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)

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)

Transposable elements are no longer considered to be “junk” DNA. Here, we review how TEs can impact gene regulation systematically. TEs encode various regulatory elements that enables them to regulate gene expression. RJ Britten and EH Davidson hypothesized that TEs can integrate the function of various transcriptional regulators into gene regulatory networks. Uniquely TEs can deposit regulatory sites across the genome when they transpose, and thereby bring multiple genes under control of the same regulatory logic. Several studies together have (...) robustly established that TEs participate in embryonic development and oncogenesis. We discuss the regulatory characteristics of TEs in context of evolution to understand the extent of their impact on gene networks. Understanding these features of TEs is central to future investigations of TEs in cellular processes and phenotypic presentations, which are applicable to development and disease studies. We re-visit the Britten–Davidson “gene-battery” model and understand the genetic and transcriptional impact of TEs in innovating gene regulatory networks. Transposable elements are exogenous sequences that have either been co-opted or repurposed for host functions. The vast amounts of TE sequence in the genome provides raw material for gene expression regulation, and still remains to be fully understood; the “gene-battery” model provides the basis for understanding this. (shrink)

The germ track is the cellular path by which genes are transmitted to future generations whereas somatic cells die with their body and do not leave direct descendants. Transposable elements (TEs) evolve to be silent in somatic cells but active in the germ track. Thus, the performance of most bodily functions by a sequestered soma reduces organismal costs of TEs. Flexible forms of gene regulation are permissible in the soma because of the self‐imposed silence of TEs, but strict licensing of (...) transcription and translation is maintained in the germ track to control proliferation of TEs. Delayed zygotic genome activation (ZGA) and maternally inherited germ granules are adaptations that enhance germ‐track security. Mammalian embryos exhibit very early ZGA associated with extensive mobilization of retroelements. This window of vulnerability to retrotransposition in early embryos is an indirect consequence of evolutionary conflicts within the mammalian genome over postzygotic maternal provisioning. (shrink)

Philosophers who study the problem of biological function often begin their deliberations by reflecting on the functions of parts of animals, or the behavior of animals. Applying theories of biological function to unconventional or borderline cases can help us to better evaluate and refine those theories. This is the case when we consider whether parts of transposable elements —bits of “selfish” DNA that move about within a host genome—have functions of their own, that is, whether the parts of TEs have (...) the function of helping the TE move about within the genome. Here I argue that whether or not the parts of TEs have functions depends crucially on whether collections of TEs form “populations,” by which I mean, here, a group of individuals of the same type that impact one another’s chances of persistence or multiplication, by impacting one another’s access to a shared resource. I think there is suggestive, but not conclusive, evidence that some TEs have functions of their own. Considering the problem of TE functionality, then, has value both for philosophy and for biology. (shrink)

The de‐repression of transposable elements (TEs) in mammalian genomes is thought to contribute to genome instability, inflammation, and ageing, yet is viewed as a cell‐autonomous event. In contrast to mammalian cells, prokaryotes constantly exchange genetic material through TEs, crossing both cell and species barriers, contributing to rapid microbial evolution and diversity in complex communities such as the mammalian gut. Here, it is proposed that TEs released from prokaryotes in the microbiome or from pathogenic infections regularly cross the kingdom barrier to (...) the somatic cells of their eukaryotic hosts. It is proposed this horizontal transfer of TEs from microbe to host is a stochastic, ongoing catalyst of genome destabilization, resulting in structural and epigenetic variations, and activation of well‐evolved host defense mechanisms contributing to inflammation, senescence, and biological ageing. It is proposed that innate immunity pathways defend against the horizontal acquisition of microbial TEs, and that activation of this pathway during horizontal transposon transfer promotes chronic inflammation during ageing. Finally, it is suggested that horizontal acquisition of prokaryotic TEs into mammalian genomes has been masked and subsequently under‐reported due to flaws in current sequencing pipelines, and new strategies to uncover these events are proposed. (shrink)

