Darwinian evolutionary theory has two key terms, variations and biological selection, which finally lead to survival of the fittest variant. With the rise of molecular genetics, variations were explained as results of error replications out of the genetic master templates. For more than half a century, it has been accepted that new genetic information is mostly derived from random error-based events. But the error replication narrative has problems explaining the sudden emergence of new species, new phenotypic traits, and (...) genome innovations as a sudden single event. Meanwhile, it is recognized that errors cannot explain the evolution of genetic information, genetic novelty, and complexity. Now, empirical evidence establishes the crucial role of non-random genetic content editors, such as viruses, diversity generating retroelements, and other RNA networks, to produce new genetic information, complex regulatory control, inheritance vectors, genetic identity, immunity, new sequence space, evolution of complex organisms, and evolutionary transitions. (shrink)

Evolution is frequently concentrated in bursts of rapid morphological change and speciation followed by long‐term stasis. We propose that this pattern of punctuated equilibria results from an evolutionary tug‐of‐war between host genomes and transposable elements (TEs) mediated through the epigenome. According to this hypothesis, epigenetic regulatory mechanisms (RNA interference, DNA methylation and histone modifications) maintain stasis by suppressing TE mobilization. However, physiological stress, induced by climate change or invasion of new habitats, disrupts epigenetic regulation and unleashes TEs. With their (...) capacity to drive non‐adaptive host evolution, mobilized TEs can restructure the genome and displace populations from adaptive peaks, thus providing an escape from stasis and generating genetic innovations required for rapid diversification. This “epi‐transposon hypothesis” can not only explain macroevolutionary tempo and mode, but may also resolve other long‐standing controversies, such as Wright's shifting balance theory, Mayr's peripheral isolates model, and McClintock's view of genome restructuring as an adaptive response to challenge. (shrink)

Plasmids are a major type of mobile genetic elements (MGEs) that mediate horizontal gene transfer. The stable maintenance of plasmids plays a critical role in the functions and survival for microbial populations. However, predicting and controlling plasmid persistence and abundance in complex microbial communities remain challenging. Computationally, this challenge arises from the combinatorial explosion associated with the conventional modeling framework. Recently, a plasmid‐centric framework (PCF) has been developed to overcome this computational bottleneck. This framework enables the derivation (...) of a simple metric, the persistence potential, to predict plasmid persistence and abundance. Here, we discuss how PCF can be extended to account for plasmid interactions. We also discuss how such model‐guided predictions of plasmid fates can benefit from the development of new experimental tools and data‐driven computational methods. (shrink)

The framework for this contribution is the transformation of the textual community, namely, modern society, into a digital community, in other words, a network society. This paper analyzes two theses. The first holds that the text, due to its genetic and historic nature, is always IMMUTABLE, STABLE, and never mobile. For this reason, the text represents the foundational element of a specific society, modern society. The second thesis is based on the assertion that within information and hypertext technologies (...) two diverse views confront and contrast each other. I locate these tendencies in the following key words: “dream” (Nelson) and “intellect” (Engelbart). Hypertext technology and culture represent the most transformative location and agency, they are the actors of the paradigm shift in which we are implicated. The hypertext revolution is based on the criticism of and attack against the material supports of writing and reading, as well as typographic technologies. Hypertext fights and wins this battle. However, hypertext technology is not able to reach the deep structure of alphabetic culture that is made not only of material support but also mental and bodily experience, consolidated and evolving, and of social relationships that are implied in the materiality of the support. La cornice di riferimento di questo contributo è la trasformazione della società testuale, cioè della società moderna, in società digitale, ovvero nella società dei network. Nell’intervento vengono analizzate due tesi: la prima afferma che il testo, per sua natura genetica e storica, è sempre IMMUTABILE, STABILE e non è mai mobile e per questo è fondativo di una società specifica, quella che noi chiamiamo la società moderna. La seconda tesi si basa sull’assunto che all’interno della cultura informatica e tecnologica che genera gli ipertesti si confrontano e si scontrano due idee diverse. Identifico queste due tendenze nelle parole chiave: dream (Nelson) e intellect (Engelbart). La tecnologia e la cultura ipertestuale sono il luogo e l’agente più fortemente trasformativi, gli attori del cambio di paradigma che ci coinvolge. La rivoluzione ipertestuale ha le sue basi nell’attacco e nella critica dei supporti materiali della scrittura e della lettura e sulle tecnologie tipografiche. L’ipertesto combatte e vince questa battaglia. La tecnologia ipertestuale non riesce però a raggiungere la struttura profonda della cultura alfabetica che è composta non solo da supporti ma da esperienze sia della mente sia del corpo, da relazioni sociali consolidate e mutanti che sono sottese e operanti con la materialità del supporto. (shrink)

Forty years’ experience as a bacterial geneticist has taught me that bacteria possess many cognitive, computational and evolutionary capabilities unimaginable in the first six decades of the twentieth century. Analysis of cellular processes such as metabolism, regulation of protein synthesis, and DNA repair established that bacteria continually monitor their external and internal environments and compute functional outputs based on information provided by their sensory apparatus. Studies of genetic recombination, lysogeny, antibiotic resistance and my own work on transposable elements (...) revealed multiple widespread bacterial systems for mobilizing and engineering DNA molecules. Examination of colony development and organization led me to appreciate how extensive multicellular collaboration is among the majority of bacterial species. Contemporary research in many laboratories on cell–cell signaling, symbiosis and pathogenesis show that bacteria utilise sophisticated mechanisms for intercellular communication and even have the ability to commandeer the basic cell biology of ‘higher’ plants and animals to meet their own needs. This remarkable series of observations requires us to revise basic ideas about biological information processing and recognise that even the smallest cells are sentient beings. Previous article in issue. (shrink)

