Extended active inference: Constructing predictive cognition beyond skulls

Cognitive niche construction is the process whereby organisms create and maintain cause-effect models of their niche as guides for fitness influencing behavior. Extended mind theory claims that cognitive processes extend beyond the brain to include predictable states of the world. Active inference and predictive processing in cognitive science assume that organisms embody predictive (i.e., generative) models of the world optimized by standard cognitive functions (e.g., perception, action, learning). This paper presents an active inference formulation that views cognitive niche construction as a cognitive function aimed at optimizing organisms' generative models. We call that process of optimization extended active inference.

Digging the channels of inheritance: On how to distinguish between cultural and biological inheritance

Theories of cultural evolution rest on the assumption that cultural inheritance is distinct from biological inheritance. Cultural and biological inheritance are two separate so-called channels of inheritance, two sub-systems of the sum total of developmental resources travelling in distinct ways between individual agents. This paper asks: what justifies this assumption? In reply, a philosophical account is offered that points at three related but distinct criteria that (taken together) make the distinction between cultural and biological inheritance not only precise but also justify it as real, i.e. as ontologically adequate. These three criteria are (i) the autonomy of cultural change, (ii) the near-decomposability of culture and (iii) differences in temporal order between cultural and biological inheritance. This article is part of the theme issue 'Foundations of cultural evolution'.

Microbial driven genetic variation in holobionts

Genetic variation in holobionts, (host and microbiome), occurring by changes in both host and microbiome genomes, can be observed from two perspectives: observable variations and the processes that bring about the variation. The observable includes the enormous genetic diversity of prokaryotes, which gave rise to eukaryotic organisms. Holobionts then evolved a rich microbiome with a stable core containing essential genes, less so common taxa, and a more diverse non-core enabling considerable genetic variation. The result being that, the human gut microbiome, for example, contains 1,000 times more unique genes than are present in the human genome. Microbial driven genetic variation processes in holobionts include: (1) Acquisition of novel microbes from the environment, which bring in multiple genes in one step, (2) amplification/reduction of certain microbes in the microbiome, that contribute to holobiont` s adaptation to changing conditions, (3) horizontal gene transfer between microbes and between microbes and host, (4) mutation, which plays an important role in optimizing interactions between different microbiota and between microbiota and host. We suggest that invertebrates and plants, where microbes can live intracellularly, have a greater chance of genetic exchange between microbiota and host, thus a greater chance of vertical transmission and a greater effect of microbiome on evolution of host than vertebrates. However, even in vertebrates the microbiome can aid in environmental fluctuations by amplification/reduction and by acquisition of novel microorganisms.

Ecosystem engineering in the Quaternary of the West Coast of South Africa

Despite advances in our understanding of the geographic and temporal scope of the Paleolithic record, we know remarkably little about the evolutionary and ecological consequences of changes in human behavior. Recent inquiries suggest that human evolution reflects a long history of interconnections between the behavior of humans and their surrounding ecosystems (e.g., niche construction). Developing expectations to identify such phenomena is remarkably difficult because it requires understanding the multi-generational impacts of changes in behavior. These long-term dynamics require insights into the emergent phenomena that alter selective pressures over longer time periods which are not possible to observe, and are also not intuitive based on observations derived from ethnographic time scales. Generative models show promise for probing these potentially unexpected consequences of human-environment interaction. Changes in the uses of landscapes may have long term implications for the environments that hominins occupied. We explore other potential proxies of behavior and examine how modeling may provide expectations for a variety of phenomena.

Children and innovation: play, play objects and object play in cultural evolution

Cultural evolutionary theory conceptualises culture as an information-transmission system whose dynamics take on evolutionary properties. Within this framework, however, innovation has been likened to random mutations, reducing its occurrence to chance or fortuitous transmission error. In introducing the special collection on children and innovation, we here place object play and play objects - especially functional miniatures - from carefully chosen archaeological contexts in a niche construction perspective. Given that play, including object play, is ubiquitous in human societies, we suggest that plaything construction, provisioning and use have, over evolutionary timescales, paid substantial selective dividends via ontogenetic niche modification. Combining findings from cognitive science, ethology and ethnography with insights into hominin early developmental life-history, we show how play objects and object play probably had decisive roles in the emergence of innovative capabilities. Importantly, we argue that closer attention to play objects can go some way towards addressing changes in innovation rates that occurred throughout human biocultural evolution and why innovations are observable within certain technological domains but not others.

