Symbols, Meaning, and Origins of Mind

The mind maps symbols and the extra-symbolic relationships amongst them to specific meanings. When symbols of various levels are placed in a hierarchical ordering, one may look at such ordered classes as distinct worlds where one class represents objects and the other represents the objects’ corresponding meanings. However, such an explanation can only be partial because the number of potential levels in such an ordering is infinite and, therefore, it engenders problems of recursion and infinite regress. There are also logical problems in the form of paradoxes that emanate from the consideration of sets of sets. Given that most prior studies only consider symbols that are classical objects in associative relationships, we argue that there is a need to also consider objects with shifting boundaries and quantum objects. We believe that objects belonging to each of these three classes—that is classical objects, objects with shifting boundaries, and quantum objects—play a role in the workings of the mind.     

GenRGenS: software for generating random genomic sequences and structures

SUMMARY: GenRGenS is a software tool dedicated to randomly generating genomic sequences and structures. It handles several classes of models useful for sequence analysis, such as Markov chains, hidden Markov models, weighted context-free grammars, regular expressions and PROSITE expressions. GenRGenS is the only program that can handle weighted context-free grammars, thus allowing the user to model and to generate structured objects (such as RNA secondary structures) of any given desired size. GenRGenS also allows the user to combine several of these different models at the same time.     

Shape Similarity,Better than Semantic Membership,Accounts for the Structure of Visual Object Representations in a Population of Monkey Inferotemporal Neurons

The anterior inferotemporal cortex (IT) is the highest stage along the hierarchy of visual areas that, in primates, processes visual objects. Although several lines of evidence suggest that IT primarily represents visual shape information, some recent studies have argued that neuronal ensembles in IT code the semantic membership of visual objects (i.e., represent conceptual classes such as animate and inanimate objects). In this study, we investigated to what extent semantic, rather than purely visual information, is represented in IT by performing a multivariate analysis of IT responses to a set of visual objects. By relying on a variety of machine-learning approaches (including a cutting-edge clustering algorithm that has been recently developed in the domain of statistical physics), we found that, in most instances, IT representation of visual objects is accounted for by their similarity at the level of shape or, more surprisingly, low-level visual properties. Only in a few cases we observed IT representations of semantic classes that were not explainable by the visual similarity of their members. Overall, these findings reassert the primary function of IT as a conveyor of explicit visual shape information, and reveal that low-level visual properties are represented in IT to a greater extent than previously appreciated. In addition, our work demonstrates how combining a variety of state-of-the-art multivariate approaches, and carefully estimating the contribution of shape similarity to the representation of object categories, can substantially advance our understanding of neuronal coding of visual objects in cortex.     

The microbiological data base of the data bank project BD1

The aim of the project BD1 (Biotechnology Data Bank 1) is to improve the data processing for research in biotechnology. In BD1, data of several classes of objects and methods are compiled. A data file conception consisting of object data files, method data files and feature data files was created, which can be easily extended to further classes, and which allows the combination of different classes of features to the same class of objects. There are two main approaches to use BD1: 1. making available informations on certain biotechnological objects, 2. the identification of unknown objects by means of their feature pattern. The microbiological data base and the possibilities of data base search are presented by example of lactic acid bacteria.     

The Effect of Age and Sex on Object Exploration and Manipulative Behavior in a Neotropical Raptor,the Chimango Caracara,Milvago chimango

We studied object exploration and manipulative behavior in wild‐caught Chimango Caracaras (Milvago chimango), an opportunistic and generalist raptor species, in relation to age and sex differences. Each bird was presented with six objects. We then recorded the latencies to approach and first contact with the objects, the number of objects explored, and the number of exploration events performed on each object. Age influenced the tendency to explore in M. chimango. Compared with adults, juveniles were more likely to explore the objects, approaching and contacting them more quickly. The number of objects explored was also higher in young than adult birds. Both age classes used a variety of manipulative behaviors to explore the objects, some of which have been described as play in others studies. Sex did not affect an individual's likelihood to explore or the number and frequency of manipulative behaviors used during object exploration. The tendency for both young and adult birds to explore and manipulate objects that not resemble prey is likely to be a distinct advantage for a generalist species like M. chimango which must cope with a high diversity of modified environments.     

