Showing papers in "Biological Theory in 2019"

Social-Ecological Theory of Maximization: Basic Concepts and Two Initial Models

Abstract: Efforts have been dedicated to the understanding of social-ecological systems, an important focus in ethnobiological studies. In particular, ethnobiological investigations have found evidence and tested hypotheses over the last 30 years on the interactions between human groups and their environments, generating the need to formulate a theory for such systems. In this article, we propose the social-ecological theory of maximization to explain the construction and functioning of these systems over time, encompassing hypotheses and evidence from previous ethnobiological studies. In proposing the theory, we present definitions and two conceptual models, an environmental maximization model and a redundancy generation model. The first model seeks to address biota selection and its use by human populations. The second emphasizes how the system organizes itself from the elements that were incorporated into it. Furthermore, we provide the theoretical scenario of plant selection and use from an evolutionary perspective, which explicitly integrates the phylogenetic relationships of plants (or other living resources) and human beings.

The Nature of Programmed Cell Death

Abstract: In multicellular organisms, cells are frequently programmed to die. This makes good sense: cells that fail to, or are no longer playing important roles are eliminated. From the cell’s perspective, this also makes sense, since somatic cells in multicellular organisms require the cooperation of clonal relatives. In unicellular organisms, however, programmed cell death (PCD) poses a difficult and unresolved evolutionary problem. The empirical evidence for PCD in diverse microbial taxa has spurred debates about what precisely PCD means in the case of unicellular organisms (how it should be defined). In this article, we survey the concepts of PCD in the literature and the selective pressures associated with its evolution. We show that definitions of PCD have been almost entirely mechanistic and fail to separate questions concerning what PCD fundamentally is from questions about the kinds of mechanisms that realize PCD. We conclude that an evolutionary definition is best able to distinguish PCD from closely related phenomena. Specifically, we define “true” PCD as an adaptation for death triggered by abiotic or biotic environmental stresses. True PCD is thus not only an evolutionary product but must also have been a target of selection. Apparent PCD resulting from pleiotropy, genetic drift, or trade-offs is not true PCD. We call this “ersatz PCD.”

Criteria for Holobionts from Community Genetics

Abstract: We address the controversy in the literature concerning the definition of holobionts and the apparent constraints on their evolution using concepts from community population genetics. The genetics of holobionts, consisting of a host and diverse microbial symbionts, has been neglected in many discussions of the topic, and, where it has been discussed, a gene-centric, species-centric view, based in genomic conflict, has been predominant. Because coevolution takes place between traits or genes in two or more species and not, strictly speaking, between species, it may affect some traits but not others in either host or symbiont. Moreover, when interacting species pairs are embedded in a larger community, indirect ecological effects can alter the expected pairwise dynamics. Mode of symbiont transmission and the degree of host inbreeding both affect the extent of microbial mixing across host lineages and thereby the degree to which selection on one trait of either partner affects other aspects of a holobiont phenotype. We discuss several potential defining criteria for holobionts using community genetics and population genetics models, suggesting their application and limitations. Using community genetics models, we show how conflict between genomes can be self-limiting, while cooperation and mutualism tend to be self-accelerating. It is likely that this bias in the evolutionary dynamics of interaction between hosts and symbionts is an important feature of holobionts. This bias in the evolutionary dynamic could contribute to explaining the absence of cheaters from natural mutualisms, although cheaters are predicted by gene-centered conflict theory to cause the evolutionary instability of mutualisms. Additionally, it may help explain the more frequent origin of mutualisms from parasitic than from free-living systems, an evolutionary trajectory opposite to that predicted by genome conflict theory.

Reciprocal Causation and the Extended Evolutionary Synthesis

Abstract: Kevin Laland and colleagues have put forward a number of arguments motivating an extended evolutionary synthesis. Here I examine Laland et al.'s central concept of reciprocal causation. Reciprocal causation features in many arguments supporting an expanded evolutionary framework, yet few of these arguments are clearly delineated. Here I clarify the concept and make explicit three arguments in which it features. I identify where skeptics can—and are—pushing back against these arguments, and highlight what I see as the empirical, explanatory, and methodological issues at stake.

