Evolutionary Plausibility Research Articles

The HOMO-LUMO Gap as Discriminator of Biotic from Abiotic Chemistries.

Low-molecular-mass organic chemicals are widely discussed as potential indicators of life in extraterrestrial habitats. However, demarcation lines between biotic chemicals and abiotic chemicals have been difficult to define. Here, we have analyzed the potential utility of the quantum chemical property, HOMO-LUMO gap (HLG), as a novel proxy variable of life, since a significant trend towards incrementally smaller HLGs has been described in the genetically encoded amino acids. The HLG is a zeroth-order predictor of chemical reactivity. Comparing a set of 134 abiotic organic molecules recovered from meteorites, with 570 microbial and plant secondary metabolites thought to be exclusively biotic, we found that the average HLG of biotic molecules was significantly narrower (-10.4 ± 0.9 eV versus -12.4 ± 1.6 eV), with an effect size of g = 1.87. Limitation to hydrophilic molecules (XlogP < 2) improved the separation of biotic from abiotic compounds (g = 2.52). The "hydrophilic reactivity" quadrant defined by |HLG| < 11.25 eV and XlogP < 2 was populated exclusively by 183 biotic compounds and 6 abiotic compounds, 5 of which were nucleobases. We conclude that hydrophilic molecules with small HLGs represent valuable indicators of biotic activity, and we discuss the evolutionary plausibility of this inference.

The Topological Characteristics of Biological Ratio-Sensing Networks

Ratio sensing is a fundamental biological function observed in signal transduction and decision making. In the synthetic biology context, ratio sensing presents one of the elementary functions for cellular multi-signal computation. To investigate the mechanism of the ratio-sensing behavior, we explored the topological characteristics of biological ratio-sensing networks. With exhaustive enumeration of three-node enzymatic and transcriptional regulatory networks, we found that robust ratio sensing was highly dependent on network structure rather than network complexity. Specifically, a set of seven minimal core topological structures and four motifs were deduced to be capable of robust ratio sensing. Further investigations on the evolutionary space of robust ratio-sensing networks revealed highly clustered domains surrounding the core motifs which suggested their evolutionary plausibility. Our study revealed the network topological design principles of ratio-sensing behavior and provided a design scheme for constructing regulatory circuits with ratio-sensing behavior in synthetic biology.

Evolution of metamemory based on self-reference to own memory in artificial neural network with neuromodulation

The ability of humans to self-monitor and control their memory processes is called metamemory and has been widely studied as a component of metacognition in cognitive psychology. Metamemory in non-human animals has also been investigated in recent years, although it had been regarded as a truly unique characteristic of human memory. We attempt to evolve artificial neural networks with neuromodulation, which have a metamemory function. Our constructive approach is expected to contribute, by introducing a novel dimension of evolutionary plausibility, to the discussion of animal experiments to detect metamemory. In this study, we demonstrate the evolution of neural networks that have a metamemory function based on the self-reference of memory, including the analysis of the evolved mechanism of metamemory. In addition, we discuss the similarity between the structure of the evolved neural network and the metamemory model defined by Nelson and Narens.

Supporting the weight of the elephant in the room: Technical intelligence propped up by social cognition and language

We consider the evolutionary plausibility of Osiurak and Reynaud's (O&R) arguments. We argue that technical reasoning is not quite the magic bullet that O&R assume, and instead propose a co-evolutionary account of the interplay between technical reasoning and social learning, with language emerging as a vital issue neglected in O&R's account.

What is the rate-limiting step towards aging? Chemical reaction kinetics might reconcile contradictory observations in experimental aging research.

