Imperfect Copies Research Articles

Representation and computation in visual working memory.

The ability to sustain internal representations of the sensory environment beyond immediate perception is a fundamental requirement of cognitive processing. In recent years, debates regarding the capacity and fidelity of the working memory (WM) system have advanced our understanding of the nature of these representations. In particular, there is growing recognition that WM representations are not merely imperfect copies of a perceived object or event. New experimental tools have revealed that observers possess richer information about the uncertainty in their memories and take advantage of environmental regularities to use limited memory resources optimally. Meanwhile, computational models of visuospatial WM formulated at different levels of implementation have converged on common principles relating capacity to variability and uncertainty. Here we review recent research on human WM from a computational perspective, including the neural mechanisms that support it.

The analogy of computing

Abstract The digital machine is analogical by design: with it, we construct models of phenomena that by definition of that term are necessarily partial approximations. For that reason, we learn more by conceiving of them as analogues rather than imperfect copies. As the foofaraw over AI would make clear to anyone who bothered to separate its strange wheat from the common chaff, analogy is key to the digital engine’s intellectual power, whether for good or for ill. (The one we must further, the other oppose, but in both cases, understand as fully as we are able.) Analogy is itself a Proteus, however, surfacing in different forms in different disciplines where the machine has found its applications. In the following essay, I chase it through a number of fields before returning to computing, with two examples of its application. I end with a brief note on worldmaking, which after all is what it’s all about, at whatever scale.

Investigating Imperfect Cloning for Extending Quantum Communication Capabilities.

Quantum computing allows the implementation of powerful algorithms with enormous computing capabilities and promises a secure quantum Internet. Despite the advantages brought by quantum communication, certain communication paradigms are impossible or cannot be completely implemented due to the no-cloning theorem. Qubit retransmission for reliable communications and point-to-multipoint quantum communication (QP2MP) are among them. In this paper, we investigate whether a Universal Quantum Copying Machine (UQCM) generating imperfect copies of qubits can help. Specifically, we propose the Quantum Automatic Repeat Request (QARQ) protocol, which is based on its classical variant, as well as to perform QP2MP communication using imperfect clones. Note that the availability of these protocols might foster the development of new distributed quantum computing applications. As current quantum devices are noisy and they decohere qubits, we analyze these two protocols under the presence of various sources of noise. Three major quantum technologies are studied for these protocols: direct transmission (DT), teleportation (TP), and telecloning (TC). The Nitrogen-Vacancy (NV) center platform is used to create simulation models. Results show that TC outperforms TP and DT in terms of fidelity in both QARQ and QP2MP, although it is the most complex one in terms of quantum cost. A numerical study shows that the QARQ protocol significantly improves qubit recovery and that creating more clones does not always improve qubit recovery.

THE LENGTH AND THE STRUCTURE OF THE COPY TEXT OF SHEVCHENKO’S POEM “THE GREAT VAULT”

stands in Subotiv village...” to the text of Shevchenko’s poem “Th e Great Vault”. Stanislav Rosovetskyi provided a detailed criticism of this decision in his time, and his counterarguments are consistently considered in the paper. Most of them are refuted or questioned, false statements and inaccurate information are corrected.
 As a result, the following vision of the history of poem’s creation and circulation has been substantiated. In the early October 1845 in Myrhorod, Shevchenko completed the poem “The Great Vault”, the text of which still might not have had an epigraph and epilogue. Probably, a later copy that belonged to Ivan Lazarevskyi indirectly comes from this autograph. While in Maryinske the poet added an epigraph and on October 21 added the epilogue “There stands in Subotiv village...”, marking the date and place of creation. At that time, according to Olexandr Afanasiev-Chuzhbynskyi, whom the poet met in Lubny on October 25 and stayed with in Iskivtsi on October 25—27, the mystery play had no name. After returning to Kyiv, in approximately April — June 1846 Shevchenko rewrote “The Great Vault” along with other works from an unknown autograph to the manuscript collection “Three Years” in such a way that the epilogue of the poem could be mistaken for a separate work, as it was misunderstood by Vasyl Bilozerskyi who copied the mystery without the final fragment. Obviously, the same mistake was made by other copyists, who started the tradition of “Th e Great Vault” without the epilogue. When Shevchenko received an imperfect copy of I. Lazarevskyi, he had no choice but to edit only what it contained.
 Apparently, he did not object to the fact that in the copy of Lev Zhemchuzhnykov the final fragment was called “Subotiv”. It is suggested to increase the distance between the end of the third part of the poem and the beginning of the epilogue in the next academic edition, as well as to reproduce all the graphics of the poetic texts in editions closer to the autographs.

