This paper explores how an evolutionary process can produce systems that learn. A general framework for the evolution of learning is outlined, and is applied to the task of evolving mechanisms suitable for supervised learning in single-layer neural networks. Dynamic properties of a network’s information-processing capacity are encoded genetically, and these properties are subjected to selective pressure based on their success in producing adaptive behavior in diverse environments. As a result of selection and genetic recombination, various successful (...) learning mechanisms evolve, including the well-known delta rule. The effect of environmental diversity on the evolution of learning is investigated, and the role of different kinds of emergent phenomena in genetic and connectionist systems is discussed. (shrink)

Every living entity requires the capacity to defend against viruses in some form. From bacteria to plants to arthropods, cells retain the capacity to capture genetic material, process it in a variety of ways, and subsequently use it to generate pathogen-specific small RNAs. These small RNAs can then be used to provide specificity to an otherwise non-specific nuclease, generating a potent antiviral system. While small RNA-based defenses in chordates are less utilized, the protein-based antiviral invention in this phylum appears (...) to have derived from components of the same ancestral small RNA machinery. Based on recent evidence, it would seem that RNase III nucleases have been reiteratively repurposed over billions of years to provide cells with the capacity to recognize and destroy unwanted genetic material. Here we describe an overview of what is known on this subject and provide a model for how these defenses may have evolved. RNase III nuclease domains are widely used in an array of RNA metabolic functions as well as antiviral defenses. Here, we review their current usage as well as provide insight into how these domains may have shaped all major antiviral pathways over the course of evolution. (shrink)

There are currently three major theories on the origin and evolution of the genetic code: the stereochemical theory, the coevolution theory, and the error-minimization theory. The first two assume that the genetic code originated respectively from chemical affinities and from metabolic relationships between codons and amino acids. The error-minimization theory maintains that in primitive systems the apparatus of protein synthesis was extremely prone to errors, and postulates that the genetic code evolved in order to minimize (...) the deleterious effects of the translation errors. This article describes a fourth theory which starts from the hypothesis that the ancestral genetic code was ambiguous and proposes that its evolution took place with a mechanism that systematically reduced its ambiguity and eventually removed it altogether. This proposal is distinct from the stereochemical and the coevolution theories because they do not contemplate any ambiguity in the genetic code, and it is distinct from the error-minimization theory because ambiguity-reduction is fundamentally different from error-minimization. The concept of ambiguity-reduction has been repeatedly mentioned in the scientific literature, but so far it has remained only an abstract possibility because no model has been proposed for its mechanism. Such a model is described in the present article and may be the first step in a new approach to the study of the evolution of the genetic code. (shrink)

We address issues of description of the origin and evolution of the genetic code from a semiotics standpoint. Developing the concept of codepoiesis introduced by Barbieri, a new idea of semio-poiesis is proposed. Semio-poiesis, a recursive auto-referential processing of semiotic system, becomes a form of organization of the bio-world when and while notions of meaning and aiming are introduced into it. The description of the genetic code as a semiotic system allows us to apply the method of (...) internal reconstruction to it: on the basis of heterogeneity and irregularity of the current state, to explicate possible previous states and various ways of forming mechanisms of coding and textualization. The revealed patterns are consistent with hypotheses about the origin and evolution of the genetic code. (shrink)

Heyes argues that human metacognitive strategies (“cognitive gadgets” or “mills”) are the products of cultural evolution based on domain‐general cognition with few simple biases. Although like Heyes, we believe that the evolution of domain‐general cognitive processes played a crucial role in the evolution of human cognition, we argue that Heyes' distinction between mills and grist is too sharp, that associative learning evolved gradually to become more complex and hierarchical, something that is not captured by the system 1/system (...) 2 distinction, and that human cognitive plasticity required the genetic accommodation of gadget‐specific processes that led to more plasticity‐enhancing human‐specific biases. (shrink)

The Segregation Distorter (SD) system of Drosophila melanogaster is one the best‐characterized meiotic drive complexes known. SD gains an unfair transmission advantage through heterozygous SD/SD+ males by incapacitating SD+‐bearing spermatids so that virtually all progeny inherit SD. Segregation distorter (Sd), the primary distorting locus in the SD complex, is a truncated duplication of the RanGAP gene, a major regulator of the small GTPase Ran, which has several functions including the maintenance of the nucleocytoplasmic RanGTP concentration gradient that mediates nuclear transport. (...) The truncated Sd‐RanGAP protein is enzymatically active but mislocalizes to the nucleus where it somehow causes distortion. Here I present data consistent with the idea that wild‐type RanGAP, and possibly other loci able to influence the RanGTP gradient, has been caught up in an ancient genetic conflict that predates the SD complex. The legacy of this conflict could include the unexpectedly rapid evolution of nuclear transport‐related proteins, the accumulation of chromosomal inversions, the recruitment of gene duplications, and the turnover of repetitive sequences in the centric heterochromatin. BioEssays 29:386–391, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

Three early 20th-century attempts at unifying separate areas of biology, in particular development, genetics, physiology, and evolution, are compared in regard to their success and fruitfulness for further research: Jacques Loeb’s reductionist project of unifying approaches by physico-chemical explanations; Richard Goldschmidt’s anti-reductionist attempts to unify by integration; and Sewall Wright’s combination of reductionist research and vision of hierarchical genetic systems. Loeb’s program, demanding that all aspects of biology, including evolution, be studied by the methods of the (...) experimental sciences, proved highly successful and indispensible for higher level investigations, even though evolutionary change and properties of biological systems up to now cannot be fully explained on the molecular level alone. Goldschmidt has been appraised as pioneer of physiological and developmental genetics and of a new evolutionary synthesis which transcended neo-Darwinism. However, this study concludes that his anti-reductionist attempts to integrate genetics, development and evolution have to be regarded as failures or dead ends. His grand speculations were based on the one hand on concepts and experimental systems that were too vague in order to stimulate further research, and on the other on experiments which in their core parts turned out not to be reproducible. In contrast, Sewall Wright, apart from being one of the architects of the neo-Darwinian synthesis of the 1930s, opened up new paths of testable quantitative developmental genetic investigations. He placed his research within a framework of logical reasoning, which resulted in the farsighted speculation that examinations of biological systems should be related to the regulation of hierarchical genetic subsystems, possibly providing a mechanism for development and evolution. I argue that his suggestion of basing the study of systems on clearly defined properties of the components has proved superior to Goldschmidt’s approach of studying systems as a whole, and that attempts to integrate different fields at a too early stage may prove futile or worse. © 2011 Elsevier Inc. (shrink)

