'...a challenging and useful book, both because it provokes a careful scrutiny of one's own basic ideas regarding evolutionary theory, and because it cuts across so many biological disciplines.' -The Quarterly Review of Biology 'In my view, this work exemplifies Theoretical Biology at its best...here is rampant speculation that is consistently based on cautious reasoning from the available data. Even more refreshing is the absence of sloganeering, grandstanding, and 'isms'.' -Biology and Philosophy 'Epigenetics is fundamental to understanding both development and (...) gene expression, and not surprisingly, evolutionary biologists have long been fascinated with its proper place in evolutionary theory...Enter Jablonka and Lamb, who provide a thoughtful review of the recent molecular literature and suggest a number of potential consequences.' -EvolutionSince first publication of this controversial book, much of the initial opposition to the ideas it contained has been replaced by a general, although often grudging, acceptance of them. Advances in knowledge, especially at the molecular level, have enhanced general awareness and interest in epigenetics and the evolution of systems that store and transmit information and put any of the authors' speculations on a more solid basis. This paperback edition contains a new Preface that sets out the major changes in the scientific world and in the authors' own thinking that have occurred since the book was published. A new Appendix provides a selected bibliography of the many books and articles about epigenetic inheritance and its role in evolution that have appeared since first publication. (shrink)

This paper argues that nothing that has been discovered in the increasingly complex delails of gene regulation has provided any grounds to retract or qualify Crick's version of the central dogma. In particular it defends the role of the genes as the sole bearers of information, and argues that the mechanism of epigenetic modification of the DNA is but another vindication of Crick's version of the central dogma. The paper shows that arguments of C.K. Waters for the distinctive causual (...) role of the genes are equivalent in important respects to the present ones and concludes with a defense of the informational role of the genes against an argument from trans-actĭng genetic regulation due to Stotz. (shrink)

Advocates of Extended Evolutionary Synthesis claim that the gene-centric framework of Modern Synthesis (MS) inadequately addresses epigenetics and extended heredity. Historically, epigenetic inheritance relates to Lamarck's inheritance of acquired characters, which was widely accepted before the dominance of MS. In this talk, I argue that the challenge posed by epigenetic inheritance to the gene-centric view arises partly from the ambiguous use of "gene," "phenotype," and "environment" concepts. A functional analysis of the gene concept played in (...) the formal evolutionary models shows that the gene can include materials like exogenes, demonstrating the flexibility of evolutionary theory beyond the verbal MS. Properly understanding the evolutionary gene concept reveals that incorporating epigenetic inheritance does not demand a radical revision of the contemporary evolutionary theory. (shrink)

Since the 1990s, the terms “Lamarckism” and “Lamarckian” have seen a significant resurgence in biological publications. The discovery of new molecular mechanisms have been interpreted as evidence supporting the reality and efficiency of the inheritance of acquired characters, and thus the revival of Lamarckism. The present paper aims at giving a critical evaluation of such interpretations. I argue that two types of arguments allow to draw a clear distinction between the genuine Lamarckian concept of inheritance of acquired characters (...) and transgenerational epigenetic inheritance. The first concerns the explanandum of the processes under consideration: molecular mechanisms of transgenerational epigenetic inheritance are understood as evolved products of natural selection. This means that the kind of inheritance of acquired characters they might be responsible for is an obligatory emergent feature of evolution, whereas traditional Lamarckisms conceived the inheritance of acquired characters as a property inherent in living matter itself. The second argument concerns the explanans of the inheritance of acquired characters: in light of current knowledge, epigenetic mechanisms are not able to drive adaptive evolution by themselves. Emergent Lamarckian phenomena would be possible if and only if individual epigenetic variation allowed the inheritance of acquired characters to be a factor of unlimited change. This implies specific requirements for epigenetic variation, which I explicitly define and expand upon. I then show that given current knowledge, these requirements are not empirically grounded. (shrink)

Sperm, eggs and embryos are made up of more than genes, and there are indications that changes to non‐genetic structures in these elements of the germline can also be inherited. It is, therefore, a mistake to treat phrases like ‘germline inheritance’ and ‘genetic inheritance’ as simple synonyms, and bioethical discussion should expand its focus beyond alterations to the genome when considering the ethics of germline modification. Moreover, additional research on non‐genetic inheritance draws attention to a variety of (...) means whereby differences can be inherited in offspring generations that do not rely on differences in germline structures. Research on these diverse forms of inheritance challenges the notion that there is some special form of ethical concern that falls on germline interventions in general, and on interventions to the nuclear genome within the germline in particular. (shrink)