Forty years’ experience as a bacterial geneticist has taught me that bacteria possess many cognitive, computational and evolutionary capabilities unimaginable in the first six decades of the twentieth century. Analysis of cellular processes such as metabolism, regulation of protein synthesis, and DNA repair established that bacteria continually monitor their external and internal environments and compute functional outputs based on information provided by their sensory apparatus. Studies of genetic recombination, lysogeny, antibiotic resistance and my own work on transposable elements (...) revealed multiple widespread bacterial systems for mobilizing and engineering DNA molecules. Examination of colony development and organization led me to appreciate how extensive multicellular collaboration is among the majority of bacterial species. Contemporary research in many laboratories on cell–cell signaling, symbiosis and pathogenesis show that bacteria utilise sophisticated mechanisms for intercellular communication and even have the ability to commandeer the basic cell biology of ‘higher’ plants and animals to meet their own needs. This remarkable series of observations requires us to revise basic ideas about biological information processing and recognise that even the smallest cells are sentient beings. (shrink)

Integrative mobile genetic elements (MGEs), such as transposons and insertion sequences, propagate within bacterial genomes, but persistence times in individual lineages are short. For long‐term survival, MGEs must continuously invade new hosts by horizontal transfer. Theoretically, MGEs that persist for millions of years in single lineages, and are thus subject to vertical inheritance, should not exist. Here we draw attention to an exception – a class of MGE termed REPIN. REPINs are non‐autonomous MGEs whose duplication depends on (...) non‐jumping RAYT transposases. Comparisons of REPINs and typical MGEs show that replication rates of REPINs are orders of magnitude lower, REPIN population size fluctuations correlate with changes in available genome space, REPIN conservation depends on RAYT function, and REPIN diversity accumulates within host lineages. These data lead to the hypothesis that REPINs form enduring, beneficial associations with eubacterial chromosomes. Given replicative nesting, our hypothesis predicts conflicts arising from the diverging effects of selection acting simultaneously on REPINs and host genomes. Evidence in support comes from patterns of REPIN abundance and diversity in two distantly related bacterial species. Together this bolsters the conclusion that REPINs are the genetic counterpart of mutualistic endosymbiotic bacteria. (shrink)

An appreciation of the life and word of Barbara McClintock, with special emphasis on what made her a unique and visionary scientist. The obituary indicates unappreciated aspects of her work on biological sensing and how organisms restructure their genomes in response to challenges.

The CRISPR-Cas systems of bacterial and archaeal adaptive immunity have become a household name among biologists and even the general public thanks to the unprecedented success of the new generation of genome editing tools utilizing Cas proteins. However, the fundamental biological features of CRISPR-Cas are of no lesser interest and have major impacts on our understanding of the evolution of antivirus defense, host-parasite coevolution, self versus non-self discrimination and mechanisms of adaptation. CRISPR-Cas systems present the best known case in point (...) for Lamarckian evolution, i.e. generation of heritable, adaptive genomic changes in response to encounters with external factors, in this case, foreign nucleic acids. CRISPR-Cas systems employ multiple mechanisms of self versus non-self discrimination but, as is the case with immune systems in general, are nevertheless costly because autoimmunity cannot be eliminated completely. In addition to the autoimmunity, the fitness cost of CRISPR-Cas systems appears to be determined by their inhibitory effect on horizontal gene transfer, curtailing evolutionary innovation. Hence the dynamic evolution of CRISPR-Cas loci that are frequently lost and acquired by archaea and bacteria. Another fundamental biological feature of CRISPR-Cas is its intimate connection with programmed cell death and dormancy induction in microbes. In this and, possibly, other immune systems, active immune response appears to be coupled to a different form of defense, namely, “altruistic” shutdown of cellular functions resulting in protection of neighboring cells. Finally, analysis of the evolutionary connections of Cas proteins reveals multiple contributions of mobile genetic elements to the origin of various components of CRISPR-Cas systems, furthermore, different biological systems that function by genome manipulation appear to have evolved convergently from unrelated MGE. The shared features of adaptive defense systems and MGE, namely the ability to recognize and cleave unique sites in genomes, make them ideal candidates for genome editing and engineering tools. (shrink)

Written for non-experts, this volume introduces the mechanisms that underlie reticulate evolution. Chapters are either accompanied with glossaries that explain new terminology or timelines that position pioneering scholars and their major discoveries in their historical contexts. The contributing authors outline the history and original context of discovery of symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow, and infectious heredity. By applying key insights from the areas of molecular (phylo)genetics, microbiology, virology, ecology, systematics, immunology, epidemiology and computational science, (...) they demonstrate how reticulate evolution impacts successful survival, fitness and speciation. Reticulate evolution brings forth a challenge to the standard Neo-Darwinian framework, which defines life as the outcome of bifurcation and ramification patterns brought forth by the vertical mechanism of natural selection. Reticulate evolution puts forward a pattern in the tree of life that is characterized by horizontal mergings and lineage crossings induced by symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow, and infective heredity, making the “tree of life” look more like a “web of life.” On an epistemological level, the various means by which hereditary material can be transferred horizontally challenges our classic notions of units and levels of evolution, fitness, modes of transmission, linearity, communities, and biological individuality. The case studies presented examine topics including the origin of the eukaryotic cell and its organelles through symbiogenesis; the origin of algae through primary and secondary symbiosis and dinoflagellates through tertiary symbiosis; the superorganism and holobiont as units of evolution; how endosymbiosis induces speciation in multicellular life forms; transferrable and non-transferrable plasmids and how they symbiotically interact with their host; the means by which pro- and eukaryotic organisms transfer genes laterally (bacterial transformation, transduction and conjugation as well as transposons and other mobile genetic elements); hybridization and divergence with gene flow in sexually-reproducing individuals; current (human) microbiome and viriome studies that impact our knowledge concerning the evolution of organismal health and acquired immunity; and how symbiosis and symbiogenesis can be modelled in computational evolution. (shrink)

James Shapiro’s view of evolution is inspired by looking at the molecular mechanisms of mutation. Finding these systems to be intelligent and the mutations non-gradual, Shapiro concludes that neither the role of DNA in development, nor and the role of natural selection in evolution are what we thought them to be. The cases discussed are interesting and may require some modification of theory in biology, but this reviewer finds many of Shapiro’s conclusions unwarranted.

