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 show that the universally axiomatized, induction-free theory equation image is a sequential theory in the sense of Pudlák's 5, in contrast to the closely related Robinson's arithmetic.

Previous studies have found that P1 and P2 components were more sensitive to configural and featural face processing, respectively, when attentional resources were sufficient, suggesting that face processing follows a coarse-to-fine sequence. However, the role of working memory load in the time course of configural and featural face processing is poorly understood, especially whether it differs during encoding and retrieval stages. This study employed a delayed recognition task with varying WM load and face spatial frequency. Our behavioral and ERP (...) results showed that WM load modulated face SF processing. Specifically, for the encoding stage, P1 and P2 were more sensitive to broadband SF faces, while N170 was more sensitive to low SF and BSF faces. For the retrieval stage, P1 on the right hemisphere was more sensitive to BSF faces relative to HSF faces, N170 was more sensitive to LSF faces than HSF faces, especially under the load 1 condition, while P2 was more sensitive to high SF faces than HSF faces, especially under load 3 condition. These results indicate that faces are perceived less finely during the encoding stage, whereas face perception follows a coarse-to-fine sequence during the retrieval stage, which is influenced by WM load. The coarse and fine information were processed especially under the low and high load conditions, respectively. (shrink)

This paper examines a specific kind of part-whole relations that exist in the molecular genetic domain. The central question is under which conditions a particular molecule, such as a DNA sequence, is a biological part of the human genome. I address this question by analyzing how biologists in fact partition the human genome into parts. This paper thus presents a case study in the metaphysics of biological practice. I develop a metaphysical account of genomic parthood by analyzing the investigative (...) and reasoning practices in the ENCODE (ENCyclopedia Of DNA Elements) project. My account reveals two conditions that determine whether a molecule is a part of the human genome (i.e., a genomic part). First, genomic parts must possess a causal role function in the genome as a whole, that is, their functions must contribute to the genome directing the overall functioning of the cell. Second, genomic parts must have a specific chemical structure and be actual segments of the DNA sequence of the genome. (shrink)

Humans possess the ability to extract highly organized perceptual structures from sequences of temporal stimuli. For instance, we can organize specific rhythmical patterns into hierarchical, or metrical, systems. Despite the evidence of a fundamental influence of the motor system in achieving this skill, few studies have attempted to investigate the organization of our motor representation of rhythm. To this aim, we studied—in musicians and non-musicians—the ability to perceive and reproduce different rhythms. In a first experiment participants performed a temporal order-judgment (...) task, for rhythmical sequences presented via auditory or tactile modality. In a second experiment, they were asked to reproduce the same rhythmic sequences, while their tapping force and timing were recorded. We demonstrate that tapping force encodes the metrical aspect of the rhythm, and the strength of the coding correlates with the individual’s perceptual accuracy. We suggest that the similarity between perception and tapping-force organization indicates a common representation of rhythm, shared between the perceptual and motor systems. (shrink)

Recent investigations have revealed 1) that the isochores of the human genome group into two super‐families characterized by two different long‐range 3D structures, and 2) that these structures, essentially based on the distribution and topology of short sequences, mold primary chromatin domains (and define nucleosome binding). More specifically, GC‐poor, gene‐poor isochores are low‐heterogeneity sequences with oligo‐A spikes that mold the lamina‐associated domains (LADs), whereas GC‐rich, gene‐rich isochores are characterized by single or multiple GC peaks that mold the topologically associating domains (...) (TADs). The formation of these “primary TADs” may be followed by extrusion under the action of cohesin and CTCF. Finally, the genomic code, which is responsible for the pervasive encoding and molding of primary chromatin domains (LADs and primary TADs, namely the “gene spaces”/“spatial compartments”) resolves the longstanding problems of “non‐coding DNA,” “junk DNA,” and “selfish DNA” leading to a new vision of the genome as shaped by DNA sequences. (shrink)

More and more research on left ventricle quantification skips segmentation due to its requirement of large amounts of pixel-by-pixel labels. In this study, a framework is developed to directly quantify left ventricle multiple indices without the process of segmentation. At first, DenseNet is utilized to extract spatial features for each cardiac frame. Then, in order to take advantage of the time sequence information, the temporal feature for consecutive frames is encoded using gated recurrent unit. After that, the attention mechanism (...) is integrated into the decoder to effectively establish the mappings between the input sequence and corresponding output sequence. Simultaneously, a regression layer with the same decoder output is used to predict multi-indices of the left ventricle. Different weights are set for different types of indices based on experience, and l2-norm is used to avoid model overfitting. Compared with the state-of-the-art, our method can not only produce more competitive results but also be more flexible. This is because the prediction results in our study can be obtained for each frame online while the SOTA only can output results after all frames are analyzed. (shrink)

