An outline of functional self-organization in V1: synchrony, STLR and Hebb rules

A model of self-organization of synapses in the striate cortex is described, and its functional implications discussed. Principal assumptions are: (a) covariance of cell firing declines with distance in cortex, (b) covariance of stimulus characteristics declines with distance in the visual field, and (c) metabolic rates are approximately uniform in all small axonal segments. Under these constraints, Hebbian learning implies a maximally stable synaptic configuration corresponding to anatomically and physiologically realistic ‘‘local maps’’, each of macro-columnar size, and each organized as Möbius projections of a “global map” of retinotopic form. Convergence to the maximally stable configuration is facilitated by the spatio-temporal learning rule. A tiling of V1, constructed of approximately mirror-image reflections of each local map by its neighbors, is formed. The model supplements standard concepts of feed-forward visual processing by introducing a new basis for contextual modulation and neural network identifications of visual signals, as perturbation of the synaptic configuration by rapid stimulus transients. On a long time-scale, synaptic development could overwrite the Möbius configuration, while LTP and LTD could mediate synaptic gain on intermediate time-scales.     

Continuum electrostatic analysis of preferred solvation sites around proteins in solution

To understand water-protein interactions in solution, the electrostatic field is calculated by solving the Poisson-Boltzmann equation, and the free energy surface of water is mapped by translating and rotating an explicit water molecule around the protein. The calculation is applied to T4 lysozyme with data available on the conservation of solvent binding sites in 18 crystallographically independent molecules. The free energy maps around the ordered water sites provide information on the relationship between water positions in crystal structure and in solution. Results show that almost all conserved sites and the majority of nonconserved sites are within 1.3 A of local free energy minima. This finding is in sharp contrast to the behavior of randomly placed water molecules in the boundary layer, which, on the average, must travel more than 3 A to the nearest free energy minimum. Thus, the solvation sites are at least partially determined by protein-water interactions rather than by crystal packing alone. The characteristic water residence times, obtained from the free energies at the local minima, are in good agreement with nuclear magnetic resonance experiments. Only about half of the potential sites show up as ordered water in the 1.7 A resolution X-ray structure. Crystal packing interactions can stabilize weak or mobile potential sites (in fact, some ordered water positions are not close to free energy minima) or can prevent water from occupying certain sites. Apart from a few buried water molecules that are strong binders, the free energies are not very different for conserved and nonconserved sites. We show that conservation of a water site between two crystals occurs if the positions of protein atoms, primarily contributing to the free energy at the local minimum, do not substantially change from one structure to the other. This requirement can be correlated with the nature of the side chain contacting the water molecule in the site.     

The value of coarse species range maps to inform local biodiversity conservation in a global context

Range maps of thousands of species, compiled and made freely available by the International Union for Conservation of Nature, are being increasingly applied to support spatial conservation planning. However, their coarse nature makes them prone to commission and omission errors, and they lack information on the variations in abundance within species’ distributions, calling into question their value to inform decisions at the fine scales at which conservation often takes place. Here, we tested if species ranges can reliably be used to estimate the responsibility of sites for the global conservation of species. We defined ‘specific responsibility’ as the fraction of a species’ population within a given site, considering it useful for prioritising species within sites; and defined ‘overall responsibility’ as the sum of specific responsibility across species within a site, assuming it informative of priorities among sites. Taking advantage of an exceptionally detailed dataset on the distribution and abundance of bird species at a near‐continental scale – a level of information rarely available to local decision‐makers – we created a benchmark against which we tested estimates of responsibility derived from range maps. We investigated approaches for improving these estimates by complementing range maps with plausibly available local data. We found that despite their coarse nature, range maps provided good estimates of sites’ overall responsibility, but relatively poor estimates of specific responsibility. Estimates were improved by combining range maps with local species lists or local abundance data, easily available through local surveys on the sites of interest, or simulated expert knowledge. Our results suggest that combining range maps with local data is a promising route for improving the effectiveness of local conservation decisions at contributing to reducing global biodiversity losses. This is all the more urgent in hyper‐diverse poorly‐known regions where conservation‐relevant decisions must proceed despite a paucity of biodiversity data.     

A modified error backpropagation algorithm for complex-value neural networks

The complex-valued backpropagation algorithm has been widely used in fields of dealing with telecommunications, speech recognition and image processing with Fourier transformation. However, the local minima problem usually occurs in the process of learning. To solve this problem and to speed up the learning process, we propose a modified error function by adding a term to the conventional error function, which is corresponding to the hidden layer error. The simulation results show that the proposed algorithm is capable of preventing the learning from sticking into the local minima and of speeding up the learning.     

