Transposons are ubiquitous genetic elements discovered so far in all investigated prokaryotes and eukaryotes. In remarkable contrast to all other genes, transposable elements are able to move to new locations within their host genomes. Transposition of transposons into coding sequences and their initiation of chromosome rearrangements have tremendous impact on gene expression and genome evolution. While transposons have long been known in bacteria, plants, and animals, only in recent years has there been a significant increase in the number of transposable (...) elements discovered in filamentous fungi. Like those of other eukaryotes, each fungal transposable element is either of class I or of class II. While class I elements transpose by a RNA intermediate and employ reverse transcriptases, class II elements transpose directly at the DNA level. We present structural and functional features for such transposons that have been identified so far in filamentous fungi. Emphasis is given to specific advantages or unique features when fungal systems are used to study transposable elements, e.g., the evolutionary impact of transposons in coenocytic organisms and possible experimental approaches toward horizontal gene transfer. Finally, we focus on the potential of transposons for tagging and identifying fungal genes. BioEssays 20:652–659, 1998.© 1998 John Wiley & Sons Inc. (shrink)

Transposable elements (TEs) are sequences currently or historically mobile, and are present across all eukaryotic genomes. A growing interest in understanding the regulation and function of TEs has revealed seemingly dichotomous roles for these elements in evolution, development, and disease. On the one hand, many gene regulatory networks owe their organization to the spread of cis‐elements and DNA binding sites through TE mobilization during evolution. On the other hand, the uncontrolled activity of transposons can generate mutations and contribute to disease, (...) including cancer, while their increased expression may also trigger immune pathways that result in inflammation or senescence. Interestingly, TEs have recently been found to have novel essential functions during mammalian development. Here, the function and regulation of TEs are discussed, with a focus on LINE1 in mammals. It is proposed that LINE1 is a beneficial endogenous dual regulator of gene expression and genomic diversity during mammalian development, and that both of these functions may be detrimental if deregulated in disease contexts. (shrink)

The Sleeping Beauty transposon system is a nonviral DNA transfer tool capable of efficiently mediating transposition‐based, stable integration of DNA sequences of choice into eukaryotic genomes. Continuous refinements of the system, including the emergence of hyperactive transposase mutants and novel approaches in vectorology, greatly improve upon transposition efficiency rivaling viral‐vector‐based methods for stable gene insertion. Current developments, such as reversible transgenesis and proof‐of‐concept RNA‐guided transposition, further expand on possible applications in the future. In addition, innate advantages such as lack (...) of preferential integration into genes reduce insertional mutagenesis‐related safety concerns while comparably low manufacturing costs enable widespread implementation. Accordingly, the system is recognized as a powerful and versatile tool for genetic engineering and is playing a central role in an ever‐expanding number of gene and cell therapy clinical trials with the potential to become a key technology to meet the growing demand for advanced therapy medicinal products. (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)

Expression and transposition of the Suppressor‐mutator (Spm) transposon of maize are controlled by interacting epigenetic and autoregulatory mechanisms. Methylation of critical element sequences prevents both transcription and transposition, heritably inactivating the element. The promoter, comprising the terminal 0.2 kb of the element, and a 0.35‐kb, highly GC‐rich, downstream sequence are the methylation target sequences. The element encodes two proteins necessary for transposition, TnpA and TnpD. There are multiple TnpA binding sites, both in the 5′ terminal promoter region and at (...) the element's 3′ end. In addition to its role in transposition, TnpA is both a positive and a negative regulator of transcription. TnpA represses the element's promoter when it is not methylated. When the element is inactive and its promoter methylated, TnpA activates the methylated promoter and facilitates both its transient and heritable demethylation. (shrink)

