Semiotic Mechanisms Underlying Niche Construction

The explanatory value of niche construction can be strengthened by firm footing in semiotic theory. Anthropologists have a unique perspective on the integration of such diverse approaches to human action and evolutionary processes. Here, we seek to open a dialogue between anthropology and biosemiotics. The overarching aim of this paper is to demonstrate that niche construction, including the underlying mechanism of reciprocal causation, is a semiotic process relating to biological development (sensu stricto) as well as cognitive development and cultural change. In making this argument we emphasize the semiotic mechanisms underlying the niche concept. We argue that the “niche” in ecology and evolutionary biology can be consistent with the Umwelt of Jakob von Uexkull. Following John Deely we therefore suggest that investigations into the organism—environment interface constituting niche construction should emphasize the semiotic basis of experience. Peircean signs are pervasive and allow for flexible interpretations of phenomena in relation to the perceptual and cognitive capacities of the behaving organism, which is particularly pertinent for understanding the relation of proximate/ultimate selective forces as co-productive (i.e., reciprocal). Additionally, theoretical work by Kinji Imanishi on the evolution of daily life and Gregory Bateson’s relational view of evolution both support the linkage between proximate and ultimate evolutionary processes of causation necessitated by the niche construction perspective. We will then apply this theoretical framework to two specific examples: 1) hominin evolution, including uniquely human cultural behaviors with niche constructive implications; and 2) the multispecies and anthropocentric niche of human-dog coevolution from which complex cognitive capacities and semiotic relationships emerged. The intended outcome of this paper is the establishment of concrete semiotic mechanisms and theory underlying niche constructive behavior which can then be applied to a broad spectrum of organisms to contextualize the reciprocal relation between proximate and ultimate drivers of behavior.     

Perceive, Co-opt, Modify, and Live! Organism as a Centre of Experience

Organic appearances are largely neglected by contemporary biology; partly because they are regarded as superficial effects of causes concealed beneath the surface. The persuasion that everything what does exist is existent for some immediately non-apparent reasons belongs to a general belief of modern science. All organisms are of the same evolutionary origin and of the same world wherein appearance coincides with existence. In this study, living beings are approached as appearing centers of experience that reflects their evolutionary history. From biohermeneutic point of view the evolution of organisms, interactions between organisms, and their relationships to environment is understood as “evolution of interpretations”. I use simple conceptual framework of perception, semiotic co-option, and modification to explain the evolution of semantic organs, i.e. organs that operate through the meaning that was given to them by an animal interpreter.     

Unearthing LTR Retrotransposon gag Genes Co-opted in the Deep Evolution of Eukaryotes

LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse functions, a process formally referred to as co-option. However, a comprehensive picture of LTR retrotransposon gag gene co-option in eukaryotes is still lacking, with several documented cases exclusively involving Ty3/Gypsy retrotransposons in animals. Here, we use a phylogenomic approach to systemically unearth co-option of retrotransposon gag genes above the family level of taxonomy in 2,011 eukaryotes, namely co-option occurring during the deep evolution of eukaryotes. We identify a total of 14 independent gag gene co-option events across more than 740 eukaryote families, eight of which have not been reported previously. Among these retrotransposon gag gene co-option events, nine, four, and one involve gag genes of Ty3/Gypsy, Ty1/Copia, and Bel-Pao retrotransposons, respectively. Seven, four, and three co-option events occurred in animals, plants, and fungi, respectively. Interestingly, two co-option events took place in the early evolution of angiosperms. Both selective pressure and gene expression analyses further support that these co-opted gag genes might perform diverse cellular functions in their hosts, and several co-opted gag genes might be subject to positive selection. Taken together, our results provide a comprehensive picture of LTR retrotransposon gag gene co-option events that occurred during the deep evolution of eukaryotes and suggest paucity of LTR retrotransposon gag gene co-option during the deep evolution of eukaryotes.     

