Polite plurals and adjective agreement

When an agreement controller such as a subject NP is a hybrid of contrasting syntactic and semantic features, the choice of syntactic versus semantic agreement depends on both the type of agreement target and the type of agreement controller. Two types of controller are contrasted: hybrid pronouns such as polite uses of the second person plural to refer to one addressee; and hybrid common nouns such as plurale tante. In some languages the pronoun type triggers singular on a predicate adjective and plural on the verb, while the common noun type triggers plural on both adjectives and verbs. The former pattern is explained in terms of underspecification of the pronoun: it is unspecified for the Concord number feature, to which adjectives are sensitive; but it carries a number feature on its referential Index, to which finite verbs are sensitive. An Agreement Marking Principle is proposed, according to which an agreement target checks the trigger for a syntactic phi feature, assigning that feature’s semantic interpretation to the trigger denotation if no syntactic feature is found.     

Reduplication and repetition of person markers in Guaporé isolates

The person marking system of the language isolate Kwazá, spoken in the Brazilian Amazon, has several unusual properties. Its bound inflectional person suffixes can be reduplicated in order to express temporal and aspectual notions in a rather un-iconic way. The reduplicated segments are not defined by phonotactic boundaries, such as the syllable, but they are based on morphological units, disregarding their phonotactic structure. The origin and nature of this rare type of reduplication are not very clear. Morphologically based reduplication is not attested in the neighbouring languages with which Kwazá forms a linguistic area. However, Kwazá person markers are also involved in an unusual type of recursive construction that is encountered in the neighbouring languages, too. Recursive application of person markers occurs in Kwazá to express quoted speech in a transparent manner and has also given rise to less transparent expressions such as the desiderative. Similar constructions in the Aikanã and Wari’ languages suggest that this quotative construction is an areal feature of at least the Brazilian part of the Guaporé region. The quotative construction may help to understand the poorly understood phenomenon of seemingly redundant person marking in Kanoê, another language isolate of the region. It remains a question whether it also plays a role in the origin of the unique morphologically determined reduplication constructions of Kwazá.     

The expression of person and number: a typologist’s perspective

The categories of person and number have been analyzed extensively, both from a generative/structural perspective and from a typological/cross-linguistic perspective. The goal of both approaches is to account for the diversity of human languages, but in practice both have a rather different take on the subject. One major difference between these approaches is the relation between language-specific and cross-linguistic analyses. This paper argues that it is crucial to strictly distinguish between the two. However, this plea is at odds with the generative/structural perspective, which attempts to deal with both kinds of analyses at the same time. In contrast, it is of central importance from a typological/cross-linguistic perspective to keep the comparison constant across the wide variation as attested among human languages, thereby often ignoring many language-specific details (for the course of the comparison). The final section of this paper summarizes some major results of recent cross-linguistic comparisons of the person/number categories in the world’s languages.     

Defining ‘periphrasis’: key notions

We examine the notion of ??(inflectional) periphrasis?? within the framework of Canonical Typology, and argue that the canonical approach allows us to define a logically coherent notion of periphrasis. We propose a set of canonical criteria for inflectional morphology and a set of canonical criteria for functional syntax, that is, syntactic constructions which include functional elements and which express grammatical features. We argue that canonical periphrasis is exemplified in our theoretical space of possibilities whenever a cell in a (canonically morphological) inflectional paradigm (??feature intersection??) is expressed by a multiword construction which respects the canonical properties of functional syntax. We compare our canonically-based approach with the approach of other authors, notably, Ackerman & Stump (2004), who argue for three sufficient conditions for a construction to be regarded as periphrastic: feature intersection, non-compositionality and distributed exponence. We argue that non-compositionality and distributed exponence, while sometimes diagnostic of periphrasis on a language-particular basis, do not constitute canonical properties of periphrasis. We also examine crucial but neglected syntactic aspects of periphrastic constructions: recursion of periphrases and headedness of periphrastic constructions. The approach we propose allows us to distinguish between constructions in actual languages which approximate the ideal of canonical periphrasis to various degrees without committing us to a categorical distinction between periphrastic and non-periphrastic constructions. At the same time we can capture the intuition that there is in some languages a distinct identifiable set of multiword constructions whose principal role is to realize grammatical features.     