The main purpose of this article is to consider the significance of different types of memory and non-genetic inheritance and different biosemiotic systems for the origin and evolution of language. It presents language and memory as distributed, heteronomous and system-determined processes implemented in biological and social domains. The article emphasises that language and other sign systems are both ecological and inductive systems that were caused by and always correlate with the environment and deductive systems (...) that are inherited by and depend on the internal development of organisms, individuals, and societies. The article also claims that the origin, re-occurrence and evolution of naturally-emerging sign systems presuppose their retention and accumulation in physical, biological, individual, and social types of memory and reinforcement and maintenance by conventional and deliberate social regulation and accumulation. All of this allows language and other sign systems to be situation-relevant and to be transmitted through generations without their constant reinvention. The novelty of the proposed theory of language origin and evolution is in interdisciplinary integration of biosemiotic studies, systems approaches to language and studies of inheritance systems presented by ‘Extended evolutionary synthesis’. (shrink)

All surviving jawed vertebrate representatives achieve diversity in immunoglobulin‐based B and T cell receptors for antigen recognition through recombinatorial rearrangement of V(D)J segments. However, the extant jawless vertebrates, lampreys and hagfish, instead generate three types of variable lymphocyte receptors (VLRs) through a template‐mediated combinatorial assembly of different leucine‐rich repeat (LRR) sequences. The clonally diverse VLRB receptors are expressed by B‐like lymphocytes, while the VLRA and VLRC receptors are expressed by lymphocyte lineages that resemble αβ and γδ T lymphocytes, respectively. These (...) findings suggest that three basic types of lymphocytes, one B‐like and two T‐like, are an essential feature of vertebrate adaptive immunity. Around 500 million years ago, a common ancestor of jawed and jawless vertebrates evolved a genetic program for the development of prototypic lymphoid cells as a foundation for an adaptive immune system. This acquisition preceded the convergent evolution of alternative types of clonally diverse receptors for antigens in all vertebrates, as reviewed in this article. (shrink)

The study of alternative genetic systems and mixed modes of reproduction, whereby sexual and asexual reproduction is combined within the same lifecycle, is of fundamental importance as they may shed light on classical evolutionary issues, such as the paradox of sex. Recently, several such cases were discovered in social insects. A closer examination of these systems has revealed many amazing facts, including the mixed use of asexual and sexual reproduction for the production of new queens and workers, (...) males that can clone themselves and the routine use of incest without deleterious genetic consequences. In addition, in several species, remarkable cases of asexually reproducing socially parasitic worker lineages have been discovered. The study of these unusual systems promises to provide insight into many basic evolutionary questions, including the maintenance of sex, the expression of sexual conflict and kin conflict and the evolution of cheating in asexual lineages. (shrink)

This chapter offers an essay on the evolution of evolvability. It investigates the most frequently cited arguments against the possibility that the evolution of evolvability might be the result of selection favoring more evolvable genotypes. The chapter argues that all these arguments have not been rigorously analyzed by their proponents, and are thus a self-inflicted blind spot in evolutionary biology, and indicates that there are no deep conceptual obstacles for population genetic theory to explain the evolution (...) of evolvability. The very focus on this subject will help shift the perspective of evolutionary biology toward a more holistic, systemic view of evolution. (shrink)

Parallels in anatomy between humans and domesticated mammals suggest that for the last 300,000 years, Homo sapiens has experienced more intense selection against the propensity for reactive aggression than any other species of Homo. Selection against reactive aggression, a process that can also be called self-domestication, would help explain various physiological, behavioral and cognitive features of humans, including the unique system of egalitarian male hierarchy in mobile hunter-gatherers. Here I review nine leading proposals that could potentially explain why self-domestication occurred (...) in H. sapiens, whether by selecting in favor of cooperation and tolerance or by selecting against aggressiveness. To account for the domestication syndrome, proposals must explain what led to a decline in fitness of highly aggressive males, and why the explanatory factor applies only to H. sapiens rather than to other species of Homo. The proposed explanations invoke genetic group selection; group-structured culture selection (also known as cultural group selection); social selection by female mate choice; social selection by male partner choice; increased self-control; cooperative breeding; high population density; use of lethal weapons; and language-based conspiracy. Most proposals face difficulties in accounting for the origins and/or maintenance of self-domestication. I conclude that the evolution of language-based conspiracy, which is a form of collective intentionality, was the key factor initiating and maintaining self-domestication in H. sapiens, because it is the most convincing mechanism for explaining the selective pressure against individually powerful fighters. Sophisticated language enabled males of low fighting prowess to coordinate in executing physically aggressive and domineering alpha males. This system is known today as a leveling mechanism in small-scale societies. Group-structured culture selection possibly accelerated the process. (shrink)

The way language as a human faculty has evolved is a question that preoccupies researchers from a wide spread of disciplines. In this book, a team of writers has been brought together to examine the evolution of language from a variety of such standpoints, including language's genetic basis, the anthropological context of its appearance, its formal structure, its relation to systems of cognition and thought, as well as its possible evolutionary antecedents. The book includes Hauser, Chomsky, and (...) Fitch's seminal and provocative essay on the subject, 'The Faculty of Language,' and charts the progress of research in this active and highly controversial field since its publication in 2002. This timely volume will be welcomed by researchers and students in a number of disciplines, including linguistics, evolutionary biology, psychology, and cognitive science. (shrink)

Ideas about heredity and evolution are undergoing a revolutionary change. New findings in molecular biology challenge the gene-centered version of Darwinian theory according to which adaptation occurs only through natural selection of chance DNA variations. In Evolution in Four Dimensions, Eva Jablonka and Marion Lamb argue that there is more to heredity than genes. They trace four "dimensions" in evolution -- four inheritance systems that play a role in evolution: genetic, epigenetic, behavioral, and symbolic. (...) These systems, they argue, can all provide variations on which natural selection can act. Evolution in Four Dimensions offers a richer, more complex view of evolution than the gene-based, one-dimensional view held by many today. The new synthesis advanced by Jablonka and Lamb makes clear that induced and acquired changes also play a role in evolution.After discussing each of the four inheritance systems in detail, Jablonka and Lamb "put Humpty Dumpty together again" by showing how all of these systems interact. They consider how each may have originated and guided evolutionary history and they discuss the social and philosophical implications of the four-dimensional view of evolution. Each chapter ends with a dialogue in which the authors engage the contrarieties of the fictional "I.M.," or Ifcha Mistabra -- Aramaic for "the opposite conjecture" -- refining their arguments against I.M.'s vigorous counterarguments. The lucid and accessible text is accompanied by artist-physician Anna Zeligowski's lively drawings, which humorously and effectively illustrate the authors' points. (shrink)

