Re-Examination of Globally Flat Space-Time

In the following, we offer a novel approach to modeling the observed effects currently attributed to the theoretical concepts of “dark energy,” “dark matter,” and “dark flow.” Instead of assuming the existence of these theoretical concepts, we take an alternative route and choose to redefine what we consider to be inertial motion as well as what constitutes an inertial frame of reference in flat space-time. We adopt none of the features of our current cosmological models except for the requirement that special and general relativity be local approximations within our revised definition of inertial systems. Implicit in our ideas is the assumption that at “large enough” scales one can treat objects within these inertial systems as point-particles having an insignificant effect on the curvature of space-time. We then proceed under the assumption that time and space are fundamentally intertwined such that time- and spatial-translational invariance are not inherent symmetries of flat space-time (i.e., observable clock rates depend upon both relative velocity and spatial position within these inertial systems) and take the geodesics of this theory in the radial Rindler chart as the proper characterization of inertial motion. With this commitment, we are able to model solely with inertial motion the observed effects expected to be the result of “dark energy,” “dark matter,” and “dark flow.” In addition, we examine the potential observable implications of our theory in a gravitational system located within a confined region of an inertial reference frame, subsequently interpreting the Pioneer anomaly as support for our redefinition of inertial motion. As well, we extend our analysis into quantum mechanics by quantizing for a real scalar field and find a possible explanation for the asymmetry between matter and antimatter within the framework of these redefined inertial systems.     

On the proposed energy switch in photosynthesis

This paper analyzes the “energy switch” that has often been proposed to direct quanta absorbed by a given photosynthetic unit alternately to the site of one and then the other primary reaction. Such a device is essential to the Franck-Rosenberg theory, but not to the Duysens-Witt-Kok (DWK) model, which needs to assume only that the reactions occur in series. If there is no energy switch, an incident quantum absorbed at any time by any particular pigment molecule stands a chance of ending up in the reactive site of either primary reaction. The “separate packages” model is a special case of this general picture. Without an energy switch, a series model requires a storage device to insure that a quantum will not be wasted if it arrives at the site of one reaction while the photosynthetic unit is set up to perform the other. Such a storage device can be appended to the DWK model. Alternatively, this model can be augmented by an energy switch. This gives what is commonly known as the “spillover model,” a confusing name which we suggest be abandoned. As a clear-cut-though perhaps technically unfeasible-test of the energy switch hypothesis, we imagine a quantum injector, a hypothetical source of flashing light which delivers a single quantum to every photosynthetic unit with each flash. We aim this useful figment at an (equally hypothetical) photosynthetic system all of whose units are set up to perform the same primary reaction. If there is an energy switch, we can now prepare a “synchronous” photosynthetic apparatus in which each photosynthetic unit is undergoing the same reaction at the same time.     

Deathly Drool: Evolutionary and Ecological Basis of Septic Bacteria in Komodo Dragon Mouths

Komodo dragons, the world''s largest lizard, dispatch their large ungulate prey by biting and tearing flesh. If a prey escapes, oral bacteria inoculated into the wound reputedly induce a sepsis that augments later prey capture by the same or other lizards. However, the ecological and evolutionary basis of sepsis in Komodo prey acquisition is controversial. Two models have been proposed. The “bacteria as venom” model postulates that the oral flora directly benefits the lizard in prey capture irrespective of any benefit to the bacteria. The “passive acquisition” model is that the oral flora of lizards reflects the bacteria found in carrion and sick prey, with no relevance to the ability to induce sepsis in subsequent prey. A third model is proposed and analyzed here, the “lizard-lizard epidemic” model. In this model, bacteria are spread indirectly from one lizard mouth to another. Prey escaping an initial attack act as vectors in infecting new lizards. This model requires specific life history characteristics and ways to refute the model based on these characteristics are proposed and tested. Dragon life histories (some details of which are reported here) prove remarkably consistent with the model, especially that multiple, unrelated lizards feed communally on large carcasses and that escaping, wounded prey are ultimately fed on by other lizards. The identities and evolutionary histories of bacteria in the oral flora may yield the most useful additional insights for further testing the epidemic model and can now be obtained with new technologies.     