Functional Characterization of a Phf8 Processed Pseudogene in the Mouse Genome.

Most pseudogenes are generated when an RNA transcript is reverse-transcribed and integrated into the genome at a new location. Pseudogenes are often considered as an imperfect and silent copy of a functional gene because of the accumulation of numerous mutations in their sequence. Here we report the presence of Pfh8-ps, a Phf8 retrotransposed pseudogene in the mouse genome, which has no disruptions in its coding sequence. We show that this pseudogene is mainly transcribed in testis and can produce a PHF8-PS protein in vivo. As the PHF8-PS protein has a well-conserved JmjC domain, we characterized its enzymatic activity and show that PHF8-PS does not have the intrinsic capability to demethylate H3K9me2 in vitro compared to the parental PHF8 protein. Surprisingly, PHF8-PS does not localize in the nucleus like PHF8, but rather is mostly located at the cytoplasm. Finally, our proteomic analysis of PHF8-PS-associated proteins revealed that PHF8-PS interacts not only with mitochondrial proteins, but also with prefoldin subunits (PFDN proteins) that deliver unfolded proteins to the cytosolic chaperonin complex implicated in the folding of cytosolic proteins. Together, our findings highlighted PHF8-PS as a new pseudogene-derived protein with distinct molecular functions from PHF8.

Mediated Identifications

Mediated Identifications

False discovery rate control in genome-wide association studies with population structure

We present a comprehensive statistical framework to analyze data from genome-wide association studies of polygenic traits, producing interpretable findings while controlling the false discovery rate. In contrast with standard approaches, our method can leverage sophisticated multivariate algorithms but makes no parametric assumptions about the unknown relation between genotypes and phenotype. Instead, we recognize that genotypes can be considered as a random sample from an appropriate model, encapsulating our knowledge of genetic inheritance and human populations. This allows the generation of imperfect copies (knockoffs) of these variables that serve as ideal negative controls, correcting for linkage disequilibrium and accounting for unknown population structure, which may be due to diverse ancestries or familial relatedness. The validity and effectiveness of our method are demonstrated by extensive simulations and by applications to the UK Biobank data. These analyses confirm our method is powerful relative to state-of-the-art alternatives, while comparisons with other studies validate most of our discoveries. Finally, fast software is made available for researchers to analyze Biobank-scale datasets.

The Evidential Statistics of Genetic Assembly: Bootstrapping a Reference Sequence

The reference sequences play an essential role in genome assembly, like type specimens in taxonomy. Those references are also samples obtained at some time and location with a specific method. How can we evaluate or discriminate uncertainties of the reference itself and assembly methods? Here we bootstrapped 50 random read data sets from a small circular genome of aEscherichia colibacteriophage, phiX174, and tried to reconstruct the reference with 14 free assembly programs. Nine out of 14 assembly programs were capable of circular genome reconstruction. Unicycler correctly reconstructed the reference for 44 out of 50 data sets, but each reconstructed contig of the failed six data sets had minor defects. The other assembly software could reconstruct the reference with minor defects. The defect regions differed among the assembly programs, and the defect locations were far from randomly distributed in the reference genome. All contigs of Trinity included one, but Minia had two perfect copies other than an imperfect reference copy. The centroid of contigs for assembly programs except Unicycler differed from the reference with 75bases at most. Nonmetric multidimensional scaling (NMDS) plots of the centroids indicated that even the reference sequence was located slightly off from the estimated location of the true reference. We propose that the combination of bootstrapping a reference, making consensus contigs as centroids in an edit distance, and NMDS plotting will provide an evidential statistic way of genetic assembly for non-fragmented base sequences.

Novelty and imitation within the brain: a Darwinian neurodynamic approach to combinatorial problems

Efficient search in vast combinatorial spaces, such as those of possible action sequences, linguistic structures, or causal explanations, is an essential component of intelligence. Is there any computational domain that is flexible enough to provide solutions to such diverse problems and can be robustly implemented over neural substrates? Based on previous accounts, we propose that a Darwinian process, operating over sequential cycles of imperfect copying and selection of neural informational patterns, is a promising candidate. Here we implement imperfect information copying through one reservoir computing unit teaching another. Teacher and learner roles are assigned dynamically based on evaluation of the readout signal. We demonstrate that the emerging Darwinian population of readout activity patterns is capable of maintaining and continually improving upon existing solutions over rugged combinatorial reward landscapes. We also demonstrate the existence of a sharp error threshold, a neural noise level beyond which information accumulated by an evolutionary process cannot be maintained. We introduce a novel analysis method, neural phylogenies, that displays the unfolding of the neural-evolutionary process.