There is growing acceptance among language evolution researchers that an increase in our ancestors’ theory of mind capacities was critical to the origins of language. However, little attention has been paid to the question of how those capacities were in fact upgraded. This article develops a novel hypothesis, grounded in contemporary cognitive neuroscience, on which our theory of mind capacities improved as a result of an increase in our System-2 thinking capacities, in turn based in an increase in our (...) working memory capacities. I contrast this hypothesis with what would appear to be the default position among language evolution researchers, namely, that our theory of mind became more powerful as a result of genetic change to a domain-specific mindreading system which we share with other great apes. While the latter hypothesis is not implausible, it arguably enjoys less empirical support at present than does the alternative hypothesis I develop. (shrink)

The term ‘breeding system’ is used to describe the morphological and behavioural aspects of the sexual life cycle of a species. The yeast breeding system provides three alternatives that enable hapoids to return to the diploid state that is necessary for meiosis: mating of unrelated haploids (amphimixis), mating between spores from the same tetrad (intratetrad mating, automixis) and mother daughter mating upon mating type switching (haplo‐selfing). The frequency of specific mating events affects the level of heterozygosity present in individuals and (...) the genetic diversity of populations. This review discuses the reproductive strategies of yeasts, in particular S. cerevisiae (Bakers' or budding yeast). Emphasis is put on intratetrad mating, its implication for diversity, and how the particular genome structure could have evolved to ensure the preservation of a high degree of heterozygosity in conjunction with frequent intratetrad matings. I also discuss how the ability of yeast to control the number of spores that are formed accounts for high intratetrad mating rates and for enhanced transmission of genomic variation. I extend the discussion to natural genetic variation and propose that a high level of plasticity is inherent in the yeast breeding system, which may allow variation of the breeding behaviour in accordance with the needs imposed by the environment. BioEssays 28: 696–708, 2006. © 2006 Wiley Periodicals, Inc. (shrink)

We set out an account of how self-domestication plays a crucial role in the evolution of language. In doing so, we focus on the growing body of work that treats language structure as emerging from the process of cultural transmission. We argue that a full recognition of the importance of cultural transmission fundamentally changes the kind of questions we should be asking regarding the biological basis of language structure. If we think of language structure as reflecting an accumulated set (...) of changes in our genome, then we might ask something like, “What are the genetic bases of language structure and why were they selected?” However, if cultural evolution can account for language structure, then this question no longer applies. Instead, we face the task of accounting for the origin of the traits that enabled that process of structure-creating cultural evolution to get started in the first place. In light of work on cultural evolution, then, the new question for biological evolution becomes, “How did those precursor traits evolve?” We identify two key precursor traits: the transmission of the communication system through learning; and the ability to infer the communicative intent associated with a signal or action. We then describe two comparative case studies—the Bengalese finch and the domestic dog—in which parallel traits can be seen emerging following domestication. Finally, we turn to the role of domestication in human evolution. We argue that the cultural evolution of language structure has its origin in an earlier process of self-domestication. (shrink)

Alternative ways to ensure mate compatibility, such as hermaphroditism and the breakdown of self‐incompatibility, evolved repeatedly when finding a mating partner is difficult. In a variety of microorganisms where compatibility is determined by mating‐types, a highly regulated form of universal compatibility system called mating‐type switching has evolved several times. This sophisticated system allows for the genetic adjustment of the mating type during asexual growth, and it most likely evolved for reproductive assurance of immotile species under low densities. In this (...) review, we compare the switching strategy to other universal compatibility systems such as “unisexual mating” and homothallism. We identify the costs of switching, including genome instability, and mechanistic costs, as well as the benefits, mainly the maintenance of important mating‐type functions. Given the potential benefits of mating‐type switching, we speculate that switching is likely to have evolved many times independently, and may be more common in groups where genetic mating types regulate mate compatibility than assumed so far. (shrink)

Genes that exert their function when they are introduced into a foreign genetic background pose many questions to our current understanding of the forces and mechanisms that promote either the maintenance or divergence of gene functions over evolutionary time. The melanoma inducing Xmrk oncogene of the Southern platyfish (Xiphophorus maculatus) is a stable constituent of the genome of this species. It displays its tumorigenic function, however, almost exclusively only after inter‐populational or, even more severely, interspecific hybridization events. The Xiphophorus (...) hybrid melanoma system has gained attention in biomedical research as a genetic model for studying tumor formation. From an evolutionary perspective, a prominent question is: how could this gene persist over millions of years? An attractive hypothesis is that Xmrk, acting as a detrimental gene in a hybrid genome, could be a speciation gene that shields the gene pool of its species from mixing with other closely related sympatric species. In this article, I briefly review our current knowledge of the molecular genetics and biochemical functions of the Xmrk gene and discuss aspects of its evolutionary history and presence with respect to this idea. While Xmrk as a potentially injurious oncogene has clearly survived for millions of years, its role as a speciation gene has to be questioned. BioEssays 30:822–832, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

Here, in textbook style, is a concise biological account of the evolution of morality. It addresses morality on three levels: moral outcomes (behavioral genetics), moral motivation or intent (psychology and neurology), and moral systems (sociality). The rationale for teaching this material is addressed in Allchin (2009). Classroom resources (including accompanying images and video links) and a discussion of teaching strategies are provided online at: http://EvolutionOfMorality.net.