Visual saliency and spike timing in the ventral visual pathway.

Visual saliency is a fundamental yet hard to define property of objects or locations in the visual world. In a context where objects and their representations compete to dominate our perception, saliency can be thought of as the "juice" that makes objects win the race. It is often assumed that saliency is extracted and represented in an explicit saliency map, which serves to determine the location of spatial attention at any given time. It is then by drawing attention to a salient object that it can be recognized or categorized. I argue against this classical view that visual "bottom-up" saliency automatically recruits the attentional system prior to object recognition. A number of visual processing tasks are clearly performed too fast for such a costly strategy to be employed. Rather, visual attention could simply act by biasing a saliency-based object recognition system. Under natural conditions of stimulation, saliency can be represented implicitly throughout the ventral visual pathway, independent of any explicit saliency map. At any given level, the most activated cells of the neural population simply represent the most salient locations. The notion of saliency itself grows increasingly complex throughout the system, mostly based on luminance contrast until information reaches visual cortex, gradually incorporating information about features such as orientation or color in primary visual cortex and early extrastriate areas, and finally the identity and behavioral relevance of objects in temporal cortex and beyond. Under these conditions the object that dominates perception, i.e. the object yielding the strongest (or the first) selective neural response, is by definition the one whose features are most "salient"--without the need for any external saliency map. In addition, I suggest that such an implicit representation of saliency can be best encoded in the relative times of the first spikes fired in a given neuronal population. In accordance with our subjective experience that saliency and attention do not modify the appearance of objects, the feed-forward propagation of this first spike wave could serve to trigger saliency-based object recognition outside the realm of awareness, while conscious perceptions could be mediated by the remaining discharges of longer neuronal spike trains.     

A Comparison of Protocols for Updating Location Information

Detailed location information of mobile objects, for example that of a user with a mobile computer or phone, is an important input for many location-aware applications. However, constantly updating the location information for thousands of mobile objects is not feasible. Therefore, special update protocols for location information are required that transmit the information as efficiently as possible, that is requiring only few update messages, while still being effective in returning the location information with the desired accuracy. Different classes of such update protocols are described in this paper and a new combined protocol is proposed. To be able to compare their effectiveness and efficiency, we present an analysis for the minimum and average resulting accuracy of the location information in comparison with the number of messages transmitted. We also present the results of simulations that we have performed to back up our analysis.     

Fragment-based learning of visual object categories

When we perceive a visual object, we implicitly or explicitly associate it with a category we know. It is known that the visual system can use local, informative image fragments of a given object, rather than the whole object, to classify it into a familiar category. How we acquire informative fragments has remained unclear. Here, we show that human observers acquire informative fragments during the initial learning of categories. We created new, but naturalistic, classes of visual objects by using a novel "virtual phylogenesis" (VP) algorithm that simulates key aspects of how biological categories evolve. Subjects were trained to distinguish two of these classes by using whole exemplar objects, not fragments. We hypothesized that if the visual system learns informative object fragments during category learning, then subjects must be able to perform the newly learned categorization by using only the fragments as opposed to whole objects. We found that subjects were able to successfully perform the classification task by using each of the informative fragments by itself, but not by using any of the comparable, but uninformative, fragments. Our results not only reveal that novel categories can be learned by discovering informative fragments but also introduce and illustrate the use of VP as a versatile tool for category-learning research.     

A Quantitative Model for Nonrandom Generalized Transduction, Applied to the Phage P22–SALMONELLA TYPHIMURIUM System

A mathematical model for nonrandom generalized transduction is proposed and analyzed. The model takes into account the finite number of transducing particle classes for any given marker. The equations for estimation of the distance between markers from contransduction frequency data are derived and standard errors of the estimates are given. The obtained relationships depend significantly on the number of classes of transducing fragments. The model was applied to estimate the number of transducing fragment classes for a given marker in transduction with phage P22 of Salmonella typhimurium. It was found that the literature data on frequencies of contransduction in crosses with mutual substitution of selective and nonselective markers can be rationalized most accurately by assuming that the mean number of classes is equal to 2. An improved method for analysis of cotransduction data is proposed on the basis of our model and the results of calculation. The method relies on solving a set of algebraic equations for cotransduction frequencies of markers located within one phage length. The method allows a relatively precise determination of distances between markers, positions of transducing particle ends and deletion or insertion lengths. The approach is applied to the trp-cysB-pyrF and aroC-hisT-purF-dhuA regions of the Salmonella typhimurium chromosome.     