Although many studies have provided evidence that abstract knowledge can be acquired in artificial grammar learning, it remains unclear how abstract knowledge can be attained in sequence learning. To address this issue, we proposed a dual simple recurrent network model that includes a surface SRN encoding and predicting the surface properties of stimuli and an abstract SRN encoding and predicting the abstract properties of stimuli. The results of Simulations 1 and 2 showed that the DSRN model can account for (...) learning effects in the serial reaction time task under different conditions, and the manipulation of the contribution weight of each SRN accounted for the contribution of conscious and unconscious processes in inclusion and exclusion tests in previous studies. The results of human performance in Simulation 3 provided further evidence that people can implicitly learn both chunking and abstract knowledge in sequence learning, and the results of Simulation 3 confirmed that the DSRN model can account for how people implicitly acquire the two types of knowledge in sequence learning. These findings extend the learning ability of the SRN model and help understand how different types of knowledge can be acquired implicitly in sequence learning. (shrink)

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

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 forms of words as they appear in text and speech are central to theories and models of lexical processing. Nonetheless, current methods for simulating their learning and representation fail to approach the scale and heterogeneity of real wordform lexicons. A connectionist architecture termed thesequence encoderis used to learn nearly 75,000 wordform representations through exposure to strings of stress‐marked phonemes or letters. First, the mechanisms and efficacy of the sequence encoder are demonstrated and shown to overcome problems with (...) traditional slot‐based codes. Then, two large‐scale simulations are reported that learned to represent lexicons of either phonological or orthographic wordforms. In doing so, the models learned the statistics of their lexicons as shown by better processing of well‐formed pseudowords as opposed to ill‐formed (scrambled) pseudowords, and by accounting for variance in well‐formedness ratings. It is discussed how the sequence encoder may be integrated into broader models of lexical processing. (shrink)

The forms of words as they appear in text and speech are central to theories and models of lexical processing. Nonetheless, current methods for simulating their learning and representation fail to approach the scale and heterogeneity of real wordform lexicons. A connectionist architecture termed thesequence encoderis used to learn nearly 75,000 wordform representations through exposure to strings of stress‐marked phonemes or letters. First, the mechanisms and efficacy of the sequence encoder are demonstrated and shown to overcome problems with (...) traditional slot‐based codes. Then, two large‐scale simulations are reported that learned to represent lexicons of either phonological or orthographic wordforms. In doing so, the models learned the statistics of their lexicons as shown by better processing of well‐formed pseudowords as opposed to ill‐formed (scrambled) pseudowords, and by accounting for variance in well‐formedness ratings. It is discussed how the sequence encoder may be integrated into broader models of lexical processing. (shrink)

Sibley et al. (2008) report a recurrent neural network model designed to learn wordform representations suitable for written and spoken word identification. The authors claim that their sequence encoder network overcomes a key limitation associated with models that code letters by position (e.g., CAT might be coded as C‐in‐position‐1, A‐in‐position‐2, T‐in‐position‐3). The problem with coding letters by position (slot‐coding) is that it is difficult to generalize knowledge across positions; for example, the overlap between CAT and TOMCAT is lost. (...) Although we agree this is a critical problem with many slot‐coding schemes, we question whether the sequence encoder model addresses this limitation, and we highlight another deficiency of the model. We conclude that alternative theories are more promising. (shrink)

Three decades ago Gilbert posited that novel proteins arise by re‐shuffling genomic sequences encoding polypeptide domains. Today, with numerous genomes and countless genes sequenced, it is well established that recombination of sequences encoding polypeptide domains plays a major role in protein evolution. There is, however, less evidence to suggest how the novel polypeptide domains, themselves, arise. Recent comparisons of genomes from closely related species have revealed numerous species‐specific exons, supporting models of domain origin based on “exonization” of intron sequences. Also, (...) a mechanism for the origin of novel polypeptide domains has been proposed based on analyses of insertion‐based polymorphisms between orthologous genes across broad phylogenetic spectra and between allelic variants of genes within species. This review discusses these processes and how each might participate in the evolutionary emergence of novel polypeptide domains. BioEssays 29: 262–270, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

Poly(ADP‐ribosyl)ation is an immediate DNA‐damage‐dependent post‐translational modification of histones and other nuclear proteins that contributes to the survival of injured proliferating cells. Poly(ADP‐ribose) polymerases (PARPs) now constitute a large family of 18 proteins, encoded by different genes and displaying a conserved catalytic domain in which PARP‐1 (113 kDa), the founding member, and PARP‐2 (62 kDa) are so far the sole enzymes whose catalytic activity has been shown to be immediately stimulated by DNA strand breaks. A large repertoire of sequences encoding (...) novel PARPs now extends considerably the field of poly(ADP‐ribosyl)ation reactions to various aspects of the cell biology including cell proliferation and cell death. Some of these new members interact with each other, share common partners and common subcellular localizations suggesting possible fine tuning in the regulation of this post‐translational modification of proteins. This review summarizes our present knowledge of this emerging superfamily, which might ultimately improve pharmacological strategies to enhance both antitumor efficacy and the treatment of a number of inflammatory and neurodegenerative disorders. A provisional nomenclature is proposed. BioEssays 26:882–893, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

