In contrast to vertical gene transfer from parent to offspring, horizontal (or lateral) gene transfer moves genetic information between different species. Bacteria and archaea often adapt through horizontal gene transfer. Recent analyses indicate that eukaryotic genomes, too, have acquired numerous genes via horizontal transfer from prokaryotes and other lineages. Based on this we raise the hypothesis that horizontally acquired genes may have contributed more to adaptive evolution of eukaryotes than previously assumed. Current candidate sets of horizontally acquired (...) eukaryotic genes may just be the tip of an iceberg. We have recently shown that adaptation of the thermoacidophilic red algaGaldieria sulphurariato its hot, acid, toxic‐metal laden, volcanic environment was facilitated by the acquisition of numerous genes from extremophile bacteria and archaea. Other recently published examples of horizontal acquisitions involved in adaptation include ice‐binding proteins in marine algae, enzymes for carotenoid biosynthesis in aphids, and genes involved in fungal metabolism.Editor's suggested further reading in BioEssaysJumping the fine LINE between species: Horizontal transfer of transposable elements in animals catalyses genome evolution Abstract. (shrink)

The concept of public participation is one of growing interest in the UK and elsewhere, with a commensurate growth in mechanisms to enable this. The merits of participation, however, are difficult to ascertain, as there are relatively few cases in which the effectiveness of participation exercises have been studied in a structured manner. This seems to stem largely from uncertainty in the research community as to how to conduct evaluations. In this article, one agenda for conducting evaluation research that might (...) lead to the systematic acquisition of knowledge is presented. This agenda identifies the importance of defining effectiveness and of operationalizing one’s definition. The article includes analysis of the nature of past evaluations, discussion of potential difficulties in the enactment of the proposed agenda, and discussion of some potential solutions. (shrink)

Contrary to Müller's claims, and in support of modular theories, genetic factors play a substantial and significant role in language. The finding that some children with specific language impairment (SLI) have nonlinguistic impairments may reflect improper diagnosis of SLI or impairments that are secondary to linguistic impairments. Thus, such findings do not argue against the modularity thesis. The lexical/functional distinction appears to be innate and specifically linguistic and could be instantiated in either symbolic or connectionist systems.

The significance of horizontal gene transfer (HGT) in eukaryotic evolution remains controversial. Although many eukaryotic genes are of bacterial origin, they are often interpreted as being derived from mitochondria or plastids. Because of their fixed gene pool and gene loss, however, mitochondria and plastids alone cannot adequately explain the presence of all, or even the majority, of bacterial genes in eukaryotes. Available data indicate that no insurmountable barrier to HGT exists, even in complex multicellular eukaryotes. In addition, (...) the discovery of both recent and ancient HGT events in all major eukaryotic groups suggests that HGT has been a regular occurrence throughout the history of eukaryotic evolution. A model of HGT is proposed that suggests both unicellular and early developmental stages as likely entry points for foreign genes into multicellular eukaryotes. (shrink)

The pseudoscience of evolutionary psychology purports to explain human behaviors by reference to an ancestral environment (essentially, a hunting‐gathering way of life) in which we evolved. Contemporary human behaviors are allegedly governed directly by genes that reflect adaptation to this environment by natural selection. However, the evolutionary process is much more complex than this reductionist approach implies, and adaptation cannot involve the fine‐tuning of structures or behaviors within individuals or species: natural selection can only affect entire organisms, not their components. (...) Similarly, genetic processes are too complex to admit this simplistic view. Instead, our flexible, complex human behaviors probably represent an emergent acquisition. (shrink)

In the multidisciplinary field of developmental cognitive neuroscience, statistical associations between levels of description play an increasingly important role. One example of such associations is the observation of correlations between relatively common gene variants and individual differences in behavior. It is perhaps surprising that such associations can be detected despite the remoteness of these levels of description, and the fact that behavior is the outcome of an extended developmental process involving interaction of the whole organism with a variable environment. (...) Given that they have been detected, how do such associations inform cognitive-level theories? To investigate this question, we employed a multiscale computational model of development, using a sample domain drawn from the field of language acquisition. The model comprised an artificial neural network model of past-tense acquisition trained using the backpropagation learning algorithm, extended to incorporate population modeling and genetic algorithms. It included five levels of description—four internal: genetic, network, neurocomputation, behavior; and one external: environment. Since the mechanistic assumptions of the model were known and its operation was relatively transparent, we could evaluate whether cross-level associations gave an accurate picture of causal processes. We established that associations could be detected between artificial genes and behavioral variation, even under polygenic assumptions of a many-to-one relationship between genes and neurocomputational parameters, and when an experience-dependent developmental process interceded between the action of genes and the emergence of behavior. We evaluated these associations with respect to their specificity, to their developmental stability, and to their replicability, as well as considering issues of missing heritability and gene–environment interactions. We argue that gene–behavior associations can inform cognitive theory with respect to effect size, specificity, and timing. The model demonstrates a means by which researchers can undertake multiscale modeling with respect to cognition and develop highly specific and complex hypotheses across multiple levels of description. (shrink)

Genes are gained and lost over the course of evolution. A recent study found that over 1,800 new genes have appeared during primate evolution and that an unexpectedly high proportion of these genes are expressed in the human brain. But what are the molecular functions of newly evolved genes and what is their impact on an organism's fitness? The acquisition of new genes may provide a rich source of genetic diversity that fuels evolutionary innovation. Although gene manipulation experiments (...) are not feasible in humans, studies in model organisms, such as Drosophila melanogaster, have shown that new genes can quickly become integrated into genetic networks and become essential for survival or fertility. Future studies of new genes, especially chimeric genes, and their functions will help determine the role of genetic novelty in the adaptation and diversification of species. (shrink)