While heredity is predominantly controlled by what deoxyribonucleic acid (DNA) sequences are passed from parents to their offspring, a small but growing number of traits have been shown to be regulated in part by the non‐genetic inheritance of information. Transgenerational epigenetic inheritance is defined as heritable information passed from parents to their offspring without changing the DNA sequence. Work of the past seven decades has transitioned what was previously viewed as rare phenomenology, into well‐established paradigms by which (...) numerous traits can be modulated. For the most part, studies in model organisms have correlated transgenerational epigenetic inheritance phenotypes with changes in epigenetic modifications. The next steps for this field will entail transitioning from correlative studies to causal ones. Here, we delineate the major molecules that have been implicated in transgenerational epigenetic inheritance in both mammalian and non‐mammalian models, speculate on additional molecules that could be involved, and highlight some of the tools which might help transition this field from correlation to causation. (shrink)

Although the promyelocytic leukemia (PML) protein is renowned for regulating a wide range of cellular processes and as an essential component of PML nuclear bodies (PML‐NBs), the mechanisms through which it exerts its broad physiological impact are far from fully elucidated. Here, we review recent studies supporting an emerging view that PML's pleiotropic effects derive, at least partially, from its role in regulating histone H3.3 chromatin assembly, a critical epigenetic mechanism. These studies suggest that PML maintains heterochromatin organization by (...) restraining H3.3 incorporation. Examination of PML's contribution to H3.3 chromatin assembly in the context of the cell cycle and PML‐NB assembly suggests that PML represses heterochromatic H3.3 deposition during S phase and that transcription and SUMOylation regulate PML's recruitment to heterochromatin. Elucidating PML’ s contributions to H3.3‐mediated epigenetic regulation will provide insight into PML's expansive influence on cellular physiology and open new avenues for studying oncogenesis linked to PML malfunction. (shrink)

Heritable traits are predominantly encoded within genomic DNA, but it is now appreciated that epigenetic information is also inherited through DNA methylation, histone modifications, and small RNAs. Several examples of transgenerational epigenetic inheritance of traits have been documented in plants and animals. These include even the inheritance of traits acquired through the soma during the life of an organism, implicating the transfer of epigenetic information via the germline to the next generation. Small RNAs appear to (...) play a significant role in carrying epigenetic information across generations. This review focuses on how epigenetic information in the form of small RNAs is transmitted from the germline to the embryos through the gametes. We also consider how inherited epigenetic information is maintained across generations in a small RNA‐dependent and independent manner. Finally, we discuss how epigenetic traits acquired from the soma can be inherited through small RNAs. (shrink)

Literature on maternal exposures and the risk of epigenetic changes or diseases in the offspring is growing. Paternal contributions are often not considered. However, some animal and epidemiologic studies on various contaminants, nutrition, and lifestyle‐related conditions suggest a paternal influence on the offspring's future health. The phenotypic outcomes may have been attributed to DNA damage or mutations, but increasing evidence shows that the inheritance of environmentally induced functional changes of the genome, and related disorders, are (also) driven by (...) epigenetic components. In this essay we suggest the existence of epigenetic windows of susceptibility to environmental insults during sperm development. Changes in DNA methylation, histone modification, and non‐coding RNAs are viable mechanistic candidates for a non‐genetic transfer of paternal environmental information, from maturing germ cell to zygote. Inclusion of paternal factors in future research will ultimately improve the understanding of transgenerational epigenetic plasticity and health‐related effects in future generations. (shrink)

I argue that too much attention has been paid to the Baldwin effect. George Gaylord Simpson was probably right when he said that the effect is theoretically possible and may have actually occurred but that this has no major implications for evolutionary theory. The Baldwin effect is not even central to Baldwin's own account of social heredity and biology-culture co-evolution, an account that in important respects resembles the modern ideas of epigenetic inheritance and niche-construction.

In criminal proceedings, offenders are sentenced based on doctrines of culpability and punishment that theorize why they are guilty and why they should be punished. Throughout human history, these doctrines have largely been grounded in legal-policy constructions around retribution, safety, deterrence, and closure, mostly derived from folk psychology, natural philosophy, sociocultural expectations, public-order narratives, and common sense. On these premises, justice systems have long been designed to account for crimes and their underlying intent, with experience and probabilistic assumptions shaping theoretical (...) discourses on the nature of crimes and offenders’ punishability. As scientific discoveries, inventions, and methodologies progressively developed to refine such doctrines and displace long-held assumptions, criminal courtrooms have increasingly witnessed counsels and judges relying on scientific evidence to submit, dispute, or validate claims. For instance, over the last century, criminal courtrooms have selectively admitted neuroscientific models, exams, and insights claiming to revolutionize our understanding of who is culpable and deserving of punishment. Most recently, advancements in epigenetics have promised even more profound challenges to long-standing criminal law doctrines. This article examines the reasons reversibility and inheritability of epigenetic markers might warrant revising culpability and punishment and concludes that epigenetic findings are not yet robust enough to justify such revisions. (shrink)