Ontology, archetypes and the definition of ‘mineral species’

AbstractOntologydeals with questions concerning what things exist, and how such things may be associated according to similarities and differences and related within a hierarchy. Ontology provides a rigorous way to develop a general definition of a mineral species. Properties may be divided into two principal groups: anintrinsic propertyis characteristic of the object and is independent of anything else; anextrinsic propertydepends on the relation between the object and other things. Auniversalis an entity that is common to all objects in a set. Here the objects are mineral samples, each entity is a specific property of these minerals, and the set of objects is all mineral samples of that mineral species. The key intrinsic properties of a mineral species are its name, its end-member formula andZ(the number of formula units in the unit cell), its space group and the bond topology of the end-member structure. These are also universals as they are common to all mineral samples belonging to that mineral species. An archetype is a pure form which embodies the fundamental characteristics of an object. Thus the archetype of a mineral species embodies the above set of universals. Real mineral samples of this mineral species are imperfect copies of that archetype, with a range of chemical composition defined by the boundaries between end-member formulae of this and other end members of the same bond topology. The result is a formal definition of a mineral species: A specific mineral species is the set of imperfect copies of the corresponding archetype and is defined by the following set of universals: name, end-member formula andZ, space group, and bond topology of the end-member structure, with the range of chemical composition limited by the compositional boundaries between end members with the same bond topology.

Contra Instrumentalism: A Translation Polemic

Contra Instrumentalism: A Translation Polemic

Chanchadas and intermediality

This audiovisual essay investigates the intermedial nature of Brazilian film comedies produced during the 1940s and 50s by exploring the musical numbers of Aviso aos navegantes (Calling All Sailors, Watson Macedo, 1950). Brazilian cinema of this period is a privileged arena of different media strategies. Its “mixed” style is informed by Hollywood cinema but also by the domestic influence of radio, Carnival, and by the local forms of comic staging of the teatro de revista (the Brazilian equivalent of music hall or vaudeville). Of particular interest in this regard are the chanchadas, a body of films made between the mid-1930s and the early 1960s, that presented musical performances intertwined with comic situations, slender narrative lines and strong connections with the world of Carnival. Our aim is to show how the relationships between the different forms of cultural production in 1950s Brazil can be identified in a specific chanchada, opening a dialogue between musical performances on stage, over the radio, at Carnival and on screen. The essay also examines similarities and differences between chanchadas and the Hollywood musical comedy tradition. One area explored is integration, both in the sense in which it is often used in film studies, to discuss the relationship between the numbers and the narrative, and in reflecting on whether the different elements which feed into the numbers of Aviso aos navegantes are seamlessly combined in the film. Despite the huge popular success of his films, Watson Macedo was considered by many as the most “Americanised” of the directors of that period, adhering less to the critical mechanisms of parody than was the case with his contemporaries. However, if we pay attention to Macedo’s musical numbers, it is evident that these performances are not imperfect copies of Hollywood originals, but have a logic of their own. This audiovisual essay complements Flávia Cesarino Costa’s other contribution to this issue of Alphaville, the article “Building an Integrated History of Musical Numbers in Brazilian Chanchadas”, by exploring related ideas in the context of a single film. As well as the interest of the video essay’s own exploration and argument, the pairing of essays—traditional and videographic—enables readers of this issue to pursue their thinking about chanchadas and intermediality with specific audiovisual material in front of them

"Ojos que no ven": Gendered Blindness in María de Zayas's Desengaños amorosos

Early modern medical discourse regarding gender and reproduction defined women as naturally inferior to men. Those who accepted Aristotle's theorization of male and female differentiation regarded the female body as an imperfect or monstrous copy of its male counterpart. This essay examines two novellas from María de Zayas's Desengaños amorosos (1647), in which Zayas confronts such patriarchal ideologies. Zayas's work has commonly been understood to challenge patriarchal norms that reinforced male dominance. This essay, however, offers a new interpretation of Zayas's resistance to misogyny by exploring her fifth and ninth desengaños through the critical discourse of disability studies. It argues that the literal blindness of Zayas's female protagonists in these stories combines with the metaphorical blindness of the men who determine women's roles within society in order to dismantle the logic upon which the social constraints placed on women were based. In these novellas, Zayas redefines the category of "monstrous" women as she rejects the idea of natural female impairment.