Mathematical theory of chemical synaptic transmission

Mathematical theory of chemical synaptic transmission is suggested in which the modes of operation of chemical synapses are given as consequencies of some fundamental theoretical principles presented in the form of systems of quantum and macroscopic postulates. These postulates establish transmitter transfer rules between 3 component parts — cytoplasmic, vesicular and external pools of neurotransmitter. The main features of the transfers are determined by special properties of the dividing membranes (synaptic and vesicle) which show high selectivity towards the direction of the transmitter quantum transfer. The formulation of a previously unknown effect of transmitter quantum transfer from the vesicular pool into the cytoplasmic one is introduced: it is postulated that each arriving presynaptic impulse not only releases a constant fraction of the current contents of the cytoplasmic pool into the synaptic cleft (external pool), but also realizes practically simultaneous transmitter transfer from the vesicular pool into the cytoplasmic one. Zone structure of the vesicular pool is postulated. In accordance with basic equations of the theory a nonlinear control system (dynamic synaptic modulator — DYSYM) of transmitter release from the terminal is constructed.Depending on the parameters relation two types of synapses are classified — those with rapid and slow demobilization. Analytical dependencies of the transmitter pools sizes on the stimulation frequency are introduced. By fitting the frequency dependencies to the empirical data model parameters are determined corresponding to a set of experimentally studied synaptic junctions. Different aspects of the chemical synapse behaviour under the influence of presynaptic stimulation are simulated.     

Revisiting Special Relativity: A Natural Algebraic Alternative to Minkowski Spacetime

Minkowski famously introduced the concept of a space-time continuum in 1908, merging the three dimensions of space with an imaginary time dimension , with the unit imaginary producing the correct spacetime distance , and the results of Einstein’s then recently developed theory of special relativity, thus providing an explanation for Einstein’s theory in terms of the structure of space and time. As an alternative to a planar Minkowski space-time of two space dimensions and one time dimension, we replace the unit imaginary , with the Clifford bivector for the plane that also squares to minus one, but which can be included without the addition of an extra dimension, as it is an integral part of the real Cartesian plane with the orthonormal basis and . We find that with this model of planar spacetime, using a two-dimensional Clifford multivector, the spacetime metric and the Lorentz transformations follow immediately as properties of the algebra. This also leads to momentum and energy being represented as components of a multivector and we give a new efficient derivation of Compton’s scattering formula, and a simple formulation of Dirac’s and Maxwell’s equations. Based on the mathematical structure of the multivector, we produce a semi-classical model of massive particles, which can then be viewed as the origin of the Minkowski spacetime structure and thus a deeper explanation for relativistic effects. We also find a new perspective on the nature of time, which is now given a precise mathematical definition as the bivector of the plane.     

Gloger's rule in plants: The species and ecosystem levels

Gloger''s rule posits that darker birds are found more often in humid environments than in arid ones, especially in the tropics. Accordingly, desert-inhabiting animals tend to be light-colored. This rule is also true for certain mammalian groups, including humans. Gloger''s rule is manifested at 2 levels: (1) at the species level (different populations of the same species have different pigmentation at different latitudes), and (2) at the species assembly level (different taxa at a certain geography have different pigmentation than other taxa found at different habitats or latitudes). Concerning plants, Gloger''s rule was first proposed to operate in many plant species growing in sand dunes, sandy shores and in deserts, because of being white, whitish, or silver colored, based on white trichomes, because of sand grains and clay particles glued to sticky glandular trichomes, or because of light-colored waxes. Recently, Gloger''s rule was shown to also be true at the intraspecific level in relation to protection of anthers from UV irradiation. While Gloger''s rule is true in certain plant taxa and ecologies, there are others where “anti-Gloger” coloration patterns exist. In some of these the selective agents are known and in others they are not. I present both Gloger and “anti-Gloger” cases and argue that this largely neglected aspect of plant biology deserves much more research attention.     

"Like Owner,Like Dog": Correlation between the Owner's Attachment Profile and the Owner-Dog Bond

During recent years, several studies have revealed that human-dog relationships are based on a well-established and complex bond. There is now evidence suggesting that the dog–human affectional bond can be characterized as an “attachment”. The present study investigated possible association between the owners'' attachment profile assessed throughout a new semi-projective test (the 9 Attachment Profile) and the owner-dog attachment bond evaluated using a modified version of those used in studying human infants: Ainsworth''s “strange situation”. The findings represented the first evidence for the presence of a correlation between the owners'' attachment profile and the owner-dog attachment bond throughout procedure and behavioural analyses involving controlled observations.     