“Antibiotic resistance is usually associated with a fitness cost” is frequently accepted as common knowledge in the field of infectious diseases. However, with the advances in high‐throughput DNA sequencing that allows for a comprehensive analysis of bacterial pathogenesis at the genome scale, including antibiotic resistance genes, it appears that this paradigm might not be as solid as previously thought. Recent studies indicate that antibiotic resistance is able to enhance bacterial fitness in vivo with a concomitant increase in virulence during (...) infections. As a consequence, strategies to minimize antibiotic resistance turn out to be not as simple as initially believed. Indeed, decreased antibiotic use may not be sufficient to let susceptible strains outcompete the resistant ones. Here, we put in perspective these findings and review alternative approaches, such as preventive and therapeutic anti‐bacterial immunotherapies that have the potential to by‐pass the classic antibiotics. (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)

We have synthesized a 582,970-base pair Mycoplasma genitalium genome. This synthetic genome, named M. genitalium JCVI-1.0, contains all the genes of wild-type M. genitalium G37 except MG408, which was disrupted by an antibiotic marker to block pathogenicity and to allow for selection. To identify the genome as synthetic, we inserted "watermarks" at intergenic sites known to tolerate transposon insertions. Overlapping "cassettes" of 5 to 7 kilobases (kb), assembled from chemically synthesized oligonucleotides, were joined by in vitro recombination to produce (...) intermediate assemblies of approximately 24 kb, 72 kb ("1/8 genome"), and 144 kb ("1/4 genome"), which were all cloned as bacterial artificial chromosomes in Escherichia coli. Most of these intermediate clones were sequenced, and clones of all four 1/4 genomes with the correct sequence were identified. The complete synthetic genome was assembled by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae, then isolated and sequenced. A clone with the correct sequence was identified. The methods described here will be generally useful for constructing large DNA molecules from chemically synthesized pieces and also from combinations of natural and synthetic DNA segments. 10.1126/science.1151721. (shrink)

Natural genome editing from a biocommunicative perspective is the competent agent-driven generation and integration of meaningful nucleotide sequences into pre-existing genomic content arrangements, and the ability to (re-)combine and (re-)regulate them according to context-dependent (i.e. adaptational) purposes of the host organism. Natural genome editing integrates both natural editing of genetic code and epigenetic marking that determines genetic reading patterns. As agents that edit genetic code and epigenetically mark genomic structures, viral and subviral agents have been suggested because they may be (...) evolutionarily older than cellular life. This hypothesis that viruses and viral-like agents edit genetic code is developed according to three well investigated examples that represent key evolutionary inventions in which non-lytic viral swarms act symbiotically in a persistent lifestyle within cellular host genomes: origin of eukaryotic nucleus, adaptive immunity, placental mammals. Additionally an abundance of various RNA elements cooperate in a variety of steps and substeps as regulatory and catalytic units with multiple competencies to act on the genetic code. Most of these RNA agents such as transposons, retroposons and small non-coding RNAs act consortially and are remnants of persistent viral infections that now act as co-opted adaptations in cellular key processes. (shrink)

The growing number of cloned eukaryotic genes lacking a defined or proven biological function poses a major challenge in ‘reverse genetics’. A method is described here that permits efficient screening for new lesions in, or close to, genes corresponding to cloned DNA sequences of interest. The technique involves transposon mutagenesis, followed by screening of DNA isolated from a population of mutagenised individuals (or their progeny) for evidence that the population contains at least one individual in which transposon insertion (...) has occurred at the target locus. Detection of rare individuals within the population is facilitated by the use of the polymerase chain reaction (PCR). Once recognised, specific individuals (or their progeny) are isolated from the population by a process of sib‐selection. In cases where insertion of the transposon has occurred close to, but not within, the target locus, secondary events involving imprecise excision of the transposon will nonetheless allow the isolation of mutant individuals. Though the method was developed specifically for the transposon‐mutagenesis of Drosophila, extensions to other organisms and to other mutagenic strategies are feasible and some of the possibilities are discussed. (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)

