What's wrong with evolutionary biology?

A mathematical framework for evo-devo dynamics

Natural selection acts on phenotypes constructed over development, which raises the question of how development affects evolution. Classic evolutionary theory indicates that development affects evolution by modulating the genetic covariation upon which selection acts, thus affecting genetic constraints. However, whether genetic constraints are relative, thus diverting adaptation from the direction of steepest fitness ascent, or absolute, thus blocking adaptation in certain directions, remains uncertain. This limits understanding of long-term evolution of developmentally constructed phenotypes. Here we formulate a general, tractable mathematical framework that integrates age progression, explicit development (i.e., the construction of the phenotype across life subject to developmental constraints), and evolutionary dynamics, thus describing the evolutionary and developmental (evo-devo) dynamics. The framework yields simple equations that can be arranged in a layered structure that we call the evo-devo process, whereby five core elementary components generate all equations including those mechanistically describing genetic covariation and the evo-devo dynamics. The framework recovers evolutionary dynamic equations in gradient form and describes the evolution of genetic covariation from the evolution of genotype, phenotype, environment, and mutational covariation. This shows that genotypic and phenotypic evolution must be followed simultaneously to yield a dynamically sufficient description of long-term phenotypic evolution in gradient form, such that evolution described as the climbing of a fitness landscape occurs in "geno-phenotype" space. Genetic constraints in geno-phenotype space are necessarily absolute because the phenotype is related to the genotype by development. Thus, the long-term evolutionary dynamics of developed phenotypes is strongly non-standard: (1) evolutionary equilibria are either absent or infinite in number and depend on genetic covariation and hence on development; (2) developmental constraints determine the admissible evolutionary path and hence which evolutionary equilibria are admissible; and (3) evolutionary outcomes occur at admissible evolutionary equilibria, which do not generally occur at fitness landscape peaks in geno-phenotype space, but at peaks in the admissible evolutionary path where "total genotypic selection" vanishes if exogenous plastic response vanishes and mutational variation exists in all directions of genotype space. Hence, selection and development jointly define the evolutionary outcomes if absolute mutational constraints and exogenous plastic response are absent, rather than the outcomes being defined only by selection. Moreover, our framework provides formulas for the sensitivities of a recurrence and an alternative method to dynamic optimization (i.e., dynamic programming or optimal control) to identify evolutionary outcomes in models with developmentally dynamic traits. These results show that development has major evolutionary effects.

Thomas S. Kuhn: key to a better understanding of the extended evolutionary synthesis

In recent years, some scholars have explicitly questioned the desirability or utility of applying the classical and "old-fashioned" theories of scientific change by the likes of Karl Popper and Thomas S. Kuhn to the question of the precise nature and significance of the extended evolutionary synthesis (EES). Supposedly, these twentieth-century philosophers are completely irrelevant for a better understanding of this new theoretical framework for the study of evolution. Here, it will be argued that the EES can be fruitfully interpreted in terms of, as yet, insufficiently considered or even overlooked elements from Kuhn's theory. First, in his original, historical philosophy of science, Kuhn not only distinguished between small and big scientific revolutions, he also pointed out that paradigms can be extended and reformulated. In contrast with what its name suggests, the mainstream EES can be interpreted as a Kuhnian reformulation of modern evolutionary theory. Second, it has, as yet, also been overlooked that the EES can be interpreted in terms of Kuhn's later, tentative evolutionary philosophy of science. With the EES, an old dichotomy in evolutionary biology is maybe being formalized and institutionalized.