Recent investigations surprisingly indicate that single RNA "stem-loops" operate solely by chemical laws that act without selective forces, and in contrast, self-ligated consortia of RNA stem-loops operate by biological selection. To understand consortial RNA selection, the concept of single quasi-species and its mutant spectra as drivers of RNA variation and evolution is rethought here. Instead, we evaluate the current RNA world scenario in which consortia of cooperating RNA stem-loops are the basic players. We thus redefine quasispecies as RNA quasispecies consortia (...) and argue that it has essential behavioral motifs that are relevant to the inherent variation, evolution and diversity in biology. We propose that qs-c is an especially innovative force. We apply qs-c thinking to RNA stem-loops and evaluate how it yields altered bulges and loops in the stem-loop regions, not as errors, but as a natural capability to generate diversity. This basic competence-not error-opens a variety of combinatorial possibilities which may alter and create new biological interactions, identities and newly emerged self identity functions. Thus RNA stem-loops typically operate as cooperative modules, like members of social groups. From such qs-c of stem-loop groups we can trace a variety of RNA secondary structures such as ribozymes, viroids, viruses, mobile genetic elements as abundant infection derived agents that provide the stem-loop societies of small and long non-coding RNAs. (shrink)

Current research on the origin of DNA and RNA, viruses, and mobile genetic elements prompts a re-evaluation of the origin and nature of genetic material as the driving force behind evolutionary novelty. While scholars used to think that novel features resulted from random genetic mutations of an individual’s specific genome, today we recognize the important role that acquired viruses and mobile genetic elements have played in introducing evolutionary novelty within the genomes of (...) species. Viral infections and subviral RNAs can enter the host genome and persist as genetic regulatory networks. Persistent viral infections are also important to understand the split between great apes and humans. Nearly all mammals and nonhuman primates rely on olfaction, i.e., chemoreception as the basis of the sense of smell for social recognition, group membership, and the coordination of organized social life. Humans, however, evolved other means to establish social bonding, because several infection waves by endogenous retroviruses caused a loss of odor receptors in human ancestors. The human independence from olfaction for social recognition was in turn one driver of the rather abrupt human transition to dependence on visual information, gesture production, and facial recognition that are at the roots of language-based communication. (shrink)

Recently improved understanding of evolutionary processes suggests that tree-based phylogenetic analyses of evolutionary change cannot adequately explain the divergent evolutionary histories of a great many genes and gene complexes. In particular, genetic diversity in the genomes of prokaryotes, phages, and plasmids cannot be fit into classic tree-like models of evolution. These findings entail the need for fundamental reform of our understanding of molecular evolution and the need to devise alternative apparatus for integrated analysis of these genomes. We advocate the (...) development of integrative phylogenomics for analyzing these genomes and their histories, with tools suited to analyzing the importance of lateral gene transfer (LGT) and of DNA evolution in extra-cellular mobile genetic elements (e.g., viruses, plasmids). These phenomena greatly increase the complexity of relationships among interacting genetic partners, as they exchange functional genetic units. We examine the ontology of functional genetic units, interacting genetic partners, and emergent genetic associations, argue that these three categories of entities are required for a successful integrated phylogenomics. We conclude with arguments to suggest that the proposed new perspective and associated tools are suitable, and perhaps required, as a replacement for the bifurcating trees that have dominated evolutionary thinking for the last 150 years. (shrink)

There is growing evidence of evolutionary genome plasticity. The evolution of repetitive DNA elements, the major components of most eukaryotic genomes, involves the amplification of various classes of mobile genetic elements, the expansion of satellite DNA, the transfer of fragments or entire organellar genomes and may have connections with viruses. In addition to various repetitive DNA elements, a plethora of large and small RNAs migrate within and between cells during individual development as well as during (...) evolution and contribute to changes of genome structure and function. Such migration of DNA and RNA molecules often results in horizontal gene transfer, thus shaping the whole genomic network of interconnected species. Here, we propose that a high evolutionary dynamism of repetitive genome components is often related to the migration/movement of DNA or RNA molecules. We speculate that the cytoplasm is probably an ideal compartment for such evolutionary experiments. (shrink)

Most molecular biological concepts derive from physical chemical assumptions about the genetic code that are basically more than 40 years old. Additionally, systems biology, another quantitative approach, investigates the sum of interrelations to obtain a more holistic picture of nucleotide sequence order. Recent empirical data on genetic code compositions and rearrangements by mobile genetic elements and non-coding RNAs, together with results of virus research and their role in evolution, does not really fit into these concepts (...) and compel a re-examination. In this review we try to find an alternate hypothesis. It seems plausible now that if we look at the abundance of regulatory RNAs and persistent viruses in host genomes, we will find more and more evidence that the key players that edit the genetic codes of host genomes are consortia of RNA agents and viruses that drive evolutionary novelty and regulation of cellular processes in all steps of development. This agent-based approach may lead to a qualitative RNA sociology that investigates and identifies relevant behavioural motifs of cooperative RNA consortia. In addition to molecular biological perspectives this may lead to a better understanding of genetic code evolution and dynamics. (shrink)