Dawkins in his The Selfish Gene(1) quite aptly applies the term “selfish” to parasitic repetitive DNA sequences endemic to eukaryotic genomes, especially vertebrates. Doolittle and Sapienza(2) as well as Orgel and Crick(3) enlivened this notion of selfish DNA with the identification of such repetitive sequences as remnants of mobile elements such as transposons. In addition, Orgel and Crick(3) associated parasitic DNA with a potential to outgrow their host genomes by propagating both vertically via conventional genome replication as well as infectiously (...) by horizontal gene transfer (HGT) to other genomes. Still later, Doolittle(4) speculated that unchecked HGT between unrelated genomes so complicates phylogeny that the conventional representation of a tree of life would have to be replaced by a thicket or a web of life.(4) In contrast, considerable data now show that reconstructions based on whole genome sequences are consistent with the conventional “tree of life”.(5–10) Here, we identify natural barriers that protect modern genome populations from the inroads of rampant HGT. BioEssays 27:741–747, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

The use of Drosophila chromosomal rearrangements and transposon constructs involving the white gene reveals the existence of repressive chromatin domains that can spread over considerable genomic distances. One such type of domain is found in heterochromatin and is responsible for classical position‐effect variegation. Another type of repressive domain is established, beginning at specific sequences, by complexes of Polycomb Group proteins. Such complexes, which normally regulate the expression of many genes, including the homeotic loci, are responsible for silencing, white gene (...) variegation, pairing‐dependent effects and insertional targeting. (shrink)

The pituitary hormone prolactin (PRL) is best known for its role in the regulation of lactation. Recent evidence furthermore indicates PRL is required for normal reproduction in rodents. Here, we report on the insertion of two transposon-like DNA sequences in the human prolactin gene, which together function as an alternative promoter directing extrapituitary PRL expression. Indeed, the transposable elements contain transcription factor binding sites that have been shown to mediate PRL transcription in human uterine decidualised endometrial cells and lymphocytes. (...) We hypothesize that the transposon insertion event has resulted in divergent (pituitary versus extrapituitary) expression of prolactin in primates, and in differential actions of pituitary versus extrapituitary prolactin in lactation versus pregnancy respectively. Importantly, the TE insertion might provide a context for some of the conflicting results obtained in studies of PRL function in mice and man. (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)

American Academy of Pediatrics (AAP) and American College of Medical Genetics (ACMG) recently provided two recommendations about predictive genetic testing of children. The Clinical Sequencing Exploratory Research Consortium's Pediatrics Working Group compared these recommendations, focusing on operational and ethical issues specific to decision making for children. Content analysis of the statements addresses two issues: (1) how these recommendations characterize and analyze locus of decision making, as well as the risks and benefits of testing, and (2) whether the guidelines conflict (...) or come to different but compatible conclusions because they consider different testing scenarios. These statements differ in ethically significant ways. AAP/ACMG analyzes risks and benefits using best interests of the child and recommends that, absent ameliorative interventions available during childhood, clinicians should generally decline to order testing. Parents authorize focused tests. ACMG analyzes risks and benefits using the interests of the child and other family members and recommends that sequencing results be examined for additional variants that can lead to ameliorative interventions, regardless of age, which laboratories should report to clinicians who should contextualize the results. Parents must accept additional analysis. The ethical arguments in these statements appear to be in tension with each other. (shrink)