Modern geroscience is divided as regards the validity of the free radical theory of aging. Thermodynamic arguments and observations from comparative zoology support it, whereas results from experimental manipulations in representative animal species sometimes strongly contradict it. From a comparison of the multi-step aging process with a linear metabolic pathway (glycolysis), we here argue that the identification of the rate-limiting kinetic steps of the aging cascade is essential to understand the overall flux through the cascade, i.e., the rate of aging. Examining free radical reactions as a case in point, these reactions usually occur as chain reactions with three kinetically independent steps: initiation, propagation, and termination, each of which can be rate-limiting. Revisiting the major arguments in favor and against a role of free radicals in aging, we find that the majority of arguments in favor point to radical propagation as relevant and rate-limiting, whereas almost all arguments in disfavor are based on experimental manipulations of radical initiation or radical termination which turned out to be ineffective. We conclude that the overall lack of efficacy of antioxidant supplementation (which fosters termination) and antioxidant enzyme overexpression (which inhibits initiation) in longevity studies is attributable to the fact that initiation and termination are not the rate-limiting steps of the aging cascade. The biological and evolutionary plausibility of this interpretation is discussed. In summary, radical propagation is predicted to be rate-limiting for aging and should be explored in more detail.

Where is the evidence for general intelligence in nonhuman animals?

This commentary contrasts evolutionary plausibility with empirical evidence and cognitive continuity with radiation and convergent evolution. So far, neither within-species nor between-species comparisons on the basis of rigorous experimental and species-appropriate tests substantiate the claims made in the target article. Caution is advisable on meta-analytical comparisons that primarily rely on publication frequencies and overgeneralizations (from murids and primates to other nonhuman animals).

Optimality and Plausibility in Language Design

The Minimalist Program in generative syntax has been the subject of much rancour, a good proportion of it stoked by Noam Chomsky’s suggestion that language may represent “a ‘perfect solution’ to minimal design specifications.” A particular flash point has been the application of Minimalist principles to speculations about how language evolved in the human species. This paper argues that Minimalism is well supported as a plausible approach to language evolution. It is claimed that an assumption of minimal design specifications like that employed in MP syntax satisfies three key desiderata of evolutionary and general scientific plausibility: Physical Optimism, Rational Optimism, and Darwin’s Problem. In support of this claim, the methodologies employed in MP to maximise parsimony are characterised through an analysis of recent theories in Minimalist syntax, and those methodologies are defended with reference to practices and arguments from evolutionary biology and other natural sciences.

Direct reciprocity in animals: The roles of bonding and affective processes

The presence of direct reciprocity in animals is a debated topic, because, despite its evolutionary plausibility, it is believed to be uncommon. Some authors claim that stable reciprocal exchanges require sophisticated cognition which has acted as a constraint on its evolution across species. In contrast, a more recent trend of research has focused on the possibility that direct reciprocity occurs within long-term bonds and relies on simple as well as more complex affective mechanisms such as emotional book-keeping, rudimentary and higher forms of empathy, and inequity aversion, among others. First, we present evidence supporting the occurrence of long-term reciprocity in the context of existing bonds in social birds and mammals. Second, we discuss the evidence for affective responses which, modulated by bonding, may underlie altruistic behaviours in different species. We conclude that the mechanisms that may underlie reciprocal exchanges are diverse, and that some act in interaction with bonding processes. From simple associative learning in social contexts, through emotional contagion and behavioural mimicry, to empathy and a sense of fairness, widespread and diverse social affective mechanisms may explain why direct reciprocity may not be a rare phenomenon among social vertebrates.

An Evolutionary Comparison of the Handicap Principle and Hybrid Equilibrium Theories of Signaling.

The handicap principle has come under significant challenge both from empirical studies and from theoretical work. As a result, a number of alternative explanations for honest signaling have been proposed. This paper compares the evolutionary plausibility of one such alternative, the “hybrid equilibrium,” to the handicap principle. We utilize computer simulations to compare these two theories as they are instantiated in Maynard Smith’s Sir Philip Sidney game. We conclude that, when both types of communication are possible, evolution is unlikely to lead to handicap signaling and is far more likely to result in the partially honest signaling predicted by hybrid equilibrium theory.