Developing classification in action: I. Human infants

Human infants’ developing manipulatory transformations involved in classifying objects from ages 6 to 24 months were investigated. Infants’ manipulations develop from predominantly serial one-at-a-time acts with one object to predominantly parallel two-at-a-time acts with two objects. This shift is marked by increasingly overt transformational consequences for the objects manipulated. When infants construct parallel transformations they are initially different. With age they are increasingly identical or reciprocal. Also during this age period, as the number of objects manipulated at the same time increases, so does the frequency with which infants coordinate them. At the same time, the kind of objects infants manipulate simultaneously changes. Six-month-olds manipulate different objects when acting on more than one object at a time. By age 12 months, infants switch to manipulating identical objects at the same time, indicating that they are beginning to construct identity classes. Since this development occurs about a half year before human infants develop any substantial naming behavior, the origins of classification cannot depend on this linguistic development     

Detection of Nonrandom Association of Alleles from the Distribution of the Number of Heterozygous Loci in a Sample

The distribution of the number of heterozygous loci in two randomly chosen gametes or in a random diploid zygote provides information regarding the nonrandom association of alleles among different genetic loci. Two alternative statistics may be employed for detection of nonrandom association of genes of different loci when observations are made on these distributions: observed variance of the number of heterozygous loci (s2k) and a goodness-of-fit criterion (X2) to contrast the observed distribution with that expected under the hypothesis of random association of genes. It is shown, by simulation, that s2k is statistically more efficient than X2 to detect a given extent of nonrandom association. Asymptotic normality of s2k is justified, and X2 is shown to follow a chi-square (chi 2) distribution with partial loss of degrees of freedom arising because of estimation of parameters from the marginal gene frequency data. Whenever direct evaluations of linkage disequilibrium values are possible, tests based on maximum likelihood estimators of linkage disequilibria require a smaller sample size (number of zygotes or gametes) to detect a given level of nonrandom association in comparison with that required if such tests are conducted on the basis of s2k. Summarization of multilocus genotype (or haplotype) data, into the different number of heterozygous loci classes, thus, amounts to appreciable loss of information.     

Relational diversity

In biology, the measurement of diversity traditionally focusses on reporting number of unambiguously distinguishable types, thus referring to qualitative (discontinuously varying) traits. Inclusion of frequencies or other weights has produced a large variety of diversity indices. Quantitative (continuously varying) traits do not readily fit into this perspective. In fact, in the context of quantitative traits, the concept of diversity is not always clearly distinguished from the (statistical) notion of dispersion. In many cases the ambiguity even extends to qualitative traits. This is at variance with the broad spectrum of diversity issues ranging, e.g., from ecological and genetic aspects of diversity to functional, structural, systematic, or evolutionary (including phylogenetic) aspects. In view of the urgent need for a more consistent perspective, it is called to attention that all of these aspects, whether of qualitative or quantitative nature, can be gathered under the common roof of binary relations (for qualitative traits two objects are related, for example, if they share the same trait state). A comprehensive concept of (relational) diversity can be developed in two steps: (1) determine the number of unrelated pairs of objects among all admissible pairs as a measure of implicit (relative) diversity, (2) invoke the concept of effective number to transform the implicit measure of diversity into an explicit (absolute) measure. The transformation operates by equating the observed implicit diversity to the implicit diversity obtained for the ideal model of an equivalence relation with classes of equal size. The number of these classes specifies the effective number as an explicit measure of diversity. The wealth of problems that can be treated from this unified perspective is briefly addressed by classifying and interpreting established diversity indices in the light of relational diversity. Desirable applications to the above-mentioned aspects are specified with the help of types of relations such as order, hierarchical, and tree relations. Corresponding biological issues including taxonomic community diversity, mating system, food web, sociological, cladistic and phylogenetic, or hypercycle diversity are suggested for future consideration.     