The recent explosion of interest in epigenetics is often portrayed as the dawning of a scientific revolution that promises to transform biomedical science along with developmental and evolutionary biology. Much of this enthusiasm surrounds what we call the epigenetic switch hypothesis, which regards certain examples of epigenetic inheritance as an adaptive organismal response to environmental change. This interpretation overlooks an alternative explanation in terms of coevolutionary dynamics between parasitic transposons and the host genome. This raises a question about whether epigenetics (...) researchers tend to overlook transposon dynamics more generally. To address this question, we surveyed a large sample of scientific publications on the topics of epigenetics and transposons over the past fifty years. We found that enthusiasm for epigenetics is often inversely related to interest in transposon dynamics across the four disciplines we examined. Most surprising was a declining interest in transposons within biomedical science and cellular and molecular biology over the past two decades. Also notable was a delayed and relatively muted enthusiasm for epigenetics within evolutionary biology. An analysis of scientific abstracts from the past twenty-five years further reveals systematic differences among disciplines in their uses of the term epigenetic, especially with respect to heritability commitments and functional interpretations. Taken together, these results paint a nuanced picture of the rise of epigenetics and the possible neglect of transposon dynamics, especially among biomedical scientists. (shrink)

The American Journal of Bioethics, Volume 12, Issue 10, Page 24-26, October 2012.

Specker sequences are constructive, increasing, bounded sequences of rationals that do not converge to any constructive real. A sequence is said to be a strong Specker sequence if it is Specker and eventually bounded away from every constructive real. Within Bishop's constructive mathematics we investigate non-decreasing, bounded sequences of rationals that eventually avoid sets that are unions of sequences of intervals with rational endpoints. This yields surprisingly straightforward proofs of certain basic results fromconstructive mathematics. Within Russian constructivism, we show how (...) to use this general method to generate Specker sequences. Furthermore, we show that any nonvoid subset of the constructive reals that has no isolated points contains a strictly increasing sequence that is eventually bounded away from every constructive real. If every neighborhood of every point in the subset contains a rational number different from that point, the subset contains a strong Specker sequence. (shrink)

In 2013, the U.S. National Institutes of Health funded four large interdisciplinary research projects exploring the “implications, challenges and opportunities associated with the possible use of g...

Five recursively axiomatizable theories extending Kleene's intuitionistic theory FIM of numbers and numbertheoretic sequences are introduced and shown to be consistent, by a modified relative realizability interpretation which verifies that every sequence classically defined by a Π11 formula is unavoidable and that no sequence can fail to be classically Δ11. The analytical form of Markov's Principle fails under the interpretation. The notion of strongly inadmissible rule of inference is introduced, with examples.

The aim of this paper is to highlight an interdependence between procedural and agential norms that undermines their neat separation when appraising argumentation. Drawing on the munāẓara tradition, we carve a space for sequencing in argumentation scholarship. Focusing on the antagonist’s sequencing of critical moves, we identify each sequence’s corresponding values of argumentation: coalescence, reliability, and efficacy. These values arise through the mediation of virtues and simultaneously underpin procedural as well as agential norms. Consequently, an ambiguity between procedure (...) and agent becomes apparent. This ambiguity hints at the potential for a virtue theory of argumentation that draws on procedural norms. (shrink)

Running head: Implicit sequence learning ABSTRACT Can we learn without awareness? Although this issue has been extensively explored through studies of implicit learning, there is currently no agreement about the extent to which knowledge can be acquired and projected onto performance in an unconscious way. The controversy, like that surrounding implicit memory, seems to be at least in part attributable to unquestioned acceptance of the unrealistic assumption that tasks are process-pure, that is, that a given task exclusively involves either implicit (...) or explicit knowledge. (shrink)

ABSTRACT There are two tenets about free agency that have proven difficult to combine: free agency is grounded in an agent’s possession or exercise of their reasons-responsiveness, only actual sequence features can ground free agency. This paper argues that and can only be reconciled if we recognise that their clash is just the particular manifestation of a wider conflict between two approaches to the notion of non-accidentality. According to modalism, p is non-accidentally connected to q iff p modally tracks q. (...) According to explanationism, p is non-accidentally connected to q iff q explains p in the right way. The conflict between these two approaches becomes manifest in Frankfurt-like cases for many notions, in which p and q are intuitively non-accidentally connected even though there is no modal tracking between them. Thus, and can’t be combined because the Frankfurt-cases upon which rests track explanationist intuitions, while the non-accidentality requirement of reasons-responsiveness in is usually spelled out in modalist terms. Hence, the possibility of an actual sequence reasons-responsiveness account depends on finding an explanationist approach to the non-accidentality requirement of reasons-responsiveness. (shrink)