The ArgumentDespite more than fifty years of debate on the Merton thesis, there have been few attempts to substantiate Merton's argument through empirically based comparative studies. This study of the Jesuit scientific tradition is intended to serve as a test of some of Merton's central claims.Jesuit science is remarkable for its scope and longevity, and is distinguished by its markedly empirical and utilitarian orientation. In this paper I examine the ideological structure of the Society of Jesus and find at its (...) core an “apostolic spirituality” that explains the legitimation of these forms of science within the Society. The values of apostolic spirituality strongly encouraged an activist mentality among Jesuits, which in turn led to the formation of apostolates in education, at court, and in the overseas missions. The values associated with apostolic spirituality led to the initial acceptance of active-empirical sciences within the Society, which became established as traditions because they were useful in fulfilling the goals of the Society's apostolates.This study, by providing a qualified confirmation of Merton's central claims, suggests the importance of a supra-confessional sanctification of labor and learning in the growth of active-empirical sciences. (shrink)

In lectures and writings in the decades following the publication of Studies in Ethnomethodology [1967], Harold Garfinkel, the founder of ethnomethodology, developed what he called a “misreading” of the phenomenological writings of Aron Gurwitsch, Maurice Merleau-Ponty and others. Garfinkel’s “misreading” included a selective and creative treatment of themes that Gurwitsch drew from Gestalt psychology, such as figure-ground, Gestalt contexture, and the phenomenal field. Rather than identifying these themes with visual perception demonstrated with picture-puzzles (for example, of animals hidden in foliage) (...) and line drawings of reversible figures, Garfinkel used them to demonstrate praxeological and interactional phenomena: organizations of embodied activity that constitute fields of collective action. Phenomenal fields, for Garfinkel, are formed through embodied work performed in concert with the actions of others. Although Harvey Sacks, the founder of Conversation Analysis, did not explicitly mention Gurwitsch, phenomenology or Gestalt psychology in his writings and transcribed lectures, some of his writings on the sequential organization of conversation seem informed, if only indirectly through his relationship with Garfinkel, by Gurwitsch’s treatment of visual and auditory phenomena. Both Garfinkel and Sacks devised innovative ways to transpose Gestalt phenomena from perceptual psychology to social formations. (shrink)

The genomes of virtually all sexually reproducing species contain transposable elements. Although active elements generally transpose more rapidly than they are inactivated by mutation or excision, their number can be kept in check by purifying selection if its effectiveness becomes disproportionately greater as their copy number increases. In sexually reproducing species, such synergistic selection can result from ectopic crossing-over or from homologous recombination under negative epistasis. In addition, there may be controls on transposon activity that are associated with meiosis. (...) Because a sexual lineage that abandons sex must lack such mechanisms, it may be driven to extinction by the unchecked proliferation of deleterious transposons inherited from its sexual progenitor. An important component of the evolutionary advantage of sex over asex may therefore lie in the ability of sex, despite facilitating the spread of deleterious elements within interbreeding populations, also to restrain their intragenomic proliferation. BioEssays 27:76–85, 2005. © 2004 Wiley Periodicals, Inc. (shrink)

The ArgumentThe paper argues for the restricted viability of the concept of style in the history of science. Since historians of science borrow this term from art history or the sociology of knowledge, the paper outlines its emergence and function in these disciplines, in order to show that the need for ever subtler stylistic distinctions in historical description inevitably leads to the dissolution of the concept of style itself.“Style” will be defined in predominantly cognitive or technical terms when imputed to (...) an individual; in social or moral terms when thought to be carried by some collective entity. Both descriptions are given normative interpretations. A good individual style, then, is regarded as the pledge for valid knowledge or insights of a “higher order,” while a collective style, understood as the vehicle of successful intra group communication, involves the acceptance of certain rhetorical norms and/or socially shared values that are supposed to structure that style. “National styles” belong to the latter category; the emergence of this dubious notion can best be explained in sociological terms.If historians of science insist on adopting the concept of style, they will have to agree on its meaning. The paper concludes, therefore, with a rough typology of its most frequent meanings and uses. (shrink)