Key transitions during the evolution of animal phototransduction: novelty, "tree-thinking," co-option, and co-duplication

Biologists are amazed by the intricacy and complexity of biologicalinteractions between molecules, cells, organisms, and ecosystems.Yet underlying all this biodiversity is a universal common ancestry.How does evolution proceed from common starting points to generatethe riotous biodiversity we see today? This "novelty problem"—understandinghow novelty and common ancestry relate—has become of criticalimportance, especially since the realization that genes anddevelopmental processes are often conserved across vast phylogeneticdistances. In particular, two processes have emerged as theprimary generators of diversity in organismal form: duplicationplus divergence and co-option. In this article, we first illustratehow phylogenetic methodology and "tree-thinking" can be usedto distinguish duplication plus divergence from co-option. Second,we review two case studies in photoreceptor evolution—onesuggesting a role for duplication plus divergence, the otherexemplifying how co-option can shape evolutionary change. Finally,we discuss how our tree-thinking approach differs from othertreatments of the origin of novelty that utilized a "linear-thinking"approach in which evolution is viewed as a linear and gradualprogression, often from simple to complex phenotype, drivenby natural selection.     

Where is Darwin 200 years later?

The theory of evolution is perceived by many people, particularly but not only in the United States, as a controversial theory not yet fully demonstrated. Yet, that living organisms, including humans, have evolved from ancestors who were very different from them is beyond reasonable doubt, confirmed by at least as much evidence as any other widely accepted scientific theory. I argue that Darwin’s contribution to science goes much beyond the theory of evolution in itself. The theory of natural selection explains the adaptations of organisms, their ‘design’. The ‘Copernican Revolution’ brought the phenomena of the physical universe into the realm of science: explanations by natural causes that can be tested by observation and experiment. However, the scientific revolution that occurred in the 16th and 17th centuries had left the living world out of scientific explanations, because organisms seemingly show that they are ‘designed,’ and thus call for an intentional designer. It was Darwin’s greatest contribution to science, to demonstrate that the adaptations of organisms, their apparent ‘design’, can be explained by natural processes governed by natural laws. At that point, science came into maturity, because all natural phenomena in the universe, living as well as nonliving, could be investigated scientifically, and explained as matter in motion governed by natural laws.     

Fecundity selection theory: concepts and evidence

Fitness results from an optimal balance between survival, mating success and fecundity. The interactions between these three components of fitness vary depending on the selective context, from positive covariation between them, to antagonistic pleiotropic relationships when fitness increases in one reduce the fitness of others. Therefore, elucidating the routes through which selection shapes life history and phenotypic adaptations via these fitness components is of primary significance to understanding ecological and evolutionary dynamics. However, while the fitness components mediated by natural (survival) and sexual (mating success) selection have been debated extensively from most possible perspectives, fecundity selection remains considerably less studied. Here, we review the theoretical basis, evidence and implications of fecundity selection as a driver of sex‐specific adaptive evolution. Based on accumulating literature on the life‐history, phenotypic and ecological aspects of fecundity, we (i) suggest a re‐arrangement of the concepts of fecundity, whereby we coin the term ‘transient fecundity’ to refer to brood size per reproductive episode, while ‘annual’ and ‘lifetime fecundity’ should not be used interchangeably with ‘transient fecundity’ as they represent different life‐history parameters; (ii) provide a generalized re‐definition of the concept of fecundity selection as a mechanism that encompasses any traits that influence fecundity in any direction (from high to low) and in either sex; (iii) review the (macro)ecological basis of fecundity selection (e.g. ecological pressures that influence predictable spatial variation in fecundity); (iv) suggest that most ecological theories of fecundity selection should be tested in organisms other than birds; (v) argue that the longstanding fecundity selection hypothesis of female‐biased sexual size dimorphism (SSD) has gained inconsistent support, that strong fecundity selection does not necessarily drive female‐biased SSD, and that this form of SSD can be driven by other selective pressures; and (vi) discuss cases in which fecundity selection operates on males. This conceptual analysis of the theory of fecundity selection promises to help illuminate one of the central components of fitness and its contribution to adaptive evolution.     