This paper studies the metric structure of the space Hr of absolutely summable sequences of real numbers with at most r nonzero terms. Hr is complete, and is located and nowhere dense in the space of all absolutely summable sequences. Totally bounded and compact subspaces of Hr are characterized, and large classes of located, totally bounded, compact, and locally compact subspaces are constructed. The methods used are constructive in the strict sense. MSC: 03F65, 54E50.

Sibley, Kello, Plaut, and Elman (2008) proposed the sequence encoder as a model that learns fixed‐width distributed representations of variable‐length sequences. In doing so, the sequence encoder overcomes problems that have restricted models of word reading and recognition to processing only monosyllabic words. Bowers and Davis (2009) recently claimed that the sequence encoder does not actually overcome the relevant problems, and hence it is not a useful component of large‐scale word‐reading models. In this reply, it is noted that the sequence (...) encoder has facilitated the creation of large‐scale word‐reading models. The reasons for this success are explained and stand as counterarguments to claims made by Bowers and Davis. (shrink)

We give an overview of the role of equicontinuity of sequences of real-valued functions on [0,1] and related notions in classical mathematics, intuitionistic mathematics, Bishop’s constructive mathematics, and Russian recursive mathematics. We then study the logical strength of theorems concerning these notions within the programme of Constructive Reverse Mathematics. It appears that many of these theorems, like a version of Ascoli’s Lemma, are equivalent to fan-theoretic principles.

Human language is a salient example of a neurocognitive system that is specialized to process complex dependencies between sensory events distributed in time, yet how this system evolved and specialized remains unclear. Artificial Grammar Learning (AGL) studies have generated a wealth of insights into how human adults and infants process different types of sequencing dependencies of varying complexity. The AGL paradigm has also been adopted to examine the sequence processing abilities of nonhuman animals. We critically evaluate this growing literature (...) in species ranging from mammals (primates and rats) to birds (pigeons, songbirds, and parrots) considering also cross‐species comparisons. The findings are contrasted with seminal studies in human infants that motivated the work in nonhuman animals. This synopsis identifies advances in knowledge and where uncertainty remains regarding the various strategies that nonhuman animals can adopt for processing sequencing dependencies. The paucity of evidence in the few species studied to date and the need for follow‐up experiments indicate that we do not yet understand the limits of animal sequence processing capacities and thereby the evolutionary pattern. This vibrant, yet still budding, field of research carries substantial promise for advancing knowledge on animal abilities, cognitive substrates, and language evolution. (shrink)

Studies of Y chromosome evolution often emphasize gene loss, but this loss has been counterbalanced by addition of new genes. The DAZ genes, which are critical to human spermatogenesis, were acquired by the Y chromosome in the ancestor of Old World monkeys and apes. We and our colleagues recently sequenced the rhesus macaque Y chromosome, and comparison of this sequence to human and chimpanzee enables us to reconstruct much of the evolutionary history of DAZ. We report that DAZ arrived on (...) the Y chromosome about 38 million years ago via the transposition of at least 1.1 megabases of autosomal DNA. This transposition also brought five additional genes to the Y chromosome, but all five genes were subsequently lost through mutation or deletion. As the only surviving gene, DAZ experienced extensive restructuring, including intragenic amplification and gene duplication, and has been the target of positive selection in the chimpanzee lineage.Editor's suggested further reading in BioEssays Should Y stay or should Y go: The evolution of non‐recombining sex chromosomes Abstract. (shrink)

We define DNA sequence by a bottom-up approach, starting with a real sequence from an actual biological sample. By providing axioms for notions of string, substring and strand, we formally define a DNA sequence, and a DNA molecule as composed of two antiparallel strands. We note that a sequence is a kind of group in which each member stands a certain relation to every other. The spatial aspects of a DNA sequence are also described.