Darwinian selection of host and bacteria supports emergence of Lamarckian-like adaptation of the system as a whole

Background

The relatively fast selection of symbiotic bacteria within hosts and the potential transmission of these bacteria across generations of hosts raise the question of whether interactions between host and bacteria support emergent adaptive capabilities beyond those of germ-free hosts.

Results

To investigate possibilities for emergent adaptations that may distinguish composite host-microbiome systems from germ-free hosts, we introduce a population genetics model of a host-microbiome system with vertical transmission of bacteria. The host and its bacteria are jointly exposed to a toxic agent, creating a toxic stress that can be alleviated by selection of resistant individuals and by secretion of a detoxification agent (“detox”). We show that toxic exposure in one generation of hosts leads to selection of resistant bacteria, which in turn, increases the toxic tolerance of the host’s offspring. Prolonged exposure to toxin over many host generations promotes anadditional form of emergent adaptation due to selection of hosts based on detox produced by their bacterial community as a whole (as opposed to properties of individual bacteria).

Conclusions

These findings show that interactions between pure Darwinian selections of host and its bacteria can give rise to emergent adaptive capabilities, including Lamarckian-like adaptation of the host-microbiome system.

Reviewers

This article was reviewed by Eugene Koonin, Yuri Wolf and Philippe Huneman.

Electronic supplementary material

The online version of this article (10.1186/s13062-018-0224-7) contains supplementary material, which is available to authorized users.

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.

Footbinding, Industrialization, and Evolutionary Explanation : An Empirical Illustration of Niche Construction and Social Inheritance

The incorporation of niche construction theory (NCT) and epigenetics into an extended evolutionary synthesis (EES) increases the explanatory power of evolutionary analyses of human history. NCT allows identification of distinct social inheritance and cultural inheritance and can thereby account for how an existing-but-dynamic social system yields variable influences across individuals and also how these individuals' microlevel actions can feed back to alter the dynamic heterogeneously across time and space. An analysis of Chinese footbinding, as it was ending during the first half of the twentieth century and China was industrializing, illustrates the evolutionary dynamics of niche construction across inheritance tracks and explains regional heterogeneity as well as the persistence of a cultural belief that was socially inaccurate. Incorporating anthropological and sociological insights into an EES with NCT has the potential to proffer source laws for relationships between individual actions and macro-patterns in beliefs, structures, climate, and demography.

Niche construction game cancer cells play

Niche construction concept was originally defined in evolutionary biology as the continuous interplay between natural selection via environmental conditions and the modification of these conditions by the organism itself. Processes unraveling during cancer metastasis include construction of niches, which cancer cells use towards more efficient survival, transport into new environments and preparation of the remote sites for their arrival. Many elegant experiments were done lately illustrating, for example, the premetastatic niche construction, but there is practically no mathematical modeling done which would apply the niche construction framework. To create models useful for understanding niche construction role in cancer progression, we argue that a) genetic, b) phenotypic and c) ecological levels are to be included. While the model proposed here is phenomenological in its current form, it can be converted into a predictive outcome model via experimental measurement of the model parameters. Here we give an overview of an experimentally formulated problem in cancer metastasis and propose how niche construction framework can be utilized and broadened to model it. Other life science disciplines, such as host-parasite coevolution, may also benefit from niche construction framework adaptation, to satisfy growing need for theoretical considerations of data collected by experimental biology.

A controvérsia em torno da atribuição de cultura a animais não humanos: uma revisão crítica

Nas últimas décadas, estudiosos do comportamento têm afirmado que animais não humanos apresentam cultura, dando início a uma controvérsia, especialmente com antropólogos socioculturais, que ainda não foi resolvida. Com o objetivo de compreender melhor essa controvérsia e identificar possíveis direções de consenso, nós revisamos o desenvolvimento da noção de cultura na antropologia sociocultural e sua utilização na literatura etológica. Argumentamos que antropólogos socioculturais e estudiosos do comportamento animal divergem em termos de suas teorias e visões de mundo. Para alcançar uma abordagem sintética do comportamento animal que inclua humanos e não humanos, sem ignorar as características próprias de cada espécie, seria desejável construir um consenso nesses dois níveis. A questão dos símbolos e significados é central para a noção antropológica de cultura e, portanto, será necessário incluí-la em uma perspectiva comparativa. Concluímos que uma direção de consenso teórico encontra-se em abordagens críticas às dualidades natureza-cultura, inato-adquirido e gene-ambiente.

