Niche construction in evolutionary theory: the construction of an academic niche?

Speciation, natural selection, and networks: three historians versus theoretical population geneticists

In 1913, the geneticist William Bateson called for a halt in studies of genetic phenomena until evolutionary fundamentals had been sufficiently addressed at the molecular level. Nevertheless, in the 1960s, the theoretical population geneticists celebrated a "modern synthesis" of the teachings of Mendel and Darwin, with an exclusive role for natural selection in speciation. This was supported, albeit with minor reservations, by historians Mark Adams and William Provine, who taught it to generations of students. In subsequent decades, doubts were raised by molecular biologists and, despite the deep influence of various mentors, Adams and Provine noted serious anomalies and began to question traditional "just-so-stories." They were joined in challenging the genetic orthodoxy by a scientist-historian, Donald Forsdyke, who suggested that a "collective variation" postulated by Darwin's young research associate, George Romanes, and a mysterious "residue" postulated by Bateson, might relate to differences in short runs of DNA bases (oligonucleotides). The dispute between a small network of historians and a large network of geneticists can be understood in the context of national politics. Contrasts are drawn between democracies, where capturing the narrative makes reversal difficult, and dictatorships, where overthrow of a supportive dictator can result in rapid reversal.

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.

Biological adaptation in light of the Lewontin-Williams (a)symmetry

Neo-Darwinism characterizes biological adaptation as a one-sided process, in which organisms adapt to their environment but not vice versa. This asymmetric relationship-here called Williams' asymmetry-is called into question by Niche Construction Theory, which emphasizes that organisms and their environments often mutually affect each other. Here, we clarify that Williams' asymmetry is specifically concerned with (quasi)-directed modifications toward phenotypes that increase individual fitness. This directedness-which drives the adaptive fit between organism and environment-entails far more than the mere presence of cause-effect relationships. We argue that difficulties with invoking fitness as the guiding principle of adaptive evolution are resolved with an appropriate definition of fitness and that objections against Williams' asymmetry reflect confusions about the nature of biological adaptation.

More Thumbs Than Rules: Is Rationality an Exaptation?

The literatures on bounded and ecological rationality are built on adaptationism-and its associated modular, cognitivist and computational paradigm-that does not address or explain the evolutionary origins of rationality. We argue that the adaptive mechanisms of evolution are not sufficient for explaining human rationality, and we posit that human rationality presents exaptive origins, where exaptations are traits evolved for other functions or no function at all, and later co-opted for new uses. We propose an embodied reconceptualization of rationality-embodied rationality-based on the reuse of the perception-action system, where many neural processes involved in the control of the sensory-motor system, salient in ancestral environments have been later co-opted to create-by tinkering-high-level reasoning processes, employed in civilized niches.

Building behavior does not drive rates of phenotypic evolution in spiders

Do animals set the course for the evolution of their lineage when manipulating their environment? This heavily disputed question is empirically unexplored but critical to interpret phenotypic diversity. Here, we tested whether the macroevolutionary rates of body morphology correlate with the use of built artifacts in a megadiverse clade comprising builders and nonbuilders-spiders. By separating the inferred building-dependent rates from background effects, we found that variation in the evolution of morphology is poorly explained by artifact use. Thus natural selection acting directly on body morphology rather than indirectly via construction behavior is the dominant driver of phenotypic diversity.

Diverse interactions and ecosystem engineering can stabilize community assembly

The complexity of an ecological community can be distilled into a network, where diverse interactions connect species in a web of dependencies. Species interact directly with each other and indirectly through environmental effects, however to our knowledge the role of these ecosystem engineers has not been considered in ecological network models. Here we explore the dynamics of ecosystem assembly, where species colonization and extinction depends on the constraints imposed by trophic, service, and engineering dependencies. We show that our assembly model reproduces many key features of ecological systems, such as the role of generalists during assembly, realistic maximum trophic levels, and increased nestedness with mutualistic interactions. We find that ecosystem engineering has large and nonlinear effects on extinction rates. While small numbers of engineers reduce stability by increasing primary extinctions, larger numbers of engineers increase stability by reducing primary extinctions and extinction cascade magnitude. Our results suggest that ecological engineers may enhance community diversity while increasing persistence by facilitating colonization and limiting competitive exclusion.