A Microscopic “Social Norm” Model to Obtain Realistic Macroscopic Velocity and Density Pedestrian Distributions

We propose a way to introduce in microscopic pedestrian models a “social norm” in collision avoiding and overtaking, i.e. the tendency, shared by pedestrians belonging to the same culture, to avoid collisions and perform overtaking in a preferred direction. The “social norm” is implemented, regardless of the specific collision avoiding model, as a rotation in the perceived velocity vector of the opponent at the moment of computation of the collision avoiding strategy, and justified as an expectation that the opponent will follow the same “social norm” (for example a tendency to avoid on the left and overtake on the right, as proposed in this work for Japanese pedestrians). By comparing with real world data, we show that the introduction of this norm allows for a better reproduction of macroscopic pedestrian density and velocity patterns.     

The “Egg of Columbus” for Making the World's Toughest Fibres

In this letter we present the “Egg of Columbus” for making fibres with unprecedented toughness: a slider, in the simplest form just a knot, is introduced as frictional element to dissipate additional energy and thus demonstrating the existence of a previously “hidden” toughness. The proof of concept is experimentally realized making the world''s toughest fibre, increasing the toughness modulus of a commercial Endumax macroscopic fibre from 44 J/g up to 1070 J/g (and of a zylon microfiber from 20 J/g up to 1400 J/g). The ideal upperbound toughness is expected for graphene, with a theoretical value of ∼10⁵ J/g. This new concept, able of maximizing (one fold increment) the structural robustness, could explain the mysterious abundance of knot formations, in spite of their incremental energy cost and topological difficulty, in biological evolved structures, such as DNA strands and proteins.     

Pathological States and Criminal Responsibility

The doctor is embarrassed in court when asked to testify to the effects of illness on a defendant''s capability “of appreciating the nature and quality of an act or omission or of knowing that an act or omission is wrong”. The source of his difficulty is traced to the legal concepts of “guilt”, “crime” and “punishment” which imply a legal view of man at variance with our modern biological view. To abolish this discrepancy we need not accept a medical model for criminal law where “crime” is analogous to “disease”, and “punishment” to “treatment”. A pragmatic approach to the handling of the criminal could exclude the notions of “guilt” and “punishment” and yet fulfil the rational goals of protecting society from the criminal and of compensating his victims.     

Pseudohypertension secondary to a noncompressible brachial artery

The interesting problem is considered of a comatose alcoholic diabetic with an extremely high systolic blood pressure, as determined by the usual means, who was subsequently found to have severe medial calcinosis and normal intraarterial blood pressure. The syndrome of the noncompressible brachial artery surely accounts for this patient''s falsely elevated blood pressure reading. Though infrequently reported, this condition can be one cause of “difficult to control” hypertension in the elderly and in the diabetic patient.     

Relativity Theory and Time Perception: Single or Multiple Clocks?

Background

Current theories of interval timing assume that humans and other animals time as if using a single, absolute stopwatch that can be stopped or reset on command. Here we evaluate the alternative view that psychological time is represented by multiple clocks, and that these clocks create separate temporal contexts by which duration is judged in a relative manner. Two predictions of the multiple-clock hypothesis were tested. First, that the multiple clocks can be manipulated (stopped and/or reset) independently. Second, that an event of a given physical duration would be perceived as having different durations in different temporal contexts, i.e., would be judged differently by each clock.

Methodology/Principal Findings

Rats were trained to time three durations (e.g., 10, 30, and 90 s). When timing was interrupted by an unexpected gap in the signal, rats reset the clock used to time the “short” duration, stopped the “medium” duration clock, and continued to run the “long” duration clock. When the duration of the gap was manipulated, the rats reset these clocks in a hierarchical order, first the “short”, then the “medium”, and finally the “long” clock. Quantitative modeling assuming re-allocation of cognitive resources in proportion to the relative duration of the gap to the multiple, simultaneously timed event durations was used to account for the results.