What role does non-genetic inheritance play in evolution? In recent work we have independently and collectively argued that the existence and scope of non-genetic inheritance systems, including epigenetic inheritance, niche construction/ecological inheritance, and cultural inheritance—alongside certain other theory revisions—necessitates an extension to the neo-Darwinian Modern Synthesis (MS) in the form of an Extended Evolutionary Synthesis (EES). However, this argument has been challenged on the grounds that non-genetic inheritance systems are exclusively proximate mechanisms that (...) serve the ultimate function of calibrating organisms to stochastic environments. In this paper we defend our claims, pointing out that critics of the EES (1) conflate non-genetic inheritance with early 20th-century notions of soft inheritance; (2) misunderstand the nature of the EES in relation to the MS; (3) confuse individual phenotypic plasticity with trans-generational non-genetic inheritance; (4) fail to address the extensive theoretical and empirical literature which shows that non-genetic inheritance can generate novel targets for selection, create new genetic equilibria that would not exist in the absence of non-genetic inheritance, and generate phenotypic variation that is independent of genetic variation; (5) artificially limit ultimate explanations for traits to gene-based selection, which is unsatisfactory for phenotypic traits that originate and spread via non-genetic inheritance systems; and (6) fail to provide an explanation for biological organization. We conclude by noting ways in which we feel that an overly gene-centric theory of evolution is hindering progress in biology and other sciences. (shrink)

Recent investigations with non‐model species and whole‐genome approaches have challenged several paradigms in animal epigenetics. They revealed that epigenetic variation in populations is not the mere consequence of genetic variation, but is a semi‐independent or independent source of phenotypic variation, depending on mode of reproduction. DNA methylation is not positively correlated with genome size and phylogenetic position as earlier believed, but has evolved differently between and within higher taxa. Epigenetic marks are usually not completely erased in the zygote (...) and germ cells as generalized from mouse, but often persist and can be transgenerationally inherited, making them evolutionarily relevant. Gene body methylation and promoter methylation are similar in vertebrates and invertebrates with well methylated genomes but transposon silencing through methylation is variable. The new data also suggest that animals use epigenetic mechanisms to cope with rapid environmental changes and to adapt to new environments. The main benefiters are asexual populations, invaders, sessile taxa and long‐lived species. (shrink)

How epigenetic mechanisms regulate genome output and response to stimuli is a fundamental question in development and disease. Past decades have made tremendous progress in deciphering the regulatory relationships involved by correlating aggregated (epi)genomics profiles with global perturbations. However, the recent development of epigenetic editing technologies now enables researchers to move beyond inferred conclusions, towards explicit causal reasoning, through 'programing’ precise chromatin perturbations in single cells. Here, we first discuss the major unresolved questions in the epigenetics field that (...) can be addressed by programable epigenome editing, including the context‐dependent function and memory of chromatin states. We then describe the epigenetic editing toolkit focusing on CRISPR‐based technologies, and highlight its achievements, drawbacks and promise. Finally, we consider the potential future application of epigenetic editing to the study and treatment of specific disease conditions. (shrink)

In recent decades, advances in the life sciences have created an unprecedentedly detailed picture of heredity and the formation of the phenotype where clusters of simplistic reductionist and deterministic views and interpretations have begun to lose ground to more complex and holistic notions. The developments in gene regulation and epigenetics have become a vivid emblem of the ongoing ‘softening’ of heredity. Despite this headway, the outlook and rhetoric widely popular in the twentieth century favoring the ‘gene’ in the ‘genegenetic plasticityphenotypeenvironment’ (...) tetrad have not been successfully tackled but continue to exist in parallel with a new, equally monochromatic, viewpoint championing genetic plasticity. An examination of epigenetics and its presentation in the public sphere, open to a conversation with the social disciplines and philosophy, could address this dichotomy and contribute to the discourse. This article outlines key biological aspects of epigenetics and discusses the language, presentation and wider resonance of this field of life science research. (shrink)

August Weismann rejected the inheritance of acquired characters on the grounds that changes to the soma cannot produce the kind of changes to the germ-plasm that would result in the altered character being transmitted to subsequent generations. His intended distinction, between germ-plasm and soma, was closer to the modern distinction between genotype and phenotype than to the modern distinction between germ cells and somatic cells. Recently, systems of epigenetic inheritance have been claimed to make possible the (...) class='Hi'>inheritance of acquired characters. I argue that the sense in which these claims are true does not challenge fundamental tenets of neo-Darwinism. Epigenetic inheritance expands the range of options available to genes but evolutionary adaptation remains the product of natural selection of ‘random’ variation. (shrink)

