Replacing academic journals.

Replacing traditional journals with a more modern solution is not a new idea. Here, we propose ways to overcome the social dilemma underlying the decades of inaction. Any solution needs to not only resolve the current problems but also be capable of preventing takeover by corporations: it needs to replace traditional journals with a decentralized, resilient, evolvable network that is interconnected by open standards and open-source norms under the governance of the scholarly community. It needs to replace the monopolies connected to journals with a genuine, functioning and well-regulated market. In this new market, substitutable service providers compete and innovate according to the conditions of the scholarly community, avoiding sustained vendor lock-in. Therefore, a standards body needs to form under the governance of the scholarly community to allow the development of open scholarly infrastructures servicing the entire research workflow. We propose a redirection of money from legacy publishers to the new network by funding bodies broadening their minimal infrastructure requirements at recipient institutions to include modern infrastructure components replacing and complementing journal functionalities. Such updated eligibility criteria by funding agencies would help realign the financial incentives for recipient institutions with public and scholarly interest.

Eco-evolution from deep time to contemporary dynamics: The role of timescales and rate modulators.

Eco-evolutionary dynamics, or eco-evolution for short, are often thought to involve rapid demography (ecology) and equally rapid heritable phenotypic changes (evolution) leading to novel, emergent system behaviours. We argue that this focus on contemporary dynamics is too narrow: Eco-evolution should be extended, first, beyond pure demography to include all environmental dimensions and, second, to include slow eco-evolution which unfolds over thousands or millions of years. This extension allows us to conceptualise biological systems as occupying a two-dimensional time space along axes that capture the speed of ecology and evolution. Using Hutchinson's analogy: Time is the 'theatre' in which ecology and evolution are two interacting 'players'. Eco-evolutionary systems are therefore dynamic: We identify modulators of ecological and evolutionary rates, like temperature or sensitivity to mutation, which can change the speed of ecology and evolution, and hence impact eco-evolution. Environmental change may synchronise the speed of ecology and evolution via these rate modulators, increasing the occurrence of eco-evolution and emergent system behaviours. This represents substantial challenges for prediction, especially in the context of global change. Our perspective attempts to integrate ecology and evolution across disciplines, from gene-regulatory networks to geomorphology and across timescales, from today to deep time.

Expanding evolutionary theories of ageing to better account for symbioses and interactions throughout the Web of Life.

How, when, and why organisms age are fascinating issues that can only be fully addressed by adopting an evolutionary perspective. Consistently, the main evolutionary theories of ageing, namely the Mutation Accumulation theory, the Antagonistic Pleiotropy theory, and the Disposable Soma theory, have formulated stimulating hypotheses that structure current debates on both the proximal and ultimate causes of organismal ageing. However, all these theories leave a common area of biology relatively under-explored. The Mutation Accumulation theory and the Antagonistic Pleiotropy theory were developed under the traditional framework of population genetics, and therefore are logically centred on the ageing of individuals within a population. The Disposable Soma theory, based on principles of optimising physiology, mainly explains ageing within a species. Consequently, current leading evolutionary theories of ageing do not explicitly model the countless interspecific and ecological interactions, such as symbioses and host-microbiomes associations, increasingly recognized to shape organismal evolution across the Web of Life. Moreover, the development of network modelling supporting a deeper understanding on the molecular interactions associated with ageing within and between organisms is also bringing forward new questions regarding how and why molecular pathways associated with ageing evolved. Here, we take an evolutionary perspective to examine the effects of organismal interactions on ageing across different levels of biological organisation, and consider the impact of surrounding and nested systems on organismal ageing. We also apply this perspective to suggest open issues with potential to expand the standard evolutionary theories of ageing.

The integrated information theory of agency.

We propose that measures of information integration can be more straightforwardly interpreted as measures of agency rather than of consciousness. This may be useful to the goals of consciousness research, given how agency and consciousness are "duals" in many (although not all) respects.

Natural Selection beyond Life? A Workshop Report.

Natural selection is commonly seen not just as an explanation for adaptive evolution, but as the inevitable consequence of "heritable variation in fitness among individuals". Although it remains embedded in biological concepts, such a formalisation makes it tempting to explore whether this precondition may be met not only in life as we know it, but also in other physical systems. This would imply that these systems are subject to natural selection and may perhaps be investigated in a biological framework, where properties are typically examined in light of their putative functions. Here we relate the major questions that were debated during a three-day workshop devoted to discussing whether natural selection may take place in non-living physical systems. We start this report with a brief overview of research fields dealing with "life-like" or "proto-biotic" systems, where mimicking evolution by natural selection in test tubes stands as a major objective. We contend the challenge may be as much conceptual as technical. Taking the problem from a physical angle, we then discuss the framework of dissipative structures. Although life is viewed in this context as a particular case within a larger ensemble of physical phenomena, this approach does not provide general principles from which natural selection can be derived. Turning back to evolutionary biology, we ask to what extent the most general formulations of the necessary conditions or signatures of natural selection may be applicable beyond biology. In our view, such a cross-disciplinary jump is impeded by reliance on individuality as a central yet implicit and loosely defined concept. Overall, these discussions thus lead us to conjecture that understanding, in physico-chemical terms, how individuality emerges and how it can be recognised, will be essential in the search for instances of evolution by natural selection outside of living systems.