Toward a Macroevolutionary Theory of Human Evolution: The Social Protocell

Abstract: Despite remarkable empirical and methodological advances, our theoretical understanding of the evolutionary processes that made us human remains fragmented and contentious. Here, we make the radical proposition that the cultural communities within which Homo emerged may be understood as a novel exotic form of organism. The argument begins from a deep congruence between robust features of Pan community life cycles and protocell models of the origins of life. We argue that if a cultural tradition, meeting certain requirements, arises in the context of such a “social protocell,” the outcome will be an evolutionary transition in individuality whereby traditions and hominins coalesce into a macroscopic bio-socio-technical system, with an organismal organization that is culturally inherited through irreversible fission events on the community level. We refer to the resulting hypothetical evolutionary individual as a “sociont.” The social protocell provides a preadapted source of alignment of fitness interests that addresses a number of open questions about the origins of shared adaptive cultural organization, and the derived genetic (and highly unusual) adaptations that support them. Also, social cooperation between hominins is no longer in exclusive focus since cooperation among traditions becomes salient in this model. This provides novel avenues for explanation. We go on to hypothesize that the fate of the hominin in such a setting would be mutualistic coadaptation into a part-whole relation with the sociont, and we propose that the unusual suite of derived features in Homo is consistent with this hypothesis.

A History of Autocatalytic Sets

Abstract: This year we celebrated Stuart Kauffman’s 80th birthday. Kauffman has contributed many original ideas to science. One of them is that of autocatalytic sets in the context of the origin of life. An autocatalytic set is a self-sustaining chemical reaction network in which all the molecules mutually catalyze each other’s formation from a basic food source. This notion is often seen as a “counterargument” against the dominant genetics-first view of the origin of life, focusing more on metabolism instead. The original notion was introduced back in 1971, but it has taken several decades for this idea to really catch on. Thanks to theoretical as well as experimental progress in more recent research on autocatalytic sets, especially over the past 15 years, the idea now seems to be gaining significant interest and support. In this tribute to Kauffman’s work and ideas, a brief history of research on autocatalytic sets is presented.

The Role of Assessor Teaching in Human Culture

Abstract: According to the dual inheritance theory, cultural learning in our species is a biased and highly efficient process of transmitting cultural traits. Here we define a model of cultural learning where social learning is integrated as a complementary element that facilitates the discovery of a specific behavior by an apprentice, and not as a mechanism that works in opposition to individual learning. In that context, we propose that the emergence of the ability to approve or disapprove of offspring behavior, orienting their learning (a process we call assessor teaching), transformed primate social learning into a cultural transmission system, like that which characterizes our species. Assessor teaching facilitates the replication and/or reconstruction of behaviors that are difficult to imitate and helps to determine which behaviors should be imitated. We also explore the form in which assessor teaching has conditioned the evolution of our abilities to develop cultures in the hominin line, converting us into individuals equipped with what we call a suadens psychology. Our main point is to defend the hypothesis that suadens psychology determines the stability and dynamics that affect the trajectories of many cultural characters. We compare our proposal with other theories about cultural evolution, specifically with dual inheritance theory and cultural attraction theory.