The c‐myc proto‐oncogene is believed to be involved in the regulation of cell growth and differentiation. Deregulation of this gene, resulting in an inappropriate increase of gene product, can contribute to cancer formation. One of the ways in which the expression of the c‐myc gene can be deregulated is by the stabilization of the labile c‐myc mRNA. The rapid degradation of the c‐myc transcript appears to be mediated by at least two distinct regions in the mRNA. One lies in the (...) 3' untranslated region, and presumably consists of (A+U)‐rich sequences. The other lies in the C‐terminal part of the coding region and colocalizes with sequences encoding protein‐dimerization motifs. The exact mechanism by which the destabilizing elements function is not yet clear. Shortening of the poly(A) tail of the c‐myc message appears to precede degradation of the transcript. When translation is blocked, this shortening is slowed down and the mRNA is stabilized. This suggests that deadenylation is required before degradation of the mRNA body can take place. (shrink)

Retroviruses encode a small, basic nucleocapsid (NC) protein that is found complexed to genomic RNA within the viral particle. The NC protein appears to function not only in a histone‐like manner in packaging the RNA into the particle but also in specifically selecting the viral genomic RNA for packaging. A cysteine‐histidine (cys‐his) region, usually composed of 14 amino acids and reminiscent of the ‘zinc fingers’ of transcription factors, is the only highly conserved sequence element among the retroviral NC proteins. (...) This review discusses the biochemical properties of NC, and its possible role(s) in retroviral replication. We also speculate on how the biochemical properties may relate to its function in RNA recognition and packaging. (shrink)

Rhythmic structure in speech is characterized by sequences of stressed and unstressed syllables. A large body of literature suggests that speakers of English attempt to achieve rhythmic harmony by evenly distributing stressed syllables throughout prosodic phrases. The question remains as to how speakers plan metrical structure during speech production and whether it is planned independently of phonemes. To examine this, we designed a tongue twister task consisting of disyllabic word pairs with overlapping phonological segments and either matching or non‐matching metrical (...) structure. Results showed that speakers had more difficulty producing metrically regular word pairs, compared to irregular pairs; that is, word pairs with irregular meter had faster productions and fewer speech errors in this production task. This finding of metrical regularity inhibiting production is inconsistent with an abstract metrical structure that is planned independently of phonemes at the point of phonological encoding. (shrink)

Eukaryotic mRNAs are monocistronic, and therefore mechanisms exist that coordinate the synthesis of multiprotein complexes in order to obtain proper stoichiometry at the appropriate intracellular locations. RNA‐binding proteins containing low‐complexity sequences are prone to generate liquid droplets via liquid‐liquid phase separation, and in this way create cytoplasmic assemblages of functionally related mRNAs. In a recent iCLIP study, we showed that the Drosophila RNA‐binding protein Imp, which exhibits a C‐terminal low‐complexity sequence, increases the formation of F‐actin by binding to 3′ (...) untranslated regions of mRNAs encoding components participating in F‐actin biogenesis. We hypothesize that phase transition is a mechanism the cell employs to increase the local mRNA concentration considerably, and in this way synchronize protein production in cytoplasmic territories, as discussed in the present review. (shrink)

Learning the structure of event sequences is a ubiquitous problem in cognition and particularly in language. One possible solution is to learn a probabilistic generative model of sequences that allows making predictions about upcoming events. Though appealing from a neurobiological standpoint, this approach is typically not pursued in connectionist modeling. Here, we investigated a sequential version of the restricted Boltzmann machine, a stochastic recurrent neural network that extracts high-order structure from sensory data through unsupervised generative learning and can encode contextual (...) information in the form of internal, distributed representations. We assessed whether this type of network can extract the orthographic structure of English monosyllables by learning a generative model of the letter sequences forming a word training corpus. We show that the network learned an accurate probabilistic model of English graphotactics, which can be used to make predictions about the letter following a given context as well as to autonomously generate high-quality pseudowords. The model was compared to an extended version of simple recurrent networks, augmented with a stochastic process that allows autonomous generation of sequences, and to non-connectionist probabilistic models. We conclude that sequential RBMs and stochastic simple recurrent networks are promising candidates for modeling cognition in the temporal domain. (shrink)