The Epistemic Revolution Induced by Microbiome Studies: An Interdisciplinary View.

Many separate fields and practices nowadays consider microbes as part of their legitimate focus. Therefore, microbiome studies may act as unexpected unifying forces across very different disciplines. Here, we summarize how microbiomes appear as novel major biological players, offer new artistic frontiers, new uses from medicine to laws, and inspire novel ontologies. We identify several convergent emerging themes across ecosystem studies, microbial and evolutionary ecology, arts, medicine, forensic analyses, law and philosophy of science, as well as some outstanding issues raised by microbiome studies across these disciplines and practices. An 'epistemic revolution induced by microbiome studies' seems to be ongoing, characterized by four features: (i) an ecologization of pre-existing concepts within disciplines, (ii) a growing interest in systemic analyses of the investigated or represented phenomena and a greater focus on interactions as their root causes, (iii) the intent to use openly multi-scalar interaction networks as an explanatory framework to investigate phenomena to acknowledge the causal effects of microbiomes, (iv) a reconceptualization of the usual definitions of which individuals are worth considering as an explanans or as an explanandum by a given field, which result in a fifth strong trend, namely (v) a de-anthropocentrification of our perception of the world.

Shifting levels of ecological network's analysis reveals different system properties.

Network analyses applied to models of complex systems generally contain at least three levels of analyses. Whole-network metrics summarize general organizational features (properties or relationships) of the entire network, while node-level metrics summarize similar organization features but consider individual nodes. The network- and node-level metrics build upon the primary pairwise relationships in the model. As with many analyses, sometimes there are interesting differences at one level that disappear in the summary at another level of analysis. We illustrate this phenomenon with ecosystem network models, where nodes are trophic compartments and pairwise relationships are flows of organic carbon, such as when a predator eats a prey. For this demonstration, we analysed a time-series of 16 models of a lake planktonic food web that describes carbon exchanges within an autumn cyanobacteria bloom and compared the ecological conclusions drawn from the three levels of analysis based on inter-time-step comparisons. A general pattern in our analyses was that the closer the levels are in hierarchy (node versus network, or flow versus node level), the more they tend to align in their conclusions. Our analyses suggest that selecting the appropriate level of analysis, and above all regularly using multiple levels, may be a critical analytical decision. This article is part of the theme issue 'Unifying the essential concepts of biological networks: biological insights and philosophical foundations'.

Revisiting darwinian teleology: A case for inclusive fitness as design explanation.

This paper elaborates a general framework to make sense of teleological explanations in Darwinian evolutionary biology. It relies on an attempt to tie natural selection to a sense of optimization. First, after assessing the objections made by any attempt to view selection as a maximising process within population genetics, it understands Grafen's Formal Darwinism (FD) as a conceptual link established between population genetics and behavioral ecology's adaptationist framework (without any empirical commitments). Thus I suggest that this provides a way to make sense of teleological explanations in biology under their various modes. Then the paper criticizes two major ways of accounting for teleology: a Darwinian one, the etiological view of biological functions, and a non-Darwinian one, here labeled "intrinsic teleology" view, which covers several subtypes of accounts, including plasticity-oriented conceptions of evolution or organizational views of function. The former is centered on traits while the latter is centered on organisms; this is shown to imply that both accounts are unable to provide a systematic understanding of biological teleology. Finally the paper argues that viewing teleology as maximization of inclusive fitness along the FD lines as understood here allows one to make sense of both the design of organisms and the individual traits as adaptions. Such notion is thereby claimed to be the proper meaning of teleology in evolutionary biology, since it avoids the opposed pitfalls of etiological views and intrinsic-teleology view, while accounting for the same features as they do.

How the Modern Synthesis Came to Ecology.

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

The Modern Synthesis: Theoretical or Institutional Event?

This paper surveys questions about the nature of the Modern Synthesis as a historical event : was it rather theoretical than institutional? When and where did it actually happen? Who was involved? It argues that all answers to these questions are interrelated, and that systematic sets of answers define specific perspectives on the Modern Synthesis that are all complementary.

