenic pathways. Furthermore, even at the molecular level, in carcinogenesis, ‘epigenetics precedes genetics’ as global DNA hypomethylation, and the hypermethylation of tumor suppressor genes are common both in cancerous and in precancerous cells, and generally precede mutations. These epigenetic models may better explain the increase of cancer and chronic/degenerative diseases in the last decades and could be useful to adopt appropriate primary prevention measures, essentially based on the reduction of maternal-fetal and child exposure to several procarcinogenic agents and factors dispersed in the environment and in the food-chains, as recently suggested by the World Health Organization.

Canalization and genetic assimilation: Reassessing the radicality of the Waddingtonian concept of inheritance of acquired characters

Genetic assimilation is often mixed up with the Baldwin effect. For Waddington, genetic assimilation was both a phenomenon and a specific mechanism of adaptive evolution which was grounded in the concept of canalization. This theoretical link between canalization and genetic assimilation, which was pivotal in Waddington's view, has been weakened since the early 1960s. The aim of the present article is to emphasize the specificity and to reassess the possible radicality of Waddington's proposal. What he claimed to have elaborated was an actual and genuine mechanism of inheritance of acquired characters that did not rely on soft Lamarckian inheritance. Consequently his "theory" of genetic assimilation, unlike the Baldwin effect, might not be as easily integrated in the framework of the Modern Synthesis.

The molecular and mathematical basis of Waddington's epigenetic landscape: a framework for post-Darwinian biology?

The Neo-Darwinian concept of natural selection is plausible when one assumes a straightforward causation of phenotype by genotype. However, such simple 1:1 mapping must now give place to the modern concepts of gene regulatory networks and gene expression noise. Both can, in the absence of genetic mutations, jointly generate a diversity of inheritable randomly occupied phenotypic states that could also serve as a substrate for natural selection. This form of epigenetic dynamics challenges Neo-Darwinism. It needs to incorporate the non-linear, stochastic dynamics of gene networks. A first step is to consider the mathematical correspondence between gene regulatory networks and Waddington's metaphoric 'epigenetic landscape', which actually represents the quasi-potential function of global network dynamics. It explains the coexistence of multiple stable phenotypes within one genotype. The landscape's topography with its attractors is shaped by evolution through mutational re-wiring of regulatory interactions - offering a link between genetic mutation and sudden, broad evolutionary changes.

On the intrinsic inevitability of cancer: from foetal to fatal attraction

The cracks in the paradigm of oncogenic mutations and somatic evolution as driving force of tumorigenesis, lucidly exposed by the dynamic heterogeneity of "cancer stem cells" or the diffuse results of cancer genome sequencing projects, indicate the need for a more encompassing theory of cancer that reaches beyond the current proximate explanations based on individual genetic pathways. One such integrative concept, derived from first principles of the dynamics of gene regulatory networks, is that cancerous cell states are attractor states, just like normal cell types are. Here we extend the concept of cancer attractors to illuminate a more profound property of cancer initiation: its inherent inevitability in the light of metazoan evolution. Using Waddington's Epigenetic Landscape as a conceptual aid, for which we present a mathematical and evolutionary foundation, we propose that cancer is intrinsically linked to ontogenesis and phylogenesis. This explanatory rather than enumerating review uses a formal argumentation structure that is atypical in modern experimental biology but may hopefully offer a new coherent perspective to reconcile many conflicts between new findings and the old thinking in the categories of linear oncogenic pathways.