The extended evolutionary synthesis: its structure, assumptions and predictions

I am a fake loop: The effects of advertising-based artificial selection

Mimicry is common among animals, plants, and other kingdoms of life. Humans in late capitalism, however, have devised an unique method of mimicking the signs that trigger evolutionarily-programmed instincts of their own species in order to manipulate them. Marketing and advertising are the most pervasive and sophisticated forms of known human mimicry, deliberately hijacking our instincts in order to select on the basis of one dimension only: profit. But marketing and advertising also strangely undermines their form of mimicry deceiving both the intended targets and the signaler simultaneously. Human forms of mimicry have the regular consequence of deceiving the imitator, reducing meta-cognitive awareness of the act and intentions surrounding such deception. Therefore, the deceiver in the end deceives himself as well as intended targets. Drawing on scholarship applying Niko Tinbergen's the ethological discovery of supernormal stimuli in animals to humans, this article analyzes sophisticated mass mimicry in contemporary culture, in both intended and unintended forms.

Plastic multicellular development of Myxococcus xanthus: genotype-environment interactions in a physical gradient

In order to investigate the contribution of the physical environment to variation in multicellular development of Myxococcus xanthus, phenotypes developed by different genotypes in a gradient of substrate stiffness conditions were quantitatively characterized. Statistical analysis showed that plastic phenotypes result from the genotype, the substrate conditions and the interaction between them. Also, phenotypes were expressed in two distinguishable scales, the individual and the population levels, and the interaction with the environment showed scale and trait specificity. Overall, our results highlight the constructive role of the physical context in the development of microbial multicellularity, with both ecological and evolutionary implications.

Plasticity-led evolution: evaluating the key prediction of frequency-dependent adaptation

Plasticity-led evolution occurs when a change in the environment triggers a change in phenotype via phenotypic plasticity, and this pre-existing plasticity is subsequently refined by selection into an adaptive phenotype. A critical, but largely untested prediction of plasticity-led evolution (and evolution by natural selection generally) is that the rate and magnitude of evolutionary change should be positively associated with a phenotype's frequency of expression in a population. Essentially, the more often a phenotype is expressed and exposed to selection, the greater its opportunity for adaptive refinement. We tested this prediction by competing against each other spadefoot toad tadpoles from different natural populations that vary in how frequently they express a novel, environmentally induced carnivore ecomorph. As expected, laboratory-reared tadpoles whose parents were derived from populations that express the carnivore ecomorph more frequently were superior competitors for the resource for which this ecomorph is specialized-fairy shrimp. These tadpoles were better at using this resource both because they were more efficient at capturing and consuming shrimp and because they produced more exaggerated carnivore traits. Moreover, they exhibited these more carnivore-like features even without experiencing the inducing cue, suggesting that this ecomorph has undergone an extreme form of plasticity-led evolution-genetic assimilation. Thus, our findings provide evidence that the frequency of trait expression drives the magnitude of adaptive refinement, thereby validating a key prediction of plasticity-led evolution specifically and adaptive evolution generally.

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

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

A problem in theory

The replication crisis facing the psychological sciences is widely regarded as rooted in methodological or statistical shortcomings. We argue that a large part of the problem is the lack of a cumulative theoretical framework or frameworks. Without an overarching theoretical framework that generates hypotheses across diverse domains, empirical programs spawn and grow from personal intuitions and culturally biased folk theories. By providing ways to develop clear predictions, including through the use of formal modelling, theoretical frameworks set expectations that determine whether a new finding is confirmatory, nicely integrating with existing lines of research, or surprising, and therefore requiring further replication and scrutiny. Such frameworks also prioritize certain research foci, motivate the use diverse empirical approaches and, often, provide a natural means to integrate across the sciences. Thus, overarching theoretical frameworks pave the way toward a more general theory of human behaviour. We illustrate one such a theoretical framework: dual inheritance theory.