Conclusions/Significance

These results indicate that the three event durations were effectively timed by separate clocks operated independently, and that the same gap duration was judged relative to these three temporal contexts. Results suggest that the brain processes the duration of an event in a manner similar to Einstein''s special relativity theory: A given time interval is registered differently by independent clocks dependent upon the context.     

The gradient clusteron: A model neuron that learns to solve classification tasks via dendritic nonlinearities,structural plasticity,and gradient descent

Synaptic clustering on neuronal dendrites has been hypothesized to play an important role in implementing pattern recognition. Neighboring synapses on a dendritic branch can interact in a synergistic, cooperative manner via nonlinear voltage-dependent mechanisms, such as NMDA receptors. Inspired by the NMDA receptor, the single-branch clusteron learning algorithm takes advantage of location-dependent multiplicative nonlinearities to solve classification tasks by randomly shuffling the locations of “under-performing” synapses on a model dendrite during learning (“structural plasticity”), eventually resulting in synapses with correlated activity being placed next to each other on the dendrite. We propose an alternative model, the gradient clusteron, or G-clusteron, which uses an analytically-derived gradient descent rule where synapses are "attracted to" or "repelled from" each other in an input- and location-dependent manner. We demonstrate the classification ability of this algorithm by testing it on the MNIST handwritten digit dataset and show that, when using a softmax activation function, the accuracy of the G-clusteron on the all-versus-all MNIST task (~85%) approaches that of logistic regression (~93%). In addition to the location update rule, we also derive a learning rule for the synaptic weights of the G-clusteron (“functional plasticity”) and show that a G-clusteron that utilizes the weight update rule can achieve ~89% accuracy on the MNIST task. We also show that a G-clusteron with both the weight and location update rules can learn to solve the XOR problem from arbitrary initial conditions.     

Impulses and Physiological States in Theoretical Models of Nerve Membrane

Van der Pol''s equation for a relaxation oscillator is generalized by the addition of terms to produce a pair of non-linear differential equations with either a stable singular point or a limit cycle. The resulting “BVP model” has two variables of state, representing excitability and refractoriness, and qualitatively resembles Bonhoeffer''s theoretical model for the iron wire model of nerve. This BVP model serves as a simple representative of a class of excitable-oscillatory systems including the Hodgkin-Huxley (HH) model of the squid giant axon. The BVP phase plane can be divided into regions corresponding to the physiological states of nerve fiber (resting, active, refractory, enhanced, depressed, etc.) to form a “physiological state diagram,” with the help of which many physiological phenomena can be summarized. A properly chosen projection from the 4-dimensional HH phase space onto a plane produces a similar diagram which shows the underlying relationship between the two models. Impulse trains occur in the BVP and HH models for a range of constant applied currents which make the singular point representing the resting state unstable.     

Affective Video Retrieval: Violence Detection in Hollywood Movies by Large-Scale Segmental Feature Extraction

Without doubt general video and sound, as found in large multimedia archives, carry emotional information. Thus, audio and video retrieval by certain emotional categories or dimensions could play a central role for tomorrow''s intelligent systems, enabling search for movies with a particular mood, computer aided scene and sound design in order to elicit certain emotions in the audience, etc. Yet, the lion''s share of research in affective computing is exclusively focusing on signals conveyed by humans, such as affective speech. Uniting the fields of multimedia retrieval and affective computing is believed to lend to a multiplicity of interesting retrieval applications, and at the same time to benefit affective computing research, by moving its methodology “out of the lab” to real-world, diverse data. In this contribution, we address the problem of finding “disturbing” scenes in movies, a scenario that is highly relevant for computer-aided parental guidance. We apply large-scale segmental feature extraction combined with audio-visual classification to the particular task of detecting violence. Our system performs fully data-driven analysis including automatic segmentation. We evaluate the system in terms of mean average precision (MAP) on the official data set of the MediaEval 2012 evaluation campaign''s Affect Task, which consists of 18 original Hollywood movies, achieving up to .398 MAP on unseen test data in full realism. An in-depth analysis of the worth of individual features with respect to the target class and the system errors is carried out and reveals the importance of peak-related audio feature extraction and low-level histogram-based video analysis.     