The biogenesis of RNAs and proteins is a threat to the cell. Indeed, the act of transcription and nascent RNAs challenge DNA stability. Both RNAs and nascent proteins can also initiate the formation of toxic aggregates because of their physicochemical properties. In reviewing the literature, I show that co-transcriptional and co-translational biophysical constraints can trigger DNA instability that in turn increases the likelihood that sequences that alleviate the constraints emerge over evolutionary time. These directed genetic variations rely on the (...) biogenesis of small RNAs that are transcribed directly from challenged DNA regions or processed from the transcripts that directly or indirectly generate constraints or aggregates. These small RNAs can then target the genomic regions from which they initially originate and increase the local mutation rate of the targeted loci. This mechanism is based on molecular pathways involved in anti-parasite genome defence systems, and implies that gene expression-related biophysical constraints represent a driving force of genome evolution. Are randomly generated mutations the only source of genetic variation during evolution? This paper describes the molecular mechanisms by which co-transcriptional and co-translational biophysical constraints trigger genetic variations in targeted-genomic sequences in an RNA-depending manner. This directed-mutational process that drives genome evolution is related to antiparasite genome defence systems. (shrink)

A simple model, illustrating the transition from a population of free swimming, solitary cells to one consisting of small colonies serves as a basis to discuss the evolution of the cooperative group. The transition is the result of a mutation of the dynamics of cell division, delayed cell separation leads to colonies of four cells. With this mutation cooperative features appear, such as synchronised cell divisions within colonies and coordinated flagellar function which enables the colony to swim in definite (...) directions. The selective advantages under given, environmental conditions are defined and the periods necessary for complete allelic replacement in small populations are calculated for asexual and sexual reproduction. The assumption of a steady-state population during allelic substitution is critically considered, particularly under conditions of competition. It is shown that density-dependent population control must operate in the process of selection. Sexual reproduction slows down the rate of selection even though all cells dre haploid. This phenomenon can be explained in general terms of `organizational dominance', where individual units coordinate the function of their neighbours which may be of a different allelotype.Cooperativity is pointed out as an a priori systemic feature which resides in the sub-units of systems, group formation and coordination appears thus as an almost inevitable event. A particular type of system described as ‘closed cycle of positive fitness interaction’ is discussed in more detail. It has the remarkable feature that its members cannot compete with each other; selection takes place between whole cycles .Gonium has a wide spectrum of `somatic plasticity' which enables it to assume various colonial configurations depending on physiological and environmental conditions. This feature can be explained as the result of dynamic flexibilities on the macro-molecular level. The particular relationship between the vast, molecular complexity and the relative simple dynamics of the cell cycle must lead eventually to the genetic fixation of an environmentally induced phenotype. (shrink)

At the core of anthropomorphism lies a false-positive cognitive bias to over-attribute the pattern of the human body and/or mind. Anthropomorphism is independently discussed in various disciplines, is presumed to have deep biological roots, but its cognitive bases are rarely explored in an integrative way. I present an inclusive, multifaceted interdisciplinary approach to refine the psychological bases of mental anthropomorphism. I have integrated 13 conceptual dissections of folk finalistic reasoning into four psychological inference systems (physical, design, basic-goal and belief (...) stances); the latter three are truly teleological and thus prone to anthropomorphisms. I then have empirically integrated the cross-disciplinary genetic, neural, cognitive, psychiatric, developmental, comparative and evolutionary/adaptive evidence that converge supporting the nature of the distinct stances. The over-reactive calibration of the three teleological systems is framed as an evolved design feature to avoid harmful ancestral contexts. Nowadays, these stances easily engage with scientific reasoning about bio-evolutionary matters with negative and positive consequences. Design, basic-goal, and belief stances benefit biology by providing cognitive foundations, expressing a high-powered explanatory system, promoting functional generalization, fostering new research questions and discoveries, enabling metaphorical/analogical thinking and explaining didactically with brevity. Hence, it is neither feasible nor advantageous to completely eliminate teleology from biology. Instead, we should engage with the eight classes of problems in bio-philosophy and bio-education that relate to the three stances: types of anthropomorphism, variety of misunderstandings, misleading appeal, legitimacy controversy, gateway to mysticism, total prohibition and its backfire effect. Recognizing the distinction among design, basic-goal, and belief stances helps to elucidate much of the logic underlying these issues, so that it enables a much more detailed taxonomy of anthropomorphisms, and organizes the various misunderstandings about evolution by natural selection. It also offers a solid psychological grounding for anchoring definitions and terminology. This tripartite framework also shed some light on how to better deal with the over-reactive stances in bio-education, by organizing previous pedagogical strategies and by suggesting new possibilities to be tested. Therefore, this framework constitutes a promising approach to advance the debate regarding the psychological underpinnings of anthropomorphisms and to further support regulating and clarifying teleology and anthropomorphism in biology. (shrink)

This paper develops computational models to monitor patients with hip replacement surgery. The Kinect camera is used to capture the movements of patients who are performing rehabilitation exercises with both lower limbs, specifically, ‘side step’ and ‘knee lift’ with each leg. The information is measured at 25 body points with their respective coordinates. Features selection algorithms are applied to the 75 attributes of the initial and final position vector of each rehab exercise. Different classification techniques have been tested and Bayesian (...) networks, supervised classifier system and genetic algorithm with neural network have been selected and jointly applied to identify the correct and incorrect movements during the execution of the rehabilitation exercises. Besides, prediction models of the evolution of a patient are developed based on the average values of some motion related variables. These models can help to fasten the recovery of these patients. (shrink)

According to most Evolutionary Psychologists, human moral attitudes are rooted in cognitive modules that evolved in the Stone Age to solve problems of social interaction. A crucial component of their view is that such cognitive modules remain unchanged since the Stone Age, and I question that here. I appeal to evolutionary rollback, the phenomenon where an organ becomes non-functional and eventually atrophies or disappears—e.g. cave-dwelling fish losing their eyes. I argue that even if cognitive modules evolved in the Stone Age (...) to solve problems of social interaction, conditions since then have favoured rollback of those modules. This is because there are institutions that solve those problems—e.g. legal systems. Moreover, evidence suggests that where external resources are available to perform cognitive tasks, humans often use them instead of internal ones. In arguing that Stone Age cognitive modules are unchanged, Evolutionary Psychologists say that evolutionary change is necessarily slow, and that there is high genetic similarity between human populations worldwide. I counter-argue that what is necessarily slow is the building-up of complex mechanisms. Undoing this can be much quicker. Moreover, rollback of cognitive mechanisms need not require any genetic change. Finally, I argue that cross-cultural similarity in some trait need not be rooted in genetic similarity. This is not intended as decisive evidence that rollback has occurred. To finish, I suggest ways we might decide whether moral attitudes are likely to be rooted in unchanged Stone Age modules, given that I have argued that cross-cultural similarity is not enough. (shrink)