How a growing organismal perspective is adding new depth to integrative studies of morphological evolution

Over the past half century, the field of Evolutionary Developmental Biology, or Evo-devo, has integrated diverse fields of biology into a more synthetic understanding of morphological diversity. This has resulted in numerous insights into how development can evolve and reciprocally influence morphological evolution, as well as generated several novel theoretical areas. Although comparative by default, there remains a great gap in our understanding of adaptive morphological diversification and how developmental mechanisms influence the shape and pattern of phenotypic variation. Herein we highlight areas of research that are in the process of filling this void, and areas, if investigated more fully, that will add new insights into the diversification of morphology. At the centre of our discussion is an explicit awareness of organismal biology. Here we discuss an organismal framework that is supported by three distinct pillars. First, there is a need for Evo-devo to adopt a high-resolution phylogenetic approach in the study of morphological variation and its developmental underpinnings. Secondly, we propose that to understand the dynamic nature of morphological evolution, investigators need to give more explicit attention to the processes that generate evolutionarily relevant variation at the population level. Finally, we emphasize the need to address more thoroughly the processes that structure variation at micro- and macroevolutionary scales including modularity, morphological integration, constraint, and plasticity. We illustrate the power of these three pillars using numerous examples from both invertebrates and vertebrates to emphasize that many of these approaches are already present within the field, but have yet to be formally integrated into many research programs. We feel that the most exciting new insights will come where the traditional experimental approaches to Evo-devo are integrated more thoroughly with the principles of this organismal framework.

Predicting mutational routes to new adaptive phenotypes

Predicting evolutionary change poses numerous challenges. Here we take advantage of the model bacterium Pseudomonas fluorescens in which the genotype-to-phenotype map determining evolution of the adaptive 'wrinkly spreader' (WS) type is known. We present mathematical descriptions of three necessary regulatory pathways and use these to predict both the rate at which each mutational route is used and the expected mutational targets. To test predictions, mutation rates and targets were determined for each pathway. Unanticipated mutational hotspots caused experimental observations to depart from predictions but additional data led to refined models. A mismatch was observed between the spectra of WS-causing mutations obtained with and without selection due to low fitness of previously undetected WS-causing mutations. Our findings contribute toward the development of mechanistic models for forecasting evolution, highlight current limitations, and draw attention to challenges in predicting locus-specific mutational biases and fitness effects.

Transgenerational plasticity and selection shape the adaptive potential of sticklebacks to salinity change

In marine climate change research, salinity shifts have been widely overlooked. While widespread desalination effects are expected in higher latitudes, salinity is predicted to increase closer to the equator. We took advantage of the steep salinity gradient of the Baltic Sea as a space-for-time design to address effects of salinity change on populations. Additionally, genetic diversity, a prerequisite for adaptive responses, is reduced in Baltic compared to Atlantic populations. On the one hand, adaptive transgenerational plasticity (TGP) might buffer the effects of environmental change, which may be of particular importance under reduced genetic variation. On the other hand, physiological trade-offs due to environmental stress may hamper parental provisioning to offspring thereby intensifying the impact of climate change across generations (nonadaptive TGP). Here, we studied both hypothesis of adaptive and nonadaptive TGP in the three-spined stickleback (Gasterosteus aculeatus) fish model along the strong salinity gradient of the Baltic Sea in a space-for-time experiment. Each population tolerated desalination well, which was not altered by parental exposure to low salinity. Despite a common marine ancestor, populations locally adapted to low salinity lost their ability to cope with fully marine conditions, resulting in lower survival and reduced relative fitness. Negative transgenerational effects were evident in early life stages, but disappeared after selection via mortality occurred during the first 12-30 days posthatch. Modeling various strengths of selection, we showed that nonadaptive transgenerational plasticity accelerated evolution by increasing directional selection within the offspring generation. Qualitatively, when genetic diversity is large, we predict that such effects will facilitate rapid adaptation and population persistence, while below a certain threshold populations suffer a higher risk of local extinction. Overall, our results suggest that transgenerational plasticity and selection are not independent of each other and thereby highlight a current gap in TGP studies.

Assortative Mating by an Obliquely Transmitted Local Cultural Trait Promotes Genetic Divergence: A Model

The effect of learned culture (e.g., birdsong dialects and human languages) on genetic divergence is unclear. Previous theoretical research suggests that because oblique learning allows phenotype transmission from individuals with no offspring to an unrelated individual in the next generation, the effect of sexual selection on the learned trait is masked. However, I propose that migration and spatially constrained learning can form statistical associations between cultural and genetic traits, which may allow selection on the cultural traits to indirectly affect the genetic traits. Here, I build a population genetic model that allows such statistical associations to form and find that sexual selection and divergent selection on the cultural trait can indeed help maintain genetic divergence through such statistical associations, while selection against genetic hybrids does not affect cultural trait divergence. Furthermore, I find that even when the cultural trait changes over time due to drift and mutation, it can still help maintain genetic divergence. These results suggest the role of obliquely transmitted traits in evolution may be underrated, and the lack of one-to-one associations between cultural and genetic traits may not be sufficient to disprove the role of culture in genetic divergence.