A generalised approach to the study and understanding of adaptive evolution

Evolutionary theory has made large impacts on our understanding and management of the world, in part because it has been able to incorporate new data and new insights successfully. Nonetheless, there is currently a tension between certain biological phenomena and mainstream evolutionary theory. For example, how does the inheritance of molecular epigenetic changes fit into mainstream evolutionary theory? Is niche construction an evolutionary process? Is local adaptation via habitat choice also adaptive evolution? These examples suggest there is scope (and perhaps even a need) to broaden our views on evolution. We identify three aspects whose incorporation into a single framework would enable a more generalised approach to the understanding and study of adaptive evolution: (i) a broadened view of extended phenotypes; (ii) that traits can respond to each other; and (iii) that inheritance can be non-genetic. We use causal modelling to integrate these three aspects with established views on the variables and mechanisms that drive and allow for adaptive evolution. Our causal model identifies natural selection and non-genetic inheritance of adaptive parental responses as two complementary yet distinct and independent drivers of adaptive evolution. Both drivers are compatible with the Price equation; specifically, non-genetic inheritance of parental responses is captured by an often-neglected component of the Price equation. Our causal model is general and simplified, but can be adjusted flexibly in terms of variables and causal connections, depending on the research question and/or biological system. By revisiting the three examples given above, we show how to use it as a heuristic tool to clarify conceptual issues and to help design empirical research. In contrast to a gene-centric view defining evolution only in terms of genetic change, our generalised approach allows us to see evolution as a change in the whole causal structure, consisting not just of genetic but also of phenotypic and environmental variables.

Inferring cultural reproduction from lithic data: A critical review

The cultural reproduction of lithic technology, long an implicit assumption of archaeological theories, has garnered increasing attention over the past decades. Major debates ranging from the origins of the human culture capacity to the interpretation of spatiotemporal patterning now make explicit reference to social learning mechanisms and cultural evolutionary dynamics. This burgeoning literature has produced important insights and methodological innovations. However, this rapid growth has sometimes led to confusion and controversy due to an under-examination of underlying theoretical and methodological assumptions. The time is thus ripe for a critical assessment of progress in the study of the cultural reproduction of lithic technology. Here we review recent work addressing the evolutionary origins of human culture and the meaning of artifact variation at both intrasite and intersite levels. We propose that further progress will require a more extended and context-specific evolutionary approach to address the complexity of real-world cultural reproduction.

Autopoiesis, Thermodynamics, and the Natural Drift of Living Beings: Another Way to the New Evolutionary Synthesis

The New Evolutionary Synthesis (NES) groups a series of theories that, departing from the gene-centric approach of Modern Synthesis evolutionary theory (MS), place the organism as the central agent of evolution. Two versions of NES, each one with advantages and disadvantages, can be distinguished in this regard; the restrictive NES and the comprehensive NES. Comparatively, the comprehensive NES is a more robust theoretical construction than the restrictive one because it comes grounded on a general, thermodynamically informed theory of living beings (something that the restrictive NES lacks). However, due to its strong teleological commitments, the comprehensive NES has serious problems fitting with modern science’s methodological framework; a problem that the restrictive version, with no explicit commitment to teleology, does not face. In this paper, we propose the autopoietic approach to evolution as a way of integrating these two versions of NES, combining the theoretical robustness of the comprehensive view with the methodological appropriateness of the restrictive one. The autopoietic approach, we show, offers a non-teleological, organism-centered theory of evolution, namely the natural drift theory (NDT), and a grounding on a thermodynamic theory of living beings, namely the embodied autopoietic theory (EAT). We conclude that, from the programmatic point of view, an autopoietic (NDT plus EAT) approach to evolution offers a promising way to develop the NES project.

Structuralism and Adaptationism: Friends? Or foes?

Historically, the empirical study of phenotypic diversification has fallen into two rough camps; (1) "structuralist approaches" focusing on developmental constraint, bias, and innovation (with evo-devo at the core); and (2) "adaptationist approaches" focusing on adaptation, and natural selection. Whilst debates, such as that surrounding the proposed "Extended" Evolutionary Synthesis, often juxtapose these two positions, this review focuses on the grey space in between. Specifically, here I present a novel analysis of structuralism which enables us to take a more nuanced look at the motivations behind the structuralist and adaptationist positions. This makes clear how the two approaches can conflict, and points of potential commensurability. The review clarifies (a) the value of the evo-devo approach to phenotypic diversity, but also (b) how it properly relates to other predominant approaches to the same issues in evolutionary biology more broadly.

Ten recent insights for our understanding of cooperation

Since Hamilton published his seminal papers in 1964, our understanding of the importance of cooperation for life on Earth has evolved beyond recognition. Early research was focused on altruism in the social insects, where the problem of cooperation was easy to see. In more recent years, research into cooperation has expanded across the entire tree of life, and has been revolutionized by advances in genetic, microbiological and analytical techniques. We highlight ten insights that have arisen from these advances, which have illuminated generalizations across different taxa, making the world simpler to explain. Furthermore, progress in these areas has opened up numerous new problems to solve, suggesting exciting directions for future research.