The intergenerational transmission of Australian Indigenous languages: why language maintenance programmes should be family-focused

By 2050, the majority of Australia’s surviving Indigenous languages are likely to become extinct. The intergenerational transmission of languages in which children acquire languages from their parents and grandparents is a key mechanism for reversing language shift, but many Australian children whose parents speak an Indigenous language do not speak that language. Using a unique, national survey of Australian Indigenous children, I identify factors associated with the successful intergenerational transmission of Indigenous languages within Aboriginal and Torres Strait Islander families. Results highlight the importance of parents’ language use. Although community-level characteristics account for some of the variance in successful language transmission, parents who use Indigenous languages at home, speak them as well as they speak English, and do not also speak a creole language are more likely to pass those languages onto their children.     

The Handicap Principle: how an erroneous hypothesis became a scientific principle

The most widely cited explanation for the evolution of reliable signals is Zahavi's so‐called Handicap Principle, which proposes that signals are honest because they are costly to produce. Here we provide a critical review of the Handicap Principle and its theoretical development. We explain why this idea is erroneous, and how it nevertheless became widely accepted as the leading explanation for honest signalling. In 1975, Zahavi proposed that elaborate secondary sexual characters impose ‘handicaps’ on male survival, not due to inadvertent signalling trade‐offs, but as a mechanism that functions to demonstrate males' genetic quality to potential mates. His handicap hypothesis received many criticisms, and in response, Zahavi clarified his hypothesis and explained that it assumes that signals are wasteful as well as costly, and that they evolve because wastefulness enforces honesty. He proposed that signals evolve under ‘signal selection’, a non‐Darwinian type of selection that favours waste rather than efficiency. He maintained that the handicap hypothesis provides a general principle to explain the evolution of all types of signalling systems, i.e. the Handicap Principle. In 1977, Zahavi proposed a second hypothesis for honest signalling, which received many different labels and interpretations, although it was assumed to be another example of handicap signalling. In 1990, Grafen published models that he claimed vindicated Zahavi's Handicap Principle. His conclusions were widely accepted and the Handicap Principle subsequently became the dominant paradigm for explaining the evolution of honest signalling in the biological and social sciences. Researchers have subsequently focused on testing predications of the Handicap Principle, such as measuring the absolute costs of honest signals (and using energetic and other proximate costs as proxies for fitness), but very few have attempted to test Grafen's models. We show that Grafen's models do not support the handicap hypothesis, although they do support Zahavi's second hypothesis, which proposes that males adjust their investment into the expression of their sexual signals according to their condition and ability to bear the costs (and risks to their survival). Rather than being wasteful over‐investments, honest signals evolve in this scenario because selection favours efficient and optimal investment into signal expression and minimizes signalling costs. This idea is very different from the handicap hypothesis, but it has been widely misinterpreted and equated to the Handicap Principle. Theoretical studies have since shown that signalling costs paid at the equilibrium are neither sufficient nor necessary to maintain signal honesty, and that honesty can evolve through differential benefits, as well as differential costs. There have been increasing criticisms of the Handicap Principle, but they have focused on the limitations of Grafen's model and overlooked the fact that it is not a handicap model. This model is better understood within a Darwinian framework of adaptive signalling trade‐offs, without the added burden and confusing logic of the Handicap Principle. There is no theoretical or empirical support for the Handicap Principle and the time is long overdue to usher this idea into an ‘honorable retirement’.     