The Semiotic Body

Most bodies in this world do not have brains and the minority of animal species that do have brained bodies are descendents from species with more distributed or decentralized nervous systems. Thus, bodies were here first, and only relatively late in evolution did the bodies of a few species grow supplementary organs, brains, sophisticated enough to support a psychological life. Psychological life therefore from the beginning was embedded in and served as a tool for corporeal life. This paper discusses the semiotically controlled dynamics of bodily existence that has allowed the evolution of these seemingly ‘unnatural’ mental and even linguistic kinds of species. It is shown how the skin, on the one hand, makes us belong in the world, and on the other hand, is part of the huge landscape of membranes across which the semiotic self incessantly must be reconstituted. The discussion moves on to the intracellular world of signal transduction through which the activity of single cells are put to service for bodily needs. The paper further considers the mechanisms behind homeostasis and the semiotics of the psycho-neuro-endocrine integration in the body. The concept of semiotic emergence is introduced and a holistic marker hypothesis for why some animals may have an experiential life is suggested.

Practical Approaches for Detecting Selection in Microbial Genomes

Microbial genome evolution is shaped by a variety of selective pressures. Understanding how these processes occur can help to address important problems in microbiology by explaining observed differences in phenotypes, including virulence and resistance to antibiotics. Greater access to whole-genome sequencing provides microbiologists with the opportunity to perform large-scale analyses of selection in novel settings, such as within individual hosts. This tutorial aims to guide researchers through the fundamentals underpinning popular methods for measuring selection in pathogens. These methods are transferable to a wide variety of organisms, and the exercises provided are designed for researchers with any level of programming experience.

This is part of the PLOS Computational Biology Education collection.

     

Contrasting post-settlement selection results in many-to-one mapping of high performance phenotypes in the Hawaiian waterfall-climbing goby <Emphasis Type="Italic">Sicyopterus stimpsoni</Emphasis>

Natural selection drives adaptive evolution, but contrasting environmental pressures may lead to trade-offs between phenotypes that confer different performances. Such trade-offs may weaken the strength of selection and/or generate complex fitness surfaces with multiple local optima that correspond to different selection regimes. We evaluated how differences in patterns of phenotypic selection might promote morphological differences between subpopulations of the amphidromous Hawaiian waterfall-climbing goby, Sicyopterus stimpsoni. We conducted laboratory experiments on fish from the islands of Kaua‘i and Hawai‘i (the “Big Island”) to compare patterns of linear and nonlinear selection, and the opportunity for selection, that result from two contrasting pressures, predator evasion and waterfall climbing, which vary in intensity between islands. We found directional and nonlinear selection were strongest when individuals were exposed to their primary selective pressures (predator evasion on Kaua‘i, waterfall climbing on the Big Island). However, the opportunity for selection was greater for the non-primary pressure: climbing on Kaua‘i, predator evasion on the Big Island. Canonical rotation of the nonlinear gamma matrix demonstrated that individuals from Kaua‘i and the Big Island occupy regions near their local fitness peaks for some traits. Therefore, selection for predator evasion on Kaua‘i and climbing on the Big Island may be less effective in promoting morphological changes in this species, because variation of functionally important traits in their respective environments may have been reduced by directional or stabilizing selection. These results demonstrate that despite constraints on the opportunities for selection, population differences in phenotypic traits can arise due to differences in selective regimes. For S. stimpsoni, sufficient variation exists in other locomotor traits, allowing for necessary levels of performance in the contrasting selective regime (i.e., climbing on Kaua‘i and predator evasion on the Big Island) through many-to-one-mapping, which may be essential for the survival of local populations in an evanescent island environment.     

The swashbuckling anthropologist: Henrich on The Secret of Our Success

In The Secret of Our Success, Joseph Henrich claims that human beings are unique—different from all other animals—because we engage in cumulative cultural evolution. It is the technological and social products of cumulative cultural evolution, not the intrinsic rationality or ‘smartness’ of individual humans, that enable us to live in a huge range of different habitats, and to dominate most of the creatures who share those habitats with us. We are sympathetic to this general view, the latest expression of the ‘California school’s’ view of cultural evolution, and impressed by the lively and interesting way that Henrich handles evidence from anthropology, economics, and many fields of biology. However, because we think it is time for cultural evolutionists to get down to details, this essay review raises questions about Henrich’s analysis of both the cognitive processes and the selection processes that contribute to cumulative cultural evolution. In the former case, we argue that cultural evolutionists need to make more extensive use of cognitive science, and to consider the evidence that mechanisms of cultural learning are products as well as processes of cultural evolution. In the latter case, we ask whether the California school is really serious about selection, or whether it is offering a merely ‘kinetic’ view of cultural evolution, and, assuming the former, outline four potential models of cultural selection that it would be helpful to distinguish more clearly.     

