Microstudies versus big picture accounts?

Microstudies and big picture accounts are often counterposed. This paper investigates the supposed dichotomy between the two historiographical approaches. In particular it investigates how the discussions are reflected in the historiography of molecular biology and the special questions posed by the disciplinary context. Taking inspiration from the microhistory tradition as exemplified by the works of Carlo Ginzburg, Jacques Revel, and David Sabean among others, the paper highlights the heuristic value of microstudies to reconstruct the multiple contexts that link apparently small events with broader structures. In a parallel fashion, the paper argues for using microstudies to open up the history of molecular biology to other fields of study and thus moving beyond the confines of the disciplinary framework. Such an approach does not dismiss the search for big pictures. Yet rather than opposing big pictures to microstudies, it sees microstudies as a valid way to gain new and broad vistas.     

Effects of picture size reduction and blurring on emotional engagement

The activity of basic motivational systems is reflected in emotional responses to arousing stimuli, such as natural pictures. The manipulation of picture properties such as size or detail allows for investigation into the extent to which separate emotional reactions are similarly modulated by perceptual changes, or, rather, may subserve different functions. Pursuing this line of research, the present study examined the effects of two types of perceptual degradation, namely picture size reduction and blurring, on emotional responses. Both manipulations reduced picture relevance and dampened affective modulation of skin conductance, possibly because of a reduced action preparation in response to degraded or remote pictures. However, the affective modulation of the startle reflex did not vary with picture degradation, suggesting that the identification of these degraded affective cues activated the neural circuits mediating appetitive or defensive motivation.     

Screening pigment,aperture and sensitivity in the dung beetle superposition eye

Summary Sensitivity to light was investigated in the refracting superposition eye of the dung beetle Onitis alexis using electrophysiological measurements and optical modelling. Intracellular recordings were made from single retinula cells over 24-h periods, with cells light and dark adapted, in order to measure the response/intensity (V-LogI) functions. The combined effects of a circadian rhythm and light adaptation allow the determination of the relative contributions of screening-pigment migration and transduction gain to changes in sensitivity in the eye. Between the extremes of dark adaptation at night and light adaptation during the day, the maximum sensitivity change possible is at least 4 log units, of which approximately 2 log units can be accounted for by changes in the transduction gain and at least 2 log units by screening-pigment migration. The role of the superposition aperture (the number of facets that contribute light to one rhabdom) in 3 species of dung beetle was investigated with an optical ray-tracing model of the eye. The facets of the superposition aperture do not contribute light equally to the target rhabdom; except in one species, the greatest contribution comes from facets located away from both the centre and periphery of the aperture. Light adaptation increases the optical density of the superposition aperture and decreases its size.     

Did neural pooling for night vision lead to the evolution of neural superposition eyes?

Observations of the infrared deep pseudopupil, optical determinations of the corneal nodal point, and histological methods were used to relate the visual fields of individual rhabdomeres to the array of ommatidial optical axes in four insects with open rhabdoms: the tenebrionid beetle Zophobas morio, the earwig Forficula auricularia, the crane fly Tipula pruinosa, and the backswimmer Notonecta glauca.The open rhabdoms of all four species have a central pair of rhabdomeres surrounded by six peripheral rhabdomeres. At night, a distal pigment aperture is fully open and the rhabdom receives light over an angle approximately six times the interommatidial angle. Different rhabdomeres within the same ommatidium do not share the same visual axis, and the visual fields of the peripheral rhabdomeres overlap the optical axes of several near-by ommatidia. During the day, the pigment aperture is considerably smaller, and all rhabdomeres share the same visual field of about two interommatidial angles, or less, depending on the degree of light adaptation. The pigment aperture serves two functions: (1) it allows the circadian rhythm to switch between the night and day sampling patterns, and (2) it works as a light driven pupil during the day.Theoretical considerations suggest that, in the night eye, the peripheral retinula cells are involved in neural pooling in the lamina, with asymmetric pooling fields matching the visual fields of the rhabdomeres. Such a system provides high sensitivity for nocturnal vision, and the open rhabdom has the potential of feeding information into parallel spatial channels with different tradeoffs between resolution and sensitivity. Modification of this operational principle to suit a strictly diurnal life, makes the contractile pigment aperture superfluous, and decreasing angular sensitivities together with decreasing pooling fields lead to a neural superposition eye.Abbreviations DPP deep pseudopupil - LMC large monopolar cell     