A wide range of anatomical features are shared by all vertebrates, but absent in our closest invertebrate relatives. The origin of vertebrate embryogenesis must have involved the evolution of new regulatory pathways to control the development of new features, but how did this occur? Mutations affecting regulatory genes, including those containing homeobox sequences, may have been important: for example, perhaps gene duplications allowed recruitment of genes to new roles. Here I ask whether comparative data on the genomic organization and (...) expression patterns of homeobox genes support this hypothesis. I propose a model in which duplications of particular homeobox genes, followed by the acquisition of gene‐specific secondary expression domains, allowed the evolution of the neural crest, extensive organogenesis and craniofacial morphogenesis. Specific details of the model are amenable to testing by extension of this comparative approach to molecular embryology. (shrink)

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In (...) our previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)

Binding of antigen or lectin to the surface of a T lymphocyte initiates a complex sequence of events which result in both T cell proliferation and the acquisition of immunologic functions. This complex sequence of events is most likely programmed and precisely timed by a series of contingent gene activations in which one member of this series activates the next. The two most obvious examples of these stages are the set of genes activated when antigen interacts with the (...) antigen receptor and the set of genes activated when IL‐2 interacts with its receptor. However, it is likely that several other parallel pathways of gene activation are necessary to bring about T‐cell division. An example would be the antigen‐induced activation of the c‐myc gene, which in turn is likely to be involved in regulating an additional group of genes not directly controlled by either IL‐2 or antigen. A fundamental understanding of T‐lymphocyte activation necessitates identification of the factors involved in initiating each of these contingent levels of gene activation. (shrink)

BackgroundHIV cure research involving cell and gene therapy has intensified in recent years. There is a growing need to identify ethical standards and safeguards to ensure cell and gene therapy (CGT) HIV cure research remains valued and acceptable to as many stakeholders as possible as it advances on a global scale.MethodsTo elicit preliminary ethical and practical considerations to guide CGT HIV cure research, we implemented a qualitative, in-depth interview study with three key stakeholder groups in the United States: (...) (1) biomedical HIV cure researchers, (2) bioethicists, and (3) community stakeholders. Interviews permitted evaluation of informants’ perspectives on how CGT HIV cure research should ethically occur, and were transcribed verbatim. We applied conventional content analysis focused on inductive reasoning to analyze the rich qualitative data and derive key ethical and practical considerations related to CGT towards an HIV cure.ResultsWe interviewed 13 biomedical researchers, 5 community members, and 1 bioethicist. Informants generated considerations related to: perceived benefits of CGT towards an HIV cure, perceived risks, considerations necessary to ensure an acceptable benefit/risk balance, CGT strategies considered unacceptable, additional ethical considerations, and considerations for first-in-human CGT HIV cure trials. Informants also proposed important safeguards to developing CGT approaches towards an HIV cure, such as the importance of mitigating off-target effects, mitigating risks associated with long-term duration of CGT interventions, and mitigating risks of immune overreactions.ConclusionOur study identified preliminary considerations for CGT-based HIV cure across three key stakeholder groups. Respondents identified an ideal cure strategy as one which would durably control HIV infection, protect the individual from re-acquisition, and eliminate transmission to others. Known and unknown risks should be anticipated and perceived as learning opportunities to preserve and honor the altruism of participants. Preclinical studies should support these considerations and be transparently reviewed by regulatory experts and peers prior to first-in-human studies. To protect the public trust in CGT HIV cure research, ethical and practical considerations should be periodically revisited and updated as the science continues to evolve. Additional ethics studies are required to expand stakeholder participation to include traditionally marginalized groups and clinical care providers. (shrink)

The target article offers an important cautionary note on the interpretation of the heritability index. However, it does not directly address how culture and genes might interact. Here, we suggest that one allele of the dopamine D4 receptor gene promotes the acquisition of cultural values and practices and likely has coevolved with the human culture over the last 50,000 years.

Evolutionary developmental systems theory stresses that selection pressures operate on entire developmental systems rather than just genes. This study extends this approach to language evolution, arguing that selection pressure may operate on two quasi-independent timescales. First, children clearly must acquire language successfully and evolution must equip them with the tools to do so. Second, while this is developing, they must also communicate with others in the moment using partially developed knowledge. These pressures may require different solutions, and their combination may (...) underlie the evolution of complex mechanisms for language development and processing. I present two case studies to illustrate how the demands of both real-time communication and language acquisition may be subtly different. The first case study examines infant-directed speech. A recent view is that IDS underwent cultural to statistical learning mechanisms that infants use to acquire the speech categories of their language. However, recent data suggest is it may not have evolved to enhance development, but rather to serve a more real-time communicative function. The second case study examines the argument for seemingly specialized mechanisms for learning word meanings. Both behavioral and computational work suggest that learning may be much slower and served by general-purpose mechanisms like associative learning. Fast-mapping, then, may be a real-time process meant to serve immediate communication, not learning, by augmenting incomplete vocabulary knowledge with constraints from the current context. Together, these studies suggest that evolutionary accounts consider selection pressure arising from both real-time communicative demands and from the need for accurate language development. (shrink)

S. Oyama’s prominent account of the Parity Thesis states that one cannot distinguish in a meaningful way between nature-based (i.e. gene-based) and nurture-based (i.e. environment-based) characteristics in development because the information necessary for the resulting characteristics is contained at both levels. Oyama as well as P. E. Griffiths and K. Stotz argue that the Parity Thesis has far-reaching implications for developmental psychology in that both nativist and interactionist developmental accounts of psychological capacities that presuppose a substantial nature/nurture dichotomy are (...) inadequate. We argue that well-motivated abandoning of the nature/nurture dichotomy, as advocated in converging versions of the Parity Thesis in biology, does not necessarily entail abandoning the distinction between biologically given abilities necessary for the development of higher psychological capacities and the learning process they enable. Thus, contrary to the claims of the aforementioned authors, developmental psychologists need not discard a substantial distinction between innate (biologically given) characteristics and those acquired by learning, even if they accept the Parity Thesis. We suggest a two-stage account of development: the first stage is maturational and involves interaction of genetic, epigenetic and environmental causes, resulting in the endogenous biological ‘machinery’ (e.g. language acquisition device), responsible for learning in the subsequent stage of the developmental process by determining the organism’s responses to the environment. This account retains the crux of nativism (the endogenous biological structure determines the way the organism learns/responds to an environment) whilst adopting the developmentalist view of biology by characterizing environments as distinctly different in terms of structure and function in two developmental stages. (shrink)