Reflections on a Biometrics of Organismal Form

Abstract: Back in 1987 the physicist/theoretical biologist Walter Elsasser reviewed a range of philosophical issues at the foundation of organismal biology above the molecular level. Two of these are particularly relevant to quantifications of form: the concept of ordered heterogeneity and the principle of nonstructural memory, the truism that typically the forms of organisms substantially resemble the forms of their ancestors. This essay attempts to weave Elsasser’s principles together with morphometrics (the biometrics of organismal form) for one prominent data type, the representation of animal forms by positions of landmark points. I introduce a new spectrum of pattern descriptors of the shape variation of landmark configurations, ranging from the most homogeneous (uniform shears) through growth gradients and focal features to a model of totally disordered heterogeneity incompatible with the rhetoric of functional explanation. An investigation may end up reporting its findings by one of these descriptors or by several. These descriptors all derive from one shared diagrammatic device: a log–log plot of sample variance against one standard formalism of today’s geometric morphometrics, the bending energies of the principal warps that represent all the scales of variability around the sample average shape. The new descriptors, which I demonstrate over a variety of contemporary morphometric examples, may help build the bridge we urgently need between the arithmetic of today’s burgeoning image-based data resources and the rhetoric of biological explanations aligned with the principles of Elsasser along with an even earlier philosopher of biology, the Viennese visionary Hans Przibram.

Neural Reuse and the Modularity of Mind: Where to Next for Modularity?

Abstract: The leading hypothesis concerning the “reuse” or “recycling” of neural circuits builds on the assumption that evolution might prefer the redeployment of established circuits over the development of new ones. What conception of cognitive architecture can survive the evidence for this hypothesis? In particular, what sorts of “modules” are compatible with this evidence? I argue that the only likely candidates will, in effect, be the columns which Vernon Mountcastle originally hypothesized some 60 years ago, and which form part of the well-known columnar hypothesis in neuroscience—systems that cannot handle gross cognitive functions (vision, olfaction, language, etc.) as distinct from strictly exiguous subfunctions (such as aspects of edge detection, depth discrimination, etc.). This is in stark contrast to the modules postulated by much of cognitive psychology, cognitive neuropsychology, and evolutionary psychology. And yet the fate of this revised notion is unclear. The main issue confronting it is the effect of the neural network context on local function. At some point the effects of context are so strong that the degree of specialization required for modularity is not able to be met. Still, despite indications from neuroimaging that peripheral and central systems deploy shared circuitry, some skills clearly do seem to display modularization and autonomy. This article: (1) provides an in-depth analytical and historical review of the fortunes of modular thinking in cognitive science; (2) offers a systematic calibration of brain regions in terms of degrees of functional specificity and robustness; and (3) suggests another way of accounting for the partially encapsulated character of expertise and other highly practiced skills without having to resort to domain-specific modules.

Code Biology, Peircean Biosemiotics, and Rosen’s Relational Biology

Abstract: The classical theories of the genetic code (the stereochemical theory and the coevolution theory) claimed that its coding rules were determined by chemistry—either by stereochemical affinities or by metabolic reactions—but the experimental evidence has revealed a totally different reality: it has shown that any codon can be associated with any amino acid, thus proving that there is no necessary link between them. The rules of the genetic code, in other words, obey the laws of physics and chemistry but are not determined by them. They are arbitrary, or conventional, rules. The result is that the genetic code is not a metaphorical entity, as implied by the classical theories, but a real code, because it is precisely the presence of arbitrary rules that divides a code from all other natural processes. In the past 20 years, furthermore, various independent discoveries have shown that many other organic codes exist in living systems, which means that the genetic code has not been an isolated case in the history of life. These experimental facts have one outstanding theoretical implication: they imply that in addition to the concept of information we must introduce in biology the concept of meaning, because we cannot have codes without meaning or meaning without codes. The problem is that at present we have two different theoretical frameworks for that purpose: one is Code Biology, where meaning is the result of coding, and the other is Peircean biosemiotics, where meaning is the result of interpretation. Recently, however, a third party has entered the scene, and it has been proposed that Robert Rosen’s relational biology can provide a bridge between Code Biology and Peircean biosemiotics.