The tower number ${\mathfrak t}$ and the ultrafilter number $\mathfrak {u}$ are cardinal characteristics from set theory. They are based on combinatorial properties of classes of subsets of $\omega $ and the almost inclusion relation $\subseteq ^*$ between such subsets. We consider analogs of these cardinal characteristics in computability theory.We say that a sequence $(G_n)_{n \in {\mathbb N}}$ of computable sets is a tower if $G_0 = {\mathbb N}$, $G_{n+1} \subseteq ^* G_n$, and $G_n\smallsetminus G_{n+1}$ is infinite for each (...) n. A tower is maximal if there is no infinite computable set contained in all $G_n$. A tower ${\left \langle {G_n}\right \rangle }_{n\in \omega }$ is an ultrafilter base if for each computable R, there is n such that $G_n \subseteq ^* R$ or $G_n \subseteq ^* \overline R$ ; this property implies maximality of the tower. A sequence $(G_n)_{n \in {\mathbb N}}$ of sets can be encoded as the “columns” of a set $G\subseteq \mathbb N$. Our analogs of ${\mathfrak t}$ and ${\mathfrak u}$ are the mass problems of sets encoding maximal towers, and of sets encoding towers that are ultrafilter bases, respectively. The relative position of a cardinal characteristic broadly corresponds to the relative computational complexity of the mass problem. We use Medvedev reducibility to formalize relative computational complexity, and thus to compare such mass problems to known ones.We show that the mass problem of ultrafilter bases is equivalent to the mass problem of computing a function that dominates all computable functions, and hence, by Martin’s characterization, it captures highness. On the other hand, the mass problem for maximal towers is below the mass problem of computing a non-low set. We also show that some, but not all, noncomputable low sets compute maximal towers: Every noncomputable (low) c.e. set computes a maximal tower but no 1-generic $\Delta ^0_2$ -set does so.We finally consider the mass problems of maximal almost disjoint, and of maximal independent families. We show that they are Medvedev equivalent to maximal towers, and to ultrafilter bases, respectively. (shrink)

This paper considers whether the available evidence from archeology, biological anthropology, primatology, and comparative gene-sequencing, can test evolutionary game theory models of cooperation as historical hypotheses about the actual course of human prehistory. The examination proceeds on the assumption that cooperation is the product of cultural selection and is not a genetically encoded trait. Nevertheless, we conclude that gene sequence data may yet shed signi cant light on the evolution of cooperation.

Prior to the genomic sequencing era, the bible for those working in clinical genetics was McKusick’s Mendelian Inheritance in Man, which appeared in multiple editions between the 1960s and the late 1990s. This catalogue was organized according to general patterns of inheritance and focused on phenotypes. Beginning in the mid-1980s, it was replaced by Online Mendelian Inheritance in Man, a continuously updated catalogue documenting molecular relationships between genetic variation and phenotypic expression. This paper explores this resource’s evolution with attention to (...) how disease is distinguished from clinically irrelevant variation and how phenotypic similarities are captured in cases where there is no obvious genotypic association. It is argued that hybrid compromises are encoded into OMIM®; in addition to serving its key original purpose of being a diagnostic catalogue, it also began to record detectable variations in the genome even if they were not known to be associated with phenotypically visible disorders or even phenotypic variations. Although the impacts of geneticization have been well recognized, particularly in popular media, this example allows exploration of some of the historic, epistemic, and methodological causes that underlie tendencies toward disease geneticization in contemporary medicine, while highlighting that such gene-focused strategies may in fact be warranted in some contexts. (shrink)

Plant MADS‐box genes encode transcriptional regulators that are critical for a number of developmental processes. In the angiosperms (the flowering plants), these include the specification of floral organ identities, flowering time and fruit development. It appears that the MADS box gene family has undergone considerable gene duplication and sequence divergence within the angiosperms. Here I discuss the possibility that these events have allowed the recruitment of these genes to new developmental pathways in particular angiosperm lineages. Recent analyses of (...) class='Hi'>sequence changes, expression patterns and, in a few cases, gene function are beginning to provide tantalizing evidence for deciphering when and how such genetic diversification has led to particular morphological innovations. In the future, comparative studies of large numbers of species will be required to assess the extent of such variation as well as to fully understand the mechanisms by which evolution of these developmental regulators has played a role in shaping new morphologies. BioEssays 25:637–646, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

In eukaryotic cells intron sequences are usually spliced out with a high degree of precision from heterogenous nuclear RNA (hnRNA) to give functional mRNA with exons in their right order. Provided with the right substrates, cell extracts can achieve the same. With exotic substrates, on the other hand, the same extracts can cut exons from one RNA and join them to exons from another RNA, a process termed trans‐splicing. In vivo, RNA trans‐splicing could lead to faulty, but also to novel (...) proteins and, through reverse transcription, to genomic rearrangements. So far, in living cells trans‐splicing has only been invoked to occur in trypanosomes. In these unicellular organisms most if not all mRNAs are made discontinuously, so that the mature mRNAs carry, at their 5′ end, a common 35‐nucleotide sequence, called a miniexon, encoded separately in the genome. The miniexon is most likely joined to the body of the mRNA by trans‐splicing. (shrink)