Antibiotic resistance has become a problem of global scale. Resistance arises through mutation or through the acquisition of resistance gene(s) from other bacteria in a process called horizontal gene transfer (HGT). While HGT is recognized as an important factor in the dissemination of resistance genes in clinical pathogens, its role in the environment has been called into question by a recent study published in Nature. The authors found little evidence of HGT in soil using a culture‐independent functional (...) metagenomics approach, which is in contrast to previous work from the same lab showing HGT between the environment and human microbiome. While surprising at face value, these results may be explained by the lack of selective pressure in the environment studied. Importantly, this work suggests the need for careful monitoring of environmental antibiotic pollution and stringent antibiotic stewardship in the fight against resistance. (shrink)

This chapter contains sections titled: Born to Be Good? Are There Moral Universals? Is There a Morality Acquisition Device? Morality Without Innateness Appendix: Moral Anti‐nativism and Moral Relativism References.

AbstractmiRNA‐mediated gene repression and ubiquitin‐dependent processes are among the oldest and most versatile mechanisms that control multiple molecular pathways, rather than just protein turnover. These systems were discovered decades ago and have become among the most studied. All systems within cells are interconnected, and these two are no exception: the plethora of studies have demonstrated that the activity of the miRNAs system depends on players of the ubiquitin‐centered universe of processes, and vice versa. This review focuses on recent progress (...) that highlights that very similar mechanisms of regulation of miRNAs by ubiquitin‐related processes are likely to be found in distantly related species, including animals, plants, and viruses. Most of them occur through the ubiquitination of Argonaute proteins, but some of the other miRNA system factors are also regulated. This suggests that their regulatory relationships are either ancient evolutionary acquisitions or have arisen independently in different kingdoms. (shrink)

In his insightful review, Eugene V. Koonin discusses various aspects of CRISPR-Cas systems with a strong focus on their qualities as "adaptive immune systems". The CRISPR-Cas system is most famous for its application as a gene-editing tool. Koonin provides a deeper insight into its biological function in bacteria, which is to immunize the cell against parasite DNA. I shall comment on one issue discussed in the text, in two steps. First, I shall elaborate on CRISPR-Cas systems and their supposed (...) Lamarckian character. Criteria for calling biological phenomena genuinely Lamarckian will be narrowed down and then applied to the CRISPR-Cas system, considering interference-driven spacer acquisition as an instantiation of a truly Lamarckian paradigm. Second, I shall consider whether Lamarckian and "canonical" instances of inheritance are a case of theoretical pluralism, being two non-reducible, yet interconnected paradigms. (shrink)

The nature-nurture debate rages so, one cannot help but wonder why the sides are so vehemently partitioned. What's at stake? It is simply not clear why a great amount of people embrace either one side or the other, but dare not even blow a kiss to the opposite opinion. Prinz does an excellent job of arguing for the nurture position, zeroing in on some of the most preciously held nature arguments including the basis of knowledge, thought, and feelings in experience (...) and cultural values, increasing as a child grows. Most prominent of the nature hypothèses that Prinz takes on may be that of language acquisition and the Chomskyean notion of inborn lingusitic knowledge, via the proposed universal language. He contends that children's language acquisition--even the notion that the supposed inborn language device shuts off somewhere in mid-childhood, meaning most people will not be fully bilingual--need not demand such a natural language faculty in the brain, as general learning strategies can account for language acquisition. His arguments can stimulate both nurturists and naturists. Yet, in the end--realizing how much of the human arise from the genes--one still cannot help wonder why the two debated positions so rally to one flag or the other. (shrink)

The ability to transfer genes from one species to another provides a powerful method to study genetic regulatory differences between species in a homogeneous genetic background. A survey of several transgenic animal experiments indicates that the vast majority of regulatory differences observed between species are due to differences in the cis‐acting elements associated with the genes under study. A corollary is that in almost all cases the host species provides the necessary regulatory proteins for expression of the transgenes in specific (...) tissues in which the endogenous homolog is not expressed. Although the details of the cis‐acting differences are unknown for most cases, it appears that these differences may consist of the acquisition or loss of unique elements or subtle variation of conserved elements. It is unknown whether much of this variation is directly related to adaptive evolution. The identification of the promoter enhancer elements responsible for these differences is an important first step in examining the functional significance of this variation. (shrink)

Classifying is a fundamental operation in the acquisition of knowledge. Taxonomic theory can help students of cognition, evolutionary psychology, ethology, anatomy, and sociobiology to avoid serious mistakes, both practical and theoretical. More positively, it helps in generating hypotheses useful to a wide range of disciplines. Composite wholes, such as species and societies, are “individuals” in the logical sense, and should not be treated as if they were classes. A group of analogous features is a natural kind, but a group (...) of homologous features is not. Imposing hypotheses justified only on the basis of nominalist, realist, phenomenalist, or conceptualist metaphysics upon the neurophysiology of organisms or upon the causes of behavior exemplifies the “psychologist's fallacy” of William James. Levels should be distinguished from their members and from classes of levels, and the ontological status of entities ranked at levels should be made clear. It is important not to confuse such categories as substance and process with one another. Several genetical terms, such as “gene” and chromosome,” are even more equivocal than has been realized. Discussions about units of selection, behavior, and thinking suffer from the ambiguity of a “unit of” an entity. An important source of misunderstanding about natural selection is the habit of treating it as an “agent”: in an important sense, natural selection does not “act” at all. (shrink)