Evolution is About Populations, But Its Causes are About Individuals

Abstract: There is a tension between, on the one hand, the view that natural selection refers to individual-level causes, and on the other hand, the view that it refers to a population-level cause. In this article, I make the case for the individual-level cause view. I respond to recent claims made by McLoone that the individual-level cause view is inconsistent. I show that if one were to follow his arguments, any causal claim in any context would have to be regarded as vindicating a form of population-level cause view. I show why this is implausible and how a consistent individual-level cause position can be held within the interventionist account of causation. Finally, I argue that there is one sense in which natural selection might be said to refer to population-level causes of evolutionary change. The upshot is that, as noted by others, natural selection can be regarded as referring to a population-level cause in the context of frequency-dependent selection and other situations of fitness-altering interactions between the individuals of a population. But whether this statement is true will depend on the empirical case investigated, not some a priori conceptual distinction. Thus, even though situations of frequency dependence might be ubiquitous, it is orthogonal to the conceptual question of whether frequency-independent natural selection—McLoone’s target—refers to individual- or population-level causes.

Why is There No Successful Whole Brain Simulation (Yet)

Abstract: With the advent of powerful parallel computers, efforts have commenced to simulate complete mammalian brains. However, so far none of these efforts has produced outcomes close to explaining even the behavioral complexities of animals. In this article, we suggest four challenges that ground this shortcoming. First, we discuss the connection between hypothesis testing and simulations. Typically, efforts to simulate complete mammalian brains lack a clear hypothesis. Second, we treat complications related to a lack of parameter constraints for large-scale simulations. To demonstrate the severity of this issue, we review work on two small-scale neural systems, the crustacean stomatogastric ganglion and the Caenorhabditis elegans nervous system. Both of these small nervous systems are very thoroughly, but not completely understood, mainly due to issues with variable and plastic parameters. Third, we discuss the hierarchical structure of neural systems as a principled obstacle to whole-brain simulations. Different organizational levels imply qualitative differences not only in structure, but in choice and appropriateness of investigative technique and perspective. The challenge of reconciling different levels also undergirds the challenge of simulating and hypothesis testing, as modeling a system is not the same thing as simulating it. Fourth, we point out that animal brains are information processing systems tailored very specifically for the ecological niches the respective animals live in.

How Did Language Evolve? Some Reflections on the Language Parasite Debate

Abstract: The language parasite approach (LPA) refers to the view that language, like a parasite, is an adaptive system that evolves to fit its human hosts. Supported by recent computer simulations, LPA proponents claim that the reason that humans can use languages with ease is not because we have evolved with genetically specified linguistic instincts but because languages have adapted to the preexisting brain structures of humans. This article examines the LPA. It argues that, while the LPA has advantages over its rival, Chomskyan nativism, there are additional factors that may limit linguistic variety that have yet to be identified by its insightful proponents. This article suggests abandoning the search for a decisive cause of language capacity and argues that language evolution is more likely to arise from balancing multiple engineering constraints.

The Bio-Evolutionary Anthropocene Hypothesis: Rethinking the Role of Human-Induced Novel Organisms in Evolution

Abstract: Anthropogenic changes in the biosphere, driven mainly by human cultural habits and technological advances, are altering the direction of evolution on Earth, with ongoing and permanent changes modifying uncountable interactions between organisms, the environment, and humankind itself. While numerous species may go extinct, others will be favored due to strong human influences. The Bio-Evolutionary Anthropocene hypothesizes that directly or indirectly human-driven organisms, including alien species, hybrids, and genetically modified organisms, will have major roles in the evolution of life on Earth, shifting the evolutionary pathways of all organisms through novel biological interactions in all habitats. We anticipate that, in future scenarios, novel organisms will be continuously created, and contemporary native organisms with no obvious economic use will decline—while anthropogenic-favored and novel organisms will spread. The Bio-Evolutionary Anthropocene hypothesis therefore predicts that humankind and novel organisms will interact within a strong evolutionary bias that will lead to unexpected, and probably irreversible, outcomes for the evolution of life on our planet.