Protein splicing is an extraordinary post‐translational reaction that removes an intact central “spacer” domain (Sp) from precursor proteins (N‐Sp‐C) while splicing together the N‐ and C‐domains of the precursor, via a peptide bond, to produce a new protein (N‐C). All of the available data on protein splicing fit a model in which these intervening sequences excise at the protein level via a self‐splicing mechanism. Several proteins have recently been discovered that undergo protein splicing, and in two such cases, the excised (...) spacer protein is an endonuclease. Such endonucleases are capable of conferring genetic mobility upon the intervening sequences that encodes them. These intervening sequences define a new family of mobile genetic elements that are translated yet remain phenotypically silent by excising at the protein rather than the RNA level. (shrink)

Hamilton’s Rule, named after the evolutionary biologist Bill Hamilton, and the related concepts of inclusive fitness and kin selection, have been the bedrock of the study of social evolution for the past half century. In ’The Philosophy of Social Evolution’, Jonathan Birch provides a comprehensive introduction to the conceptual foundations of the Hamiltonian view of social evolution, and a passionate defence of its enduring value in face of the recent high profile criticism. In this review essay, I first outline the (...) version of Hamilton’s Rule defended by Birch, dubbed Hamilton’s Rule General, and its derivation. With this in place, I then navigate through the fierce disagreements that Hamilton’s Rule generates among social evolution researchers and evaluate Birch’s central argument of the book that HRG serves as an organizing framework for social evolution research under which we can compare and interpret more detailed causal models. I then spend the remainder of the review discussing what I take to be three of the most exciting implications of Hamilton’s thinking raised by Birch: the extension of Hamilton’s Rule to mobile genetic elements, maximization of inclusive fitness models and the idea of adaptation as organism design, and the relationship between Hamilton’s approaches to social behaviour and the gene’s-eye view of evolution. (shrink)

Barbara McClintock won the Nobel Prize in 1983 for her discovery of mobile genetic elements. Her Nobel work began in 1944, and by 1950 McClintock began presenting her work on "controlling elements." McClintock performed her studies through the use of controlled breeding experiments with known mutant stocks, and read the action of controlling elements (transposons) in visible patterns of pigment and starch distribution. She taught close colleagues to "read" the patterns in her maize kernels, "seeing" (...) pigment and starch genes turning on and off. McClintock illustrated her talks and papers on controlling elements or transposons with photographs of the spotted and streaked maize kernels which were both her evidence and the key to her explanations. Transposon action could be read in the patterns by the initiated, but those without step by step instruction by McClintock or experience in maize often found her presentations confusing. The photographs she displayed became both McClintock's means of communication, and a barrier to successful presentation of her results. The photographs also had a second and more subtle effect. As images of patterns arrived at through growth and development of the kernel, they highlight what McClintock believed to be the developmental consequences of transposition, which in McClintock's view was her central contribution, over the mechanism of transposition, for which she was eventually recognized by others. Scientific activities are extremely visual, both at the sites of investigation and in communication through drawings, photographs, and movies. Those visual messages deserve greater scrutiny by historians of science. (shrink)

This article argues for a shift in evolutionary metaphor-from fitness and the elimination of the less fit to fragility and passage through fragile periods of change. Childhood, for example, can be viewed as state of protected weakness, allowing time for more neural development, learning, and play. Similarly, evolutionary change can be released precisely when competitive pressure is relaxed. The fragility of evolution in time extends to several biological domains. The genetic system exhibits a surprising fluidity, whether from mobile (...) genetic elements or hypermutation due to stress. Through gene duplication, organisms build up redundancy, which can more readily diverge into novelty. With endo-symbiosis one organism becomes incorporated into another, merging genomes, membranes, and metabolisms. As a result novel structures and genetic restructuring occur, making for profound evolutionary change. In a sexual life cycle, gametes within a species group fuse and amplify subtle variation. Hybridization, or unions between atypical sexual partners, can cause instant speciation and an instability that leads to more evolution. With development organisms go through rapid morphological change and sensitive transition phases. Importantly, dissociation of developmental modules in both temporal and spatial ways allow for evolutionary novelty to emerge. Several lines of evidence lead to the hypothesis that the organism's inner matrix can respond to stresses and help shape a fluid genome. In a second article, three more biological domains will be examined, in which organisms and environment more obviously interpenetrate: the remarkably plastic neural/behavioral system, novel synergisms between organisms, and the multiple, complex dynamics of ecosystems-all of which help to generate life's outstanding diversity. Last, the protection of fragile human populations will be discussed. (shrink)

Supernumerary B chromosomes are dispensable elements of the genome which can be retained in populations at high frequencies, despite being deleterious, through the ability to undergo non‐Mendelian inheritance. Their mode of origin is, however, obscure. Recent work on gynogenetic fish has demonstrated the incorporation of small, unstable, centromere‐containing microchromosomes, probably of interspecific derivation, into an asexual lineage(1). That these resemble B chromosomes both in structure and behaviour is consistent with the proposal that hybridisation between closely related species may be (...) a significant mode of origin for such selfish genetic elements. Additional work on the B chromosome of a parasitoid wasp and observations on patterns of chromosome breakage from somatic cell hybrids also support this hypothesis. (shrink)