An Attempt to Increase the Longevity of Cut Daffodils (Narcissus pseudonarcissus) by Chemical Treatments

The use of pictures to illustrate science text is not usually taken to be problematic. However, the ‘picture superiority effect’ (PSE), whereby pictures are deemed to enhance learning from text, has been examined systematically over the last decade and has been found to be more equivocal than was hitherto believed. Part 1 of this review of the PSE in learning biology examines a number of perceptual considerations that need to be given to picture construction. It examines the major parameters which appear to attract the learner's attention to the picture in the first place, and then directs their subsequent viewing. These parameters are important because they exert control over the information the learner extracts from the picture. They are also important because, once recognized, it should be possible to control their influence in such a way as to optimize learning. These parameters fall into two main categories: those residing within the picture itself (for example, figure-ground differentiation) and those within the learner (for example, cultural bias). The review discusses ways in which within-picture variables such as depth of field and colour can be manipulated to re-inforce the intended message. It also suggests that more explicit instructions need to be given to learners to guide their use of texts with picture adjuncts. The importance of teaching children how to read pictures is complicated by the ways in which picture and text interact in the mind of the learner, and future comment on this aspect of the learning process is deferred to Part 2 of the article, which deals specifically with aspects of picture-text processing.     

Out of mind, out of sight: language affects perceptual vividness in memory

We examined whether language affects the strength of a visual representation in memory. Participants studied a picture, read a story about the depicted object, and then selected out of two pictures the one whose transparency level most resembled that of the previously presented picture. The stories contained two linguistic manipulations that have been demonstrated to affect concept availability in memory, i.e., object presence and goal-relevance. The results show that described absence of an object caused people to select the most transparent picture more often than described presence of the object. This effect was not moderated by goal-relevance, suggesting that our paradigm tapped into the perceptual quality of representations rather than, for example, their linguistic availability. We discuss the implications of these findings within a framework of grounded cognition.     

Timed picture naming norms for Mandarin Chinese

The present study reports timed norms for 435 object pictures in Mandarin Chinese. These data include naming latency, name agreement, concept agreement, word length, and age of acquisition (AoA) based on children's naming and adult ratings, and several other adult ratings of concept familiarity, subjective word frequency, image agreement, image variability, and visual complexity. Furthermore, we examined factors that influence the naming latencies of the pictures. The results show that concept familiarity, AoA, concept agreement, name agreement, and image agreement are significant predictors of naming latencies, whereas subjective word frequency is not a reliable determinant. These results are discussed in light of picture naming data in other languages. An item-based index for the norms is provided in the Table S1.     

DNA and cell resonance: magnetic waves enable cell communication

DNA generates a longitudinal wave that propagates in the direction of the magnetic field vector. Computed frequencies from the structure of DNA agree with those of the predicted biophoton radiation. The optimization of efficiency by minimizing the conduction losses leads to the double-helix structure of DNA. The vortex model of the magnetic scalar wave not only covers many observed structures within the nucleus perfectly, but also explains the hyperboloid channels in the matrix when two cells communicate with each other. Potential vortexes are an essential component of a scalar waves, as discovered in 1990. The basic approach for an extended field theory was confirmed in 2009 with the discovery of magnetic monopoles. For the first time, this provides the opportunity to explain the physical basis of life not only from the biological discipline. Nature covers the whole spectrum of known scientific fields of research, and interdisciplinary understanding is required to explain its complex relationships. The characteristics of the potential vortex are significant. With its concentration effect, it provides for miniaturization down to a few nanometers, which allows enormously high information density in the nucleus. With this first introduction of the magnetic scalar wave, it becomes clear that such a wave is suitable to use genetic code chemically stored in the base pairs of the genes and electrically modulate them, so as to "piggyback" information from the cell nucleus to another cell. At the receiving end, the reverse process takes place and the transported information is converted back into a chemical structure. The necessary energy required to power the chemical process is provided by the magnetic scalar wave itself.     