Adaptation and niche construction in human prehistory: a case study from the southern Scandinavian Late Glacial

The niche construction model postulates that human bio-social evolution is composed of three inheritance domains, genetic, cultural and ecological, linked by feedback selection. This paper argues that many kinds of archaeological data can serve as proxies for human niche construction processes, and presents a method for investigating specific niche construction hypotheses. To illustrate this method, the repeated emergence of specialized reindeer (Rangifer tarandus) hunting/herding economies during the Late Palaeolithic (ca 14.7-11.5 kyr BP) in southern Scandinavia is analysed from a niche construction/triple-inheritance perspective. This economic relationship resulted in the eventual domestication of Rangifer. The hypothesis of whether domestication was achieved as early as the Late Palaeolithic, and whether this required the use of domesticated dogs (Canis familiaris) as hunting, herding or transport aids, is tested via a comparative analysis using material culture-based phylogenies and ecological datasets in relation to demographic/genetic proxies. Only weak evidence for sustained niche construction behaviours by prehistoric hunter-gatherer in southern Scandinavia is found, but this study nonetheless provides interesting insights into the likely processes of dog and reindeer domestication, and into processes of adaptation in Late Glacial foragers.

Human niche construction in interdisciplinary focus

Niche construction is an endogenous causal process in evolution, reciprocal to the causal process of natural selection. It works by adding ecological inheritance, comprising the inheritance of natural selection pressures previously modified by niche construction, to genetic inheritance in evolution. Human niche construction modifies selection pressures in environments in ways that affect both human evolution, and the evolution of other species. Human ecological inheritance is exceptionally potent because it includes the social transmission and inheritance of cultural knowledge, and material culture. Human genetic inheritance in combination with human cultural inheritance thus provides a basis for gene-culture coevolution, and multivariate dynamics in cultural evolution. Niche construction theory potentially integrates the biological and social aspects of the human sciences. We elaborate on these processes, and provide brief introductions to each of the papers published in this theme issue.

Flowering-time plasticity facilitates niche shifts in adjacent populations

The potential for a habitat shift is enhanced when selection against immigrants is augmented by a temporal difference between them and inhabitants of core populations. Genetically mediated changes in flowering time often accompany niche shifts in plants. The possibility that temporal change may arise from plastic responses to novel, stressful, environments rather than from genetic alteration has not been explored. This option is considered here, and it may be quite common. The substantial literature on transplant and common garden experiments shows that invaders of novel habitats are likely to undergo a developmentally based phenological shift. A phenological change in the invading population leads to assortative mating within populations, which in turn facilitates the evolution of local adaptation by the invader. Environmental induction may be the sole contributor to temporal change, or this factor may act in concert with genetic change. Flowering shifts based on developmental responses are immediate, not subject to remediation by gene flow and not affected by a paucity of genetic variation, negative genetic correlations or antagonistic pleiotropy, all of which might constrain phenological evolution.

The evolutionary reduction principle for linear variation in genetic transmission

The evolution of genetic systems has been analyzed through the use of modifier gene models, in which a neutral gene is posited to control the transmission of other genes under selection. Analysis of modifier gene models has found the manifestations of an "evolutionary reduction principle": in a population near equilibrium, a new modifier allele that scales equally all transition probabilities between different genotypes under selection can invade if and only if it reduces the transition probabilities. Analytical results on the reduction principle have always required some set of constraints for tractability: limitations to one or two selected loci, two alleles per locus, specific selection regimes or weak selection, specific genetic processes being modified, extreme or infinitesimal effects of the modifier allele, or tight linkage between modifier and selected loci. Here, I prove the reduction principle in the absence of any of these constraints, confirming a twenty-year-old conjecture. The proof is obtained by a wider application of Karlin's Theorem 5.2 (Karlin in Evolutionary biology, vol. 14, pp. 61-204, Plenum, New York, 1982) and its extension to ML-matrices, substochastic matrices, and reducible matrices.