When a Text Is Translated Does the Complexity of Its Vocabulary Change? Translations and Target Readerships

In linguistic studies, the academic level of the vocabulary in a text can be described in terms of statistical physics by using a “temperature” concept related to the text''s word-frequency distribution. We propose a “comparative thermo-linguistic” technique to analyze the vocabulary of a text to determine its academic level and its target readership in any given language. We apply this technique to a large number of books by several authors and examine how the vocabulary of a text changes when it is translated from one language to another. Unlike the uniform results produced using the Zipf law, using our “word energy” distribution technique we find variations in the power-law behavior. We also examine some common features that span across languages and identify some intriguing questions concerning how to determine when a text is suitable for its intended readership.     

It's a Wonderful Life: A Career as an Academic Scientist

Many years of training are required to obtain a job as an academic scientist. Is this investment of time and effort worthwhile? My answer is a resounding “yes.” Academic scientists enjoy tremendous freedom in choosing their research and career path, experience unusual camaraderie in their lab, school, and international community, and can contribute to and enjoy being part of this historical era of biological discovery. In this essay, I further elaborate by listing my top ten reasons why an academic job is a desirable career for young people who are interested in the life sciences.Students are attracted to careers in academic science because of their interest in the subject rather than for financial reward. But then they hear messages that make them think twice about this career choice. It is difficult to find a job: “Hear about Joe? Three publications as a postdoc and still no job offers.” The NIH pay line is low: “Poor Patricia, she is now on her third submission of her first NIH grant.” Publishing is painful: “Felix''s grad school thesis work has been rejected by three journals!” Academic jobs are demanding: “Cathy has spent her last three weekends writing grants rather than being with her family.”Such scenarios do take place, but if you think that this is what a career in academic science is about, then you need to hear the other side of the story. And this is the purpose of this article—a chance to reflect on the many good things about the academic profession. In the classic movie It''s a Wonderful Life, George Bailey is at the point of despair but regains his confidence through the wisdom and perspective of a guardian angel, Clarence. Doubt and setbacks also are bound to happen in science (as is true of other careers), but pessimism should not rule the day. It is a great profession and there are many happy endings. I would like to share my top ten reasons of why being an academic professor is a “wonderful life,” one that bright and motivated young people should continue to aspire to pursue.     

Molecular Characterization of “Candidatus Similichlamydia latridicola” gen. nov., sp. nov. (Chlamydiales: “Candidatus Parilichlamydiaceae”), a Novel Chlamydia-Like Epitheliocystis Agent in the Striped Trumpeter,Latris lineata (Forster)

Histological analysis of gill samples taken from individuals of Latris lineata reared in aquaculture in Tasmania, Australia, and those sampled from the wild revealed the presence of epitheliocystis-like basophilic inclusions. Subsequent morphological, in situ hybridization, and molecular analyses were performed to confirm the presence of this disease and discovered a Chlamydia-like organism associated with this condition, and the criteria set by Fredericks and Relman''s postulates were used to establish disease causation. Three distinct 16S rRNA genotypes were sequenced from 16 fish, and phylogenetic analyses of the nearly full-length 16S rRNA sequences generated for this bacterial agent indicated that they were nearly identical novel members of the order Chlamydiales. This new taxon formed a well-supported clade with “Candidatus Parilichlamydia carangidicola” from the yellowtail kingfish (Seriola lalandi). On the basis of sequence divergence over the 16S rRNA region relative to all other members of the order Chlamydiales, a new genus and species are proposed here for the Chlamydia-like bacterium from L. lineata, i.e., “Candidatus Similichlamydia latridicola” gen. nov., sp. nov.     

Roles of leader and follower cells in collective cell migration

Collective cell migration is a widely observed phenomenon during animal development, tissue repair, and cancer metastasis. Considering its broad involvement in biological processes, it is essential to understand the basics behind the collective movement. Based on the topology of migrating populations, tissue-scale kinetics, called the “leader–follower” model, has been proposed for persistent directional collective movement. Extensive in vivo and in vitro studies reveal the characteristics of leader cells, as well as the special mechanisms leader cells employ for maintaining their positions in collective migration. However, follower cells have attracted increasing attention recently due to their important contributions to collective movement. In this Perspective, the current understanding of the molecular mechanisms behind the “leader–follower” model is reviewed with a special focus on the force transmission and diverse roles of leaders and followers during collective cell movement.