Sexual selection,sexual isolation and the evolution of song in the Drosophila repleta group of species

The evolution of male courtship song pattern in fruit flies of the repleta group within the genus Drosophila is described. We suggest that the archetypal song was composed of two distinct components, an ‘A’ song with short, regular pulse trains which occurred at the beginning of courtship, and a ‘B’ song consisting of longer pulse trains of more widely spaced pulses occurring later in courtship. During evolution of the repleta group some species have lost the A song, others the B song and, in many species, the latter has become less regular and more complex in form. A songs appear to be involved primarily in species recognition and have been subject to stabilizing selection while the B songs sexually stimulate females and have therefore evolved rapidly through the action of sexual selection. Other factors influencing the evolution of song patterns have been certain physiological and energetic constraints.     

Dicent Symbols in Non-Human Semiotic Processes

Against the view that symbol-based semiosis is a human cognitive uniqueness, we have argued that non-human primates such as African vervet monkeys possess symbolic competence, as formally defined by Charles S. Peirce. Here I develop this argument by showing that the equivocal role ascribed to symbols by ??folk semiotics?? stems from an incomplete application of the Peircean logical framework for the classification of signs, which describes three kinds of symbols: rheme, dicent and argument. In an attempt to advance in the classifying semiotic processes, Peirce proposed several typologies, with different degrees of refinement. Around 1903, he developed a division into ten classes. According to this typology, symbols can be further analysed in three subclasses (rheme, dicent, argument). I proceed to demonstrate that vervet monkeys employ dicent symbols. There are remarkable implications of this argument since ??symbolic species theory?? fails to explore the vast Peircean semiotic philosophy to frame questions regarding the emergence and evolution of symbolic processes.     

Evolution of living organisms as a multilevel process

There is inherent capacity to increase the degree of aggregation within each of the levels of structural organization of living matter. At the macromolecular level (MML), this is an increase in the gene number in the genomes of evolving organisms; at the cellular level (CL), an increase in cell size; and at the multicellular level (MCL), an increase in the number of cells in the multicellular aggregate. However, the increase in the degree of aggregation causes gene incompatibility in case of genome evolution and instability in case of large cells and multicellular aggregates with simple structure. Gene incompatibility may be neutralized by spacio-temporal disconnection of the products of incompatible genes at the cellular and multicellular levels. The larger cells and multicellular aggregates are stabilized by increased structural complexity which is a consequence of the origin of new genes. There is a feedback between the processes of evolution at different levels MML→CL→ MCL.The processes of evolutionary development at different levels of structural organization are also relatively independent. The coincidence of these processes gives rise to stable organisms of higher complexity, which are then subjected to natural selection and population processes to establish a new step in progressive biological evolution. In all of the normal organisms of newly evolved species there is a correspondence between the different levels of structural organization, i.e. in their degree of aggregation, their complexity and functional organization. The form of correspondence for multicellular organisms is presented.     

Modality matters for the expression of inducible defenses: introducing a concept of predator modality

Background

Inducible defenses are a common and widespread form of phenotypic plasticity. A fundamental factor driving their evolution is an unpredictable and heterogeneous predation pressure. This heterogeneity is often used synonymously to quantitative changes in predation risk, depending on the abundance and impact of predators. However, differences in ‘modality’, that is, the qualitative aspect of natural selection caused by predators, can also cause heterogeneity. For instance, predators of the small planktonic crustacean Daphnia have been divided into two functional groups of predators: vertebrates and invertebrates. Predators of both groups are known to cause different defenses, yet predators of the same group are considered to cause similar responses. In our study we question that thought and address the issue of how multiple predators affect the expression and evolution of inducible defenses.