Understanding how culture evolves in society is an extremely difficult task. The bifocal stance theory (BST) deploys two copying strategies which can be linked to dual-system theories of behavior. BST would benefit from incorporating results from these theories, such as the evolution of attention to goals or steps of a behavioral sequence, and the role of the environment in prompting different copying strategies.

We prove several results giving lower bounds for the large cardinal strength of a failure of the singular cardinal hypothesis. The main result is the following theorem: Theorem. Suppose κ is a singular strong limit cardinal and 2κ λ where λ is not the successor of a cardinal of cofinality at most κ. If cf > ω then it follows that o λ, and if cf = ωthen either o λ or {α: K o α+n} is confinal in κ for (...) each n ε ω.We also prove several results which extend or are related to this result, notably Theorem. If 2ω ω1 then there is a sharp for a model with a strong cardinal.In order to prove these theorems we give a detailed analysis of the sequences of indiscernibles which come from applying the covering lemma to nonoverlapping sequences of extenders. (shrink)

Genetic analysis of the signals within bacterial exported proteins have shown that the information required for proper localization is contained in both the amino‐terminal signal sequence and the mature protein. Several types of signal sequence mutations can be isolated, suggesting that the signal sequence may be involved in more than one step in the export process. Export information within the mature portion of the protein is present at several locations.

As linguistic competence so clearly illustrates, processing sequences of events is a fundamental aspect of human cognition. For this reason perhaps, sequence learning behavior currently attracts considerable attention in both cognitive psychology and computational theory. In typical sequence learning situations, participants are asked to react to each element of sequentially structured visual sequences of events. An important issue in this context is to determine whether essentially associative processes are sufficient to understand human performance, or whether more powerful learning mechanisms are (...) necessary. To address this issue, we explore how well human participants and connectionist models are capable of learning sequential material that involves complex, disjoint, longdistance contingencies. We show that the popular Simple Recurrent Network model (Elman, 1990), which has otherwise been shown to account for a variety of empirical findings (Cleeremans, 1993), fails to account for human performance in several experimental situations meant to test the model’s specific predictions. In previous research (Cleeremans, 1993) briefly described in this paper, the structure of center-embedded sequential structures was manipulated to be strictly identical or probabilistically different as a function of the elements surrounding the embedding. While the SRN could only learn in the second case, human subjects were found to be insensitive to the manipulation. In the new experiment described in this paper, we tested the idea that performance benefits from “starting small effects” (Elman, 1993) by contrasting two conditions in which the training regimen was either incremental or not. Again, while the SRN is only capable of learning in the first case, human subjects were able to learn in both. We suggest an alternative model based on Maskara & Noetzel’s (1991) Auto-Associative Recurrent Network as a way to overcome the SRN model’s failure to account for the empirical findings.. (shrink)

A model of gestural sequencing in speech is proposed that aspires to producing biologically plausible fluent and efficient movement in generating an utterance. We have previously proposed a modification of the well-known task dynamic implementation of articulatory phonology such that any given articulatory movement can be associated with a quantification of effort (Simko & Cummins, 2010). To this we add a quantitative cost that decreases as speech gestures become more precise, and hence intelligible, and a third cost component that (...) places a premium on the duration of an utterance. Together, these three cost elements allow us to derive algorithmically optimal sequences of gestures and dynamical parameters for generating articulator movement. We show that the optimized movement displays many timing characteristics that are representative of real speech movement, capturing subtle details of relative timing between gestures. Optimal movement sequences also display invariances in timing that suggest syllable-level coordination for CV sequences. We explore the behavior of the model as prosodic context is manipulated in two dimensions: clarity of articulation and speech rate. Smooth, fluid, and efficient movements result. (shrink)