Functional information means an encoded network of functions in living organisms from molecular signaling pathways to an organism’s behavior. It is represented by two components: code and an interpretation system, which together form a self-sustaining semantic closure. Semantic closure allows some freedom between components because small variations of the code are still interpretable. The interpretation system consists of inference rules that control the correspondence between the code and the function (phenotype) and determines the shape of the fitness landscape. The utility (...) factor operates at multiple time scales: short-term selection drives evolution towards higher survival and reproduction rate within a given fitness landscape, and long-term selection favors those fitness landscapes that support adaptability and lead to evolutionary expansion of certain lineages. Inference rules make short-term selection possible by shaping the fitness landscape and defining possible directions of evolution, but they are under control of the long-term selection of lineages. Communication normally occurs within a set of agents with compatible interpretation systems, which I call communication system. Functional information cannot be directly transferred between communication systems with incompatible inference rules. Each biological species is a genetic communication system that carries unique functional information together with inference rules that determine evolutionary directions and constraints. This view of the relation between utility and inference can resolve the conflict between realism/positivism and pragmatism. Realism overemphasizes the role of inference in evolution of human knowledge because it assumes that logic is embedded in reality. Pragmatism substitutes usefulness for truth and therefore ignores the advantage of inference. The proposed concept of evolutionary pragmatism rejects the idea that logic is embedded in reality; instead, inference rules are constructed within each communication system to represent reality, and they evolve towards higher adaptability on a long time scale. (shrink)

The article proposes to further develop the ideas of the Extended Evolutionary Synthesis by including into evolutionary research an analysis of phenomena that occur above the organismal level. We demonstrate that the current Extended Synthesis is focused more on individual traits (genetically or non-genetically inherited) and less on community system traits (synergetic/organizational traits) that characterize transgenerational biological, ecological, social, and cultural systems. In this regard, we will consider various communities that are made up of interacting populations, and for which (...) the individual members can belong to the same or to different species. Examples of communities include biofilms, ant colonies, symbiotic associations resulting in holobiont formation, and human societies. The proposed model of evolution at the level of communities revises classic theorizing on the major transitions in evolution by analyzing the interplay between community/social traits and individual traits, and how this brings forth ideas of top-down regulations of bottom-up evolutionary processes (collaboration of downward and upward causation). The work demonstrates that such interplay also includes reticulate interactions and reticulate causation. In this regard, we exemplify how community systems provide various non-genetic ‘scaffoldings’, ‘constraints’, and ‘affordances’ for individual and sociocultural evolutionary development. Such research complements prevailing models that focus on the vertical transmission of heritable information, from parent to offspring, with research that instead focusses on horizontal, oblique and even reverse information transmission, going from offspring to parent. We call this reversed information transfer the ‘offspring effect’ to contrast it from the ‘parental effect’. We argue that the proposed approach to inheritance is effective for modelling cumulative and distributed developmental process and for explaining the biological origins and evolution of language. (shrink)

In a macroevolutionary timescale, evolvability itself evolves. Lineages are sorted based on their ability to generate adaptive novelties, which leads to the optimization of their genotype-phenotype map. The system of translation of genetic or epigenetic changes to the phenotype may reach significant horizontal and vertical complexity, and may even exhibit certain aspects of learning behaviour. This continuously evolving semiotic system probably enables the origin of complex yet functional and internally compatible adaptations. However, it also has a second, “darker”, side. (...) As was pointed out by several authors, the same process gradually reduces the probability of the origination of significant evolutionary novelties. In a similar way to the evolution of societies, teachings, or languages, in which the growing number of internal linkages gradually solidifies their overall structure and the structure or interpretation of their constitutive elements, the evolutionary potential of lineages decreases during biological evolution. Possible adaptations become limited to small “peripheral” modifications. According to the Frozen Evolution theory, some of the proximate causes of this “macroevolutionary freezing” are more pronounced or present exclusively in sexual lineages. Sorting based on the highest evolvability probably leads to the establishment of certain structural features of complex organisms, e.g. the modular character of their development and morphology. However, modules also “macroevolutionary freeze” whereas the hypothetical “thawing” of modules or their novel adaptive combinations becomes rarer and rarer. Some possible ways out of this dead end include the rearrangement of individual development, e.g. neoteny, radical simplification, i.e. sacculinization, and transition to a higher level of organization, e.g. symbiosis or symbiogenesis. The evolution of evolvability is essentially a biosemiotic process situated at the intersection of the genocentric modern synthesis and the evo-devo-centric extended synthesis. Therefore, evolvability may eventually connect these three not necessarily contradictory approaches. (shrink)

Humans are uncontroversially better than other species at learning from their peers. A key example of this is imitation, the ability to reproduce both the means and ends of others’ behaviours. Imitation is critical to the acquisition of a number of uniquely human cultural and cognitive traits. However, while authors largely agree on the importance of imitation, they disagree about the origins of imitation in humans. Some argue that imitation is an adaptation, connected to the ‘Mirror Neuron System’ that evolved (...) to facilitate action understanding and the learning of social behaviours. Others argue that imitation is a cultural practice learned in childhood, and that there is no evidence that it evolved genetically. We offer a third alternative that is consistent with both data that the human brain is optimised for imitation, and consistent with its being substantially learned. We hypothesise that at some point in human history humans underwent natural selection for two imitation-relevant abilities – specifically, (i) the tendency to be more attentive to our peers, and (ii) fine motor skill in the manual and oro-facial domains. These changes enabled us to excel at both learning to imitate, and learning by imitating. (shrink)

The review focuses on Huxley’s debt to Richard Goldschmidt and Cyril Darlington. I discuss the conceptions of the genome developed by Goldschmidt and Darlington and their continuing relevance.