The CRISPR-Cas systems of bacterial and archaeal adaptive immunity have become a household name among biologists and even the general public thanks to the unprecedented success of the new generation of genome editing tools utilizing Cas proteins. However, the fundamental biological features of CRISPR-Cas are of no lesser interest and have major impacts on our understanding of the evolution of antivirus defense, host-parasite coevolution, self versus non-self discrimination and mechanisms of adaptation. CRISPR-Cas systems present the best known case in point (...) for Lamarckian evolution, i.e. generation of heritable, adaptive genomic changes in response to encounters with external factors, in this case, foreign nucleic acids. CRISPR-Cas systems employ multiple mechanisms of self versus non-self discrimination but, as is the case with immune systems in general, are nevertheless costly because autoimmunity cannot be eliminated completely. In addition to the autoimmunity, the fitness cost of CRISPR-Cas systems appears to be determined by their inhibitory effect on horizontal gene transfer, curtailing evolutionary innovation. Hence the dynamic evolution of CRISPR-Cas loci that are frequently lost and acquired by archaea and bacteria. Another fundamental biological feature of CRISPR-Cas is its intimate connection with programmed cell death and dormancy induction in microbes. In this and, possibly, other immune systems, active immune response appears to be coupled to a different form of defense, namely, “altruistic” shutdown of cellular functions resulting in protection of neighboring cells. Finally, analysis of the evolutionary connections of Cas proteins reveals multiple contributions of mobile genetic elements to the origin of various components of CRISPR-Cas systems, furthermore, different biological systems that function by genome manipulation appear to have evolved convergently from unrelated MGE. The shared features of adaptive defense systems and MGE, namely the ability to recognize and cleave unique sites in genomes, make them ideal candidates for genome editing and engineering tools. (shrink)

A promising recent development in molecular biology involves viewing the genome as a miniecosystem, where genetic elements are compared to organisms and the surrounding cellular and genomic structures are regarded as the local environment. Here we critically evaluate the prospects of Ecological Neutral Theory, a popular model in ecology, as it applies at the genomic level. This assessment requires an overview of the controversy surrounding neutral models in community ecology. In particular, we discuss the limitations of using ENT (...) both as an explanation of community dynamics and as a null hypothesis. We then analyze a case study in which ENT has been applied to genomic data. Our central finding is that genetic elements do not conform to the requirements of ENT once its assumptions and limitations are made explicit. We further compare this genome-level application of ENT to two other, more familiar approaches in genomics that rely on neutral mechanisms: Kimura’s Molecular Neutral Theory and Lynch’s Mutational Hazard Model. Interestingly, this comparison reveals that there are two distinct concepts of neutrality associated with these models which we dub ‘fitness-neutrality’ and ‘competitive neutrality’. This distinction helps to clarify the various roles for neutral models in genomics, for example, in explaining the evolution of genome size. (shrink)

In the October issue of BioEssays (vol. 3, no. 4), H. P. Döring reviewed the general molecular biology of transposable elements in plants. In this review by P. A. Peterson, the effects of transposable genetic elements are considered, with special attention being paid to investigation of mobile‐element‐induced mutations at loci that control identifiable enzymes, and the specific alterations in enzyme properties that result. Together with DNA sequence analysis, these studies have begun to reveal the complexity of (...) insertion/excision events, and their potential in protein evolution. (shrink)

Cet article propose d’examiner les incidences affectives des affordances numériques observées à travers un corpus authentique d’échanges par WhatsApp. La notion d’affordance, définie dans le champ de la psychologie sociale comme l’ensemble des potentialités d’action offertes par l’environnement, sera intégrée ici dans une perspective linguistique et saisie comme un concept-clé pour analyser la parole située. Ainsi, la présente étude sur les interactions WhatsApp appréhendera les affordances de l’objet mobile parallèlement à celles de l’interface d’application. WhatsApp donne aux usagers la (...) possibilité de converser par écrit tout en communiquant en temps réel une photo à leur correspondant. Ce partage d’« images conversationnelles » constitue d’une part, une trace de l’affordance générée par l’application mobile et d’autre part, un observable d’une discursivité à caractère composite qui met au m... (shrink)

Cooperation is rife in the microbial world, yet our best current theories of the evolution of cooperation were developed with multicellular animals in mind. Hamilton’s theory of inclusive fitness is an important case in point: applying the theory in a microbial setting is far from straightforward, as social evolution in microbes has a number of distinctive features that the theory was never intended to capture. In this article, I focus on the conceptual challenges posed by the project of extending Hamilton’s (...) theory to accommodate the effects of gene mobility. I begin by outlining the basics of the theory of inclusive fitness, emphasizing the role that the concept of relatedness is intended to play. I then provide a brief history of this concept, showing how, over the past fifty years, it has departed from the intuitive notion of genealogical kinship to encompass a range of generalized measures of genetic similarity. I proceed to argue that gene mobility forces a further revision of the concept. The reason in short is that, when the genes implicated in producing social behaviour are mobile, we cannot talk of an organism’s genotype simpliciter; we can talk only of an organism’s genotype at a particular stage in its life cycle. We must therefore ask: with respect to which stage(s) in the life cycle should relatedness be evaluated? For instance: is it genetic similarity at the time of social interaction that matters to the evolution of social behaviour, or is it genetic similarity at the time of reproduction? I argue that, strictly speaking, it is neither of these: what really matters to the evolution of social behaviour is diachronic genetic similarity between the producers of fitness benefits at the time they produce them and the recipients of those benefits at the end of their life-cycle. I close by discussing the implications of this result. The main payoff is that it makes room for a possible new mechanism for the evolution of altruism in microbes that does not require correlated interaction among bearers of the genes for altruism. The importance of this mechanism in nature remains an open empirical question. (shrink)