Mimicry of food intake: the dynamic interplay between eating companions

Numerous studies have shown that people adjust their intake directly to that of their eating companions; they eat more when others eat more, and less when others inhibit intake. A potential explanation for this modeling effect is that both eating companions'' food intake becomes synchronized through processes of behavioral mimicry. No study, however, has tested whether behavioral mimicry can partially account for this modeling effect. To capture behavioral mimicry, real-time observations of dyads of young females having an evening meal were conducted. It was assessed whether mimicry depended on the time of the interaction and on the person who took the bite. A total of 70 young female dyads took part in the study, from which the total number of bites (N = 3,888) was used as unit of analyses. For each dyad, the total number of bites and the exact time at which each person took a bite were coded. Behavioral mimicry was operationalized as a bite taken within a fixed 5-second interval after the other person had taken a bite, whereas non-mimicked bites were defined as bites taken outside the 5-second interval. It was found that both women mimicked each other''s eating behavior. They were more likely to take a bite of their meal in congruence with their eating companion rather than eating at their own pace. This behavioral mimicry was found to be more prominent at the beginning than at the end of the interaction. This study suggests that behavioral mimicry may partially account for social modeling of food intake.     

Exploring rate variation among and within sites in a densely sampled tree: species level phylogenetics of north american tiger beetles (genus cicindela)

Species-level phylogenetic studies require fast-evolving nucleotide positions to resolve relationships among close relatives, but these sites may be highly homoplastic and perhaps uninformative or even misleading deeper in the tree. Here we describe a species-level analysis of tiger beetles in the genus Cicindela (Coleoptera: Cicindelidae) for 132 terminal taxa and 1897 nucleotide positions from three regions of mtDNA, comprising 75% coverage of species occurring in North America. Evenly weighted parsimony analysis recovered four major clades representing radiations confined to North and Central America. Relationships near the tips were well supported but signal was contradictory at deeper nodes. Two major categories (3rd positions and all others) can be distinguished in likelihood analysis of character variation, of which only the fast-changing 3rd position characters were affected by saturation. However, their downweighting under a variety of criteria did not improve the tree topology at basal nodes. There was weak conflict between 3rd and non-3rd position characters deep in the tree, but support levels declined towards the root for all categories, even on trees that were reconstructed from 3rd and non-3rd positions separately. Statistical analysis of parsimony-based character transitions along branches showed a largely homogeneous distribution of change along the root-to-tip axis. The comparison of character transitions among the four major portions of the tree revealed deviations from stochastic distribution for the non-3rd positions, but not for 3rd positions. Hence, variability of functionally constrained non-3rd positions differs between clades and may be dependent on the character states at other sites, consistent with the covarion model of molecular evolution. The results suggest that some properties of 3rd positions are less problematic for phylogenetic reconstruction than other categories despite their high total homoplasy. In densely sampled data sets of closely related species, the disadvantages of weighting schemes according to homoplasy levels outweigh the benefits, showing the difficulty of devising meaningful weighting schemes that are applicable universally throughout the tree.     

Prediction of β-turns in proteins by 1-4 and 2-3 correlation model

A 1–4 and 2–3 residue-correlation model is proposed to predict the β-turns in proteins. The average rate of correct prediction for the 455 β-turn tetrapeptides and 4018 non-β-turn tetrapeptides in the training data base is 80.1%, and that for the 223 β-turn tetrapeptides and 12562 non-β-turn tetrapeptides in the testing data base is 80.9%. Compared with the rates of correct prediction based on the residue-independent model reported previously, the quality of prediction is significantly improved by the new model, implying that the correlation effect between the 1st and the 4th residues and that between the 2nd and 3rd residues along a tetrapeptide are important for forming a β-turn in a protein during the process of its folding. © 1997 John Wiley & Sons, Inc. Biopoly 41: 673–702, 1997     

Genome structure described by formal languages

Nucleic acid sequences may be looked upon as words over the alphabet of nucleotides. Naturally occurring DNAs and RNAs form subsets of the set of all possible words. The use of formal languages is proposed to describe the structure of these subsets. Regular languages defined by finite automata are introduced to demonstrate the application of the concept on RNA-phages of group I. This approach permits a concise characterization of grammatical patterns in genetic information.     