Early in life effects and heredity: reconciling neo-Darwinism with neo-Lamarckism under the banner of the inclusive evolutionary synthesis.

Recent discoveries show that early in life effects often have long-lasting influences, sometimes even spanning several generations. Such intergenerational effects of early life events appear not easily reconcilable with strict genetic inheritance. However, an integrative evolutionary medicine of early life effects needs a sound view of inheritance in development and evolution. Here, we show how to articulate the gene-centred and non-gene-centred visions of inheritance. We first recall the coexistence of two gene concepts in scientific discussions, a statistical one (focused on patterns of parent-offspring resemblance, and implicitly including non-DNA-sequence-based resemblance), and a molecular one (based on the DNA sequence). We then show how all the different mechanisms of inheritance recently discovered can be integrated into an inclusive theory of evolution where different mechanisms would enable adaptation to changing environments at different timescales. One surprising consequence of this integrative vision of inheritance is that early in life effects start much earlier than fertilization. This article is part of the theme issue 'Developing differences: early-life effects and evolutionary medicine'.

Towards a Dynamic Interaction Network of Life to unify and expand the evolutionary theory.

The classic Darwinian theory and the Synthetic evolutionary theory and their linear models, while invaluable to study the origins and evolution of species, are not primarily designed to model the evolution of organisations, typically that of ecosystems, nor that of processes. How could evolutionary theory better explain the evolution of biological complexity and diversity? Inclusive network-based analyses of dynamic systems could retrace interactions between (related or unrelated) components. This theoretical shift from a Tree of Life to a Dynamic Interaction Network of Life, which is supported by diverse molecular, cellular, microbiological, organismal, ecological and evolutionary studies, would further unify evolutionary biology.

Realizability and the varieties of explanation.

What realization is has been convincingly presented in relation to the way we determine what counts as the realizers of realized properties. The way we explain a fact of realization includes a reference to what realization should be; therefore it informs in turn our understanding of the nature of realization. Conceptions of explanation are thereby included in the views of realization as a metaphysical property. Recently, several major views of realization such as Polger and Shapiro's or Gillett and Aizawa's, however competing, have relied on the neo-mechanicist theory of explanations (e.g,. Darden and Caver 2013), currently popular among philosophers of science. However, it has also been increasingly argued that some explanations are not mechanistic (e.g., Batterman 2009). Using an account given in Huneman (2017), I argue that within those explanations the fact that some mathematical properties are instantiated is explanatory, and that this defines a specific explanatory type called "structural explanation", whose subtypes could be: optimality explanations (usually found in economics), topological explanations, etc. This paper thereby argues that all subtypes of structural explanation define several kinds of realizability, which are not equivalent to the usual notion of realization tied to mechanistic explanations, onto which many of the philosophical investigations are focused. Then it draws some consequences concerning the notion of multiple realizability.

The behavioural ecology of irrational behaviours.

Natural selection is often envisaged as the ultimate cause of the apparent rationality exhibited by organisms in their specific habitat. Given the equivalence between selection and rationality as maximizing processes, one would indeed expect organisms to implement rational decision-makers. Yet, many violations of the clauses of rationality have been witnessed in various species such as starlings, hummingbirds, amoebas and honeybees. This paper attempts to interpret such discrepancies between economic rationality (defined by the main axioms of rational choice theory) and biological rationality (defined by natural selection). After having distinguished two kinds of rationality we introduce irrationality as a negation of economic rationality by biologically rational decision-makers. Focusing mainly on those instances of irrationalities that can be understood as exhibiting inconsistency in making choices, i.e. as non-conformity of a given behaviour to axioms such as transitivity or independence of irrelevant alternatives, we propose two possible families of Darwinian explanations that may account for these apparent irrationalities. First, we consider cases where natural selection may have been an indirect cause of irrationality. Second, we consider putative cases where violations of rationality axioms may have been directly favored by natural selection. Though the latter cases (prima facie) seem to clearly contradict our intuitive representation of natural selection as a process that maximizes fitness, we argue that they are actually unproblematic; for often, they can be redescribed as cases where no rationality axiom is violated, or as situations where no adaptive solution exists in the first place.

From a religious view of madness to religious mania: the Encyclopédie, Pinel, Esquirol.

This paper focuses on the shift from a concept of insanity understood in terms of religion to another (as entertained by early psychiatry, especially in France) according to which it is believed that forms of madness tinged by religion are difficult to cure. The traditional religious view of madness, as exemplified by Pascal (inter alia), is first illustrated by entries from the Encyclopédie. Then the shift towards a medical view of madness, inspired by Vitalistic physiology, is mapped by entries taken from the same publication. Firmed up by Pinel, this shift caused the abandonment of the religious view. Esquirol considered religious mania to be a vestige from the past, but he also believed that mental conditions carrying a religious component were difficult to cure.