Given a sequence of sets An⊆{0,…,n−1}, the Furstenberg correspondence principle provides a shift-invariant measure on2N that encodes combinatorial information about infinitely many of the An's. Here it is shown that this process can be inverted, so that for any such measure, ergodic or not, there are finite sets whose combinatorial properties approximate it arbitarily well. The finite approximations are obtained from the measure by an explicit construction, with an explicit upper bound on how large n has to be to (...) yield a sufficiently good approximation. We draw conclusions for computable measure theory, and show, in particular, that given any computable shift-invariant measure on 2N, there is a computable element of 2N that is generic for the measure. We also consider a generalization of the correspondence principle to countable discrete amenable groups, and once again provide an effective inverse. (shrink)

The gelsolin gene family encodes a number of higher eukaryotic actin-binding proteins that are thought to function in the cytoplasm by severing, capping, nucleating or bundling actin filaments. Recent evidence, however, suggests that several members of the gelsolin family may have adopted unexpected nuclear functions including a role in regulating transcription. In particular, flightless I, supervillin and gelsolin itself have roles as coactivators for nuclear receptors, despite the fact that their divergence appears to predate the evolutionary appearance of nuclear receptors. (...) Flightless I has been shown to bind both actin and the actin-related BAF53a protein, which are subunits of SWI/SNF-like chromatin remodelling complexes. The primary sequences of some actin-related proteins such as BAF53a exhibit conservation of residues that, in actin itself, are known to interact with gelsolin-related proteins. In summary, there is a growing body of evidence supporting a biological role in the nucleus for actin, Arps and actin-binding proteins and, in particular, the gelsolin family of actin-binding proteins. (c) 2005 Wiley Periodicals, Inc. (shrink)

The expression of protein‐encoding genes is a complex process culminating in the production of mature mRNA and its translation by the ribosomes. The production of a mature mRNA involves an intricate series of processing steps. The majority of eukaryotic protein‐encoding genes contain intron sequences that disrupt the protein‐encoding frame, and hence have to be removed from immature mRNA prior to translation into protein. The mechanism involved in the selection of correct splice sites is incompletely understood. A considerable body of evidence (...) suggests that the splicing machinery has suboptimal efficiency and fidelity leading to substantial processing inaccuracy. Here we discuss a recently published article1 that extends observations that cells rely on nonsense‐mediated mRNA decay (NMD) to compensate for such suboptimal processing accuracy. Intriguingly these authors provide evidence for a strong selective pressure in favour of premature termination of mRNA translation in the event of intron retention. The analysis presented implies a positive role of NMD in transcript diversification through alternative splicing and suggest that this ancient surveillance mechanism may have co‐evolved with intron acquisition born from the need for quality control of splicing patterns. BioEssays 30:926–928, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

The vav proto‐oncogene encodes a 95 kDa protein which is expressed exclusively in hematopoietic cells. Analysis of the deduced amino acid sequence has revealed the presence of a src‐homology 2 (SH2) domain, 2 SH3 domains, a cysteine‐rich region with similarity to protein kinase C, and a region highly similar to proteins with guanine nucleotide exchange activity on ras‐like GTPases. Recent work has shown that vav is tyrosine phosphorylated in response to stimulation of surface membrane receptors in a variety of (...) hematopoietic cell lines. Vav may play a role in hematopoietic cell signaling by coupling tyrosine kinase pathways to ras‐like GTPases through the regulation of guanine nucleotide exchange. (shrink)

Biologists rely heavily on the language of information, coding, and transmission that is commonplace in the field of information theory developed by Claude Shannon, but there is open debate about whether such language is anything more than facile metaphor. Philosophers of biology have argued that when biologists talk about information in genes and in evolution, they are not talking about the sort of information that Shannon’s theory addresses. First, philosophers have suggested that Shannon’s theory is only useful for developing a (...) shallow notion of correlation, the so-called causal sense of information. Second, they typically argue that in genetics and evolutionary biology, information language is used in a semantic sense, whereas semantics are deliberately omitted from Shannon’s theory. Neither critique is well-founded. Here we propose an alternative to the causal and semantic senses of information: a transmission sense of information, in which an object X conveys information if the function of X is to reduce, by virtue of its sequence properties, uncertainty on the part of an agent who observes X. The transmission sense not only captures much of what biologists intend when they talk about information in genes, but also brings Shannon’s theory back to the fore. By taking the viewpoint of a communications engineer and focusing on the decision problem of how information is to be packaged for transport, this approach resolves several problems that have plagued the information concept in biology, and highlights a number of important features of the way that information is encoded, stored, and transmitted as genetic sequence. (shrink)