Task Allocation and the Logic of Research Questions: How Ants Challenge Human Sociobiology

Abstract: After biologist Deborah Gordon made a series of experimental discoveries in the 1980s, she argued that a change in terminology regarding the division of labor among castes of specialists was needed. Gordon’s investigations of the interactive effects of ants in colonies led her to believe that the established approach Edward O. Wilson had pioneered was biased in a way that made some alternative candidate adaptive explanations invisible. Gordon argued that this was because the term “division of labor” implied a division among specialists that was unwarranted, and proposed “task allocation” as a better description that did not bias research against the alternative causes she had discovered. Gordon’s empirical findings and theoretical proposals also vindicate the initial critics of Wilson’s human sociobiology who have been dismissed as political radicals, but her proposals have been widely misunderstood by many contemporary behavioral ecologists. The terminological and methodological confusions rampant in contemporary discourse can be clarified by applying a framework developed by Elisabeth Lloyd involving an analysis of the constraints imposed by different research questions. Applying this framework will show how the methodological problems involving description raised by the initial critics of Wilson’s human sociobiology extended to his analysis of ants, indicating that they were not challenging Wilson’s naturalistic approach to the study of human evolution, but rather his methods. It will also show how confusion over how Gordon’s proposed research questions have been conflated with the possible answers she has argued ought to be investigated. This in turn will clarify contemporary disputes over her proposal to abandon the term “division of labor.”

Revisiting Clarence King’s "Catastrophism and Evolution" (1877)

Abstract: Published comments by American scientists on Darwin’s evolutionary theory are rather rare in the latter half of the 19th century. Clarence King, the founding director of the U.S. Geological Survey in 1879, and an experienced field geologist, focused on the relation between Darwin’s evolutionary concepts and the larger context of Hutton/Lyell’s uniformitarianism versus Cuvier’s catastrophism in his 1877 paper, “Catastrophism and Evolution.” King knew that the fossil record contains little or no data supporting Darwin’s vision of gradual evolutionary change (indeed, Darwin himself was also painfully aware of that fact). Instead, using horse evolution seen in the rocks of the American West, the very example that by the 1920s had become the shining exemplar of gradual evolutionary change, King argued for catastrophic extinction and evolutionary replacement by “plastic” species that were able to survive in modified form as components of the succeeding biota. Though he could not see such change as involving natural selection, in this novel (for the times, whether in Europe or elsewhere, insofar as I am aware) use of the term “plasticity,” there may well be adumbrations of modern evolutionary biology. King’s themes became muted as Americans began to embrace more fully Darwin’s work. But his version of catastrophism never entirely disappeared, especially in paleobiological circles. And it came back in more fully modern form with force beginning with the work of Norman D. Newell on mass extinctions in the mid-20th century—and with that of two of his students: Eldredge and Gould’s (1972) “Punctuated Equilibria.” This essay introduces King’s “Catastrophism and Evolution” (published in The American Naturalist, vol. 11, no. 8, August 1877, pp. 449–470) for the journal’s “Classics in Biological Theory” collection; King’s article is available as supplementary material in the online version of this introduction.

Are Verbal-Narrative Models More Suitable than Mathematical Models as Information Processing Devices for Some Behavioral (Biosemiotic) Problems?

Abstract: This article argues that many, if not most, behavior descriptions and sequencing are in essence an interpretation of signs, and are evaluated as sequences of signs by researchers. Thus, narrative analysis, as developed by Barthes and others, seems best suited to be used in behavioral/biosemiotic studies rather than mathematical modeling, and is very similar to some classic ethology methods. As our brain interprets behaviors as signs and attributes meaning to them, narrative analysis seems more suitable than mathematical modeling to describe and study behavior. Mathematical models are, on many occasions, extremely reductionist and simplifying because of computational and/or numerical representation limitations that lead to errors and straitjacketing interpretations of reality. Since actual animals (and our analysis of their behavior) are not as optimal in real life as our mathematical models, here it is proposed that we should consider logical/verbal models and semantic interpretations as equally or even better suited for behavioral analysis, and refrain from enforcing mathematical modeling as the only (right) way to study and understand biological problems, especially those of a behavioral and biosemiotic nature.