A simple completion of Fisher's fundamental theorem of natural selection

Fisher's fundamental theorem of natural selection shows that the part of the rate of change of mean fitness that is due to natural selection equals the additive genetic variance in fitness. Fisher embedded this result in a model of total fitness, adding terms for deterioration of the environment and density dependence. Here, a quantitative genetic version of this neglected model is derived that relaxes its assumptions that the additive genetic variance in fitness and the rate of deterioration of the environment do not change over time, allows population size to vary, and includes an input of mutational variance. The resulting formula for total rate of change in mean fitness contains two terms more than Fisher's original, representing the effects of stabilizing selection, on the one hand, and of mutational variance, on the other, making clear for the first time that the fundamental theorem deals only with natural selection that is directional (as opposed to stabilizing) on the underlying traits. In this model, the total (rather than just the additive) genetic variance increases mean fitness. The unstructured population allows an explanation of Fisher's concept of fitness as simply birth rate minus mortality rate, and building up to the definition in structured populations.

Synthesising arguments and the extended evolutionary synthesis

Synthesising arguments motivate changes to the conceptual tools, theoretical structure, and evaluatory framework employed in a given scientific domain. Recently, a broad coalition of researchers has put forward a synthesising argument in favour of an Extended Evolutionary Synthesis ('EES'). Often this synthesising argument is evaluated using a virtue-based approach, which construes the EES as a wholesale alternative to prevailing practice. Here I argue this virtue-based approach is not fit for purpose. Taking the central concept of niche construction as a case study, I show that an agenda-based approach better captures the pragmatic and epistemological goals of the EES synthesising argument and diagnoses areas of empirical disagreement with prevailing practice.

Inclusive fitness is an indispensable approximation for understanding organismal design

For some decades most biologists interested in design have agreed that natural selection leads to organisms acting as if they are maximizing a quantity known as "inclusive fitness." This maximization principle has been criticized on the (uncontested) grounds that other quantities, such as offspring number, predict gene frequency changes accurately in a wider range of mathematical models. Here, we adopt a resolution offered by Birch, who accepts the technical difficulties of establishing inclusive fitness maximization in a fully general model, while concluding that inclusive fitness is still useful as an organizing framework. We set out in more detail why inclusive fitness is such a practical and powerful framework, and provide verbal and conceptual arguments for why social biology would be more or less impossible without it. We aim to help mathematicians understand why social biologists are content to use inclusive fitness despite its theoretical weaknesses. Here, we also offer biologists practical advice for avoiding potential pitfalls.

Computational mechanisms in genetic regulation by RNA

The evolution of the genome has led to very sophisticated and complex regulation. Because of the abundance of non-coding RNA (ncRNA) in the cell, different species will promiscuously associate with each other, suggesting collective dynamics similar to artificial neural networks. A simple mechanism is proposed allowing ncRNA to perform computations equivalent to neural network algorithms such as Boltzmann machines and the Hopfield model. The quantities analogous to the neural couplings are the equilibrium constants between different RNA species. The relatively rapid equilibration of RNA binding and unbinding is regulated by a slower process that degrades and creates new RNA. The model requires that the creation rate for each species be an increasing function of the ratio of total to unbound RNA. Similar mechanisms have already been found to exist experimentally for ncRNA regulation. With the overall concentration of RNA regulated, equilibrium constants can be chosen to store many different patterns, or many different input-output relations. The network is also quite insensitive to random mutations in equilibrium constants. Therefore one expects that this kind of mechanism will have a much higher mutation rate than ones typically regarded as being under evolutionary constraint.

Natural Selection and Pangenesis: The Darwinian Synthesis of Evolution and Genetics

Since the end of the 19th century, Lamarck's name has been tightly linked to the notion of the inheritance of acquired characters. Darwin regarded Lamarck as a great zoologist and a forerunner of evolution, and repeatedly expressed the opinion that "natural selection has been the main but not the exclusive means of modification." The original Darwinism not only includes natural selection, but also the inheritance of acquired characters and mutation. Neo-Darwinism considers natural selection as the one controlling process of evolution, but denies the inheritance of acquired characters. Lysenkoism accepts the inheritance of acquired characters and graft hybridization, but denies the significance of Malthusism and Mutationism. It has been suggested that the "modern synthesis", which evolved from neo-Darwinism, needs a rethink. I propose that there is a need to go back to Darwin's own synthesis which combined his theory of evolution by natural selection with his theory of heredity and variation - Pangenesis.