Within a physicalist-mechanistic worldview, in which we cannot be more than intelligent, self-reproducing biomachines or biobots, fundamentals of a new approach to the science of human self-explanation are outlined. Some a priori logical necessities, or determinants, of any biobot’s control system design are recognized. Evolution had to satisfy them, but neuroscience and cognitive science so far do not clearly see these basics. It is concluded that the old part of the brain still contains the genetically fixed drives, responses, and (...) the physiological control. Here is the seat of an ancient somatic self that is not intelligent but is still the active center of our life. The neocortex has evolved to serve the somatic self with intelligence by individually building a virtual model of the external material and social world. This model is used by the somatic self to “pre-play” intended actions and responses to see whether they would satisfy its needs. This schema of global brain function provides the neurological foundation for the ego-id dichotomy in analytic psychology, as well as some critique of it. Following the groundbreaking experiments by Benjamin Libet and John-Dylan Haynes et al. , consciousness is taken as a “theater” that presents what the neural networks already have worked out, and freedom of the will is limited. The explosive growth of culture and civilization began when neocortical power exceeded a certain threshold. This can be taken as a quasi-mutation that projected us into a supra-biological space of existence that is new to natural history. It is not clear whether this event will lead to a positive future for humanity or to doom. Functional religion is seen as a neurosystemic attempt to bring back the earlier natural state. Thus, it can be valuable when cleared of mythological ballast. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Species Counterpoint:Darwin and the Evolution of FormsRandall Everett AllsupMy intention is to tell of bodies changed to different forms; the gods, who made the changes, will help me—or so I hope—with a poem that runs from the World's beginning to our own days.1I.A recent article in a progressive monthly magazine asked by way of a thesis, "Whose music is the blues?" Under the title, the tag line read, (...) "2003 is the 'Year of the Blues.' But as a music born of oppression becomes a feel-good soundtrack for white America, just what are we celebrating?"2 I recall feeling puzzled by this rather old-fashioned topic of investigation. Anyone with access to the Internet knows that music is not for one group or another. Global file sharing has made ownership as easy as, well, sharing a file. Furthermore, the tendency to depart from ancestral forms, whether as rebellious teenagers, rock guitarists, or both, seems genetically built into us. Life is a metamorphosis and music—like life—evolves.To advance the notion that music is made for one people and not another, that it has absolute or essential qualities, opens a terribly large can of worms. We know, for example, that identity and music are linked, but the relationship is not [End Page 159] mono-directional, causal, or fixed. My relationship to the blues or Broadway show tunes for that matter is defined somewhere within a dense web of group associations, educational opportunities, even closet desires. With regard to psychological research on identity, slippery and impermanent as identity is, this research is really about similarities.3 Conservative in this light, such studies look for commonalities: their goal is to identify "what is."4Fear is often the dominant response to the evolution of a cherished form. Change, however, holds equal parts fear and promise. The Chinese word for crisis, wei-ji, means "opportunity with danger." This essay will contextualize the latter, but focus on the former. It is worth asking, for example, what might result from an examination of anomalies? Rather than attempt to identify "what is," such an inquiry would be concerned with "what else" [the abnormality] as well as "what might be" [the opportunity]. Located, I think, within the anomalies and mutations that seem to fit so well our globally connected world are new codes, altered methods for self-understanding, and interaction in the arts.Charles Darwin and The Origins of Species will provide the conceptual framework for this discussion.5 To look for help in the work of Darwin will require a crossbreeding of scientific theory and metaphor, a cross-pollination of hypothesis and the hypothetical. We will look at how the production of new forms, particularly musical forms, is shaped. Speaking metaphorically, a work of art or entertainment can be seen as an adaptation to and of its environment. We know that cultural products, like all living species, are not permanent entities. Change, Darwin stressed, carries with it purpose. To that end, he looked for variation to help him understand how and why an organism or system developed the way it did. What might be revealed if we apply this procedure to the field of music and music education? We might see eco-systems in various stages of growth, health, and decline. A look at musical forms as mutable, living creations that spring from and reflect a particular condition raises interesting questions about place and purpose.II.Only a hundred and fifty years ago, a single event—a theory!—precipitated a cultural crisis that threw down two thousand years of scientific and philosophic thought. The popular revolt that Charles Darwin's The Origin of Species fueled (and continues to fuel) called into question fundamental beliefs about how the world is made. Darwin's theory that matter and energy are in steady flux, that life is in need of constant variation, implied that fixed or universal truths are nothing more than comforts created by the mind. The Origin of Species was therefore more than a scientific revolution.6 A core tenet of Western culture was challenged by its publication: the so-called immaterial spirit, whether viewed in the [End... (shrink)

Some central ideas associated with developmental systems theory are outlined for non-specialists. These ideas concern the nature of biological development, the alleged distinction between “genetic” and “environmental” traits, the relations between organism and environment, and evolutionary processes. I also discuss some criticisms of the DST approach.

Feed-forward Pavlovian conditioning can serve as a proximate mechanism for the evolution of social behavior. Feed-forward can provide the impetus for animals to associate other individuals' presence, and cooperation with them, with the acquisition of resources, whether or not the animals are genetically related. Other social behaviors such as play and grooming may develop as conditioned stimuli in feed-forward social systems.

This article is about ‘genogeographic’ maps produced by late-Soviet geneticists and published during post-Soviet time. It focuses on the visual and numerical techniques scientists used to project genetic data onto geographic space. Rather than discussing their representational character, I follow these visuals as ‘folded objects’, describing the layering and realigning of measurements and temporalities as well as the shifts in the practices and meanings of genetics. In the 1970s Soviet biological anthropologists transformed scattered data points by means of spatial (...) statistics into visually coherent maps for a ‘genogeographical atlas’, by interpolating data for the entire USSR territory. Computer-aided modelling rendered ‘populations’ as systemic entities and enacted specific cybernetic versions of population, evolution and difference. Tracing the history of their making helps one in understanding what these folded objects hold in store, in terms of data ranging from Russian imperial and colonial anthropology, through early Soviet traditions, to cold war technologies. Folded into those maps in intricate ways, they have co-shaped post-Soviet human genetics as an ever-active site for possible reinscriptions of difference. (shrink)

Darwinism is defined here as an evolving research tradition based upon the concepts of natural selection acting upon heritable variation articulated via background assumptions about systems dynamics. Darwin’s theory of evolution was developed within a context of the background assumptions of Newtonian systems dynamics. The Modern Evolutionary Synthesis, or neo-Darwinism, successfully joined Darwinian selection and Mendelian genetics by developing population genetics informed by background assumptions of Boltzmannian systems dynamics. Currently the Darwinian Research Tradition is changing as (...) it incorporates new information and ideas from molecular biology, paleontology, developmental biology, and systems ecology. This putative expanded and extended synthesis is most perspicuously deployed using background assumptions from complex systems dynamics. Such attempts seek to not only broaden the range of phenomena encompassed by the Darwinian Research Tradition, such as neutral molecular evolution, punctuated equilibrium, as well as developmental biology, and systems ecology more generally, but to also address issues of the emergence of evolutionary novelties as well as of life itself. (shrink)