The dynamics of ecological communities depends on interactions between species as well as those between species and their environment, however the effects of the latter are poorly understood. Here, Yeakel et al. reveal how species that modify their environment (ecosystem engineers) impact community dynamics and the risk of extinction.

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.

Scale-invariant topology and bursty branching of evolutionary trees emerge from niche construction

Phylogenetic trees describe both the evolutionary process and community diversity. Recent work has established that they exhibit scale-invariant topology, which quantifies the fact that their branching lies in between the two extreme cases of balanced binary trees and maximally unbalanced ones. In addition, the backbones of phylogenetic trees exhibit bursts of diversification on all timescales. Here, we present a simple, coarse-grained statistical model of niche construction coupled to speciation. Finite-size scaling analysis of the dynamics shows that the resultant phylogenetic tree topology is scale-invariant due to a singularity arising from large niche construction fluctuations that follow extinction events. The same model recapitulates the bursty pattern of diversification in time. These results show how dynamical scaling laws of phylogenetic trees on long timescales can reflect the indelible imprint of the interplay between ecological and evolutionary processes.

Cognition blindness and cognitive gadgets

Responding to commentaries from psychologists, neuroscientists, philosophers, and anthropologists, I clarify a central purpose of Cognitive Gadgets – to overcome “cognition blindness” in research on human evolution. I defend this purpose against Brunerian, extended mind, and niche construction critiques of computationalism – that is, views prioritising meaning over information, or asserting that behaviour and objects can be intrinsic parts of a thinking process. I argue that empirical evidence from cognitive science is needed to locate distinctively human cognitive mechanisms on the continuum between gadgets and instincts. Focussing on that requirement, I also address specific challenges, and applaud extensions and refinements, of the evidence surveyed in my book. It has been said that “a writer's idea of sound criticism is ten thousand words of closely reasoned adulation.” I cannot disagree with this untraceable wag, but the 30 commentators on Cognitive Gadgets provided some 30,000 words of criticism that are of much greater scientific value than adulation. I am grateful to them all. The response that follows is V-shaped. It starts with the broadest conceptual and methodological issues and funnels down to matters arising from specific empirical studies.

The Extended Evolutionary Synthesis: what is the debate about, and what might success for the extenders look like?

Debate over the Extended Evolutionary Synthesis (EES) ranges over three quite different domains of enquiry. Protagonists are committed to substantive positions regarding (1) empirical questions concerning (for example) the properties and prevalence of systems of epigenetic inheritance; (2) historical characterizations of the modern synthesis; and (3) conceptual/philosophical matters concerning (among other things) the nature of evolutionary processes, and the relationship between selection and adaptation. With these different aspects of the debate in view, it is possible to demonstrate the range of cross-cutting positions on offer when well-informed evolutionists consider their stance on the EES. This overview of the multiple dimensions of debate also enables clarification of two philosophical elements of the EES debate, regarding the status of niche-construction and the role of selection in explaining adaptation. Finally, it points the way to a possible resolution of the EES debate, via a pragmatic approach to evolutionary enquiry.

Why Gupta et al.'s critique of niche construction theory is off target

Gupta et al., in their article in this issue ('Niche construction in evolutionary theory: the construction of an academic niche?'. doi:10.1007/s12041-017-0787-6), lament 'serious problems with the way science is being done' and suggest that 'niche construction theory exemplifies this state of affairs.' However, their aggressively confrontational but superficial critique of niche construction theory (NCT) only contributes to these problems by attacking claims that NCT does not make. This is unfortunate, as their poor scholarship has done a disservice to the evolutionary biology community through propagating misinformation.We correct Gupta et al.'s misunderstandings, stressing that NCT does not suggest that the fact that organisms engage in niche construction is neglected, nor does it make strong claims on the basis of its formal theory. Moreover, the treatment of niche construction as an evolutionary process has been highly productive, and is both theoretically and empirically well-validated.We end by reflecting on the potentially deleterious implications of their publication for evolutionary science.

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 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.

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.