Results

We exposed D. barbata to chemical cues released by Triops cancriformis and Notonecta glauca, respectively. We found for the first time that two invertebrate predators induce different shapes of the same morphological defensive traits in Daphnia, rather than showing gradual or opposing reaction norms. Additionally, we investigated the adaptive value of those defenses in direct predation trials, pairing each morphotype (non-induced, Triops-induced, Notonecta-induced) against the other two and exposed them to one of the two predators. Interestingly, against Triops, both induced morphotypes offered equal protection. To explain this paradox we introduce a ‘concept of modality’ in multipredator regimes. Our concept categorizes two-predator-prey systems into three major groups (functionally equivalent, functionally inverse and functionally diverse). Furthermore, the concept includes optimal responses and costs of maladaptions of prey phenotypes in environments where both predators co-occur or where they alternate.

Conclusion

With D. barbata, we introduce a new multipredator-prey system with a wide array of morphological inducible defenses. Based on a ‘concept of modality’, we give possible explanations how evolution can favor specialized defenses over a general defense. Additionally, our concept not only helps to classify different multipredator-systems, but also stresses the significance of costs of phenotype-environment mismatching in addition to classic ‘costs of plasticity’. With that, we suggest that ‘modality’ matters as an important factor in understanding and explaining the evolution of inducible defenses.

     

The Landscape as a Semiotic Interface between Organisms and Resources

Despite an impressive number of investigations and indirect evidence, the mechanisms that link patterns and processes across the landscape remain a debated point. A new definition of landscape as a semiotic interface between resources and organisms opens up a new perspective to a better understanding of such mechanisms. If the landscape is considered a source of signals converted by animal cognition into signs, it follows that spatial configurations, extension, shape and contagion are not only landscape patterns but categories of identifiable signals. The eco-field hypothesis, by which cognitive templates are used to identify spatial configurations as carriers of meaning according to an active function, are combined with the sign theory to create an eco-semiotic model of landscape representation. Signs from landscape change in efficacy according to mechanisms of degradation, and metric sign categories have to be considered. An interdisciplinary coalescence is expected by using the theoretical approach in different fields of conservation and resource management and planning.     

A Maximum Likelihood Method for Detecting Functional Divergence at Individual Codon Sites, with Application to Gene Family Evolution

The tailoring of existing genetic systems to new uses is called genetic co-option. Mechanisms of genetic co-option have been difficult to study because of difficulties in identifying functionally important changes. One way to study genetic co-option in protein-coding genes is to identify those amino acid sites that have experienced changes in selective pressure following a genetic co-option event. In this paper we present a maximum likelihood method useful for measuring divergent selective pressures and identifying the amino acid sites affected by divergent selection. The method is based on a codon model of evolution and uses the nonsynonymous-to-synonymous rate ratio () as a measure of selection on the protein, with =1, <1, and >1 indicating neutral evolution, purifying selection, and positive selection, respectively. The model allows variation in among sites, with a fraction of sites evolving under divergent selective pressures. Divergent selection is indicated by different s between clades, such as between paralogous clades of a gene family. We applied the codon model to duplication followed by functional divergence of (i) the and globin genes and (ii) the eosinophil cationic protein (ECP) and eosinophil-derived neurotoxin (EDN) genes. In both cases likelihood ratio tests suggested the presence of sites evolving under divergent selective pressures. Results of the and globin analysis suggested that divergent selective pressures might be a consequence of a weakened relationship between fetal hemoglobin and 2,3-diphosphoglycerate. We suggest that empirical Bayesian identification of sites evolving under divergent selective pressures, combined with structural and functional information, can provide a valuable framework for identifying and studying mechanisms of genetic co-option. Limitations of the new method are discussed.     