The dispersion analysis of cell suspensions by a conductometric method

A conductometric device-analyser ADS-05 designed by the authors is proposed for dispersive analysis of cell suspensions. The device makes it possible to do a wide range express analysis of suspensions (0.1-600 microns) according to any required number of classes (from 2 to 2(10)). The results of dispersion analysis of the yeast cells of Saccharomyces aragilis crop are given (according to the 16 classes).     

Euclidian space and grouping of biological objects

MOTIVATION: Biological objects tend to cluster into discrete groups. Objects within a group typically possess similar properties. It is important to have fast and efficient tools for grouping objects that result in biologically meaningful clusters. Protein sequences reflect biological diversity and offer an extraordinary variety of objects for polishing clustering strategies. Grouping of sequences should reflect their evolutionary history and their functional properties. Visualization of relationships between sequences is of no less importance. Tree-building methods are typically used for such visualization. An alternative concept to visualization is a multidimensional sequence space. In this space, proteins are defined as points and distances between the points reflect the relationships between the proteins. Such a space can also be a basis for model-based clustering strategies that typically produce results correlating better with biological properties of proteins. RESULTS: We developed an approach to classification of biological objects that combines evolutionary measures of their similarity with a model-based clustering procedure. We apply the methodology to amino acid sequences. On the first step, given a multiple sequence alignment, we estimate evolutionary distances between proteins measured in expected numbers of amino acid substitutions per site. These distances are additive and are suitable for evolutionary tree reconstruction. On the second step, we find the best fit approximation of the evolutionary distances by Euclidian distances and thus represent each protein by a point in a multidimensional space. The Euclidian space may be projected in two or three dimensions and the projections can be used to visualize relationships between proteins. On the third step, we find a non-parametric estimate of the probability density of the points and cluster the points that belong to the same local maximum of this density in a group. The number of groups is controlled by a sigma-parameter that determines the shape of the density estimate and the number of maxima in it. The grouping procedure outperforms commonly used methods such as UPGMA and single linkage clustering.     

On Countable Mixtures of Bivariate Binomial Distributions

A unified treatment is given for mixtures of bivariate binomial distributions with respect to their index parameter(s). The use of probability generating functions is employed and a number of interesting properties including probabilities, factorial moments, factorial cumulants and conditional distributions are derived. Five classes of such mixtures are examined and several well known bivariate discrete distributions are used as illustrative examples. Biological applications are indicated including the fit of three bivariate distributions to an actual set of human family data.     

Having sex,yes, but with whom? Inferences from fungi on the evolution of anisogamy and mating types

The advantage of sex has been among the most debated issues in biology. Surprisingly, the question of why sexual reproduction generally requires the combination of distinct gamete classes, such as small and large gametes, or gametes with different mating types, has been much less investigated. Why do systems with alternative gamete classes (i.e. systems with either anisogamy or mating types or both) appear even though they restrict the probability of finding a compatible mating partner? Why does the number of gamete classes vary from zero to thousands, with most often only two classes? We review here the hypotheses proposed to explain the origin, maintenance, number, and loss of gamete classes. We argue that fungi represent highly suitable models to help resolve issues related to the evolution of distinct gamete classes, because the number of mating types vary from zero to thousands across taxa, anisogamy is present or not, and because there are frequent transitions between these conditions. We review the nature and number of gamete classes in fungi, and we attempt to draw inferences from these data on the evolutionary forces responsible for their appearance, loss or maintenance, and number.     

Correlation model of object recognition by echolocating animals]

The model proposed in an attempt to find out physical bases of object perception during echolocation. It is shown that echolocational perception can be provided with correlational treatment of corresponding signals. The character of objects is determined by the comparison by echo probing accepted in the given cycle with typical distortions remembered in the course of individual experience of the animal. The distortions take place during the reflection of the probing impulse from these or those objects. "Binding" of the objects according to distance may be carried out by using the choice of typical distortions for corresponding correction of the copy of probing impulse, serving as a bearing signal of distance correlometer. The response of correlometer to the echo from correctly perceived target increases. The block-scheme of such correlation perception during echolocation is given. Performance of some experiments allowing to check and refine the model considered.