Free-energy minimization in joint agent-environment systems: A niche construction perspective

The free-energy principle is an attempt to explain the structure of the agent and its brain, starting from the fact that an agent exists (Friston and Stephan, 2007; Friston et al., 2010). More specifically, it can be regarded as a systematic attempt to understand the 'fit' between an embodied agent and its niche, where the quantity of free-energy is a measure for the 'misfit' or disattunement (Bruineberg and Rietveld, 2014) between agent and environment. This paper offers a proof-of-principle simulation of niche construction under the free-energy principle. Agent-centered treatments have so far failed to address situations where environments change alongside agents, often due to the action of agents themselves. The key point of this paper is that the minimum of free-energy is not at a point in which the agent is maximally adapted to the statistics of a static environment, but can better be conceptualized an attracting manifold within the joint agent-environment state-space as a whole, which the system tends toward through mutual interaction. We will provide a general introduction to active inference and the free-energy principle. Using Markov Decision Processes (MDPs), we then describe a canonical generative model and the ensuing update equations that minimize free-energy. We then apply these equations to simulations of foraging in an environment; in which an agent learns the most efficient path to a pre-specified location. In some of those simulations, unbeknownst to the agent, the 'desire paths' emerge as a function of the activity of the agent (i.e. niche construction occurs). We will show how, depending on the relative inertia of the environment and agent, the joint agent-environment system moves to different attracting sets of jointly minimized free-energy.

Sciences of Observation

Multiple sciences have converged, in the past two decades, on a hitherto mostly unremarked question: what is observation? Here, I examine this evolution, focusing on three sciences: physics, especially quantum information theory, developmental biology, especially its molecular and “evo-devo” branches, and cognitive science, especially perceptual psychology and robotics. I trace the history of this question to the late 19th century, and through the conceptual revolutions of the 20th century. I show how the increasing interdisciplinary focus on the process of extracting information from an environment provides an opportunity for conceptual unification, and sketch an outline of what such a unification might look like.

Pre-imaginal conditioning alters adult sex pheromone response in Drosophila

Pheromones are chemical signals that induce innate responses in individuals of the same species that may vary with physiological and developmental state. In Drosophila melanogaster, the most intensively studied pheromone is 11-cis-vaccenyl acetate (cVA), which is synthezised in the male ejaculatory bulb and is transferred to the female during copulation. Among other effects, cVA inhibits male courtship of mated females. We found that male courtship inhibition depends on the amount of cVA and this effect is reduced in male flies derived from eggs covered with low to zero levels of cVA. This effect is not observed if the eggs are washed, or if the eggs are laid several days after copulation. This suggests that courtship suppression involves a form of pre-imaginal conditioning, which we show occurs during the early larval stage. The conditioning effect could not be rescued by synthetic cVA, indicating that it largely depends on conditioning by cVA and other maternally-transmitted factor(s). These experiments suggest that one of the primary behavioral effects of cVA is more plastic and less stereotypical than had hitherto been realised.

Information Theory, Developmental Psychology, and the Baldwin Effect

As part of the extended evolutionary synthesis, there has recently been a new emphasis on the effects of biological development on genetic inheritance and variation. The exciting new directions taken by those in the community have by a pre-history filled with related ideas that were never given a rigorous foundation or combined coherently. Part of the historical background of the extended synthesis is the work of James Mark Baldwin on his so-called “Baldwin Effect.” Many variant re-interpretations of his work obscure the original meaning of the Baldwin Effect. This paper emphasizes a new approach to the Baldwin Effect, focusing on his work in developmental psychology and how that would impact evolution. We propose a novel population genetics model of the Baldwin Effect. First, the impact of a kind of learning process motivated by motor babbling, in the developmental psychology literature, on evolution; second, that Information-theoretic phenotype reshaping speeds up evolution compared to populations without this kind of learning. The basic idea behind the model is to allow the organism to apply abstraction to his initial phenotype to situate it within one of a few different classes of phenotypes in the local neighborhood of a fitness maximum. The reshaping of the phenotype space thereby allows the organism to reach a nearby fitness maximum. By so doing, valleys in the fitness landscape are leveled out, making a rugged fitness landscape into a set of mesas and plateaus with increasing height. Using this model we can show the first sizeable speed-up for the Baldwin Effect compared to ordinary population genetics. We also introduce an information-theoretic foundation for the Baldwin Effect, which may be of independent interest.