We hypothesize that heritable epigenetic changes can affect rates of fitness increase as well as patterns of genotypic and phenotypic change during adaptation. In particular, we suggest that when natural selection acts on pure epigenetic variation in addition to genetic variation, populations adapt faster, and adaptive phenotypes can arise before any genetic changes. This may make it difficult to reconcile the timing of adaptive events detected using conventional population genetics tools based on DNA sequence data with environmental drivers (...) of adaptation, such as changes in climate. Epigenetic modifications are frequently associated with somatic cell differentiation, but recently epigenetic changes have been found that can be transmitted over many generations. Here, we show how the interplay of these heritable epigenetic changes with genetic changes can affect adaptive evolution, and how epigenetic changes affect the signature of selection in the genetic record. (shrink)

Recent epidemiological reports of associations between socioeconomic status and epigenetic markers that predict vulnerability to diseases are bringing to light substantial biological effects of social inequalities. Here, we start the discussion of the moral consequences of these findings. We firstly highlight their explanatory importance in the context of the research program on the Developmental Origins of Health and Disease (DOHaD) and the social determinants of health. In the second section, we review some theories of the moral status of health (...) inequalities. Rather than a complete outline of the debate, we single out those theories that rest on the principle of equality of opportunity and analyze the consequences of DOHaD and epigenetics for these particular conceptions of justice. We argue that DOHaD and epigenetics reshape the conceptual distinction between natural and acquired traits on which these theories rely and might provide important policy tools to tackle unjust distributions of health. (shrink)

The recent explosion of interest in epigenetics is often portrayed as the dawning of a scientific revolution that promises to transform biomedical science along with developmental and evolutionary biology. Much of this enthusiasm surrounds what we call the epigenetic switch hypothesis, which regards certain examples of epigenetic inheritance as an adaptive organismal response to environmental change. This interpretation overlooks an alternative explanation in terms of coevolutionary dynamics between parasitic transposons and the host genome. This raises a question (...) about whether epigenetics researchers tend to overlook transposon dynamics more generally. To address this question, we surveyed a large sample of scientific publications on the topics of epigenetics and transposons over the past fifty years. We found that enthusiasm for epigenetics is often inversely related to interest in transposon dynamics across the four disciplines we examined. Most surprising was a declining interest in transposons within biomedical science and cellular and molecular biology over the past two decades. Also notable was a delayed and relatively muted enthusiasm for epigenetics within evolutionary biology. An analysis of scientific abstracts from the past twenty-five years further reveals systematic differences among disciplines in their uses of the term epigenetic, especially with respect to heritability commitments and functional interpretations. Taken together, these results paint a nuanced picture of the rise of epigenetics and the possible neglect of transposon dynamics, especially among biomedical scientists. (shrink)

Our paper aims at bringing to the fore the crucial role that habits play in Charles Darwin’s theory of evolution by means of natural selection. We have organized the paper in two steps: first, we analyse value and functions of the concept of habit in Darwin's early works, notably in his Notebooks, and compare these views to his mature understanding of the concept in the Origin of Species and later works; second, we discuss Darwin’s ideas on habits in the light (...) of today’s theories of epigenetic inheritance, which describe the way in which the functioning and expression of genes is modified by the environment, and how these modifications are transmitted over generations. We argue that Darwin’s lasting and multifaceted interest in the notion of habit, throughout his intellectual life, is both conceptually and methodologically relevant. From a conceptual point of view, intriguing similarities can be found between Darwin’s (early) conception of habit and contemporary views on epigenetic inheritance. From a methodological point of view, we suggest that Darwin’s plastic approach to habits, from his early writings up to the mature works, can provide today’s evolutionary scientists with a viable methodological model to address the challenging task of extending and expanding evolutionary theory, with particular reference to the integration of epigenetic mechanisms into existing models of evolutionary change. Over his entire life Darwin has modified and reassessed his views on habits as many times as required by evidence: his work on this notion may represent the paradigm of a habit of good scientific research methodology. (shrink)

The environment can have a long‐lasting influence on an individual's physiology and behavior. While some environmental conditions can be beneficial and result in adaptive responses, others can lead to pathological behaviors. Many studies have demonstrated that changes induced by the environment are expressed not only by the individuals directly exposed, but also by the offspring sometimes across multiple generations. Epigenetic alterations have been proposed as underlying mechanisms for such transmissible effects. Here, we review the most relevant literature on these (...) changes and the developmental stages they affect the most. We discuss current evidence for transgenerational effects of prenatal and postnatal factors on bodily functions and behavioral responses, and the potential epigenetic mechanisms involved. We also discuss the need for a careful evaluation of the evolutionary importance with respect to health and disease, and possible directions for future research in the field. (shrink)