From enclitic to prefix: diachrony of personal absolutive markers in Q’eqchi’

Q’eqchi’ (Mayan stock, K’ichean subgroup) is an ergative language; a finite verb form obligatorily carries information on the person and number of the absolutive participant, i.e., the unique argument of an intransitive verb or the direct object of a transitive one. The set of personal absolutive markers includes five morphemes; the third person singular has no overt marker. These morphemes in Modern Q’eqchi’ are prefixes in a finite verbal predication and enclitics in a non-finite predication. In a finite verb form, the place of an absolutive prefix is between the tense-aspect prefix and personal ergative prefix (in a transitive predication) or verb root (in an intransitive one). This paper argues that during Colonial Q’eqchi’ (used in the second half of the 16th century and slightly later) the general structure of a verbal complex was completely different, and all personal absolutive markers were in fact enclitics. They were enclitisized to tense-aspect morphemes that functioned syntactically as main predicates of a complex construction. Further diachronic change consolidated a verbal complex, conditioning the transition to affixation.     

Dynamic visuomotor transformation involved with remote flying of a plane utilizes the 'Mirror Neuron' system

Brain regions involved with processing dynamic visuomotor representational transformation are investigated using fMRI. The perceptual-motor task involved flying (or observing) a plane through a simulated Red Bull Air Race course in first person and third person chase perspective. The third person perspective is akin to remote operation of a vehicle. The ability for humans to remotely operate vehicles likely has its roots in neural processes related to imitation in which visuomotor transformation is necessary to interpret the action goals in an egocentric manner suitable for execution. In this experiment for 3(rd) person perspective the visuomotor transformation is dynamically changing in accordance to the orientation of the plane. It was predicted that 3(rd) person remote flying, over 1(st), would utilize brain regions composing the 'Mirror Neuron' system that is thought to be intimately involved with imitation for both execution and observation tasks. Consistent with this prediction differential brain activity was present for 3(rd) person over 1(st) person perspectives for both execution and observation tasks in left ventral premotor cortex, right dorsal premotor cortex, and inferior parietal lobule bilaterally (Mirror Neuron System) (Behaviorally: 1(st)>3(rd)). These regions additionally showed greater activity for flying (execution) over watching (observation) conditions. Even though visual and motor aspects of the tasks were controlled for, differential activity was also found in brain regions involved with tool use, motion perception, and body perspective including left cerebellum, temporo-occipital regions, lateral occipital cortex, medial temporal region, and extrastriate body area. This experiment successfully demonstrates that a complex perceptual motor real-world task can be utilized to investigate visuomotor processing. This approach (Aviation Cerebral Experimental Sciences ACES) focusing on direct application to lab and field is in contrast to standard methodology in which tasks and conditions are reduced to their simplest forms that are remote from daily life experience.     

The fallacy of the Principle of Procreative Beneficence

The claim that we have a moral obligation, where a choice can be made, to bring to birth the 'best' child possible, has been highly controversial for a number of decades. More recently Savulescu has labelled this claim the Principle of Procreative Beneficence. It has been argued that this Principle is problematic in both its reasoning and its implications, most notably in that it places lower moral value on the disabled. Relentless criticism of this proposed moral obligation, however, has been unable, thus far, to discredit this Principle convincingly and as a result its influence shows no sign of abating. I will argue that while criticisms of the implications and detail of the reasoning behind it are well founded, they are unlikely to produce an argument that will ultimately discredit the obligation that the Principle of Procreative Beneficence represents. I believe that what is needed finally and convincingly to reveal the fallacy of this Principle is a critique of its ultimate theoretical foundation, the notion of impersonal harm. In this paper I argue that while the notion of impersonal harm is intuitively very appealing, its plausibility is based entirely on this intuitive appeal and not on sound moral reasoning. I show that there is another plausible explanation for our intuitive response and I believe that this, in conjunction with the other theoretical criticisms that I and others have levelled at this Principle, shows that the Principle of Procreative Beneficence should be rejected.     