Displaying inter-main chain hydrogen bond patterns in proteins

Two computer graphics techniques for displaying hydrogen bonds between the main chains of different proteins are described, and illustrated for two thiol proteases. (The X-ray crystallography was performed by Kamphuis et al. in 1984,¹ and by Baker and Dodson in 1980.²) One is a three-dimensional model that can be manipulated in space; the hydrogen bonds are represented with the smoothed α-carbon plot of the polypeptide chain. In the other type of display, hydrogen bonds are viewed in relation to the one-dimensional sequence. Both types of picture facilitate visualization of hydrogen bond patterns, such that loop motifs, as well as α-helices and β-sheets, can be examined easily. We suggest that such displays are useful as a general means of displaying whole proteins and whole domains because they reveal more information than do conventional simplified pictures of proteins, which focus exclusively on α-helices and β-sheets. These techniques can be implemented on a UNIX-based computer graphics workstation. (UNIX is a trademark of Bell Telephone laboratories.)     

In search of morphological modules: a systematic review

Morphological modularity arises in complex living beings due to a semi‐independent inheritance, development, and function of body parts. Modularity helps us to understand the evolvability and plasticity of organismal form, and how morphological variation is structured during evolution and development. For this reason, delimiting morphological modules and establishing the factors involved in their origins is a lively field of inquiry in biology today. Although it is thought that modularity is pervasive in all living beings, actually we do not know how often modularity is present in different morphological systems. We also do not know whether some methodological approaches tend to reveal modular patterns more easily than others, or whether some factors are more related to the formation of modules or the integration of the whole phenotype. This systematic review seeks to answer these type of questions through an examination of research investigating morphological modularity from 1958 to present. More than 200 original research articles were gathered in order to reach a quantitative appraisal on what is studied, how it is studied, and how the results are explained. The results reveal an heterogeneous picture, where some taxa, systems, and approaches are over‐studied, while others receive minor attention. Thus, this review points out various trends and gaps in the study of morphological modularity, offering a broad picture of current knowledge and where we can direct future research efforts.     

rCUR:an R package for CUR matrix decomposition

ABSTRACT: BACKGROUND: Many methods for dimensionality reduction of large data sets such as those generated in microarray studies boil down to the Singular Value Decomposition (SVD). Although singular vectors associated with the largest singular values have strong optimality properties and can often be quite useful as a tool to summarize the data, they are linear combinations of up to all of the data points, and thus it is typically quite hard to interpret those vectors in terms of the application domain from which the data are drawn. Recently, an alternative dimensionality reduction paradigm, CUR matrix decompositions, has been proposed to address this problem and has been applied to genetic and internet data. CUR decompositions are low-rank matrix decompositions that are explicitly expressed in terms of a small number of actual columns and/or actual rows of the data matrix. Since they are constructed from actual data elements, CUR decompositions are interpretable by practitioners of the eld from which the data are drawn. RESULTS: We present an implementation to perform CUR matrix decompositions, in the form of a freely available, open source R-package called rCUR. This package will help users to perform CUR-based analysis on large-scale data, such as those obtained from different high-throughput technologies, in an interactive and exploratory manner. We show two examples that illustrate how CUR-based techniques make it possible to reduce signicantly the number of probes, while at the same time maintaining major trends in data and keeping the same classication accuracy. CONCLUSIONS: The package rCUR provides functions for the users to perform CUR-based matrix decompositions in the R environment. In gene expression studies, it gives an additional way of analysis of differential expression and discriminant gene selection based on the use of statistical leverage scores. These scores, which have been used historically in diagnostic regression analysis to identify outliers, can be used by rCUR to identify the most informative data points with respect to which to express the remaining data points.     

Biological networks

Recent advances in high-throughput methods have provided us with a first glimpse of the overall structure of molecular interaction networks in biological systems. Ultimately, we expect that such information will change how we think about biological systems in a fundamental way. Instead of viewing the genetic parts list of an organism as a loose collection of biochemical activities, in the best case, we anticipate discrete networks of function to bridge the gap between genotype and phenotype, and to do so in a more profound way than the current qualitative classification of linked reactions into familiar pathways, such as glycolysis and the MAPK signal transduction cascades. At the present time, however, we are still far from a complete answer to the most basic question: what can we learn about biology by studying networks? Promising steps in this direction have come from such diverse approaches as mathematical analysis of global network structure, partitioning networks into functionally related modules and motifs, and even de novo design of networks. A complete picture will probably require integrating the data obtained from all of these approaches with modeling efforts at many different levels of detail.     