This essay is a response to Robert Norton's "The Myth of the Counter-Enlightenment". Norton's essay raises two issues. Is Isaiah Berlin's interpretation of Hamann and Herder based on one-sided and faulty scholarship, naively putting itself in the service of an anti-liberal myth about those figures originated by early twentieth-century German ideologues? A second issue flows from the first: if Berlin was mistaken in his reading of the work of Hamann and Herder, mistaking what they contributed to the Enlightenment, is Berlin's (...) very notion of a Counter-Enlightenment a fiction-a myth? Thorough analysis of those issues would require several essays. Instead, I try to sketch an alternative reading of Berlin's style of doing intellectual history, while highlighting the limitations of Norton's critique. (shrink)

The origin and prevalence of transposable elements may best be understood as resulting from “selfish” evolutionary processes at the within-genome level, with relevant populations being all members of the same TE family or all potentially mobile DNAs in a species. But the maintenance of families of TEs as evolutionary drivers, if taken as a consequence of selection, might be better understood as a consequence of selection at the level of species or higher, with the relevant populations being species or ecosystems (...) varying in their possession of TEs. In 2015, Brunet and Doolittle made the case for legitimizing claims for an evolutionary role for TEs by recasting such claims as being about species selection. Here I further develop this “how possibly” argument. I note that with a forgivingly broad construal of evolution by natural selection we might come to appreciate many aspects of Life on earth as its products, and TEs as—possibly—contributors to the success of Life by selection at several levels of a biological hierarchy. Thinking broadly makes this proposition a testable Darwinian one. (shrink)

Robert Kirk; III*—Goodbye to Transposed Qualia, Proceedings of the Aristotelian Society, Volume 82, Issue 1, 1 June 1982, Pages 33–44, https://doi.org/10.1093/a.

Robert Kirk; III*—Goodbye to Transposed Qualia, Proceedings of the Aristotelian Society, Volume 82, Issue 1, 1 June 1982, Pages 33–44, https://doi.org/10.1093/a.

We tell the tale of the first writing of a partial transpose, without guaranteeing historical authenticity.

Since the Second Vatican Council (1962-65), particularly its Pastoral Constitution on the Church and the Modern World, many Catholic theologians, including J. B. Metz, Karl Rahner, and Edward Schillebeeckx, have taken note of the need to see the practical implications of our theoretical doctrines. Taking its cue from a remark of Karl Rahner (1970) that the theological as such must be a principle of action, this article studies the implications of this for Christology, soteriology, and ecclesiology. The Christological implications are (...) rooted in the long overdue recovery of the faith and hope of Jesus himself as the basis of the church’s faith in Jesus. The soteriological implications are rooted in recovering Jesus’ proclamation of the reign of God as the center of Christian soteriology. Finally, the ecclesiological implications are rooted in seeing the church as existing not for itself, but for the sake of the ongoing proclamation and realization of God’s reign in the present. (shrink)

Considerable variation exists not only in the kinds of transposable elements (TEs) occurring within the genomes of different species, but also in their abundance and distribution. Noting a similarity to the assortment of organisms among ecosystems, some researchers have called for an ecological approach to the study of transposon dynamics. However, there are several ways to adopt such an approach, and it is sometimes unclear what an ecological perspective will add to the existing co-evolutionary framework for explaining transposon-host interactions. This (...) review aims to clarify the conceptual foundations of transposon ecology in order to evaluate its explanatory prospects. We begin by identifying three unanswered questions regarding the abundance and distribution of TEs that potentially call for an ecological explanation. We then offer an operational distinction between evolutionary and ecological approaches to these questions. By determining the amount of variance in transposon abundance and distribution that is explained by ecological and evolutionary factors, respectively, it is possible empirically to assess the prospects for each of these explanatory frameworks. To illustrate how this methodology applies to a concrete example, we analyzed whole-genome data for one set of distantly related mammals and another more closely related group of arthropods. Our expectation was that ecological factors are most informative for explaining differences among individual TE lineages, rather than TE families, and for explaining their distribution among closely related as opposed to distantly related host genomes. We found that, in these data sets, ecological factors do in fact explain most of the variation in TE abundance and distribution among TE lineages across less distantly related host organisms. Evolutionary factors were not significant at these levels. However, the explanatory roles of evolution and ecology become inverted at the level of TE families or among more distantly related genomes. Not only does this example demonstrate the utility of our distinction between ecological and evolutionary perspectives, it further suggests an appropriate explanatory domain for the burgeoning discipline of transposon ecology. The fact that ecological processes appear to be impacting TE lineages over relatively short time scales further raises the possibility that transposons might serve as useful model systems for testing more general hypotheses in ecology. (shrink)