Parametric construction of episode networks from pseudoperiodic time series based on mutual information

Recently, the construction of networks from time series data has gained widespread interest. In this paper, we develop this area further by introducing a network construction procedure for pseudoperiodic time series. We call such networks episode networks, in which an episode corresponds to a temporal interval of a time series, and which defines a node in the network. Our model includes a number of features which distinguish it from current methods. First, the proposed construction procedure is a parametric model which allows it to adapt to the characteristics of the data; the length of an episode being the parameter. As a direct consequence, networks of minimal size containing the maximal information about the time series can be obtained. In this paper, we provide an algorithm to determine the optimal value of this parameter. Second, we employ estimates of mutual information values to define the connectivity structure among the nodes in the network to exploit efficiently the nonlinearities in the time series. Finally, we apply our method to data from electroencephalogram (EEG) experiments and demonstrate that the constructed episode networks capture discriminative information from the underlying time series that may be useful for diagnostic purposes.     

Acoustic correlates of individual features of functional and emotional states

General theoretic and applied studies on the effects of emotional and functional states on the acoustic parameters of human speech were analyzed. In most studies, the number of frequency, time, and power characteristics of vocalization were used as the most informative acoustic correlates of emotional and functional states. As a rule, sthenic states lead to the increase, and asthenic states induce the decrease in pitch, formant, and intensity. The relationship between acoustic parameters of speech and emotional and functional states was found, which depended on individual features of the subject and appeared as diverse changes in time and power parameters. For more accurate identification of psychoemotional state of an individual, the study of general tonal phonemes that are common and easily recognizable in different languages may be helpful. The research of acoustic correlates of individual speech parameters is a promising approach to diagnosis of functional and emotional states of a person using the vocalization parameters.     

MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments

Hi-C is a genome-wide chromosome conformation capture technology that detects interactions between pairs of genomic regions and exploits higher order chromatin structures. Conceptually Hi-C data counts interaction frequencies between every position in the genome and every other position. Biologically functional interactions are expected to occur more frequently than transient background and artefactual interactions. To identify biologically relevant interactions, several background models that take biases such as distance, GC content and mappability into account have been proposed. Here we introduce MaxHiC, a background correction tool that deals with these complex biases and robustly identifies statistically significant interactions in both Hi-C and capture Hi-C experiments. MaxHiC uses a negative binomial distribution model and a maximum likelihood technique to correct biases in both Hi-C and capture Hi-C libraries. We systematically benchmark MaxHiC against major Hi-C background correction tools including Hi-C significant interaction callers (SIC) and Hi-C loop callers using published Hi-C, capture Hi-C, and Micro-C datasets. Our results demonstrate that 1) Interacting regions identified by MaxHiC have significantly greater levels of overlap with known regulatory features (e.g. active chromatin histone marks, CTCF binding sites, DNase sensitivity) and also disease-associated genome-wide association SNPs than those identified by currently existing models, 2) the pairs of interacting regions are more likely to be linked by eQTL pairs and 3) more likely to link known regulatory features including known functional enhancer-promoter pairs validated by CRISPRi than any of the existing methods. We also demonstrate that interactions between different genomic region types have distinct distance distributions only revealed by MaxHiC. MaxHiC is publicly available as a python package for the analysis of Hi-C, capture Hi-C and Micro-C data.     

The origin of eukaryotes: a reappraisal

Ever since the elucidation of the main structural and functional features of eukaryotic cells and subsequent discovery of the endosymbiotic origin of mitochondria and plastids, two opposing hypotheses have been proposed to account for the origin of eukaryotic cells. One hypothesis postulates that the main features of these cells, including their ability to capture food by endocytosis and to digest it intracellularly, were developed first, and later had a key role in the adoption of endosymbionts; the other proposes that the transformation was triggered by an interaction between two typical prokaryotic cells, one of which became the host and the other the endosymbiont. Re-examination of this question in the light of cell-biological and phylogenetic data leads to the conclusion that the first model is more likely to be the correct one.     

On the skew distribution of immunoglobulins and the inverted protein-folding problem

The question of antibody specificity is discussed in the framework of the inverted protein-folding problem (i.e. the characterization of protein sequences with a common fold). A stochastic model of the immune response, patterned after a model for the distribution of words in natural languages is proposed. It is shown that the steady-state probability distribution of immunoglobulin variable-region frequencies is the Yule distribution.