Quantitative epigenetics and evolution

Epigenetics refers to chemical modifications of chromatin or transcribed DNA that can influence gene activity and expression without changes in DNA sequence. The last 20 years have yielded breakthroughs in our understanding of epigenetic processes that impact many fields of biology. In this review, we discuss how epigenetics relates to quantitative genetics and evolution. We argue that epigenetics is important for quantitative genetics because: (1) quantitative genetics is increasingly being combined with genomics, and therefore we should expand our thinking to include cellular-level mechanisms that can account for phenotypic variance and heritability besides just those that are hard-coded in the DNA sequence; and (2) epigenetic mechanisms change how phenotypic variance is partitioned, and can thereby change the heritability of traits and how those traits are inherited. To explicate these points, we show that epigenetics can influence all aspects of the phenotypic variance formula: VP (total phenotypic variance) = VG (genetic variance) + VE (environmental variance) + VGxE (genotype-by-environment interaction) + 2COVGE (the genotype-environment covariance) + Vɛ (residual variance), requiring new strategies to account for different potential sources of epigenetic effects on phenotypic variance. We also demonstrate how each of the components of phenotypic variance not only can be influenced by epigenetics, but can also have evolutionary consequences. We argue that no sources of epigenetic effects on phenotypic variance can be easily cast aside in a quantitative genetic research program that seeks to understand evolutionary processes.

The emerging structure of the Extended Evolutionary Synthesis: where does Evo-Devo fit in?

The Extended Evolutionary Synthesis (EES) debate is gaining ground in contemporary evolutionary biology. In parallel, a number of philosophical standpoints have emerged in an attempt to clarify what exactly is represented by the EES. For Massimo Pigliucci, we are in the wake of the newest instantiation of a persisting Kuhnian paradigm; in contrast, Telmo Pievani has contended that the transition to an EES could be best represented as a progressive reformation of a prior Lakatosian scientific research program, with the extension of its Neo-Darwinian core and the addition of a brand-new protective belt of assumptions and auxiliary hypotheses. Here, we argue that those philosophical vantage points are not the only ways to interpret what current proposals to 'extend' the Modern Synthesis-derived 'standard evolutionary theory' (SET) entail in terms of theoretical change in evolutionary biology. We specifically propose the image of the emergent EES as a vast network of models and interweaved representations that, instantiated in diverse practices, are connected and related in multiple ways. Under that assumption, the EES could be articulated around a paraconsistent network of evolutionary theories (including some elements of the SET), as well as models, practices and representation systems of contemporary evolutionary biology, with edges and nodes that change their position and centrality as a consequence of the co-construction and stabilization of facts and historical discussions revolving around the epistemic goals of this area of the life sciences. We then critically examine the purported structure of the EES-published by Laland and collaborators in 2015-in light of our own network-based proposal. Finally, we consider which epistemic units of Evo-Devo are present or still missing from the EES, in preparation for further analyses of the topic of explanatory integration in this conceptual framework.

Rapid adaptive response to a Mediterranean environment reduces phenotypic mismatch in a recent amphibian invader

Invasive species frequently cope with ecological conditions that are different from those to which they adapted, presenting an opportunity to investigate how phenotypes change across short time scales. In 2000, the guttural toad Sclerophrys gutturalis was first detected in a peri-urban area of Cape Town, where it is now invasive. The ability of the species to invade Cape Town is surprising as the area is characterized by a Mediterranean climate significantly drier and colder than that of the native source area. We measured field hydration state of guttural toads from the invasive Cape Town population and a native source population from Durban. We also obtained from laboratory trials: rates of evaporative water loss and water uptake, sensitivity of locomotor endurance to hydration state, critical thermal minimum (CT_min) and sensitivity of CT_min to hydration state. Field hydration state of invasive toads was significantly lower than that of native toads. Although the two populations had similar rates of water loss and uptake, invasive toads were more efficient in minimizing water loss through postural adjustments. In locomotor trials, invasive individuals noticeably outperformed native individuals when dehydrated but not when fully hydrated. CT_min was lower in invasive individuals than in native individuals, independent of hydration state. Our results indicate that an invasive population that is only 20 years old shows adaptive responses that reduce phenotypic mismatch with the novel environment. The invasion potential of the species in Cape Town is higher than we could infer from its characteristics in the native source population.