Cast in Plastic: Semiotic Plasticity and the Pragmatic Reading of Darwin

As Darwin portended but failed to develop, and of which Gould made much, the forensic evidence of evolution points toward Punctuated Equilibrium rather than Phyletic Gradualism; however Gould’s empirical postulation has long suffered from its lack of a testable theoretical basis. This is rectified by the work of Jaroslav Flegr and the Frozen Plasticity Theory, a hypothesis with striking application within semiotic theory and hence to questions of epistemology and ontology. The consequences of applying FPT within Biosemiotics is this: when any particular sign carries a great range of interpretation (semiotic polymorphism) combined with a high degree of mutually supportive referencing (semiotic pleiotropy), that sign is less likely to exhibit plasticity—less able to find new expressions capable of taking on a life of their own (as it were), but more likely to exhibit elasticity, and the flexibility necessary to survive a wide variety of niches. By contrast, much Darwinian and most Neo-Darwinian thought presumes that plasticity is equally and necessarily present in all living things, and that all populations thus slowly evolve. This devalues the point of interplay of such processes, which is the instigation of a specific instance of relating both delineated by and delineating its own unique heritage, and a phenomenon of signage. The presumption that these moments of transaction are all of a singular type has generated certain failures in extrapolating from evolutionary theory to understanding the experience of life. However Darwin was read differently by Darwin’s philosophical champion and Peirce’s “boxing master” Chauncey Wright. Using the historical encounter of the early Pragmatists with Origin, the hypothesis that Peirce’s Pragmatism and Semiotics originated within a study of the ontology implicit within Darwin’s one long argument, and also an evocative import from Sir Edward Strachey, this essay approaches Frozen Plasticity as a theoretical semiosis, so as to clarify the functioning of signage in evolution and cognition.     

Phenomenology of Psychoanalytic Data. A Biosemiotic Framework

In my continuing efforts to build a bridge between psychoanalytic findings and biosemiotics here, as in previous works, ‘biosemiotic’ refers to the hierarchy of meaning-forms (from biological to semiotic-organizations) underlying an updated psychoanalytic model of mind. Within this framework I present a broad range of bio-semiotic phenomena, processes, dynamics, defenses, and universal and unique internalized interpersonal patterns, that in psychoanalysis all commonly fall under the broad heading of the “Unconscious.” Reconceptualized as interpretive data within the purview of a psychoanalytic discourse-semantic this biosemiotic framework posits an epigenetic continuum of human meaning-organizations originating at basic organic levels, moving upward through biological, psycho-somatic and affective expression, proto-semiotic transmissions, represented forms, and finally to explicit linguistic signs and complex symbol systems. In addition to assuming an uninterrupted epigenetic continuum crystallizing in hierarchic organization, this framework accentuates the multilayered and increasingly condensed quality of higher more elaborate organizations of meaning in human communication, drawing attention to persisting biological undercurrents in implied sense, intent, and motivation, all of which impact on repressive/defensive mechanisms. Drawing from previous works (Aragno 1997, 2005, 2008a, b, Psychoanalytic Inquiry 29(1):30–47, 2009, Biosemiotics 3:57–77, 2010, 2011a, Signs 5:71–74, 2011b, Journal of the American Psychoanalytic Association, Centennial Paper, Special Centennial Issue 59(2):239–288, 2011b, Signs 5:29–70, 2011c) in which I labored to update and revise Freud’s first topographical theory of mind, this paper presents the phenomenology of unconscious ‘data’ for the purpose of introducing a diverse range of non-linguistic signifying forms from which psychoanalysts infer mental processes and ‘interpret’ meanings. An important underlying premise regarding psychoanalytic data and its relation to the basic biosemiotic ‘agenda’ is that until grounded in an updated developmental theory of mind inclusive of pre- and proto-semiotic-forms, that is evolutionarily plausible, epistemologically based, and correlates with contemporary neuroscience, the term “sign” is merely an abstract linguistic ‘label’ rather than a mental act with antecedent developmental stages manifesting meanings through different forms and modes of expression. Drawn from the yields of the psychoanalytic method and semantic this revised metatheoretical approach provides insights into the sensory-emotive, bodily origins of unconscious layers of non-linguistic signification thereby expanding our understanding of the formative stages of the ‘semiotic function’ in human evolution. This being the third in a series of papers integrating the yields of psychoanalytic methodology with the underlying premises of ‘Biosemiotics,’ some familiarity with the background knowledge provided in the previous two is strongly recommended.