Epigenetic information is encoded by DNA methylation and by covalent modifications of histone tails. While defined epigenetic modification patterns have been frequently correlated with particular states of gene activity, very little is known about the integration level of epigenetic signals. Recent experiments have resulted in the characterization of several epigenetic adaptors that mediate interactions between distinct modifications. These adaptors include methyl‐DNA binding proteins, chromatin remodelling enzymes and siRNAs. Complex interactions between epigenetic modifiers and adaptors provide (...) the foundation for the stability of epigenetic inheritance. In addition, they also provide an explanation for the long‐range effects of epigenetic mechanisms. We propose that a major aspect of epigenetic regulation lies in the modification of chromosome architecture and that local changes in gene expression would be secondary consequences. This view is consistent with many results from recent genomic analyses. BioEssays 25:792–797, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

The information contained within the linear sequence of bases (the genome) must be faithfully replicated in each cell cycle, with a balance of constancy and variation taking place over the course of evolution. Recently, it has become clear that additional information important for genetic regulation is contained within the chromatin proteins associated with DNA (the epigenome). Epigenetic information also must be faithfully duplicated in each cell cycle, with a balance of constancy and variation taking place during the course of (...) development to achieve differentiation while maintaining identity within cell lineages. Both the genome and the epigenome are synthesized at the replication fork, so the events occurring during S‐phase provide a critical window of opportunity for eliciting change or maintaining existing genetic states. Cells discriminate between different states of chromatin through the activities of proteins that selectively modify the structure of chromatin. Several recent studies report the localization of certain chromatin modifying proteins to replication forks at specific times during S‐phase. Since transcriptionally active and inactive chromosome domains generally replicate at different times during S‐phase, this spatiotemporal regulation of chromatin assembly proteins may be an integral part of epigenetic inheritance. BioEssays 25:647–656, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

Organisms inherit various kinds of developmental information and cues from their parents. The study of inheritance systems is aimed at identifying and classifying the various mechanisms and processes of heredity, the types of hereditary information that is passed on by each, the functional interaction between the different systems, and the evolutionary consequences of these properties. We present the discussion of inheritance systems in the context of several debates. First, between proponents of monism about heredity (gene-centric views), holism about (...) heredity (Developmental Systems Theory), and those stressing the role of multiple systems of inheritance. Second, between those analyzing inheritance solely in terms of replication and transmission, and views that stress the multi-generation reproduction of phenotypic traits. A third debate is concerned with different criteria that have been proposed for identifying and delimiting inheritance systems. A fourth controversy revolves around the significance of the “Lamarckian” aspects of some of the inheritance systems that have been identified, such as epigenetic inheritance and behavioral inheritance, that allow the transmission of environmentally induced characters (i.e., “soft inheritance”). (shrink)

Ideas about heredity and evolution are undergoing a revolutionary change. New findings in molecular biology challenge the gene-centered version of Darwinian theory according to which adaptation occurs only through natural selection of chance DNA variations. In Evolution in Four Dimensions, Eva Jablonka and Marion Lamb argue that there is more to heredity than genes. They trace four "dimensions" in evolution -- four inheritance systems that play a role in evolution: genetic, epigenetic, behavioral, and symbolic. These systems, they argue, (...) can all provide variations on which natural selection can act. Evolution in Four Dimensions offers a richer, more complex view of evolution than the gene-based, one-dimensional view held by many today. The new synthesis advanced by Jablonka and Lamb makes clear that induced and acquired changes also play a role in evolution.After discussing each of the four inheritance systems in detail, Jablonka and Lamb "put Humpty Dumpty together again" by showing how all of these systems interact. They consider how each may have originated and guided evolutionary history and they discuss the social and philosophical implications of the four-dimensional view of evolution. Each chapter ends with a dialogue in which the authors engage the contrarieties of the fictional "I.M.," or Ifcha Mistabra -- Aramaic for "the opposite conjecture" -- refining their arguments against I.M.'s vigorous counterarguments. The lucid and accessible text is accompanied by artist-physician Anna Zeligowski's lively drawings, which humorously and effectively illustrate the authors' points. (shrink)