A variational approach to niche construction

In evolutionary biology, niche construction is sometimes described as a genuine evolutionary process whereby organisms, through their activities and regulatory mechanisms, modify their environment such as to steer their own evolutionary trajectory, and that of other species. There is ongoing debate, however, on the extent to which niche construction ought to be considered a bona fide evolutionary force, on a par with natural selection. Recent formulations of the variational free-energy principle as applied to the life sciences describe the properties of living systems, and their selection in evolution, in terms of variational inference. We argue that niche construction can be described using a variational approach. We propose new arguments to support the niche construction perspective, and to extend the variational approach to niche construction to current perspectives in various scientific fields.

Phenotypic plasticity, canalization, and the origins of novelty: Evidence and mechanisms from amphibians

A growing number of biologists have begun asking whether environmentally induced phenotypic change--'phenotypic plasticity'--precedes and facilitates the origin and canalization of novel, complex phenotypes. However, such 'plasticity-first evolution' (PFE) remains controversial. Here, we summarize the PFE hypothesis and describe how it can be evaluated in natural systems. We then review the evidence for PFE from amphibians (a group in which phenotypic plasticity is especially widespread) and describe how phenotypic plasticity might have facilitated macroevolutionary change. Finally, we discuss what is known about the proximate mechanisms of PFE in amphibians. We close with suggestions for future research. As we describe, amphibians offer some of the best support for plasticity's role in the origin of evolutionary novelties.

Modelling the influence of parental effects on gene-network evolution

Understanding the importance of nongenetic heredity in the evolutionary process is a major topic in modern evolutionary biology. We modified a classical gene-network model by allowing parental transmission of gene expression and studied its evolutionary properties through individual-based simulations. We identified ontogenetic time (i.e. the time gene networks have to stabilize before being submitted to natural selection) as a crucial factor in determining the evolutionary impact of this phenotypic inheritance. Indeed, fast-developing organisms display enhanced adaptation and greater robustness to mutations when evolving in presence of nongenetic inheritance (NGI). In contrast, in our model, long development reduces the influence of the inherited state of the gene network. NGI thus had a negligible effect on the evolution of gene networks when the speed at which transcription levels reach equilibrium is not constrained. Nevertheless, simulations show that intergenerational transmission of the gene-network state negatively affects the evolution of robustness to environmental disturbances for either fast- or slow-developing organisms. Therefore, these results suggest that the evolutionary consequences of NGI might not be sought only in the way species respond to selection, but also on the evolution of emergent properties (such as environmental and genetic canalization) in complex genetic architectures.

Divergent axial morphogenesis and early shh expression in vertebrate prospective floor plate

Background

The notochord has organizer properties and is required for floor plate induction and dorsoventral patterning of the neural tube. This activity has been attributed to sonic hedgehog (shh) signaling, which originates in the notochord, forms a gradient, and autoinduces shh expression in the floor plate. However, reported data are inconsistent and the spatiotemporal development of the relevant shh expression domains has not been studied in detail. We therefore studied the expression dynamics of shh in rabbit, chicken and Xenopus laevis embryos (as well as indian hedgehog and desert hedgehog as possible alternative functional candidates in the chicken).

Results

Our analysis reveals a markedly divergent pattern within these vertebrates: whereas in the rabbit shh is first expressed in the notochord and its floor plate domain is then induced during subsequent somitogenesis stages, in the chick embryo shh is expressed in the prospective neuroectoderm prior to the notochord formation and, interestingly, prior to mesoderm immigration. Neither indian hedgehog nor desert hedgehog are expressed in these midline structures although mRNA of both genes was detected in other structures of the early chick embryo. In X. laevis, shh is expressed at the beginning of gastrulation in a distinct area dorsal to the dorsal blastopore lip and adjacent to the prospective neuroectoderm, whereas the floor plate expresses shh at the end of gastrulation.

Conclusions

While shh expression patterns in rabbit and X. laevis embryos are roughly compatible with the classical view of "ventral to dorsal induction" of the floor plate, the early shh expression in the chick floor plate challenges this model. Intriguingly, this alternative sequence of domain induction is related to the asymmetrical morphogenesis of the primitive node and other axial organs in the chick. Our results indicate that the floor plate in X. laevis and chick embryos may be initially induced by planar interaction within the ectoderm or epiblast. Furthermore, we propose that the mode of the floor plate induction adapts to the variant topography of interacting tissues during gastrulation and notochord formation and thereby reveals evolutionary plasticity of early embryonic induction.