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.

Evolutionary biology today and the call for an extended synthesis

Evolutionary theory has been extended almost continually since the evolutionary synthesis (ES), but except for the much greater importance afforded genetic drift, the principal tenets of the ES have been strongly supported. Adaptations are attributable to the sorting of genetic variation by natural selection, which remains the only known cause of increase in fitness. Mutations are not adaptively directed, but as principal authors of the ES recognized, the material (structural) bases of biochemistry and development affect the variety of phenotypic variations that arise by mutation and recombination. Against this historical background, I analyse major propositions in the movement for an 'extended evolutionary synthesis'. 'Niche construction' is a new label for a wide variety of well-known phenomena, many of which have been extensively studied, but (as with every topic in evolutionary biology) some aspects may have been understudied. There is no reason to consider it a neglected 'process' of evolution. The proposition that phenotypic plasticity may engender new adaptive phenotypes that are later genetically assimilated or accommodated is theoretically plausible; it may be most likely when the new phenotype is not truly novel, but is instead a slight extension of a reaction norm already shaped by natural selection in similar environments. However, evolution in new environments often compensates for maladaptive plastic phenotypic responses. The union of population genetic theory with mechanistic understanding of developmental processes enables more complete understanding by joining ultimate and proximate causation; but the latter does not replace or invalidate the former. Newly discovered molecular phenomena have been easily accommodated in the past by elaborating orthodox evolutionary theory, and it appears that the same holds today for phenomena such as epigenetic inheritance. In several of these areas, empirical evidence is needed to evaluate enthusiastic speculation. Evolutionary theory will continue to be extended, but there is no sign that it requires emendation.

Why we don't want another "Synthesis"

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

REVIEWERS

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

On Reciprocal Causation in the Evolutionary Process

Recent calls for a revision of standard evolutionary theory (SET) are based partly on arguments about the reciprocal causation. Reciprocal causation means that cause-effect relationships are bi-directional, as a cause could later become an effect and vice versa. Such dynamic cause-effect relationships raise questions about the distinction between proximate and ultimate causes, as originally formulated by Ernst Mayr. They have also motivated some biologists and philosophers to argue for an Extended Evolutionary Synthesis (EES). The EES will supposedly expand the scope of the Modern Synthesis (MS) and SET, which has been characterized as gene-centred, relying primarily on natural selection and largely neglecting reciprocal causation. Here, I critically examine these claims, with a special focus on the last conjecture. I conclude that reciprocal causation has long been recognized as important by naturalists, ecologists and evolutionary biologists working in the in the MS tradition, although it it could be explored even further. Numerous empirical examples of reciprocal causation in the form of positive and negative feedback are now well known from both natural and laboratory systems. Reciprocal causation have also been explicitly incorporated in mathematical models of coevolutionary arms races, frequency-dependent selection, eco-evolutionary dynamics and sexual selection. Such dynamic feedback were already recognized by Richard Levins and Richard Lewontin in their bok The Dialectical Biologist. Reciprocal causation and dynamic feedback might also be one of the few contributions of dialectical thinking and Marxist philosophy in evolutionary theory. I discuss some promising empirical and analytical tools to study reciprocal causation and the implications for the EES. Finally, I briefly discuss how quantitative genetics can be adapated to studies of reciprocal causation, constructive inheritance and phenotypic plasticity and suggest that the flexibility of this approach might have been underestimated by critics of contemporary evolutionary biology.

The purpose of adaptation

A central feature of Darwin's theory of natural selection is that it explains the purpose of biological adaptation. Here, I: emphasize the scientific importance of understanding what adaptations are for, in terms of facilitating the derivation of empirically testable predictions; discuss the population genetical basis for Darwin's theory of the purpose of adaptation, with reference to Fisher's ‘fundamental theorem of natural selection'; and show that a deeper understanding of the purpose of adaptation is achieved in the context of social evolution, with reference to inclusive fitness and superorganisms.