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)‐based “active genetic” elements developed in 2015 bypassed the fundamental rules of traditional genetics. Inherited in a super‐Mendelian fashion, such selfish genetic entities offered a variety of potential applications including: gene‐drives to disseminate gene cassettes carrying desired traits throughout insect populations to control disease vectors or pest species, allelic drives biasing inheritance of preferred allelic variants, neutralizing genetic elements to delete and replace or to halt the spread of gene‐drives, (...) split‐drives with the core constituent Cas9 endonuclease and guide RNA (gRNA) components inserted at separate genomic locations to accelerate assembly of complex arrays of genetic traits or to gain genetic entry into novel organisms (vertebrates, plants, bacteria), and interhomolog based copying systems in somatic cells to develop tools for treating inherited or infectious diseases. Here, we summarize the substantial advances that have been made on all of these fronts and look forward to the next phase of this rapidly expanding and impactful field. (shrink)

Mobile Health (m-health) technologies, such as wearables, apps, and smartwatches, are increasingly viewed as tools for improving health and well-being. In particular, such technologies are conceptualized as means for laypersons to master their own health, by becoming “engaged” and “empowered” “managers” of their bodies and minds. One notion that is especially prevalent in the discussions around m-health technology is that of empowerment. In this paper, I analyze the notion of empowerment at play in the m-health arena, identifying five (...) class='Hi'>elements that are required for empowerment. These are (1) knowledge, (2) control, (3) responsibility, (4) the availability of good choices, and (5) healthy desires. I argue that at least sometimes, these features are not present in the use of these technologies. I then argue that instead of empowerment, it is plausible that m-health technology merely facilitates a feeling of empowerment. I suggest this may be problematic, as it risks placing the burden of health and behavior change solely on the shoulders of individuals who may not be in a position to affect such change. (shrink)

Birth localities of spouses from two generations are examined, to assess the extent to which the observed patterns of marital mobility link the spatially separated and kin-structured sub-populations within the ‘shahrestan’ of Nowshahr. The results indicate localised marriages and short range movements from the village of birth in both generations. Temporal increase in the range of movement indicates the breaking down of isolation, thus providing greater possibilities for admixture and genetic homogeneity.

Purpose Genetic research, via the mainstream media, presents the public with novel, profound findings almost on a daily basis. However, it is not clear how much laypeople understand these presentations and how they integrate such new findings into their knowledge base. Genetic knowledge (GK), existing causal beliefs, and genetic essentialist tendencies (GET) have been implicated in such processes; the current study assesses the relationships between these elements and how brief presentations of media releases of scientific findings (...) about genetics are consumed and affect the readers. -/- Methods An Australian national survey of GK, GET, and existing causal beliefs about health phenomena (heart disease and obesity) was conducted. Participants were also exposed to news headlines that offered genetic and non-genetic partial explanations of the same health phenomena and reported their evaluations of these headlines, as well as the effects of the headlines on their personal understanding of the health phenomena. -/- Results GK was negatively-associated with GET. Whereas GK did not directly predict the evaluation and effects of the genetic headlines, GET did. GK predicted the effects of the headlines indirectly via GET and via GET and existing causal beliefs. -/- Conclusion GET seem to predict unwarranted effects of exposure to news headlines about genetic science, whereas GK seems to indirectly mitigate the same unwarranted effects. (shrink)

Genetic drift (variously called “random drift”, “random genetic drift”, or sometimes just “drift”) has been a source of ongoing controversy within the philosophy of biology and evolutionary biology communities, to the extent that even the question of what drift is has become controversial. There seems to be agreement that drift is a chance (or probabilistic or statistical) element within population genetics and within evolutionary biology more generally, and that the term “random” isn’t invoking indeterminism or any technical mathematical (...) meaning, but that’s about where agreement ends. Yet genetic drift models are a staple topic in population genetics textbooks and research, with genetic drift described as one of the main factors of evolution alongside selection, mutation, and migration. Some claim that genetic drift has played a major role in evolution (particularly molecular evolution), while others claim it to be minor. This article examines these and other controversies. -/- In order to break through the logjam of competing definitions of drift, this entry begins with a brief history of the concept, before examining various philosophical claims about the proper characterization of drift and whether it can be distinguished from natural selection; the relation of drift to debates over statisticalism; whether drift can be detected empirically and if so, how; and the proper understanding of drift as a model and as a (purported) law. (shrink)

On December 18, 2014, a yellow female fly quietly emerged from her pupal case. What made her unique was that she had only one parent carrying a mutant allele of this classic recessive locus. Then, one generation later, after mating with a wild‐type male, all her offspring displayed the same recessive yellow phenotype. Further analysis of other such yellow females revealed that the construct causing the mutation was converting the opposing chromosome with 95% efficiency. These simple results, seen also in (...) mosquitoes and yeast, open the door to a new era of genetics wherein the laws of traditional Mendelian inheritance can be bypassed for a broad variety of purposes. Here, we consider the implications of this fundamentally new form of “active genetics,” its applications for gene drives, reversal and amplification strategies, its potential for contributing to cell and gene therapy strategies, and ethical/biosafety considerations associated with such active genetic elements. (shrink)