On the Evolutionary Plausibility of Religion as Engagement with Ultimacy

On the Evolutionary Plausibility of Religion as Engagement with Ultimacy

Comments on Nathaniel F. Barrett’s “On the Evolutionary Plausibility of Religion as Engagement with Ultimacy”

Comments on Nathaniel F. Barrett’s “On the Evolutionary Plausibility of Religion as Engagement with Ultimacy”

Interspecific social dominance mimicry in birds

Interspecific social dominance mimicry (ISDM) is a proposed form of social parasitism in which a subordinate species evolves to mimic and deceive a dominant ecological competitor in order to avoid attack by the dominant, model species. The evolutionary plausibility of ISDM has been established previously by the Hairy-Downy game (Prum & Samuelson). Psychophysical models of avian visual acuity support the plausibility of visual ISDM at distances ∼>2–3 m for non-raptorial birds, and ∼>20 m for raptors. Fifty phylogenetically independent examples of avian ISDM involving 60 model and 93 mimic species, subspecies, and morphs from 30 families are proposed and reviewed. Patterns of size differences, phylogeny, and coevolutionary radiation generally support the predictions of ISDM. Mimics average 56–58% of the body mass of the proposed model species. Mimics may achieve a large potential deceptive social advantage with <20% reduction in linear body size, which is well within the range of plausible, visual size confusion. Several, multispecies mimicry complexes are proposed (e.g. kiskadee-type flycatchers) which may coevolve through hierarchical variation in the deceptive benefits, similar to Müllerian mimicry. ISDM in birds should be tested further with phylogenetic, ecological, and experimental investigations of convergent similarity in appearance, ecological competition, and aggressive social interactions between sympatric species. Evolutionary explanations of mimicry must consider the possibility that mimics evolve to deceive model species themselves.

Evolution, Perfection, and Theories of Language

In this article it is argued that evolutionary plausibility must be made an important constraining factor when building theories of language. Recent suggestions that presume that language is necessarily a perfect or optimal system are at odds with this position, evolutionary theory showing us that evolution is a meliorizing agent often producing imperfect solutions. Perfection of the linguistic system is something that must be demonstrated, rather than presumed. Empirically, examples of imperfection are found not only in nature and in human cognition, but also in language — in the form of ambiguity, redundancy, irregularity, movement, locality conditions, and extra-grammatical idioms. Here it is argued that language is neither perfect nor optimal, and shown how theories of language which place these proper-ties at their core run into both conceptual and empirical problems.

Food Addiction

The evidence for food's addictive properties is steadily growing. In addition to clinical and evolutionary plausibility, the possibility of addiction to food is supported by animal model research and increasingly by research with humans. Much as classic drugs of abuse "hijack" the brain, accumulating evidence with food suggests a similar impact, but with weaker effects. Although neurobiological evidence for food addiction is compelling, dependence as conceptualized with respect to alcohol and other drugs of abuse is fundamentally a behavioral disorder. Thus, we review the current state of food addiction research in the context of each of the diagnostic criterion for dependence (ie, tolerance, withdrawal, loss of control) and briefly explore other relevant addiction topics such as expectancies, reinforcement, and incentive salience. There is substantial evidence that some people lose control over their food consumption, suffer from repeated failed attempts to reduce their intake, and are unable to abstain from certain types of food or reduce consumption in the face of negative consequences. Although there is some evidence for other dependence criterion, further research is needed to examine tolerance and withdrawal to high-fat sweets, time spent in obtaining, using, and recovering from excess food consumption and the degree to which important activities are given up due to overconsumption. As science continues forward and both the public and elected leaders become aware that food may trigger an addictive process, this information will likely be used to inform policy. Thus, researchers need to carefully consider the implications of their work and the way in which the results may be interpreted.

Modes of evolution in a parasite–host interaction: Dis-entangling factors determining the evolution of regulated fimbriation in E. coli

Escherichia coli expresses type-I fimbriae; these are protrusions from the outer cell wall and have been identified as a virulence factor. They are also expressed by commensal strains of E. coli although (at any one time) only by a small proportion of the population. The orthodox interpretation of this is that fimbriation is regulated so as (i) to trigger a host-based release of nutrients in the form of inflammation signals by slightly activating host defenses and (ii) while avoiding a full scale inflammatory response. This article presents a number of computer simulations of the evolution of fimbriae to scrutinize the evolutionary plausibility of this orthodox view. It turns out that these simulations suggest a revised interpretation of the fimbriae mediated parasite–host interaction. Rather than being a passive victim the host is actively providing a niche that evolutionary favors less virulent parasites. The article closes with a number of testable predictions of this model.