This book argues the case for a foundationalist ethics centrally based on an empirical understanding of human nature. For Maxine Sheets-Johnstone, “an ethics formulated on the foundations of anything other than human nature, hence on anything other than an identification of pan-cultural human realities, lacks solid empirical moorings. It easily loses itself in isolated hypotheticals, reductionist scenarios, or theoretical abstractions—in the prisoner’s dilemma, selfish genes, dedicated brain modules, evolutionary altruism, or psychological egoism, for example—or it easily becomes itself an ethical (...) system over and above the ethics it formulates,” such as the deontological ethics of Kantian categorical imperatives, the utilitarianism of Bentham and Mill, or the ethics of care. Taking her cue from Hume, especially his _Treatise on Human Nature_, where he grounds “the moral sense” in human nature seen as always in tension between the natural tendencies of selfish acquisitiveness and sympathy for others, Sheets-Johnstone pursues her phenomenological investigation of the natural basis of human morality by directing her attention, first in Part I, to what is traditionally considered the dark side of human nature, and then, in Part II, to the positive side. The tension between the two calls for an interdisciplinary therapeutic resolution, which she offers in the Epilogue by arguing for the value of a moral education that enlightens humans about their own human nature, highlighting both the socialization of fear and the importance of play and creativity. (shrink)

Aging of the organism is associated with highly reproducible DNA methylation (DNAm) changes, which facilitate estimation of donor age. Cancer is also associated with DNAm changes, which may contribute to disease development. Here, we speculate that age‐associated DNAm changes may increase the risk of tumor initiation. Notably, when using epigenetic signatures for age‐estimations tumor cells are often predicted to be much older than the chronological age of the patient. We demonstrate that aberrant hypermethylation within the gene DNA methyltransferase 3A (...) (DNMT3A) – which may contribute to initiation of acute myeloid leukemia (AML) – is particularly observed in AML samples that reveal significantly more age‐associated DNAm changes. The functional relevance of age‐associated DNAm changes remains to be elucidated, but they occur genome wide, in a highly reproducible manner, and most likely influence chromatin organization – and hence may favor acquisition of aberrant DNAm patterns contributing to cancer in the elderly. (shrink)

The expression of protein‐encoding genes is a complex process culminating in the production of mature mRNA and its translation by the ribosomes. The production of a mature mRNA involves an intricate series of processing steps. The majority of eukaryotic protein‐encoding genes contain intron sequences that disrupt the protein‐encoding frame, and hence have to be removed from immature mRNA prior to translation into protein. The mechanism involved in the selection of correct splice sites is incompletely understood. A considerable body of evidence (...) suggests that the splicing machinery has suboptimal efficiency and fidelity leading to substantial processing inaccuracy. Here we discuss a recently published article1 that extends observations that cells rely on nonsense‐mediated mRNA decay (NMD) to compensate for such suboptimal processing accuracy. Intriguingly these authors provide evidence for a strong selective pressure in favour of premature termination of mRNA translation in the event of intron retention. The analysis presented implies a positive role of NMD in transcript diversification through alternative splicing and suggest that this ancient surveillance mechanism may have co‐evolved with intron acquisition born from the need for quality control of splicing patterns. BioEssays 30:926–928, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

Research in the neurosciences continues to provide evidence that sleep plays a role in the processes of learning and memory. There is less of a consensus, however, regarding the precise stages of memory development during which sleep is considered a requirement, simply favorable, or not important. This article begins with an overview of recent studies regarding sleep and learning, predominantly in the procedural memory domain, and is measured against our current understanding of the mechanisms that govern memory formation. Based on (...) these considerations, I offer a new neurocognitive framework of procedural learning, consisting first of acquisition, followed by two specific stages of consolidation, one involving a process of stabilization, the other involving enhancement, whereby delayed learning occurs. Psychophysiological evidence indicates that initial acquisition does not rely fundamentally on sleep. This also appears to be true for the stabilization phase of consolidation, with durable representations, resistant to interference, clearly developing in a successful manner during time awake (or just time, per se). In contrast, the consolidation stage, resulting in additional/enhanced learning in the absence of further rehearsal, does appear to rely on the process of sleep, with evidence for specific sleep-stage dependencies across the procedural domain. Evaluations at a molecular, cellular, and systems level currently offer several sleep specific candidates that could play a role in sleep-dependent learning. These include the upregulation of select plasticity-associated genes, increased protein synthesis, changes in neurotransmitter concentration, and specific electrical events in neuronal networks that modulate synaptic potentiation. Key Words: consolidation; enhancement; learning; memory; plasticity; sleep; stabilization. (shrink)

An increasing number of studies indicate that virtues affect brain structure. These studies might shed new light on some neuroethical perspectives suggesting that our brain network activity determines the acquisition and permanence of virtues. According to these perspectives, virtuous behavior could be interpreted as the product of a brain mechanism supervised by genes and environment and not as the result of free choice. In this respect, the neural correlates of virtues would confirm the deterministic theory. In contrast, I maintain (...) that these findings do not undermine the role of willpower and freedom while reinforcing an interactionist view of free will. If virtues affect our neural system, then the predictability of the virtuous behavior follows. The likelihood of our future actions is primarily virtue-dependent; therefore, the acquired naturality of virtuous behavior is a source of predictable behavioral patterns outlining expected actions, which I propose to call Hypotheses of Action. However, the predictability of an action indicates its likeliness and not its certainty or necessity. The neural traces of virtues can be interpreted as major indicators of HAs. It is always possible for the agents to depart from their more likely, virtue-induced actions, but their deviations from the virtuous behavioral pattern are rare, as it is rare for the vicious/non-virtuous person to behave well systematically. This implies a reaffirmation of the notions of veto and consent as they provide a universal practical power affecting the subject’s use of moral virtues. (shrink)