Everyone has heard of ‘epigenetics’, but the term means different things to different researchers. Four important contemporary meanings are outlined in this paper. Epigenetics in its various senses has implications for development, heredity, and evolution, and also for medicine. Concerning development, it cements the vision of a reactive genome strongly coupled to its environment. Concerning heredity, both narrowly epigenetic and broader ‘exogenetic’ systems of inheritance play important roles in the construction of phenotypes. A thoroughly epigenetic model of (...) development and evolution was Waddington’s aim when he introduced the term ‘epigenetics’ in the 1940s, but it has taken the modern development of molecular epigenetics to realize this aim. In the final sections of the paper we briefly outline some further implications of epigenetics for medicine and for the nature/nurture debate. (shrink)

Current knowledge of the genetic, epigenetic, behavioural and symbolic systems of inheritance requires a revision and extension of the mid-twentieth-century, gene-based, 'Modern Synthesis' version of Darwinian evolutionary theory. We present the case for this by first outlining the history that led to the neo-Darwinian view of evolution. In the second section we describe and compare different types of inheritance, and in the third discuss the implications of a broad view of heredity for various aspects of evolutionary theory. (...) We end with an examination of the philosophical and conceptual ramifications of evolutionary thinking that incorporates multiple inheritance systems. (shrink)

This article examines how people of color can biologically inherit the deleterious effects of white racism. Drawing primarily on the field of epigenetics, I demonstrate how transgenerational racial disparities are in fact racist disparities that can be manifest physiologically, helping constitute the chemicals, hormones, cells, and fibers of the human body. Epigenetics can be used to demonstrate how white racism can have durable effects on the biological constitution of human beings that are not limited to the specific person who is (...) the target of white racism, but instead extend to that person's offspring. In this way, the field of epigenetics can help philosophers and others understand the transgenerational biological impact of social forces such as white racism. It reveals that the damage done by white racism is more extensive than critical philosophers of race might have realized, and also that interventions against white racism must address not just the economic, geographical, social, and psychological, but also the biological aspects of human existence. In particular, the article examines racist disparities in preterm birth rates and argues that the scope and significance of prenatal care for African American women must be expanded intergenerationally and include wide-scale forms of racial justice. (shrink)

We describe an approach to measuring biological information where ‘information’ is understood in the sense found in Francis Crick’s foundational contributions to molecular biology. Genes contain information in this sense, but so do epigenetic factors, as many biologists have recognized. The term ‘epigenetic’ is ambiguous, and we introduce a distinction between epigenetic and exogenetic inheritance to clarify one aspect of this ambiguity. These three heredity systems play complementary roles in supplying information for development. -/- We then (...) consider the evolutionary significance of the three inheritance systems. Whilst the genetic inheritance system was the key innovation in the evolution of heredity, in modern organisms the three systems each play important and complementary roles in heredity and evolution. -/- Our focus in the earlier part of the paper is on ‘proximate biology’, where information is a substantial causal factor that causes organisms to develop and causes offspring to resemble their parents. But much philosophical work has focused on information in ‘ultimate biology’. Ultimate information is a way of talking about the evolutionary design of the mechanisms of development and inheritance. We conclude by clarifying the relationship between the two. Ultimate information is not a causal factor that acts in development or heredity, but it can help to explain the evolution of proximate information, which is. (shrink)

We compared two digital humanities methods in the analysis of a contested scientific term. “Epigenetics” is as enigmatic as it is popular. Some authors argue that its meaning has diluted over time as this term has come to describe a widening range of entities and mechanisms (Haig, International Journal of Epidemiology 41:13–16, 2012). Others propose both a Waddingtonian “broad sense” and a mechanistic “narrow sense” definition to capture its various scientific uses (Stotz and Griffiths, History and Philosophy of the Life (...) Sciences 38:22, 2016). We evaluated these proposals by first replicating a recent analysis by (Linquist and Fullerton, Theoretical Medicine and Bioethics 42:137–154, 2021). We analyzed the 1100 most frequently cited abstracts on epigenetics across four disciplines: proximal biology, biomedicine, general biology, and evolution. Each abstract was coded for its heritability commitments (if any) and functional interpretation. A second study applied LDA topic modelling to the same corpus, thus providing a useful methodological comparison. The two methods converged on a discipline-relative ambiguity. Within such disciplines as biomedicine or molecular biology that focus on proximate mechanisms, “epigenetic(s)” refers to a range of molecular structures while specifying nothing in particular about their heritability. This proximal conception was primarily associated with the functions of gene regulation and disease. In contrast, a second relatively uncommon sense of “epigenetic(s)” is restricted to a small proportion of evolutionary abstracts. It refers to many of the same molecular structures, but regards them as trans-generationally inherited and associated with adaptive phenotypic plasticity. This finding underscores the benefit of digital tools in complementing traditional conceptual analysis. Philosophers should be cautious not to conflate the relatively uncommon evolutionary sense of epigenetics with the more widely used proximal conception. (shrink)