Emotional stimulation alters olfactory sensitivity and odor judgment

Emotions have a strong influence on the perception of visual and auditory stimuli. Only little is known about the relation between emotional stimulation and olfactory functions. The present study investigated the relationship between the presentation of affective pictures, olfactory functions, and sex. Olfactory performance was assessed in 32 subjects (16 male). Olfactory sensitivity was significantly reduced following unpleasant picture presentation for all subjects and following pleasant picture presentation for male subjects only. Pleasantness and intensity ratings of a neutral suprathreshold odor were related to the valence of the pictures: After unpleasant picture presentation, the odor was rated as less pleasant and more intense, whereas viewing positive pictures induced a significant increase in reported odor pleasantness. We conclude that inducing a negative emotional state reduces olfactory sensitivity. A relation to functional deviations within the primary olfactory cortices is discussed.     

‘Tailception’: using neural networks for assessing tail lesions on pictures of pig carcasses

Tail lesions caused by tail biting are a widespread welfare issue in pig husbandry. Determining their prevalence currently involves labour intensive, subjective scoring methods. Increased societal interest in tail lesions requires fast, reliable and cheap systems for assessing tail status. In the present study, we aimed to test the reliability of neural networks for assessing tail pictures from carcasses against trained human observers. Three trained observers scored tail lesions from automatically recorded pictures of 13 124 pigs. Nearly all pigs had been tail docked. Tail lesions were classified using a 4-point score (0=no lesion, to 3=severe lesion). In addition, total tail loss was recorded. Agreement between observers was tested prior and during the assessment in a total of seven inter-observer tests with 80 pictures each. We calculated agreement between observer pairs as exact agreement (%) and prevalence-adjusted bias-adjusted κ (PABAK; value 1=optimal agreement). Out of the 13 124 scored pictures, we used 80% for training and 20% for validating our neural networks. As the position of the tail in the pictures varied (high, low, left, right), we first trained a part detection network to find the tail in the picture and select a rectangular part of the picture which includes the tail. We then trained a classification network to categorise tail lesion severity using pictures scored by human observers whereby the classification network only analysed the selected picture parts. Median exact agreement between the three observers was 80% for tail lesions and 94% for tail loss. Median PABAK for tail lesions and loss were 0.75 and 0.87, respectively. The agreement between classification by the neural network and human observers was 74% for tail lesions and 95% for tail loss. In other words, the agreement between the networks and human observers were very similar to the agreement between human observers. The main reason for disagreement between observers and thereby higher variation in network training material were picture quality issues. Therefore, we expect even better results for neural network application to tail lesions if training is based on high quality pictures. Very reliable and repeatable tail lesion assessment from pictures would allow automated tail classification of all pigs slaughtered, which is something that some animal welfare labels would like to do.     

Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars

Recognizing that certain biological functions can be associated with specific DNA sequences has led various fields of biology to adopt the notion of the genetic part. This concept provides a finer level of granularity than the traditional notion of the gene. However, a method of formally relating how a set of parts relates to a function has not yet emerged. Synthetic biology both demands such a formalism and provides an ideal setting for testing hypotheses about relationships between DNA sequences and phenotypes beyond the gene-centric methods used in genetics. Attribute grammars are used in computer science to translate the text of a program source code into the computational operations it represents. By associating attributes with parts, modifying the value of these attributes using rules that describe the structure of DNA sequences, and using a multi-pass compilation process, it is possible to translate DNA sequences into molecular interaction network models. These capabilities are illustrated by simple example grammars expressing how gene expression rates are dependent upon single or multiple parts. The translation process is validated by systematically generating, translating, and simulating the phenotype of all the sequences in the design space generated by a small library of genetic parts. Attribute grammars represent a flexible framework connecting parts with models of biological function. They will be instrumental for building mathematical models of libraries of genetic constructs synthesized to characterize the function of genetic parts. This formalism is also expected to provide a solid foundation for the development of computer assisted design applications for synthetic biology.     