The three processes needed to create life, compartmentalization, metabolism, and information transfer (memory stored in nucleic acids and manipulation operated by proteins) are embedded in organized genome features. The core of life puts together growth and maintenance (which drives survival), while life in context explores and exploits specific niches. Analysis of gene persistence in a large number of genomes shows that the former constitutes the paleome, which recapitulates the three phases of the origin of life: metabolism of small molecules (...) on surfaces, substitution of surfaces by an RNA-world where transfer RNA played a central role, and invention of template mediated information transfer. Colonization of each niche is performed using an almost unlimited set of genes, forming the cenome. The agreement of the paleome structure with a consistent scenario for the origin of life is such that we may consider extant genomes as providing us with an archive of the origin rather than as a palimpsest where most of our past would be irremediably hidden. (shrink)

It is predicted that the rapid acquisition of new genetic knowledge and related applications during the next decade will have significant implications for virtually all members of society. Currently, most people get exposed to information about genes and genetics only through stories publicized in the media. We sought to understand how individuals in the general population used and understood the concepts of ???genetics??? and ???genes.??? During in-depth one-on-one telephone interviews with adults in the United States, we asked questions exploring (...) their basic understanding of these terms, as well as their belief as to the location of genes in the human body. A wide range of responses was received. Despite conversational familiarity with genetic terminology, many noted frustration or were hesitant when trying to answer these questions. In addition, some responses reflected a lack of understanding about basic genetic science that may have significant implications for broader public education measures in genetic literacy, genetic counseling, public health practices, and even routine health care. (shrink)

Obesity and type 2 diabetes arise from a set of complex gene–environment interactions. Explanations for the heritability of these syndromes and the environmental contribution to disease susceptibility are addressed by the “thrifty genotype” and the “thrifty phenotype” hypotheses. Here, the merits of both models are discussed and elements of them are used to synthesize a “thrifty epigenotype” hypothesis. I propose that: (1) metabolic thrift, the capacity for efficient acquisition, storage and use of energy, is an ancient, complex trait, (...) (2) the environmentally responsive gene network encoding this trait is subject to genetic canalization and thereby has become robust against mutational perturbations, (3) DNA sequence polymorphisms play a minor role in the aetiology of obesity and type 2 diabetes—instead, disease susceptibility is predominantly determined by epigenetic variations, (4) corresponding epigenotypes have the potential to be inherited across generations, and (5) Leptin is a candidate gene for the acquisition of a thrifty epigenotype. BioEssays 30:156–166, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

It is widely assumed that human learning and the structure of human languages are intimately related. This relationship is frequently suggested to derive from a language-specific biological endowment, which encodes universal, but communicatively arbitrary, principles of language structure (a Universal Grammar or UG). How might such a UG have evolved? We argue that UG could not have arisen either by biological adaptation or non-adaptationist genetic processes, resulting in a logical problem of language evolution. Specifically, as the processes of language change (...) are much more rapid than processes of genetic change, language constitutes a both over time and across different human populations, and, hence, cannot provide a stable environment to which language genes could have adapted. We conclude that a biologically determined UG is not evolutionarily viable. Instead, the original motivation for UG arises because language has been shaped to fit the human brain, rather than vice versa. Following Darwin, we view language itself as a complex and interdependent which evolves under selectional pressures from human learning and processing mechanisms. That is, languages themselves are shaped by severe selectional pressure from each generation of language users and learners. This suggests that apparently arbitrary aspects of linguistic structure may result from general learning and processing biases deriving from the structure of thought processes, perceptuo-motor factors, cognitive limitations, and pragmatics. (shrink)

Cambridge Quarterly of Healthcare Ethics. What values and principles should inform the regulation of new human genetic technologies? To adequately answer this question we need an account of genetic justice. That is, an account of what constitutes a fair distribution of genetic endowments that influence our expected life-time acquisition of natural primary goods. These are goods that every rational person has an interest in. The decisions we now make regarding the regulation of human genetic technologies will determine how quickly (...) and effectively these benefits are brought into existence, as well as who receives these benefits. In this paper I argue that a necessary condition of a defensible account of genetic justice is that it must track genetic complexity. Genetic complexity encompasses phenomena such as polygenetic traits, gene-gene interactions and complex environmental influences. More specifically, I argue that pluralistic prioritarianism is a theoretical position well-suited for tracking genetic complexity. (shrink)

For decades, interdisciplinary research efforts have accumulated insights that diminish the significance of the classic nature versus nurture dichotomy, instead calling for a nuanced, multifactorial approach to ontogeny. Similarly, the role of genes in both phylogeny and ontogeny, once seen as rather deterministic, is now conceptualized as highly dependent on environmental factors, including behavior. Linguistic theories have, in principle, made an effort to incorporate these changing views. However, the central claim of the given paper is that this apparent compliance with (...) biological insights remains superficial. As such, considerable disconnects between linguistic theory and what is known about the biological underpinnings of complex traits persist, negatively impacting pertinent views on language acquisition, language universals and the evolution of language. Given the breadth of these fields of study, the aim of this paper is to tackle the root of the problem: It begins by sketching out linguistic nativism as conceptualized within generativism, pointing to aspects within this position that stand in conflict with the interdisciplinary literature. It will then review select areas of research in a succinct manner in order to substantiate the criticism and characterize the counterposition as found within the biological sciences. The paper will culminate in addressing these disconnects on conceptual grounds, i.e. invoking the term emergence as employed in neuroscience as a possible means to reconcile those biological insights with linguistic nativism. (shrink)