The article offers an insight into road traffic accidents by unravelling both the internal elements and the social context of the so-called car–driver hybrid. It takes a critical perspective on the art of designing road safety. More importantly, it seeks to contribute to social studies of transport and mobility through development of analytical concepts within the discipline. The points of departure are the inherent ambiguities of mobility. The author suggests that ‘being in traffic’ is always determined by coexisting forms (...) of mobility and immobility. This ambivalent stage is then called motility. The author discusses car-drivers as motile hybrids, as they are mobile and immobile, as well as subjects and objects at the same time. In order to apply these concepts, the question of what happens to hybrids in crashes is addressed, employing Bruno Latour’s concept of ‘immutable mobiles’. The article concludes with a discussion of the social role of road safety experts, arguing that transport safety experts create a specific kind of spatio-temporal order within which the motile hybrid exists. It is the safety professional who decides when to take agency away from the subject and give it to the object, and it s/he who determines where to slow down and where to speed up the car–driver hybrid. (shrink)

Mobile devices with health apps, direct-to-consumer genetic testing, crowd-sourced information, and other data sources have enabled research by new classes of researchers. Independent researchers, citizen scientists, patient-directed researchers, self-experimenters, and others are not covered by federal research regulations because they are not recipients of federal financial assistance or conducting research in anticipation of a submission to the FDA for approval of a new drug or medical device. This article addresses the difficult policy challenge of promoting the welfare and (...) interests of research participants, as well as the public, in the absence of regulatory requirements and without discouraging independent, innovative scientific inquiry. The article recommends a series of measures, including education, consultation, transparency, self-governance, and regulation to strike the appropriate balance. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Philosophy and Rhetoric 35.2 (2002) 120-137 [Access article in PDF] Discursive Mobility and Double Consciousness in S. Weir Mitchell and W.E.B. Du Bois 1 Susan Wells Here are two stories about double consciousness: they will become, eventually, stories about the public sphere: W. E. B. Du Bois formulating the theory of double consciousness, and S. Weir Mitchell presenting Mary Reynolds's case history, an instance of a mental disorder known (...) in the nineteenth century as double consciousness. I will begin with Du Bois's story, by far the most familiar to us: few texts are more central to contemporary rhetoric or cultural studies than the discussion of double consciousness in the opening pages of The Souls of Black Folk. 2 In the theory of double consciousness, Du Bois concentrated his contradictory experiences of scholarship, activism, social isolation, and active cosmopolitanism. Double consciousness was a methodological constraint that enabled Du Bois to build into the structure of The Souls of Black Folk a recognition that the complexity of African American life requires more than one perspective. And double consciousness was also a technique of writing, shaping the ironic and urgent voice of the book, by turns indignant and tender, eloquent and colloquial, a form of double address to both African American and Caucasian readers that allowed Du Bois to be two places at once. Double consciousness therefore controlled both the development and the presentation of The Souls of Black Folk, from the arc of its argument to its formal elements, includingDu Bois's famous use of chapter epigraphs to link canonic poetry with the melodies of the sorrow songs. Like the most relentlessly formal high modernist poem, the book continually enacts in its form not only its informing idea, but the circumstances of its composition and the constraints that shape its reading.The book's initial essay, "Of Our Spiritual Strivings," offers an analysis of double consciousness as it is shaped by three central categories of modernity: temporality, embodiment, and expertise. Double consciousness is located in time, in history; it is placed in a story of the epochal succession [End Page 120] of races, and in the specific history of slavery. Double consciousness emerges as strategically shaping African American responses to the problems of disenfranchisement, poverty, and the denial of civil rights after the suppression of Reconstruction. The historical sections of The Souls of Black Folk, therefore, do not simply rectify the facts, setting the record straight on Reconstruction or Afrocentric scholar and theorist Alexander Crumell. These local arguments all motivate an understanding of consciousness as temporally constituted, so that the work of previous generations can be effective only when it is appropriated in the present. Such appropriation is supported and mediated by the form of the book: Du Bois ends with an invocation to "God the Reader," who alone can ensure that "these crooked marks on a fragile leaf be not indeed THE END" (19).Double consciousness is also connected with embodiment, specifically the embodiment of African Americans, externalized and displaced in two images: blood, which I will discuss later in the essay, and the veil or caul that grants second sight. Like skin color, the caul is an inconsequential physical object invested with enormous symbolic power (8); it is a mark of origins that foretells the future. The "second sight" offered to the Negro is a vision of "two warring ideals," a vision that can barely be supported by "one dark body, whose dogged strength alone keeps it from being torn asunder"(9). At moments in The Souls of Black Folk, the veil is generalized, and becomes a physical barrier between the white world and the world of African American culture; the work of separating these worlds, of rendering them invisible to one another, is staged on the bodies of African Americans. The veil is usually seen as a separation between the races, something that has happened ("Feeling deeply and keenly the tendencies and opportunities of the age in which they live, their souls are bitter at the fate which drops the Veil... (shrink)

The article examines the relationship between Aby Warburg and his library by analysing the media which is involved: first, the arrangement of the books according to the library’s principle of the ‘law of thse good neighbour’, which helps to order the books on the shelves. Second, the handling of the library is even more determined by Aby Warburg’s use of index cards and card indexes. Like his card index which is situated between him and the library, Aby Warburg himself is (...) in between two library paradigms: on the one hand, as a person of the nineteenth century, Warburg belongs to the supporters of the systematic shelving instead of cataloguing the book collection. On the other hand his work is based on swift associations and direct responses to research questions, the associations not only thought up by words, but also visually, manually to be re-arranged on the shelves, which turns out to be a rather clumsy practice. The motor and initiator of these new orders is the card index with its mobile elements, allowing quick connections between the entities and resulting in enormous processes of re-shuffling of whole shelves and systematic arrangements in the book collection. It is especially the combination of these usually incompatible paradigms that makes the Kulturwissenschaftliche Bibliothek Warburg such a unique institution and rich example of knowledge practices in the twentieth century. (shrink)