Agonism Management Through Agonistic Vocal Signaling in Subterranean Rodents: A Neglected Factor Facilitating Sociality?

Abstract: Communication is inherent to social relationships. Previous papers addressed the correlation between social and communicative complexity, and the origin of sociality in rodents. In subterranean social species, as the number of animals in the same burrow increases, so do interindividual contact rates. This is because of limitations in actually used tunnel length and diameter, leading to an increasing number of agonistic situations probably resulting in time loss, threatening, and fighting with danger of injuries. To avoid this, social species are expected to have an increase in the number of particular vocalizations. Comparison of the adult vocal repertoire of 12 species (seven genera) through regression and phylogenetically independent contrasts (PIC) suggests three main conclusions: (1) social species increase their repertoire both in number and categories of vocal signals in relation to solitary species, although the coefficient was smaller in the PIC model; (2) the number of agonistic vocalizations was also different between solitary and social species, with the latter displaying higher numbers of these calls; (3) the percentage of agonistic vocalizations in relation to total repertoire was similar between social and solitary species, with no significant relationship between this parameter and the social structure. These results imply that agonistic vocalizations have also increased in number in social species, indicating the importance of these calls in the establishment of new relationships. As repertoire changes are essential to cope with new and frequent kinds of interactions sociality originates, these results suggest that at least for these organisms, communicative changes, especially at the level of agonistic signals, could be a necessary condition to fulfill in the path to the possibility of group living.

A New , New Definition of Evolution by Natural Selection

Abstract: This note provides a definition of evolution by natural selection that is compatible with the extended evolutionary synthesis.

Mating Markets: A Naturally Selected Sex Allocation Theory of Sexual Selection

Abstract: This article utilizes three premises. (1) There are commonly ecologically oriented, naturally selected specialized differences in frequency and/or quality as well as sexually selected differences between the sexes. (2) Sex in the sense of coming together and going apart (syngamy and meiosis in haploids) or going apart and coming together (meiosis and syngamy in diploids) is trade in these naturally selected differences, i.e., there is a mating market in sexual species. (3) While such trade is beneficial to the population as a whole, sexual competition and selection is conflict over the profits of that trade and can be detrimental to the population as a whole. These premises yield a naturally selected sex allocation theory of the possible directions and forms of sexual selection, i.e., one that includes costs as well as frequencies. This can explain conventional sex roles, the sex-role reversed, inter- as well as intrasexual selection, and passive as well as active choice. Any of these alternatives may be over mates, over gametes, or both. A hypothetical example based on density dependence relative to resources is provided, one that suggests that centrioles may be a cytoplasmic resource in males in multicellular animals, and which are the target of active choice and the mechanism of manipulation in passive female choice. As a whole, the approach yields a truly general theory of sexual selection, provides an alternative to the mechanism for Fisher’s principle, and gives a theoretical explanation for Mayr’s biological species definition.

Multicellular individuality: the case of bacteria

Abstract: Recent attention to complex group-level behavior amongst bacteria has led some to conceive of multicellular clusters of bacteria as individuals. In this article, I assess these recent claims by first drawing a distinction between two concepts of individuality: physiological and evolutionary. I then survey cases that are representative of three different modes of growth: myxobacteria (surface-attached agglomerative growth), Bacillus subtilis (agglomerative growth not attached to a surface), and cyanobacteria (filamentous growth). A closer look at these cases indicates that multicellular individuality among bacteria is remarkably complex. Physiologically, the three cases of multicellular clusters do not form physiological individuals. But matters are different when it comes to evolutionary individuality; although multicellular clusters that grow by agglomeration are not highly individuated, filament-forming groups achieve a relatively high degree of individuality. I also suggest that debates about bacterial multicellular individuality may have been obscured by a failure to see that selection on highly individuated groups is by no means the only mechanism to bring about the complex group-level behaviors that have led some to view bacteria as multicellular individuals.