Current knowledge of the genetic, epigenetic, behavioural and symbolic systems of inheritance requires a revision and extension of the mid-twentieth-century, gene-based, 'Modern Synthesis' version of Darwinian evolutionary theory. We present the case for this by first outlining the history that led to the neo-Darwinian view of evolution. In the second section we describe and compare different types of inheritance, and in the third discuss the implications of a broad view of heredity for various aspects of evolutionary theory. (...) We end with an examination of the philosophical and conceptual ramifications of evolutionary thinking that incorporates multiple inheritance systems. (shrink)

Considering the recent epigenetic studies on the transgenerational transmission of trauma, this article aims to 1) explore its ethical implications for the concept and nature of moral damage, and 2) offer normative suggestions on collective responsibilities both synchronic and diachronic. To do so, I first address recent epigenetic studies’ showing the crystallization of emotional information through generations, and second, defend that a unified approach to the concept of ghost damage may be useful to categorize this phenomenon, facilitate future (...) research on this type of moral damage, and recognize its importance in the identification of hermeneutical injustice. Finally, I suggest that granting a right to transgenerational information may help avoid the perpetuation of inherited damage that jeopardize mental and physical health in the offspring. (shrink)

Bourdieu suggested that the habitus contains the ‘genetic information’ which both allows and disposes successive generations to reproduce the world they inherit from their parents’ generation. While his writings on habitus are concerned with embodied dispositions, biological processes are not a feature of the practical reason of habitus. Recent critiques of the separate worlds of biology and culture, and the rise in epigenetics, provide new opportunities for expanding theoretical concepts like habitus. Using obesity science as a case study we attempt (...) to conceptualise the enfolding of biological and social processes (via a Deleuzian metaphor) to develop a concept of biohabitus – reconfiguring how social and biological environments interact across the life course, and may be transmitted and transformed intergenerationally. In conclusion we suggest that the enfolding and reproduction of social life that Bourdieu articulated as habitus is a useful theoretical frame that can be enhanced to critically develop epigenetic understandings of obesity, and vice versa. (shrink)

Every cell, tissue, organ and organism is competent to use signs to exchange information reaching common coordinations and organisations of both single cell and group behavior. These sign-mediated interactions we term biological communication. The regulatory system that works in development, morphology, cell fate and identity, physiology, genetic instructions, immunity, memory/learning, physical and mental disease depends on epigenetic marks. The communication of cells, persistent viruses and their defectives such as mobile genetic elements and RNA networks ensures both the transport of (...) regulatory instructions and the reprogramming of these instructions. But how are the different states of the epigenome orchestrated? The epigenetic pathways respond to various signaling cues such as DNA methylation, histone variants, histone modifications, chromatin structure, nucleosome remodeling, and epigenetic interactions. Epigenetic signals are responsible for the establishment, maintenance and reversal of transcriptional states that are fundamental for the cell's ability to memorize past events, such as changes in the external environment, socio-sphere or developmental cues. External signals trigger changes in the epigenome, allowing cells to respond dynamically. Internal signals direct activities that are necessary for body maintenance, and repairing damaged tissues and organs. With the emergence of epigenetic memory, organisms can fix historical and context dependent impressive experiences. Evolution from now on learnt to learn. Learning means organisms can avoid reproduction of always the same. This is key to adaptation. However, inheritance of acquired characteristics is only one of the many examples of the explanatory power of epigenetics. Behavioral epigenetics demonstrates the way in which environmental and social experiences produce individual differences in behaviour, cognition, personality, and mental health. This book assembles experts to outline the various motifs of all kinds of epigenetic regulation of cells throughout their lives. (shrink)

Our view of heredity can potentially be distorted by the ease of introducing heritable changes in the replicating gene sequences but not in the cycling assembly of regulators around gene sequences. Here, key experiments that have informed the understanding of heredity are reinterpreted to highlight this distortion and the possible variety of heritable changes are considered. Unlike heritable genetic changes, which are always associated with mutations in gene sequence, heritable epigenetic changes can be associated with physical or chemical changes (...) in molecules or only changes in the system. The transmission of cycling stores along the continuous lineage of cells that connects successive generations creates waves of activity and localization of the molecules that together form the cell code for development in each generation. As a result, heritable epigenetic changes can include any that can alter a wave such as changes in form, midline, frequency, amplitude, or phase. Testing this integrated view of all heritable information will require the concerted application of multiple experimental approaches across generations. (shrink)