A representation is a remnant of previous experience that allows that experience to affect later behavior. This paper develops a metatheoretical view of representation and applies it to issues concerning representation in animals. To describe a representational system one must specify the following: thedomainor range of situations in the represented world to which the system applies; thecontentor set of features encoded and preserved by the system; thecodeor transformational rules relating features of the representation to the corresponding features of the represented (...) world; themedium, or the representation's physical instantiation; and thedynamics, or how the system changes with time. In part because of the behaviorist assumption that the hypothetical, covert changes occurring in an organism during learning correspond to the overt physical changes that are observed, issues of representation in animal behavior have been largely ignored as irrelevant or misleading. However, it can be inferred that representations, acting as models of environmental regularities, operate at many levels of behavioral functioning, both cognitive and noncognitive. Objections to the use of this concept in explanations of animal behavior, based on the claim that it is indeterminate and on behaviorist considerations of parsimony, can be answered. Animal representations may be specialized in terms of tasks and species. Data from tasks involving spatial memory, delayed matching-to-sample, and sequence learning suggest some foundations for a general theory of animal representations. (shrink)

This chapter offers a review of standard views about the requirements for natural selection to shape evolution and for the sorts of ‘units’ on which selection might operate. It then summarizes traditional arguments for genic selectionism, i.e., the view that selection operates primarily on genes (e.g., those of G. C. Williams, Richard Dawkins, and David Hull) and traditional counterarguments (e.g., those of William Wimsatt, Richard Lewontin, and Elliott Sober, and a diffuse group based on life history strategies). It then offers (...) a series of responses to the arguments, based on more contemporary considerations from molecular genetics, offered by Carmen Sapienza. A key issue raised by Sapienza concerns the degree to which a small number of genes might be able to control much of the variation relevant to selection operating on such selectively critical organs as hearts. The response to these arguments suggests that selection acts on many levels at once and that sporadic selection, acting with strong effects, can act successively on different key traits (and genes) while maintaining a balance among many potentially conflicting demands faced by organisms within an evolving lineage. (shrink)

The traditional verbal/nonverbal dichotomy is inadequate for completely describing cerebral lateralization. Musical functions are not necessarily mediated by the right hemisphere; evidence for a specialist left-hemisphere mechanism dedicated to the encoded speech signal is weakening, and the right hemisphere possesses considerable comprehensional powers. Right-hemisphere processing is often said to be characterized by holistic or gestalt apprehension, and face recognition may be mediated by this hemisphere partly because of these powers, partly because of the right hemisphere's involvement in emotional affect, and (...) possibly through the hypothesized existence of a specialist face processor or processors in the right. The latter hypothesis may, however, suffer the same fate as the one relating to a specialist encodedness processor for speech in the left. Verbal processing is largely the province of the left because of this hemisphere's possession of sequential, analytic, time-dependent mechanisms. Other distinctions are special cases of an analytic/holistic dichotomy. More fundamentally, however, the left hemisphere is characterized by its mediation of discriminations involving duration, temporal order, sequencing, and rhythm, at thesensory level, and especially at themotorlevel. Spatial aspects characterize the right, the mapping of exteroceptive body space, and the positions of fingers, limbs, and perhaps articulators, with respect to actual and target positions. Thus there is a continuum of function between the hemispheres, rather than a rigid dichotomy, the differences being quantitative rather than qualitative, of degree rather than of kind. (shrink)

A number of ways of taxonomizing human learning have been proposed. We examine the evidence for one such proposal, namely, that there exist independent explicit and implicit learning systems. This combines two further distinctions, (1) between learning that takes place with versus without concurrent awareness, and (2) between learning that involves the encoding of instances (or fragments) versus the induction of abstract rules or hypotheses. Implicit learning is assumed to involve unconscious rule learning. We examine the evidence for implicit learning (...) derived from subliminal learning, conditioning, artificial grammar learning, instrumental learning, and reaction times in sequence learning. We conclude that unconscious learning has not been satisfactorily established in any of these areas. The assumption that learning in some of these tasks (e.g., artificial grammar learning) is predominantly based on rule abstraction is questionable. When subjects cannot report the rules that govern stimulus selection, this is often because their knowledge consists of instances or fragments of the training stimuli rather than rules. In contrast to the distinction between conscious and unconscious learning, the distinction between instance and rule learning is a sound and meaningful way of taxonomizing human learning. We discuss various computational models of these two forms of learning. (shrink)