With the advent of evolutionary developmental research, or EvoDevo, there is hope of discovering the roles that the genetic bases of development play in morphological evolution. Studies in EvoDevo span several levels of organismal organization. Low-level studies identify the ultimate genetic changes responsible for morphological variation and diversity. High-level studies of development focus on how genetic differences affect the dynamics of gene networks and epigenetic interactions to modify morphology. Whereas an increasing number of studies link independent acquisition of (...) homoplastic or convergent morphologies to similar changes in the genomes, homoplasies are not always found to have identical low-level genetic underpinnings. This suggests that a combination of low- and high-level approaches may be useful in understanding the relationship between genetic and morphological variation. Therefore, as an empirical and conceptual framework, we propose the causality horizon to signify the lowest level that allows linking homoplastic morphologies to similar changes in the development. A change in a system below the causality horizon cannot be generalized. In more concrete terms, homoplastic morphologies cannot be reduced to the same change in gene regulation when that change occurs below the causality horizon; rather, a higher-level mechanism should be identified. (shrink)

. Progress in technology has allowed dynamic research on the development of the human brain that has revolutionized concepts. Particularly, the notions of plasticity, neuronal selection, and the effects of afferent stimuli have entered into thinking about brain development. Here I focus on development from the age of four years to early adulthood, during which a 30 percent reduction in some brain synapses occurs that is out of proportion to changes in neuronal numbers. This corresponds temporally with changes in normal (...) child behavior from the loose‐associative, almost schizoid, thinking and art of the four‐year‐old to the more trained, or disciplined, or acculturated—and restrained—personality of the young adult. I propose that the synaptic changes can best be thought of as a winnowing process likely subject to environmental influences. Acquisition of language and the ability to link linguistic cognition to the plastic development of the brain provide a potentially powerful means of explaining the evolutionally explosive development of human cognition and culture. Schizophrenia, a disease that can be envisioned as representing a derangement of synaptic maturation, may provide an entry into the search for genes controlling the processes mediating the unprecedented development of Homo sapiens over the past 40,000 to 70,000 years. The recently completed mapping of the genome of the chimpanzee provides a new frame of reference that may speed the search. (shrink)

The Modern Synthesis of Darwinism and genetics regards non-genetic factors as merely constraints on the genetic variations that result in the characteristics of organisms. Even though the environment (including social interactions and culture) is as necessary as genes in terms of selection and inheritance, it does not contain the information that controls the development of the traits. S. Oyama’s account of the Parity Thesis, however, states that one cannot conceivably distinguish in a meaningful way between nature-based (i.e., gene-based) and (...) nurture-based (i.e., environment-based) characteristics in development because the information necessary for the resulting characteristics is contained at both levels. Oyama and others argue that the Parity Thesis has far-reaching implications for developmental psychology, in that both nativist and interactionist developmental accounts of motor, cognitive, affective, social, and linguistic capacities that presuppose a substantial nature/nurture dichotomy are inadequate. After considering these arguments, we conclude that either Oyama’s version of the Parity Thesis does not differ from the version advocated by liberal interactionists, or it renders precarious any analysis involving abilities present at birth (despite her claim to the contrary). More importantly, developmental psychologists need not discard the distinction between innate characteristics present at birth and those acquired by learning, even if they abandon genocentrism. Furthermore, we suggest a way nativists can disentangle the concept of maturation from a genocentric view of biological nature. More specifically, we suggest they can invoke the maturational segment of the developmental process (which involves genetic, epigenetic and environmental causes) that results in the biological “machinery” (e.g. language acquisition device) which is necessary for learning as a subsequent segment of the developmental process. (shrink)

Recent studies indicate that plakoglobin may have a similar function to that of β-catenin within the Wnt signaling pathway. β-catenin is known to be an oncogene in many forms of human cancer, following acquisition of stabilizing mutations in amino terminal sequences. Kolligs1 and coworkers show, however, that unlike β-catenin, plakoglobin induces neoplastic transformation of rat epithelial cells in the absence of such stabilizing mutations. Cellular transformation by plakoglobin also appears to be distinct from that of β-catenin in that it (...) requires activation of the proto-oncogene c-myc. Surprisingly, c-myc is activated more efficiently by plakoglobin than β-catenin, despite its previous identification as a target of Tcf/β-catenin.2 In contrast, a synthetic Tcf reporter gene is activated to a much greater extent by β-catenin than plakoglobin. Plakoglobin and β-catenin may therefore have different roles in Wnt signaling and cancer, which reflect their differential effects on target gene activity. BioEssays 22:961–965, 2000. © 2000 John Wiley & Sons, Inc. (shrink)

Within the next few years scientists will almost certainly have pieced together a broad map of the major gene locations on the twenty‐three human chromosomes. The rapid unfolding of this new knowledge raises new questions: What limits, if any, should be imposed on its acquisition? Who should control the wealth of resulting data? How should it be used? If, because of a deep‐seated need for certitude, many persons are likely to perceive a positive gene probe test as (...) an indicator of biologic destiny, probes may acquire a misleading status in our medical armamentarium. (shrink)

Issues arising in connection with genes and nutrition policy include both nutrigenomics and nutrigenetics. Nutrigenomics considers the relationship between specifc nutrients or diet and gene expression and, it is envisaged, will facilitate prevention of diet-related common diseases. Nutrigenetics is concerned with the effects of individual genetic variation on response to diet, and in the longer term may lead to personalised dietary recommendations. It is important also to consider the surrounding context of other issues such as novel and functional foods (...) in so far as they are related to genetic modification. Ethical issues fall into a number of categories: why nutrigenomics? Will it have important public health benefits? questions about research, e.g. concerning the acquisition of information about individual genetic variation; questions about who has access to this information, and its possible misuse; the applications of this information in terms of public health policy, and the negotiation of the potential tension between the interests of the individual in relation to, for example, prevention of conditions such as obesity and allergy; the appropriate ethical approach to the issues, e.g. the moral difference, if any, between therapy and enhancement in relation to individualised diets; whether the 'technological fix' is always appropriate, especially in the wider context of the purported lack of public confidence in science, which has special resonance in the sphere of nutrition. (shrink)