Whoever compares the genomes of distantly related species might find aberrantly high sequence similarity at certain loci. Such anomaly can only be explained by genetic material being transferred through other means than reproduction, that is, a horizontal transfer. Between multicellular organisms, the transferred material will likely turn out to be a transposable element. Because TEs can move between loci and invade chromosomes by replicating themselves, HT of TEs profoundly impacts genome evolution. Yet, very few studies have quantified HTT at large (...) taxonomic scales. Indeed, this task currently faces difficulties that range from the variable quality of available genome sequences to limitations of analytical procedures, some of which have been overlooked. Here we review the many challenges that an extensive analysis of HTT must overcome, we expose biases and limits of current methods, suggest solutions or workarounds, and reflect upon approaches that could be developed to better quantify this phenomenon. With the large amount of genomic resources now available, horizontal transfer of transposable elements can be studied as an evolutionary process, rather than as isolated cases. We discuss some of the difficulties encountered in detecting and counting such transfers and propose guidelines and directions for future research in this area. (shrink)

Biochemical and genetical analysis of plant transposons has shown that these elements can induce unstable mutations and also that the transposon structure can be altered in different ways. Upon insertion, a transposon can give rise to a variety of chromosomal changes in the vicinity of the insertion site. The alterations range from the nucleotide level to large‐scale rearrangements.

Autonomous transposable elements, generally considered as junk and selfish, encode transposition proteins that can bind, copy, break, join or degrade nucleic acids as well as process or interact with other proteins. Such a repertoire of activities might be of interest for the host cell. There is indeed substantial evidence that mobile DNA can serve as a dynamic reservoir for new cellular functions. Transposable element genes encoding transposase, integrase, reverse transcriptase as well as structural and envelope proteins have been repeatedly recruited (...) by their host during evolution in most eukaryotic lineages. Such domesticated sequences protect us against infections, are necessary for our reproduction, allow the replication of our chromosomes and control cell proliferation and death; others are essential for plant development. Many new candidates for domesticated sequences have been revealed by sequencing projects. Their functional analysis will uncover new aspects of evolutionary alchemy, the turning of junk into gold within genomes. BioEssays 28: 913–922, 2006. © 2006 Wiley periodicals, Inc. (shrink)

The media attention and subsequent scientific backlash engendered by the claim, announced by spokespeople for the Encyclopedia of DNA Elements project, that 80% of the human genome has a “biochemical function” highlights the need for a clearer understanding of function concepts in biology. This article provides an overview of two major function concepts that have been developed in the philosophy of science – the “causal role” concept and the “selected effects” concept – and their relevance to ENCODE. Unlike some previous (...) critiques, the ENCODE project is not considered problematic because it employed a causal role definition of function, but because of how this concept was misused. In addition, several unique challenges that arise when dealing with transposable elements, but which were ignored by ENCODE, are highlighted. These include issues surrounding TE-level versus organism-level selection, the origins versus the persistence of elements, and accidental versus functional organism-level benefits. Finally, some key questions are presented that should be addressed in any studies aiming to ascribe functions to major portions of large eukaryotic genomes, the majority of which is made up of transposable elements. (shrink)

Theories of the genetics underlying punctuated equilibrium (PE) have been vague to date. Here the developmental gene hypothesis is proposed, which states that: 1) developmental regulatory (DevReg) genes are responsible for the orchestration of metazoan morphogenesis and their extreme conservation and mutation intolerance generates the equilibrium or stasis present throughout much of the fossil record and 2) the accumulation of regulatory elements and recombination within these same genes—often derived from transposable elements—drives punctuated bursts of morphological divergence and speciation across metazoa. (...) This two‐part hypothesis helps to explain the features that characterize PE, providing a theoretical genetic basis for the once‐controversial theory. Also see the video abstract here https://youtu.be/C-fu-ks5yDs. (shrink)

In this essay I argue that Thomas Aquinas is not as naively optimistic about the noetic effects of sin as is often portrayed by standard neo-Calvinist objections. Still, his metaphysics of the human person requires some development to better explain the mind’s impairment by sin, a development made possible by the work of Bernard Lonergan and the resulting Lonergan/Aquinas (L/A) model of the noetic effects of sin.