A number of ways of taxonomizing human learning have been proposed. We examine the evidence for one such proposal, namely, that there exist independent explicit and implicit learning systems. This combines two further distinctions, between learning that takes place with versus without concurrent awareness, and between learning that involves the encoding of instances versus the induction of abstract rules or hypotheses. Implicit learning is assumed to involve unconscious rule learning. We examine the evidence for implicit learning derived from subliminal learning, (...) conditioning, artificial grammar learning, instrumental learning, and reaction times in sequence learning. We conclude that unconscious learning has not been satisfactorily established in any of these areas. The assumption that learning in some of these tasks is predominantly based on rule abstraction is questionable. When subjects cannot report the “implicitly learned” rules that govern stimulus selection, this is often because their knowledge consists of instances or fragments of the training stimuli rather than rules. In contrast to the distinction between conscious and unconscious learning, the distinction between instance and rule learning is a sound and meaningful way of taxonomizing human learning. We discuss various computational models of these two forms of learning. (shrink)

How should a machine intelligence perform unsupervised structure discovery over streams of sensory input? One approach to this problem is to cast it as an apperception task [1]. Here, the task is to construct an explicit interpretable theory that both explains the sensory sequence and also satisfies a set of unity conditions, designed to ensure that the constituents of the theory are connected in a relational structure. However, the original formulation of the apperception task had one fundamental limitation: it (...) assumed the raw sensory input had already been parsed using a set of discrete categories, so that all the system had to do was receive this already-digested symbolic input, and make sense of it. But what if we don't have access to pre-parsed input? What if our sensory sequence is raw unprocessed information? The central contribution of this paper is a neuro-symbolic framework for distilling interpretable theories out of streams of raw, unprocessed sensory experience. First, we extend the definition of the apperception task to include ambiguous (but still symbolic) input: sequences of sets of disjunctions. Next, we use a neural network to map raw sensory input to disjunctive input. Our binary neural network is encoded as a logic program, so the weights of the network and the rules of the theory can be solved jointly as a single SAT problem. This way, we are able to jointly learn how to perceive (mapping raw sensory information to concepts) and apperceive (combining concepts into declarative rules). (shrink)

To explore the question of physical thinking – using the body as an instrument of cognition – we collected extensive video and interview data on the creative process of a noted choreographer and his company as they made a new dance. A striking case of physical thinking is found in the phenomenon of marking. Marking refers to dancing a phrase in a less than complete manner. Dancers mark to save energy. But they also mark to explore the tempo of a (...) phrase, or its movement sequence, or the intention behind it. Because of its representational nature, marking can serve as a vehicle for thought. Importantly, this vehicle is less complex than the version of the same phrase danced ‘full-out’. After providing evidence for distinguishing different types of marking, three ways of understanding marking as a form of thought are considered: marking as a gestural language for encoding aspects of a target movement, marking as a method of priming neural systems involved in the target movement, and marking as a method for improving the precision of mentally projecting aspects of the target. (shrink)

In this paper we propose an extension of Defeasible Logic to represent and compute different concepts of defeasible permission. In particular, we discuss some types of explicit permissive norms that work as exceptions to opposite obligations or encode permissive rights. Moreover, we show how strong permissions can be represented both with, and without introducing a new consequence relation for inferring conclusions from explicit permissive norms. Finally, we illustrate how a preference operator applicable to contrary-to-duty obligations can be combined with a (...) new operator representing ordered sequences of strong permissions. The logical system is studied from a computational standpoint and is shown to have linear computational complexity. (shrink)

Classical mutations at the mouse Brachyury (T) locus were discovered because they lead to shortened tails in heterozygous newborns. no tail (ntl) mutants in the zebrafish, as their name suggests, show a similar phenotype. In Drosophila, mutants in the brachyenteron (byn) gene disrupt hindgut formation. These genes all encode T-box proteins, a class of sequence-specific DNA binding proteins and transcription factors. Mutations in the C. elegans mab-9 gene cause massive defects in the male tail because of failed fate decisions (...) in two tail progenitor cells. In a recent paper, Woollard and Hodgkin1 have cloned the mab-9 gene and found that it too encodes a T-box protein, similar to Brachyury in vertebrates and brachyenteron in Drosophila. The authors suggest that their results support models for an evolutionarily ancient role for these genes in hindgut formation. We will discuss this proposal and try to decide whether the gene sequences, gene interactions and gene expression patterns allow any conclusions to be made about the rear end of the ancestral metazoan. BioEssays 22:781–785, 2000. © 2000 John Wiley & Sons, Inc. (shrink)

The standard representation of the Central Dogma (CD) of Molecular Biology conspicuously ignores metabolism. However, both the metabolites and the biochemical fluxes behind any biological phenomenon are encrypted in the DNA sequence. Metabolism constrains and even changes the information flow when the DNA‐encoded instructions conflict with the homeostasis of the biochemical network. Inspection of adaptive virulence programs and emergence of xenobiotic‐biodegradation pathways in environmental bacteria suggest that their main evolutionary drive is the expansion of their metabolic networks towards new (...) chemical landscapes rather than perpetuation and spreading of their DNA sequences. Faulty enzymatic reactions on suboptimal substrates often produce reactive oxygen species (ROS), a process that fosters DNA diversification and ultimately couples catabolism of the new chemicals to growth. All this calls for a revision of the CD in which metabolism (rather than DNA) has the leading role. (shrink)