There is increasing evidence for epigenetically mediated transgenerational inheritance across taxa. However, the evolutionary implications of such alternative mechanisms of inheritance remain unclear. Herein, we show that epigenetic mechanisms can serve two fundamentally different functions in transgenerational inheritance: (i) selection-based effects, which carry adaptive information in virtue of selection over many generations of reliable transmission; and (ii) detection-based effects, which are a transgenerational form of adaptive phenotypic plasticity. The two functions interact differently with a third form (...) of epigenetic information transmission, namely information about cell state transmitted for somatic cell heredity in multicellular organisms. Selection-based epigenetic information is more likely to conflict with somatic cell inheritance than is detection-based epigenetic information. Consequently, the evolutionary implications of epigenetic mechanisms are different for unicellular and multicellular organisms, which underscores the conceptual and empirical importance of distinguishing between these two different forms of transgenerational epigenetic effect. (shrink)

Jablonka & Lamb's (J&L's) book is refreshing in that it debunks the exclusively gene-centered approach used these days to explain almost anything about life and human behavior. The book is very accessible and most convincing when the authors discuss biological theories of genetic and epigenetic inheritance, but it does not shy away from the more slippery terrain of behavioral and symbolic inheritance, and specifically the origins of language. But is the analogy appropriate?

Transcriptome sequencing has identified more than a thousand potentially imprinted genes in the mouse brain. This comes as a revelation to someone who cut his teeth on the identification of imprinted genes when only a handful was known. Genomic imprinting, an epigenetic mechanism that determines expression of alleles according to sex of transmitting parent, was discovered over 25 years ago in mice but remains an enigmatic phenomenon. Why do these genes disobey the normal Mendelian logic of inheritance, do (...) they function in specific processes, and how is their imprinting conferred? Next generation sequencing technologies are providing an unprecedented opportunity to survey the whole genome for imprinted genes and are beginning to reveal that imprinting may be more pervasive than we had come to believe. Such advances should lay the foundation for a definitive account of imprinting, but may also challenge accepted views on what it means to be imprinted.Editor's suggested further reading in BioEssays RNA as the substrate for epigenome‐environment interactions Abstract. (shrink)

What are the effects of our environment on human development and the next generation? Numerous studies have provided ample evidence that a healthy environment and lifestyle of the mother is important for her offspring. Biological mechanisms underlying these environmental influences have been proposed to involve alterations in the epigenome. Is there enough evidence to suggest a similar contribution from the part of the father? Animal models provide proof of a transgenerational epigenetic effect through the paternal germ line, but can (...) this be translated to humans? To date, literature on fathers is scarce. Human studies do not always incorporate appropriate tools to evaluate paternal influences or epigenetic effects. In reviewing the literature, I stress the need to explore and recognize paternal contributions to offspring's health within the Developmental Origins of Health and Disease hypothesis, and coin this new concept the Paternal Origins of Health and Disease paradigm. A better understanding of preconceptional origins of disease through the totality of paternal exposures, or the paternal exposome, will provide evidence-based public health recommendations for future fathers. A father's hereditary contribution exceeds that of his DNA sequence. The environment can regulate systems such as the sperm epigenome, which is inheritable as well and may steer the genome and health status of his offspring. We here suggest a new concept, the Paternal Origins of Health and Disease, as part of the DOHaD theory. (shrink)

Throughout evolution, there has been interaction and exchange between RNA pools in the environment, and DNA and RNA pools of eukaryotic organisms. Metagenomic and metatranscriptomic sequencing of invertebrate hosts and their microbiota has revealed a rich evolutionary history of RNA virus shuttling between species. Horizontal transfer adapted the RNA pool for successful future interactions which lead to zoonotic transmission and detrimental RNA viral pandemics like SARS‐CoV2. In eukaryotes, noncoding RNA (ncRNA) is an established mechanism derived from prokaryotes to defend against (...) viral attack through innate immunity and regulation of host‐derived mRNA. Transgenerational inheritance of ncRNA is evidence for feedforward adaptive immunity and epigenetically encoded environmental change across generations, which may explain the ‘‘missing heritability’’ of common disease. Causal graph theory and the Price Equation can model epigenetic inheritance involving dynamic internal and external RNA pools. Experimental designs should include metatranscriptomic analyses to understand how ncRNA responds to rapidly changing environmental conditions, within and between organisms, and across generations. (shrink)

Back in 1942, C.H. Waddington proposed a new mechanism of evolutionary change, which he termed “genetic assimilation”.1,2 The idea was that certain environmental or genetic factors can disrupt the normally canalized (i.e., stable) course of development of living organisms. This disruption may then generate phenotypic variation that could allow a population to persist in a novel or stressful environment until new mutations would eventually let natural selection fix (“assimilate”) the advantageous phenotypic variants.