The nature of the language faculty and its implications for evolution of language (Reply to Fitch, Hauser, and Chomsky)

In a continuation of the conversation with Fitch, Chomsky, and Hauser on the evolution of language, we examine their defense of the claim that the uniquely human, language-specific part of the language faculty (the “narrow language faculty”) consists only of recursion, and that this part cannot be considered an adaptation to communication. We argue that their characterization of the narrow language faculty is problematic for many reasons, including its dichotomization of cognitive capacities into those that are utterly unique and those that are identical to nonlinguistic or nonhuman capacities, omitting capacities that may have been substantially modified during human evolution. We also question their dichotomy of the current utility versus original function of a trait, which omits traits that are adaptations for current use, and their dichotomy of humans and animals, which conflates similarity due to common function and similarity due to inheritance from a recent common ancestor. We show that recursion, though absent from other animals' communications systems, is found in visual cognition, hence cannot be the sole evolutionary development that granted language to humans. Finally, we note that despite Fitch et al.'s denial, their view of language evolution is tied to Chomsky's conception of language itself, which identifies combinatorial productivity with a core of “narrow syntax.” An alternative conception, in which combinatoriality is spread across words and constructions, has both empirical advantages and greater evolutionary plausibility.

It is not evolution, but a better game would need a better agent

steels &amp; belpaeme (s&amp;b) refer to the neural plausibility and evolutionary plausibility of their algorithms. although this is not central to their goal of effective artificial agents, their algorithms are not neurally or evolutionarily plausible. their communication games are interesting, and more complex games would lead to more effective agents. however, the algorithms could be improved either by using standard subsymbolic algorithms or by algorithms that are really neurally or evolutionarily plausible.

The number and probability of canalizing functions

Canalizing functions have important applications in physics and biology. For example, they represent a mechanism capable of stabilizing chaotic behavior in Boolean network models of discrete dynamical systems. When comparing the class of canalizing functions to other classes of functions with respect to their evolutionary plausibility as emergent control rules in genetic regulatory systems, it is informative to know the number of canalizing functions with a given number of input variables. This is also important in the context of using the class of canalizing functions as a constraint during the inference of genetic networks from gene expression data. To this end, we derive an exact formula for the number of canalizing Boolean functions of n variables. We also derive a formula for the probability that a random Boolean function is canalizing for any given bias p of taking the value 1. In addition, we consider the number and probability of Boolean functions that are canalizing for exactly k variables. Finally, we provide an algorithm for randomly generating canalizing functions with a given bias p and any number of variables, which is needed for Monte Carlo simulations of Boolean networks.

Dual-process theories and hybrid systems

The distinction between such differing approaches to cognition as connectionism and rule-based models is paralleled by a distinction between two basic modes of cognition postulated in the so-called dual-process theories. Integrating these theories with insights from hybrid systems might help solve the dilemma of combining the demands of evolutionary plausibility and computational universality. No single approach alone can achieve this.

Does Art have Selective Value?

In the absence of satisfactory accounts by evolutionary biologists to explain the ubiquity and persistence of art in all human societies, a number of reasons offered by other writers for the existence and effects of art are critically examined for their evolutionary plausibility. These are found to be inadequate because they are only partial and because their “selective value” is more parsimoniously attributed to other behaviors and attributes which art resembles (e.g., play, ritual, fantasy, ordering, and so forth). The necessity for invoking a concept “art” at all is questioned. Instead it is posited that a universal human behavior, “making special,” from which art in the modern sense is derived had evolutionary value because it reinforced the adoption of other selectively-valuable behaviors. Aesthetic ingredients and responses can be called enabling mechanisms to this end. A concluding section discusses peculiarities of advanced technological society that contribute to modern confusion about art and its place — necessary or unnecessary — in human life.