The Propedeutic of the Theory of Judgment in Ancient Philosophy from the Sophists to Plato’s Theaetetus

In the ancient epistemology, precisely stated definition of judgment (axioma) appears only in the 3rd century B.C. It was formulated by Chrysippus of Soli, the founder of the Stoic logic. However, on the other hand, the analysis of the extant utterances in which the knowledge had been objectified since the first Greek thinkers, allows us to state that the evolution of the theory of judgment was a long process. In this development, Greek epistemology had to deal with a number of problems connected with the object of the judgment –– knowledge, with the form of its objectification –– predication, and also with the predicates of the true and false judgment –– categories of “truth” (aletheia) and “falsehood” (pseudos). The first definition of the false judgement (logos pseudes) and the true judgment (logos alethes) can be found only in the late dialogue of Plato, Sophist, which delivers precisely established terminology of the theorem. Yet, such a definition could be formulated only when Greek epistemology re-defined the scope of the meaning of the key terms-concepts, aletheia and pseudos. The term-concept aletheia was identified with the term-concept being, functioning in the ontological-axiological sphere. On the other hand, pseudos did not mean false in the sense of negating the truth, but something, which is different than truth, is its imperfect copy. Thus, the pre-Platonic philosophy has not yet formulated the terminology in which predication of something inconsistent with the actual state of being, with the truth, could be verbalized. Often to express such a form of predication, a phrase “to utter things, which are not” was used. The other problem was connected with –– characteristic ofthe Greek language –– dual function of the verb to be/einai, which included both existential and truthful function. Accordingly, every utterance, in which the predicate was the verb einai or its derivates, was ex definitione a true predication –– “it spoke beings (things, which are).” In such a situation, there was noneed in epistemology to precisely define judgment as such, and to state the conditions which the true judgment hadto meet. The problem is definitely solved by Plato in his dialogue Theaetetus, in which the philosopher defines the object of the judgment, which is knowledge (however, its object is not stated yet) and introduces the project of verification of the utterances/opinion, thanks to which an opinion ––doxa can reach the status of judgment ––logos. An opinion needs to be verified with the dialectical procedures.

Multistate voter model with imperfect copying.

The voter model with multiple states has found applications in areas as diverse as population genetics, opinion formation, species competition, and language dynamics, among others. In a single step of the dynamics, an individual chosen at random copies the state of a random neighbor in the population. In this basic formulation, it is assumed that the copying is perfect, and thus an exact copy of an individual is generated at each time step. Here, we introduce and study a variant of the multistate voter model in mean field that incorporates a degree of imperfection or error in the copying process, which leaves the states of the two interacting individuals similar but not exactly equal. This dynamics can also be interpreted as a perfect copying with the addition of noise: a minimalistic model for flocking. We found that the ordering properties of this multistate noisy voter model, measured by a parameter ψ in [0,1], depend on the amplitude η of the copying error or noise and the population size N. In the case of perfect copying η=0, the system reaches an absorbing configuration with complete order (ψ=1) for all values of N. However, for any degree of imperfection η>0, we show that the average value of ψ at the stationary state decreases with N as 〈ψ〉≃6/(π^{2}η^{2}N) for η≪1 and η^{2}N≳1, and thus the system becomes totally disordered in the thermodynamic limit N→∞. We also show that 〈ψ〉≃1-π^{2}/6η^{2}N in the vanishing small error limit η→0, which implies that complete order is never achieved for η>0. These results are supported by Monte Carlo simulations of the model, which allow to study other scenarios as well.

Small Open Reading Frames, Non-Coding RNAs and Repetitive Elements in Bradyrhizobium japonicum USDA 110.

Small open reading frames (sORFs) and genes for non-coding RNAs are poorly investigated components of most genomes. Our analysis of 1391 ORFs recently annotated in the soybean symbiont Bradyrhizobium japonicum USDA 110 revealed that 78% of them contain less than 80 codons. Twenty-one of these sORFs are conserved in or outside Alphaproteobacteria and most of them are similar to genes found in transposable elements, in line with their broad distribution. Stabilizing selection was demonstrated for sORFs with proteomic evidence and bll1319_ISGA which is conserved at the nucleotide level in 16 alphaproteobacterial species, 79 species from other taxa and 49 other Proteobacteria. Further we used Northern blot hybridization to validate ten small RNAs (BjsR1 to BjsR10) belonging to new RNA families. We found that BjsR1 and BjsR3 have homologs outside the genus Bradyrhizobium, and BjsR5, BjsR6, BjsR7, and BjsR10 have up to four imperfect copies in Bradyrhizobium genomes. BjsR8, BjsR9, and BjsR10 are present exclusively in nodules, while the other sRNAs are also expressed in liquid cultures. We also found that the level of BjsR4 decreases after exposure to tellurite and iron, and this down-regulation contributes to survival under high iron conditions. Analysis of additional small RNAs overlapping with 3’-UTRs revealed two new repetitive elements named Br-REP1 and Br-REP2. These REP elements may play roles in the genomic plasticity and gene regulation and could be useful for strain identification by PCR-fingerprinting. Furthermore, we studied two potential toxin genes in the symbiotic island and confirmed toxicity of the yhaV homolog bll1687 but not of the newly annotated higB homolog blr0229_ISGA in E. coli. Finally, we revealed transcription interference resulting in an antisense RNA complementary to blr1853, a gene induced in symbiosis. The presented results expand our knowledge on sORFs, non-coding RNAs and repetitive elements in B. japonicum and related bacteria.