Establishment of cell lineage identity from multipotent progenitors is controlled by cooperative actions of lineage‐specific and stably expressed transcription factors, combined with input from environmental signals. Lineage‐specific master transcription factors activate and repress gene expression by recruiting consistently expressed transcription factors and chromatin modifiers to their target loci. Recent technical advances in genome‐wide and multi‐omics analysis have shed light on unexpected mechanisms that underlie more complicated actions of transcription factors in cell fate decisions. In this review, we discuss functional (...) dynamics of stably expressed and continuously required factors, Notch and Runx family members, throughout developmental stages of early T cell development in the thymus. Pre‐ and post‐commitment stage‐specific transcription factors induce dynamic redeployment of Notch and Runx binding genomic regions. Thus, together with stage‐specific transcription factors, shared transcription factors across distinct developmental stages regulate acquisition of T lineage identity. (shrink)

Historical language change (), like evolution itself, is a fact; and its implications for the biological evolution of the human capacity for language acquisition () have been ably explored by many contemporary theorists. However, Christiansen & Chater's (C&C's) revolutionary call for a replacement of phylogenetic models with glossogenetic cultural models is based on an inadequate understanding of either. The solution to their lies before their eyes, but they mistakenly reject it due to a supposed Gene/;culture co-evolution poses a (...) series of difficult theoretical and empirical problems that will be resolved by subtle thinking, adequate models, and careful cross-disciplinary research, not by oversimplified manifestos. (shrink)

The veins are cuticular structures that differentiate in precise patterns in insect wings. The genetic and molecular basis of vein pattern formation in Drosophila melanogaster is beginning to be unravelled with the identification and characterisation of the gene products that position the veins and direct their differentiation. Genes affecting the veins fall into two groups: transcriptional regulators that specify individual veins, and members of signalling pathways involved in patterning and differentiation of the veins. The elaboration of the vein pattern (...) is progressive in time and requires the coordinated activities of these signalling pathways and the transcription factors regulated by them. Although the network of genetic interactions that determine vein cell fate is well understood, very little is known about the cellular biology underlying the acquisition of vein histotype. BioEssays 25:443–451, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

Species evolve, very slowly, through selection of genes which give rise to phenotypes well adapted to their environments. The cultures, including the languages, of human communities evolve, much faster, maintaining at least a minimum level of adaptedness to the external, non- cultural environment. In the phylogenetic evolution of species, the transmission of information across generations is via copying of molecules, and innovation is by mutation and sexual recombination. In cultural evolution, the transmission of information across generations is by learning, and (...) innovation is by sporadic invention or borrowing from other cultures. This much is the foundational bedrock of evolutionary theory. But things get more complicated; there can be gene-culture co-evolution. Prior to the rise of culture, the physical environment is the only force shaping biological evolution from outside the organism, and cultures themselves are clearly constrained by the evolved biological characteristics of their members. But cultures become part of the external environment, and influence the course of biological evolution. For example, altruistic cultures with developed medical knowledge reduce the cost to the individual of carrying genes disposing to certain pathologies (such as diabetes); and such genes become more widespread in the populations maintaining such cultures. Assortative mating can affect biological evolution, and particular cultures may influence the factors which are sorted for in mating. (For a careful discussion of the effects of cultural evolution on natural selection, see Cavalli-Sforza and Bodmer, 1971:774- 804). This paper examines mechanisms involved in the co-evolution of a biological trait, the critical period for language acquisition, and a property of human cultures, the size of their languages. A gene/culture interaction will be shown that can be described as a kind of symbiosis, but perhaps more aptly as an `arms race'. In this introduction, we will sketch the basic mechanics of the interaction in very broad terms; the rest of the paper will explain and justify the details. The implications of our model for second language acquisition are given toward the end of the paper. (shrink)

Genomic conflicts are potentially involved in the evolution and maintenance of culture. Maternal genes contributing to neocortical development could influence biases in the acquisition of information. Specifically, relatedness asymmetries due to multiple paternity are expected to lead to an increased reliability and receptivity of matrilineally-transmitted information. This view complements the gene-culture coevolutionary model adopted by Rendell and Whitehead.

The last two centuries have been the centuries of the discovery of the cell evolution: in the XIX century of the germinal cells and in the XX century of two groups of somatic cells, namely those of the brain-mind and of the immune systems. Since most cells do not behave in this way, the evolutionary character of the brain-mind and of the immune systems renders human beings formed by two different groups of somatic cells, one with a deterministic and another (...) with an indeterministic (say Darwinian) behavior. An inherent consequence is that of the generation, during ontogenesis, of a dual biological identity. The concept of the dual biological identity may be used to explain the Kantian concept of the two metaphysical worlds, namely of the causal necessity and of the free will (Azzone, 2001). Two concepts, namely those of complex adaptive systems (CAS) and of emergence (Holland, 2002), are useful tools for understanding the mechanisms of adaptation and of evolution. The concept of complex adaptive systems indicates that living organisms contain series of stratified components, denoted as building blocks, forming stratified layers of increasing complexity. The concept of emergence implies the use of repeating patterns and of building blocks for the generation of structures of increasing levels of complexity, structures capable of exchanging communications both in the top-down and in the bottom-up direction. Against the concept of emergence it has been argued that nothing can produce something which is really new and endowed of causal efficacy. The defence of the concept of emergence is based on two arguments. The first is the interpretation of the variation-selection mechanism as a process of generation of information and of optimization of free energy dissipation in accord with the second principle of thermodynamics. The second is the objective evidence of the cosmological evolution from the Big Bang to the human mind and its products. Darwin has defended the concept of the continuity of evolution. However evolution should be considered as continuous when there is no increase of information and as discontinuous when there is generation of new information. Examples of such generation of information are the acquisition of the innate structures for language and the transition from absence to presence of morality. There are several discontinuity thresholds during both phylogenesis and ontogenesis. Morality is a relational property dependent on the interactions of human beings with the environment. Piaget and Kohlberg have shown that the generation of morality during childhood occurs through several stages and is accompanied by reorganization of the child mental organization. The children respect the conventions in the first stage and gradually generate their autonomous morality. The transition from absence to presence of morality, a major adaptive process, then, not only has occurred during phylogenesis but it occurs again in every human being during ontogenesis. The religious faith does not provide a logical justification of the moral rules (Ayala, 1987) but rather a psychological and anthropological justification of two fundamental needs of human beings: that of rendering Nature an understandable entity, and that of increasing the cooperation among members of the human societies. The positive effects of the altruistic genes in the animal societies are in accord with the positive effects of morality for the survival and development of the human societies. (shrink)