Behavioural responses to photographs by pictorially naïve baboons (Papio anubis), gorillas (Gorilla gorilla) and chimpanzees (Pan troglodytes)

This study assessed how pictorially naïve nonhuman primates understand pictures. Fifty-five baboons with no prior exposure to pictures were trained to grasp a slice of banana presented against a pebble in a two alternative forced choice task. Post-training testing involved three stimulus pairs: (1) real banana slice vs. its picture, (2) the banana picture vs. a real pebble and (3) banana picture vs. a pebble picture which were presented twice. Preliminary data were also collected on naïve gorillas (n = 4) and chimpanzees (n = 7) using the same procedure. Baboons revealed a preference for the food picture in (2) and (3) and often ate this stimulus, but the food item and its picture were accurately discriminated in (1). These results suggest that baboons mistook the pictorial stimulus and its referent, but processed the banana pictures as poor exemplars of the real banana category. Among apes, only gorillas ate the banana pictures, suggesting that picture–object confusion may also occur in this species. Findings are discussed as pertaining to the general issue of representational abilities in nonhuman primates, and its evolution.     

Are viruses a source of new protein folds for organisms? – Virosphere structure space and evolution

A crucially important part of the biosphere - the virosphere - is too often overlooked. Inclusion of the virosphere into the global picture of protein structure space reveals that 63 protein domain superfamilies in viruses do not have any structural and evolutionary relatives in modern cellular organisms. More than half of these have functions which are not virus-specific and thus might be a source of new folds and functions for cellular life. The number of viruses on the planet exceeds that of cells by an order of magnitude and viruses evolve up to six orders of magnitude faster. As a result, cellular species are subject to a constitutive 'flow-through' of new viral genetic material. Due to this and the relaxed evolutionary constraints in viruses, the transfer of domains between host-to-virus could be a mechanism for accelerated protein evolution. The virosphere could be an engine for the genesis of protein structures, and may even have been so before the last universal common ancestor of cellular life.     

Improved efficiency in cryo-em secondary structure topology determination from inaccurate data

The determination of the secondary structure topology is a critical step in deriving the atomic structure from the protein density map obtained from electron cryo-microscopy technique. This step often relies on the matching of two sources of information. One source comes from the secondary structures detected from the protein density map at the medium resolution, such as 5-10 ?. The other source comes from the predicted secondary structures from the amino acid sequence. Due to the inaccuracy in either source of information, a pool of possible secondary structure positions needs to be sampled. This paper studies the question, that is, how to reduce the computation of the mapping when the inaccuracy of the secondary structure predictions is considered. We present a method that combines the concept of dynamic graph with our previous work of using constrained shortest path to identify the topology of the secondary structures. We show a reduction of 34.55% of run-time as comparison to the na?ve way of handling the inaccuracies. We also show an improved accuracy when the potential secondary structure errors are explicitly sampled verses the use of one consensus prediction. Our framework demonstrated the potential of developing computationally effective exact algorithms to identify the optimal topology of the secondary structures when the inaccuracy of the predicted data is considered.     

A perspective of synthetic biology: assembling building blocks for novel functions

Synthetic biology is a recently emerging field that applies engineering formalisms to design and construct new biological parts, devices, and systems for novel functions or life forms that do not exist in nature. Synthetic biology relies on and shares tools from genetic engineering, bioengineering, systems biology and many other engineering disciplines. It is also different from these subjects, in both insights and approach. Applications of synthetic biology have great potential for novel contributions to established fields and for offering opportunities to answer fundamentally new biological questions. This article does not aim at a thorough survey of the literature and detailing progress in all different directions. Instead, it is intended to communicate a way of thinking for synthetic biology in which basic functional elements are defined and assembled into living systems or biomaterials with new properties and behaviors. Four major application areas with a common theme are discussed and a procedure (or "protocol") for a standard synthetic biology work is suggested.     

Picture – Object Recognition in Kea (Nestor notabilis)

Although pictures are widely used as stimuli in cognitive experiments with both humans and animals, the question of how subjects interpret pictures receives less attention. Gaining a better understanding of this is especially important when working with avian subjects, as their visual anatomy and processing is different from that of humans, and even differs from one avian species to another. Successful testing for picture recognition in birds has been carried out mainly with pigeons, but no such research has been explicitly performed with ‘brainy’ birds like parrots, despite the fact that these have been the subject of exciting cognitive research. This study tested kea (Nestor notabilis) mountain parrots for picture–object recognition using a procedure which required the transfer of a learned discrimination task between pictures and objects. Kea successfully showed both picture‐to‐object and object‐to‐picture transfer and performed at a comparable level when pictures were displayed on a touch screen or as printed photographs.