From the Neutral Theory to a Comprehensive and Multiscale Theory of Ecological Equivalence.

The neutral theory of biodiversity assumes that coexisting organisms are equally able to survive, reproduce, and disperse (ecological equivalence), but predicts that stochastic fluctuations of these abilities drive diversity dynamics. It predicts remarkably well many biodiversity patterns, although substantial evidence for the role of niche variation across organisms seems contradictory. Here, we discuss this apparent paradox by exploring the meaning and implications of ecological equivalence. We address the question whether neutral theory provides an explanation for biodiversity patterns and acknowledges causal processes. We underline that ecological equivalence, although central to neutral theory, can emerge at local and regional scales from niche-based processes through equalizing and stabilizing mechanisms. Such emerging equivalence corresponds to a weak conception of neutral theory, as opposed to the assumption of strict equivalence at the individual level in strong conception. We show that this duality is related to diverging views on hypothesis testing and modeling in ecology. In addition, the stochastic dynamics exposed in neutral theory are pervasive in ecological systems and, rather than a null hypothesis, ecological equivalence is best understood as a parsimonious baseline to address biodiversity dynamics at multiple scales.

Introduction: the plurality of modeling.

Philosophers of science have recently focused on the scientific activity of modeling phenomena, and explicated several of its properties, as well as the activities embedded into it. A first approach to modeling has been elaborated in terms of representing a target system: yet other epistemic functions, such as producing data or detecting phenomena, are at least as relevant. Additional useful distinctions have emerged, such as the one between phenomenological and mechanistic models. In biological sciences, besides mathematical models, models now come in three forms: in vivo, in vitro and in silico. Each has been investigated separately, and many specific problems they raised have been laid out. Another relevant distinction is disciplinary: do models differ in significant ways according to the discipline involved-medicine or biology, evolutionary biology or earth science? Focusing on either this threefold distinction or the disciplinary boundaries reveals that they might not be sufficient from a philosophical perspective. On the contrary, focusing on the interaction between these various kinds of models, some interesting forms of explanation come to the fore, as is exemplified by the papers included in this issue. On the other hand, a focus on the use of models, rather than on their content, shows that the distinction between biological and medical models is theoretically sound.

Mapping an expanding territory: computer simulations in evolutionary biology.

The pervasive use of computer simulations in the sciences brings novel epistemological issues discussed in the philosophy of science literature since about a decade. Evolutionary biology strongly relies on such simulations, and in relation to it there exists a research program (Artificial Life) that mainly studies simulations themselves. This paper addresses the specificity of computer simulations in evolutionary biology, in the context (described in Sect. 1) of a set of questions about their scope as explanations, the nature of validation processes and the relation between simulations and true experiments or mathematical models. After making distinctions, especially between a weak use where simulations test hypotheses about the world, and a strong use where they allow one to explore sets of evolutionary dynamics not necessarily extant in our world, I argue in Sect. 2 that (weak) simulations are likely to represent in virtue of the fact that they instantiate specific features of causal processes that may be isomorphic to features of some causal processes in the world, though the latter are always intertwined with a myriad of different processes and hence unlikely to be directly manipulated and studied. I therefore argue that these simulations are merely able to provide candidate explanations for real patterns. Section 3 ends up by placing strong and weak simulations in Levins' triangle, that conceives of simulations as devices trying to fulfil one or two among three incompatible epistemic values (precision, realism, genericity).

Assessing statistical views of natural selection: Room for non-local causation?

Recently some philosophers (the "statisticalists") have emphasized a potentially irreconcilable conceptual antagonism between the statistical characterization of natural selection (derived from population genetics) and the standard scientific discussion of natural selection in terms of forces and causes. Other philosophers have developed an account of the causal character of selectionist statements represented in terms of counterfactuals. I examine the compatibility between such statisticalism and counterfactually based causal accounts of natural selection (and related arguments about counterfactuals and causality) by distinguishing two distinct statisticalist claims: firstly the suggested impossibility for natural selection to be a cause acting upon populations and secondly the conceptualization that all evolutionary causes occur at the level of interactions between individual organisms. I argue that deriving the latter from the former involves supplementary assumptions concerning precisely what causation is. I critically examine two of these assumptions purportedly preventing natural selection being regarded as a cause: the locality claim and the modularity claim. I conclude that justifying the strongest version of statisticalism-i.e. evolutionary causation only occurs at the level of individual interactions between organisms-would require further metaphysical arguments that are likely to be deemed highly problematic. Additionally, I argue that such a metaphysical position would be considered incongruous with both our scientific and ordinary use of the concepts of causality and explanation as employed within our everyday epistemological framework.