Imperfect mirror copies of the standard model

Inspired by the Standard Model of particle physics, we discuss a mechanism for constructing chiral, anomaly-free gauge theories. The gauge symmetries and particle content of such theories are identified using subgroups and complex representations of simple anomaly-free Lie groups, such as $SO(10)$ or $E_6$. We explore, using mostly $SO(10)$ and the $\mathbf{16}$ representation, several of these "imperfect copies" of the Standard Model, including $U(1)^N$ theories, $SU(5)\otimes U(1)$ theories, $SU(4)\otimes U(1)^2$ theories with 4-plets and 6-plets, and chiral $SU(3)\otimes SU(2)\otimes U(1)$. A few general properties of such theories are discussed, as well as how they might shed light on nonzero neutrino masses, the dark matter puzzle, and other phenomenologically relevant questions.

Extreme variation in patterns of tandem repeats in mitochondrial control region of yellow-browed tits (Sylviparus modestus, Paridae).

To investigate the evolutionary pattern and origins of tandem repeats in the mitochondrial control region of the yellow-browed tit (Sylviparus modestus), the control region and another four mitochondrial loci from fifteen individuals were analyzed. A 117-bp tandem repeat unit that repeated once, twice or three times in different individuals was found, and a rarely reported arrangement for this tandem repeats region that a 5′ imperfect copy at its downstream and a 3′ imperfect copy at its upstream was observed. The haplotype network, phylogenetic trees, and ancestral state reconstruction of the combined dataset of five loci suggested multiple origins of the same repeat number. The turnover model via slipped-strand mispairing was introduced to interpret the results, because mispairing occurred so frequently that multiple origins of certain repeat number were observed. Insertion via recombination should be a better explanation for the origin of this tandem repeat unit, considering characteristics of the combined sequence of the 3′ and 5′ imperfect copy, including identification of its homolog in other passerines and its predicted secondary structure.

Quantum Chernoff bound as a measure of the efficiency of quantum cloning for mixed states

In this paper we investigate the efficiency of quantum cloning of N identical mixed qubits. We employ a recently introduced measure of distinguishability of quantum states called the quantum Chernoff bound. We evaluate the quantum Chernoff bound between the output clones generated by the cloning machine and the initial mixed qubit state. Our analysis is illustrated by performing numerical calculation of the quantum Chernoff bound for different scenarios that involves the number of initial qubits N and the number of output imperfect copies M.

Field estimates of survival do not reflect ratings of mimetic similarity in wasp-mimicking hover flies

The evolution of mimicry, and particularly the persistence of undefended Batesian mimetic forms that are imperfect copies of their defended models, remains a central question in evolutionary biology. Previous work has demonstrated that variation in mimetic fidelity in artificial prey can alter survival. However, no studies have validated the assumption that detailed laboratory-based measurements of mimetic fidelity are actually reflected in survival in natural field experiments. Here, we demonstrate that, in line with previous studies, the mimetic similarity of 77 hover fly (Diptera: Syrphidae) species to the common wasp Vespula alascensis is strongly related to the number of abdominal stripes exhibited by the flies. We then produce three artificial pastry baits: (1) a “model” which is chemically defended and has two stripes, (2) a one-stripe mimic, and (3) an unstriped mimic. Based on the ratings study, we predicted that the one-stripe mimic would exhibit survival intermediate between the unstriped mimic and the model. Baits were deployed in experiments each involving 81 baits (27 of each kind), at 3 sites, with experiments replicated 10 times at each site for a total deployment of 2,430 baits. Proportional hazards models show that both one-striped and model baits survived equally well and significantly better than the unstriped baits, suggesting categorical prey identification rather than the use of stripe number as a continuous trait, as was suggested by the laboratory study. These findings suggest that, while humans and avian predators can distinguish mimics from models in the laboratory using a range of traits, behaviour in the field may not reflect this ability. This absence of a link between continuous measures of mimetic fidelity and prey selection may contribute to the maintenance of imperfect mimicry, but more studies using near-natural experimental paradigms are needed to investigate the phenomenon further.