Evolutionary adaptations to new environments generally reverse plastic phenotypic changes

Organismal adaptation to a new environment may start with plastic phenotypic changes followed by genetic changes, but whether the plastic changes are stepping stones to genetic adaptation is debated. Here we address this question by investigating gene expression and metabolic flux changes in the two-phase adaptation process using transcriptomic data from multiple experimental evolution studies and computational metabolic network analysis, respectively. We discover that genetic changes more frequently reverse than reinforce plastic phenotypic changes in virtually every adaptation. Metabolic network analysis reveals that, even in the presence of plasticity, organismal fitness drops after environmental shifts, but largely recovers through subsequent evolution. Such fitness trajectories explain why plastic phenotypic changes are genetically compensated rather than strengthened. In conclusion, although phenotypic plasticity may serve as an emergency response to a new environment that is necessary for survival, it does not generally facilitate genetic adaptation by bringing the organismal phenotype closer to the new optimum.

Phenotypic plasticity has been suggested to facilitate survival in new environments and subsequent adaptation. Here, the authors reanalyze transcriptomic data from experimental evolution studies in combination with computational metabolic network analysis and show that genetic adaptation tends to reverse plastic changes in order to recover fitness.

The sources of adaptive variation

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

Evolutionary epistemology: Reviewing and reviving with new data the research programme for distributed biological intelligence

Numerous studies in microbiology, eukaryotic cell biology, plant biology, biomimetics, synthetic biology, and philosophy of science appear to support the principles of the epistemological theory inspired by evolution, also known as "Evolutionary Epistemology", or EE. However, that none of the studies acknowledged EE suggests that its principles have not been formulated with sufficient clarity and depth to resonate with the interests of the empirical research community. In this paper I review evidence in favor of EE, and also reformulate EE principles to better inform future research. The revamped programme may be tentatively called Research Programme for Distributed Biological Intelligence. Intelligence I define as the capacity of organisms to gain information about their environment, process that information internally, and translate it into phenotypic forms. This multistage progression may be expressed through the acronym IGPT (information-gain-process-translate). The key principles of the programme may be summarized as follows. (i) Intelligence, a universal biological phenomenon promoting individual fitness, is required for effective organism-environment interactions. Given that animals represent less than 0.01% of the planetary biomass, neural intelligence is not the evolutionary norm. (ii) The basic unit of intelligence is a single cell prokaryote. All other forms of intelligence are derived. (iii) Intelligence is hierarchical. It ranges from bacteria to the biosphere or Gaia. (iv) The concept of "information" acquires a new meaning because information processing is at the heart of biological intelligence. All biological systems, from bacteria to Gaia, are intelligent, open thermodynamic systems that exchange information, matter and energy with the environment. (v) The organism-environment interaction is cybernetic. As much as the organism changes due to the influence of the environment, the organism's responses to induced changes affect the environment and subsequent organism-environment interactions. Based on the above principles a new research agenda can be formulated to explore different forms of biological intelligence.

Epigenetics: A way to bridge the gap between biological fields

The concept of epigenetics has evolved since Waddington defined it from the late 1930s as the study of the causal mechanisms at work in development. It has become a multi-faceted notion with different meanings, depending on the disciplinary context it is used. In this article, we first analyse the transformations of the concept of epigenetics, from Waddington to contemporary accounts, in order to identify its different meanings and traditions, and to come up with a typology of epigenetics throughout its history. Second, we show on this basis that epigenetics has progressively turned its main focus from biological problems regarding development, toward issues concerning evolution. Yet, both these different epistemological aspects of epigenetics still coexist. Third, we claim that the classical opposition between epigenesis and preformationism as ways of thinking about the developmental process is part of the history of epigenetics and has contributed to its current various meanings. With these objectives in mind, we first show how Waddington introduced the term "epigenetics" in a biological context in order to solve a developmental problem, and we then build on this by presenting Nanney's, Riggs' and Holliday's definitions, which form the basis for the current conception of "molecular epigenetics". Then, we show that the evo-devo research field is where some particular uses of epigenetics have started shifting from developmental issues to evolutionary problems. We also show that epigenetics has progressively focused on the issue of epigenetic inheritance within the Extended Evolutionary Synthesis' framework. Finally, we conclude by presenting a typology of the different conceptions of epigenetics throughout time, and analyse the connections between them. We argue that, since Waddington, epigenetics, as an integrative research area, has been used to bridge the gap between different biological fields.