Thomas Kuhn described the progress of science as comprising occasional paradigm shifts separated by interludes of ‘normal science’. The paradigm that has held sway since the inception of molecular biology is that genes (mainly) encode proteins. In parallel, theoreticians posited that mutation is random, inferred that most of the genome in complex organisms is non‐functional, and asserted that somatic information is not communicated to the germline. However, many anomalies appeared, particularly in plants and animals: the strange genetic phenomena of paramutation (...) and transvection; introns; repetitive sequences; a complex epigenome; lack of scaling of (protein‐coding) genes and increase in ‘noncoding’ sequences with developmental complexity; genetic loci termed ‘enhancers’ that control spatiotemporal gene expression patterns during development; and a plethora of ‘intergenic’, overlapping, antisense and intronic transcripts. These observations suggest that the original conception of genetic information was deficient and that most genes in complex organisms specify regulatory RNAs, some of which convey intergenerational information. Also see the video abstract here: https://youtu.be/qxeGwahBANw. (shrink)

Do children’s single words related to motion and change also encode aspects of environmental events highlighted by Talmy’s motion event analysis? If so, these meanings may predict children’s early verb meanings. Analyzing the kinds of meanings expressed in single “dynamic event words” through motion event semantics yields links between early true verbs in sentences and the semantics encoded in these single words. Dynamic event words reflect the sense of temporal and spatial reversibility established in the late sensorimotor period. We propose (...) that these dynamic meanings provide the semantic foundation for the most common verbs included in early sentences, and thus a bootstrap to full development of the verb repertoire. In this study, we followed the spoken language development of five children. We identified dynamic event words as encoding dynamic change in the following dimensions: spatial direction in relation to self; vertical spatial direction; figure/ground relationships; and temporal event sequences. Verbs continuing the semantics previously identified in dynamic event words occurred early and dominated the verb repertoire through 24 months of age. (shrink)

Infants are sensitive to statistical regularities (i.e., transitional probabilities, or TPs) relevant to segmenting words in fluent speech. However, there is debate about whether tracking TPs results in representations of possible words. Infants show preferential learning of sequences with high TPs (HTPs) as object labels relative to those with low TPs (LTPs). Such findings could mean that only the HTP sequences have a word‐like status, and they are more readily mapped to a referent for that reason. But these findings could (...) also suggest that HTP sequences are easier to encode, just like any other predictable sequence. Here we aimed to distinguish between these explanations. To do so, we built on findings that infants become resistant to learning labels that are not typical of their native language as they approach 2 years of age and add words to their lexicons. If tracking TPs in speech results in identifying candidate words, at this age TPs may have reduced power to confer lexical status when they yield a unit that is very dissimilar to word forms that are typical of infants’ native language. Indeed, we found that at 20 months, English‐learning infants with relatively small vocabularies learned HTP Italian words (but not LTP words) as object labels, while infants with larger vocabularies resisted learning HTP Italian words. These findings suggest that the HTP sequences may be represented as candidate words, and more broadly, that TP statistics are relevant to word learning. (shrink)

In recent years we have seen a dramatic shift, in several different areas of communication studies, from an information-theoretic to a dynamic systems paradigm. In an information processing system, communication, whether between cells, mammals, apes, or humans, is said to occur when one organism encodes information into a signal that is transmitted to another organism that decodes the signal. In a dynamic system, all of the elements are continuously interacting with and changing in respect to one another, and an aggregate (...) pattern emerges from this mutual co-action. Whereas the information-processing paradigm looks at communication as a linear, binary sequence of events, the dynamic systems paradigm looks at the relation between behaviors and how the whole configuration changes over time. One of the most dramatic examples of the significance of shifting from an information processing to a dynamic systems paradigm can be found in the debate over the interpretation of recent advances in ape language research (ALR). To some extent, many of the early ALR studies reinforced the stereotype that animal communication is functional and stimulus bound, precisely because they were based on an information-processing paradigm that promoted a static model of communicative development. But Savage-Rumbaugh's recent results with bonobos has introduced an entirely new dimension into this debate. Shifting the terms of the discussion from an information-processing to a dynamic systems paradigm not only highlights the striking differences between Savage-Rumbaugh's research and earlier ALR studies, but further, it sheds illuminating light on the factors that underpin the development of communication skills in great apes and humans, and the relationship between communicative development and the development of language. Key Words: apes; ape language research (ALR); brain development; co-regulation; communication; dynamic systems; language development; symbols. (shrink)