I criticize Herbert Simon 's argument for the claim that complex natural systems must constitute decomposable, mereological or functional hierarchies. The argument depends on certain assumptions about the requirements for the successful evolution of complex systems, most importantly, the existence of stable, intermediate stages in evolution. Simon offers an abstract model of any process that succeeds in meeting these requirements. This model necessarily involves construction through a decomposable hierarchy, and thus suggests that any complex, natural, i.e., (...) evolved, system is constituted by a decomposable hierarchy. I argue that Stuart Kauffman's recent models of genetic regulatory networks succeed in specifying processes that could meet Simon 's requirements for evolvability without requiring construction through a decomposable hierarchy. Since Kauffman's models are at least as plausible as Simon 's model, Simon 's argument that complex natural systems must constitute decomposable, mereological or functional hierarchies does not succeed. (shrink)

The compound eyes of insects exhibit stunning variation in size, structure, and function, which has allowed these animals to use their vision to adapt to a huge range of different environments and lifestyles, and evolve complex behaviors. Much of our knowledge of eye development has been learned from Drosophila, while visual adaptations and behaviors are often more striking and better understood from studies of other insects. However, recent studies in Drosophila and other insects, including bees, beetles, and butterflies, have begun (...) to address this gap by revealing the genetic and developmental bases of differences in eye morphology and key new aspects of compound eye structure and function. Furthermore, technical advances have facilitated the generation of high‐resolution connectomic data from different insect species that enhances our understanding of visual information processing, and the impact of changes in these processes on the evolution of vision and behavior. Here, we review these recent breakthroughs and propose that future integrated research from the development to function of visual systems within and among insect species represents a great opportunity to understand the remarkable diversification of insect eyes and vision. (shrink)

This paper is about representations for Artificial Intelligence systems. All of the results described in it involve engineering the representation to make AI systems more effective. The main AI techniques studied here are varieties of search: path-finding in graphs, and probablilistic searching via simulated annealing and genetic algorithms. The main results are empirical findings about the granularity of representation in implementations of genetic algorithms. We conclude by proposing a new algorithm, called “Long-Term Evolution,” which is (...) a genetic algorithm running on an evolving problem description. We see this as modelling the evolution of a species from simpler (more coarsely described— fewer genes) types of organisms to more complex ones. The results, which are reported here of our experiments with the algorithm make it seem a promising optimisation technique. (shrink)

The genetic communication system includes the following components: the parent, which represents the information source and which emits messages; the gametes, which are the messenger carriers; and the offspring, which results from the decoding of two of these messages and can, in turn, become an information source.In a diploid species, a pair of heterozygous homologous loci may emit two equally probable messages, the quantity of genetic information (Q) produced being equivalent to: Q=log2 2=1 bit. For n independent pairs (...) of heterozygous homologous loci, Q=n.log2 2=n bits. The evolution of Q is examined whenever the parent is used in inbreeding or crossbreeding. In the case of inbreeding, the initial Q is depleted as the loci become homozygous; for hybridization the evolution of Q is unpredictable. (shrink)

Since the 1930’s, several attempts have been made to develop a general theory of technical systems or objects and their evolution: in France, Jacques Lafitte, André Leroi-Gourhan, Bertrand Gille, Yves Deforge, and Gilbert Simondon are the main representatives of this trend. In this paper, we focus on the work of Simondon: his analysis of technical progress is based on the hypothesis that technology has its own laws and that customer demand has no paramount influence upon the evolution (...) of technical systems. We first describe the process Simondon called “concretization” and compare it with the process of “idealization” as defined by Genrich Altshuller. We then explain how the progress of technical lineages can be characterized as following a specific rhythm of relaxation and how it thus obeys a “law” of evolution in the industrial context. Simondon’s theoretical approach, although similar to some aspects of methodologies of conception, emphasized a more accurate understanding of technical progress over possible operational applications. Simondon never intended to optimize the engineer’s tasks from an economic point of view and, in fact, his conception of technical progress can be considered as independent from the capitalistic trend of innovation. However, the philosophy of Simondon provides a better understanding of what is at stake theoretically in the modeling of laws of technical evolution. (shrink)

This volume describes features of biological autonomy and integrates them into the recent discussion of factors in evolution. In recent years ideas about major transitions in evolution are undergoing a revolutionary change. They include questions about the origin of evolutionary innovation, their genetic and epigenetic background, the role of the phenotype, and of changes in ontogenetic pathways. In the present book, it is argued that it is likewise necessary to question the properties of these innovations and what (...) was qualitatively generated during the macroevolutionary transitions. The author states that a recurring central aspect of macroevolutionary innovations is an increase in individual organismal autonomy whereby it is emancipated from the environment with changes in its capacity for flexibility, self-regulation and self-control of behavior. The first chapters define the concept of autonomy and examine its history and its epistemological context. Later chapters demonstrate how changes in autonomy took place during the major evolutionary transitions and investigate the generation of organs and physiological systems. They synthesize material from various disciplines including zoology, comparative physiology, morphology, molecular biology, neurobiology and ethology. It is argued that the concept is also relevant for understanding the relation of the biological evolution of man to his cultural abilities. Finally the relation of autonomy to adaptation, niche construction, phenotypic plasticity and other factors and patterns in evolution is discussed. The text has a clear perspective from the context of systems biology, arguing that the generation of biological autonomy must be interpreted within an integrative systems approach. (shrink)

Many complex behaviors are genetically hardwired. Based on previous findings on genetic control of mating and other behaviors in invertebrate and mammalian systems, I suggest that genetic control of complex behaviors is modular: first, dedicated genes specify different behavioral patterns; secondly, separable genetic networks govern distinct behavioral components. I speculate that modular genetic encoding of complex behaviors may in part reflect modularity in brain development and function.Editor's suggested further reading in BioEssays From songs to synapses: (...) Molecular mechanisms of birdsong memory Abstract. (shrink)