In this paper, rather than focusing on genes as an organising concept around which historical considerations of theory and practice in genetics are elucidated, we place genetic markers at the heart of our analysis. This reflects their central role in the subject of our account, livestock genetics concerning the domesticated pig, Sus scrofa. We define a genetic marker as a element existing in different forms in the genome, that can be identified and mapped using a variety of quantitative, (...) classical and molecular genetic techniques. The conjugation of pig genome researchers around the common object of the marker from the early-1990s allowed the distinctive theories and approaches of quantitative and molecular genetics concerning the size and distribution of gene effects to align in projects to populate genome maps. Critical to this was the nature of markers as ontologically inert, internally heterogeneous and relational. Though genes as an organising and categorising principle remained important, the particular concatenation of limitations, opportunities, and intended research goals of the pig genetics community, meant that a progressively stronger focus on the identification and mapping of markers rather than genes per se became a hallmark of the community. We therefore detail a different way of doing genetics to more gene-centred accounts. By doing so, we reveal the presence of practices, concepts and communities that would otherwise be hidden. (shrink)

In this paper, rather than focusing on genes as an organising concept around which historical considerations of theory and practice in genetics are elucidated, we place genetic markers at the heart of our analysis. This reflects their central role in the subject of our account, livestock genetics concerning the domesticated pig, Sus scrofa. We define a genetic marker as a element existing in different forms in the genome, that can be identified and mapped using a variety of quantitative, (...) classical and molecular genetic techniques. The conjugation of pig genome researchers around the common object of the marker from the early-1990s allowed the distinctive theories and approaches of quantitative and molecular genetics concerning the size and distribution of gene effects to align in projects to populate genome maps. Critical to this was the nature of markers as ontologically inert, internally heterogeneous and relational. Though genes as an organising and categorising principle remained important, the particular concatenation of limitations, opportunities, and intended research goals of the pig genetics community, meant that a progressively stronger focus on the identification and mapping of markers rather than genes per se became a hallmark of the community. We therefore detail a different way of doing genetics to more gene-centred accounts. By doing so, we reveal the presence of practices, concepts and communities that would otherwise be hidden. (shrink)

Transposable elements (TEs) are powerful facilitators of genome evolution, and hence of phenotypic diversity as they can cause genetic changes of great magnitude and variety. TEs are ubiquitous and extremely ancient, and although harmful to some individuals, they can be very beneficial to lineages. TEs can build, sculpt, and reformat genomes by both active and passive means. Lineages with active TEs or with abundant homogeneous inactive populations of TEs that can act passively by causing ectopic recombination are potentially (...) fecund, adaptable, and taxonate readily. Conversely, taxa deficient in TEs or possessing heterogeneous populations of inactive TEs may be well adapted in their niche, but tend to prolonged stasis and may risk extinction by lacking the capacity to adapt to change, or diversify. Because of recurring intermittent waves of TE infestation, available data indicate a compatibility with punctuated equilibrium, in keeping with widely accepted interpretations of evidence from the fossil record. We propose a general and holistic synthesis on how the presence of TEs within genomes makes them flexible and dynamic, so that genomes themselves are powerful facilitators of their own evolution. (shrink)

The description Ausonius has given us of his family and of the teachers and professors of Bordeaux in the mid-fourth century is exceptional among our sources because of its detail and completeness. There is no reason to suppose that the picture he gives is untypical of life in the provinces and it makes a welcome change from the histories of aristocratic politics at Rome or Constantinople. It provides an excellent opportunity for a pilot study in which we may see how (...) the conflicting elements of social status were in practice reconciled and applied. In the traditional, and still prevalent view, the society of the Later Roman Empire was ‘crushed … in the iron clamp of castes separated from one another by barriers which could not be passed’. The evidence of Ausonius suggests that this judgement should be qualified. The society of the fourth century may have been stable. It was not static. (shrink)

The style of arithmetic in the treatises the Neo-Pythagorean authors is strikingly different from that of the "Elements". Namely, it is characterised by the absence of proof in the Euclidean sense and a specific genetic approach to the construction of arithmetic that we are going to describe in our paper. Lack of mathematical sophistication has led certain historians to consider this type of mathematics as a feature of decadence of mathematics in this period [Tannery 1887; Heath 1921]. The (...) alleged absence of originality in these works has also given grounds to believe that “the arithmetic presented in these works derives substantially from an ancient, primitive stage of Pythagorean arithmetic” and to use them as “an index of the character of arithmetic science in the 5th century” [Knorr 1975]. In this paper, we take Nicomachus’ Introduction to Arithmetic for point of departure, because it is the richest and most well organised treatise representing this tradition. However, we also take into account the works of other Neo-Pythagorean authors. We are going to show that the Neo-Pythagorean arithmetic might have been developed in a natural, self-contained manner as a simple theory of counting over a domain of concrete initial objects, designated by fixed signs. This approach can be comfortably realised without appealing to assumptions of axiomatic character, but relying upon some ‘genetic’ constructions intented to be carried out by means of the designated entities. (shrink)

The use of reproductive techniques and the eventual reproductive negligence from the provider of reproductive services gave rise to situations in which the intended parents are deprived of raising a child genetically connected to them. Courts have been dealing with cases of those for years, but have systemically denied claimants compensation, failing to recognise as damage the loss of genetic connection. In 2017, for the first time, the Singapore High Court provided compensation for that damage, labelled “loss of (...) class='Hi'>genetic affinity”. This paper will argue that the damage in question is the loss of genetic connection and results from a violation of reproductive rights because a key element of reproductive rights is to have children with whom we keep a genetic bond and raise them. The paper will explain why the arguments classically argued against such compensation are unfounded and it will argue for a compensation covering both patrimonial and non-patrimonial damages. (shrink)