Antievolution arguments of Christian and Hindu creationists often critique Darwin's metaphor of the geological record as an ill‐preserved book of life, while highlighting the problem of anomalous fossils. For instance, Bible‐based young‐Earth creationists point to anomalous humanlike prints alongside authenticated dinosaur tracks to argue for the creation of all life some few thousand years ago. But Vedic‐based ancient‐hominid creationists view the same sort of evidence as indicating the existence of all species, including the hominids, billions of years ago. I examine (...) the roots of this Hindu Vedic creationism and its recent elaboration among scientifically minded members of the International Society for Krishna Consciousness (ISKCON). Similarities in the methods and rhetorical strategies of the two creationist groups are considered, as well as the underlying motives that have brought together such otherwise disparate religious worldviews. (shrink)

A combination of cytogenetic and molecular analyses has shown that several different transposable elements are involved in the restructuring of Drosophila chromosomes. Two kinds of elements, P and hobo, are especially prone to induce chromosome rearrangements. The mechanistic details of this process are unclear, but, at least some of the time, it seems to involve ectopic recombination between elements inserted at different chromosomal sites; the available data suggest that these ectopic recombination events are much more likely to occure between elements (...) in the same chromosome than between elements in different chromosomes. Other Drosophila transposons also appear to mediate chromosome restructuring by ectopic recombination; these include the retrotransposons BEL, roo, Docand I and the foldback element FB. In addition, two retrotransposons, HeT‐A and TART, have been found to be associated specifically with the ends of Drosophila chromosomes. Very limited data indicate that transposon‐mediated chromosome restructuring is occurring in natural populations of Drosophila. This suggests that transposable elements may help to shape the structure of the Drosophila genome and implies that they may have a similar role in other organisms. (shrink)

Studies on transposable elements of the Ac family have led to different models for excision gap repair in either plants or Drosophila. Excision products generated by the plant transposable elements Ac and Tam3 imply a more or less straightforward ligation of broken ends; excision products of the Drosophila P element indicate the involvement of ‘double‐strand break’ (DSB) repair. Recent findings that excision products of Ac and Tam3 can also contain traces of the element ends indicate, however, that DSB repair might (...) be an alternative repair mechanism in plants. A functional DSB repair mechanism in plants can also be deduced from the observed rapid increases of Ac copy number during plant development and from the involvement of Ac in the generation of internal Ac deletions. On the other hand, alternative repair mechanisms may also be functional in Drosophila, because some of the ‘footprints’ generated upon P excision can be explained by a mechanism that has been postulated for excision gap repair in plants. It is concluded that plants and Drosophila can use similar repair mechanisms, but that the predominance of a certain repair mechanism is determined by the host. (shrink)

Horizontal transfer (HT) is the transmission of genetic material between non‐mating species, a phenomenon thought to occur rarely in multicellular eukaryotes. However, many transposable elements (TEs) are not only capable of HT, but have frequently jumped between widely divergent species. Here we review and integrate reported cases of HT in retrotransposons of the BovB family, and DNA transposons, over a broad range of animals spanning all continents. Our conclusions challenge the paradigm that HT in vertebrates is restricted to infective long (...) terminal repeat (LTR) retrotransposons or retroviruses. This raises the possibility that other non‐LTR retrotransposons, such as L1 or CR1 elements, believed to be only vertically transmitted, can horizontally transfer between species. Growing evidence indicates that the process of HT is much more general across different TEs and species than previously believed, and that it likely shapes eukaryotic genomes and catalyses genome evolution. (shrink)

Information about the structure, function and regulation of the maize Suppressormutator (Spm) transposable element has emerged from the genetic and molecular characterization of both deletion mutations and an unconventional type of reversible genetic change (epimutation). The element is subject to an epigenetic mechanism that can either stably inactivate it or specify one of a variety of heritable programs of differential element expression in development. The essay explores the relationship between the Spm element's epigenetic developmental programming mechanism and the determinative events (...) central to plant development and differentiation. (shrink)