Nonhuman primates don’t have formal kinship systems, but genetic relatedness shapes patterns of residence, behavior, mating preferences, and cognition in the primate order. The goal of this article is to provide insight about the ancestral foundations on which the first human kinship systems were built. In order for evolution to favor nepotistic biases in behavior, individuals need to have opportunities to interact with their relatives and to be able to identify them. Both these requirements impose constraints (...) on the evolution of kinship bonds in primate species. For nonhuman primates and many other mammals, maternal care generates close ties between mothers and offspring and among littermates. For species in which mother–offspring bonds extend beyond weaning, associations with the mother also generate familiarity among siblings of different ages. For species with female philopatry, mother–offspring ties provide the foundation for lifelong relationships between mothers and daughters, and dense matrilineal kin networks. However, several factors constrain the development of kinship bonds in nonhuman primates. First, dispersal strategies, which are designed to reduce inbreeding, bias kinship networks in favor of the philopatric sex. Second, hostile relationships between groups mean that kin ties are usually severed when individuals move from one group to another. Third, in species with polygynandrous mating systems, uncertainty about paternity and restricted periods of male reproductive monopoly limit the scope for development of ties among fathers and offspring, paternal siblings, or extended paternal kin networks. In this article, I explore the impact of these factors on the evolution of ancestral human kinship systems. (shrink)

What role does non-genetic inheritance play in evolution? In recent work we have independently and collectively argued that the existence and scope of non-genetic inheritance systems, including epigenetic inheritance, niche construction/ecological inheritance, and cultural inheritance—alongside certain other theory revisions—necessitates an extension to the neo-Darwinian Modern Synthesis (MS) in the form of an Extended Evolutionary Synthesis (EES). However, this argument has been challenged on the grounds that non-genetic inheritance systems are exclusively proximate mechanisms that serve (...) the ultimate function of calibrating organisms to stochastic environments. In this paper we defend our claims, pointing out that critics of the EES (1) conflate non-genetic inheritance with early 20th-century notions of soft inheritance; (2) misunderstand the nature of the EES in relation to the MS; (3) confuse individual phenotypic plasticity with trans-generational non-genetic inheritance; (4) fail to address the extensive theoretical and empirical literature which shows that non-genetic inheritance can generate novel targets for selection, create new genetic equilibria that would not exist in the absence of non-genetic inheritance, and generate phenotypic variation that is independent of genetic variation; (5) artificially limit ultimate explanations for traits to gene-based selection, which is unsatisfactory for phenotypic traits that originate and spread via non-genetic inheritance systems; and (6) fail to provide an explanation for biological organization. We conclude by noting ways in which we feel that an overly gene-centric theory of evolution is hindering progress in biology and other sciences. (shrink)

The theory of evolution settled at what was thought to be its definitive form after the affiliation of Darwin’s theory with the new science of genetics. This historical event explains not only the success but also the vulnerability of evolutionary theory. The close affinity with genetics helped to provide the tools required for managing phylogenetic evolution, which was controlled by the molecular machinery of the genome, localized in most cells of each individual. This setup worked well for organizing (...) the basics of Darwinism but it faltered when applied to the evolution of culture. This is so because, as I argue in this article, under the given conditions the active support of a system of similar complexity as the genome would be required. At some point in the process of evolution the large brains of primates may have begun experimenting with phenotypic equivalents of genomic functions like memory, adaptation, fitness, processing information, and organizing replication. In this way the brain may have weakened its ties to the genome and by exploiting its new status have become, so to speak, for the phenotype what the genome is for the genotype, thus preparing the stage on which the complexity of human behavior might unfold. (shrink)

Advances in developmental genetics and evo-devo in the last several decades have enabled the growth of novel developmental approaches to the classic theme of homology. These approaches depart from the more standard phylogenetic view by contending that homology between morphological characters depends on developmental-genetic individuation and explanation. This article provides a systematic re-examination of the relationship between developmental and phylogenetic homology in light of current evidence from developmental and evolutionary genetics and genomics. I present a qualitative model of the (...) processes that cause de-coupling of morphological and molecular evolution by developmental system drift (DSD), and hypothesize that DSD is a widespread and regular stochastic process that is predictable from parameters such as population size, pleiotropy, and regulatory redundancy. These theoretical findings support an integrative approach in which models of DSD aid in determining when developmental-genetic explanations of homology apply and when other explanations such as stabilizing selection are needed. I argue that a phylogenetic monism about the definition and criteria of homology supports the integration of different explanations into a theory of homology better than pluralism does. (shrink)

Young songbirds draw the source material for their learned songs from parents, peers, and unrelated adults, as well as from innovation. These learned songs are used for intraspecific communication, and have well-documented roles for such functions as territory maintenance and mate attraction. The songs of wild populations differ, forming local “dialects” that may shift over time, suggesting that cultural evolution is at work. Recent work has focused on the mechanisms responsible for the cultural evolution of bird songs within (...) a population, including drift, learning biases, and selection. In many songs or song repertoires, variability is partitioned, with some songs or song segments being stable and consistent, while others vary within the population and across time, and still others undergo population-wide transitions over time. This review explores the different mechanisms that shape the cultural evolution of songs in wild populations, with specific reference to a long-term investigation of a single population of philopatric Savannah sparrows. Males learn a single four-segment song during their 1st year and sing the same song thereafter. Within this song, the buzz segment is a population marker, and may be stable for decades – variant forms occur but eventually disappear. In contrast, the middle segment is highly variable both within the population and over time; changes in relative prevalence of different forms may be due to cultural drift or a rare-form learning bias. Within the introductory segment, a high note cluster was replaced by a click train between 1982 and 2010, following an S-shaped trajectory characteristic of both selective sweeps in population genetics and the replacement of one form by another in human language. In the case of the Savannah sparrows, this replacement may have been due to sexual selection. In subsequent generations, the number of clicks within trains increased, a form of cultural directional selection. In contrast to the narrowing of a trait's range during directional selection in genetic systems, variation in the number of clicks in a train increased as the mean value shifted because improvisation during song learning allowed the range of the trait to expand. Thus, in the single short song of the Savannah sparrow, at least four different mechanisms appear to contribute to three different types of cultural evolutionary outcomes. In the future, it will be import to explore the conditions that favor the application of specific learning rules, and studies such as the ongoing song seeding experiment in the Kent Island Savannah sparrow population will help in understanding the mechanisms that promote or repress changes in a population's song. (shrink)