Darwinian theories of culture need to show that they improve upon the commonsense view that cultural change is explained by humans? skillful pursuit of their conscious goals. In order for meme theory to pull its weight, it is not enough to show that the development and spread of an idea is, broadly speaking, Darwinian, in the sense that it proceeds by the accumulation of change through the differential survival and transmission of varying elements. It could still be the case that (...) the best explanation of why the idea has developed and spread is the conscious pursuit of human goals. Meme theory has the potential to do explanatory work in diverse ways. It can challenge the goal-based account of cultural change directly. Other possibilities for meme theory include explaining the acquisition of our goals and showing that memes and genes evolve together, each affecting the selective forces acting on the other. Raising the question of meme theory?s explanatory payoff brings out the importance of the ?selfish-meme? idea and the idea of non-content biases. Both have the potential to challenge the claim that our goals are in the driver?s seat. In order to show that a Darwinian theory of culture is more than an idle redescription, however, it is necessary to make the case that it offers explanatory gain over its competitors, in particular over the common sense goal-based account. (shrink)

This dissertation explores issues in the philosophy of psychology and metaphysics through the lens of the emotion of disgust, and its corresponding property, disgustingness. The first chapter organizes an extremely large body of data about disgust, imposes two constraints any theory must meet, and offers a cognitive model of the mechanisms underlying the emotion. The second chapter explores the evolution of disgust, and argues for the Entanglement thesis: this uniquely human emotion was formed when two formerly distinct mechanisms, one dedicated (...) to monitoring food intake and protecting against poisons, the other dedicated to protecting against parasitic infection, where driven together until they became functionally integrated. The third chapter explores the sorts of acquisition mechanisms that could give rise to the patterns of individual and cultural level variation we find with disgust elicitors. It argues for the Empathic Acquisition thesis, which holds that one important route for the social acquisition and transmission of disgust elicitors is linked to empathic recognition of facial expressions of the emotion. The fourth chapter builds on the Entanglement thesis, and embeds the emotion of disgust in gene-culture coevolutionary theory and the tribal instincts hypothesis. The Co-opt thesis is defended, which maintains that disgust was co-opted to play an important role in our moral psychology, particularly in our cognition of social norms and ethnic boundary markers. In doing so, however, it brings to bear many features initially linked to poisons and parasites. This explains the puzzling and troublesome character of moral judgments linked to disgust. After shifting gears from psychology to metaphysics, the fifth chapter recasts the Humean tradition of projectivism in the terminology of cognitive science. Using examples such as disgust, I argue that a psychologized projectivism is able to make sense of the idea that some properties are projected onto the world, rather than found there to begin with. The final chapter criticizes three other accounts of the property of disgustingness, two inspired by functionalism in the philosophy of color, one inspired by fittingness accounts in metaethics. I argue that none provide nearly as satisfactory account of the property as the psychologized projectivism articulated previously. (shrink)

The vertebrate immune system provides a remarkable showcase of the different ways the genome can be used to specify cellular identity and to mediate cellular function. It is arguably the leading mammalian system in which gene regulation programs that drive the acquisition of specific cell-type identities have been elucidated at the single cell level. More broadly for molecular genomics, the activation-induced gene expression pathways used in immune effector responses have provided textbook cases for fundamental elements of transcription (...) factor assembly at enhancers ; and immune system genes and gene clusters have provided key paradigms for the roles of long-range.. (shrink)

Mechanistic models in molecular systems biology are generally mathematical models of the action of networks of biochemical reactions, involving metabolism, signal transduction, and/or gene expression. They can be either simulated numerically or analyzed analytically. Systems biology integrates quantitative molecular data acquisition with mathematical models to design new experiments, discriminate between alternative mechanisms and explain the molecular basis of cellular properties. At the heart of this approach are mechanistic models of molecular networks. We focus on the articulation and development (...) of mechanistic models, identifying five constraints which guide the articulation of models in molecular systems biology. These constraints are not independent of one another, with the result that modeling becomes an iterative process. We illustrate the use of these constraints in the modeling of the mechanism for bistability in the lac operon. (shrink)

The special properties of the Y chromosome stem form the fact that it is a non‐recombining degenerate derivative of the X chromosome. The absence of homologous recombination between the X and the Y chromosome leads to gradual degeneration of various Y chromosome genes on an evolutionary timescale. The absence of recombination, however, also favors the accumulation of transposable elements on the Y chromosome during its evolution, as seen with both Drosophila and mammalian Y chromosomes. Alongside these processes, the acquisition (...) and amplification of autosomal male benefit genes occur. This review will focus on recent studies that reveal the autosome‐acquired genes on the Y chromosome of both Drosophila and humans. The evolution of the acquired and amplified genes on the Y chromosome is also discussed. Molecular and comparative analyses of Y‐linked repeats in the Drosophila melanogaster genome demonstrate that there was a period of their degeneration followed by a period of their integration into RNAi silencing, which was beneficial for male fertility. Finally, the function of non‐coding RNA produced by amplified Y chromosome genetic elements will be discussed. BioEssays 27:1256–1262, 2005. © 2005 Wiley Periodicals, Inc. (shrink)