Cover-Encodings of Fitness Landscapes

The traditional way of tackling discrete optimization problems is by using local search on suitably defined cost or fitness landscapes. Such approaches are however limited by the slowing down that occurs when the local minima that are a feature of the typically rugged landscapes encountered arrest the progress of the search process. Another way of tackling optimization problems is by the use of heuristic approximations to estimate a global cost minimum. Here, we present a combination of these two approaches by using cover-encoding maps which map processes from a larger search space to subsets of the original search space. The key idea is to construct cover-encoding maps with the help of suitable heuristics that single out near-optimal solutions and result in landscapes on the larger search space that no longer exhibit trapping local minima. We present cover-encoding maps for the problems of the traveling salesman, number partitioning, maximum matching and maximum clique; the practical feasibility of our method is demonstrated by simulations of adaptive walks on the corresponding encoded landscapes which find the global minima for these problems.     

Energy landscapes and properties of biomolecules

Thermodynamic and dynamic properties of biomolecules can be calculated using a coarse-grained approach based upon sampling stationary points of the underlying potential energy surface. The superposition approximation provides an overall partition function as a sum of contributions from the local minima, and hence functions such as internal energy, entropy, free energy and the heat capacity. To obtain rates we must also sample transition states that link the local minima, and the discrete path sampling method provides a systematic means to achieve this goal. A coarse-grained picture is also helpful in locating the global minimum using the basin-hopping approach. Here we can exploit a fictitious dynamics between the basins of attraction of local minima, since the objective is to find the lowest minimum, rather than to reproduce the thermodynamics or dynamics.     

A neural field model of the somatosensory cortex: formation, maintenance and reorganization of ordered topographic maps

We investigate the formation and maintenance of ordered topographic maps in the primary somatosensory cortex as well as the reorganization of representations after sensory deprivation or cortical lesion. We consider both the critical period (postnatal) where representations are shaped and the post-critical period where representations are maintained and possibly reorganized. We hypothesize that feed-forward thalamocortical connections are an adequate site of plasticity while cortico-cortical connections are believed to drive a competitive mechanism that is critical for learning. We model a small skin patch located on the distal phalangeal surface of a digit as a set of 256 Merkel ending complexes (MEC) that feed a computational model of the primary somatosensory cortex (area 3b). This model is a two-dimensional neural field where spatially localized solutions (a.k.a. bumps) drive cortical plasticity through a Hebbian-like learning rule. Simulations explain the initial formation of ordered representations following repetitive and random stimulations of the skin patch. Skin lesions as well as cortical lesions are also studied and results confirm the possibility to reorganize representations using the same learning rule and depending on the type of the lesion. For severe lesions, the model suggests that cortico-cortical connections may play an important role in complete recovery.     

Conformational switching upon phosphorylation: a predictive framework based on energy landscape principles

We investigate how post-translational phosphorylation modifies the global conformation of a protein by changing its free energy landscape using two test proteins, cystatin and NtrC. We first examine the changes in a free energy landscape caused by phosphorylation using a model containing information about both structural forms. For cystatin the free energy cost is fairly large indicating a low probability of sampling the phosphorylated conformation in a perfectly funneled landscape. The predicted barrier for NtrC conformational transition is several times larger than the barrier for cystatin, indicating that the switch protein NtrC most probably follows a partial unfolding mechanism to move from one basin to the other. Principal component analysis and linear response theory show how the naturally occurring conformational changes in unmodified proteins are captured and stabilized by the change of interaction potential. We also develop a partially guided structure prediction Hamiltonian which is capable of predicting the global structure of a phosphorylated protein using only knowledge of the structure of the unphosphorylated protein or vice versa. This algorithm makes use of a generic transferable long-range residue contact potential along with details of structure short range in sequence. By comparing the results obtained with this guided transferable potential to those from the native-only, perfectly funneled Hamiltonians, we show that the transferable Hamiltonian correctly captures the nature of the global conformational changes induced by phosphorylation and can sample substantially correct structures for the modified protein with high probability.     

Effect of branching in 4-alkylpyrazoles on liver alcohol dehydrogenase inhibition: A shape analysis study

Shape analysis methodology is applied to the study of 4-alkylpyrazoles which are known inhibitors of liver alcohol dehydrogenase. Elongation of the alkyl chain increases the inhibitory power, whereas branching of the chain diminishes the activity. These two counterpoised effects are studied simultaneously in a selected set of 4-alkylpyrazoles. A systematic conformational analysis followed by topological characterization of the van der Waals surfaces of all the local minima restricts the conformational space to potential bioactive structures. The analysis of the interrelation between the molecular electrostatic potential and van der Waals surfaces provides certain shape codes characteristic of each 4-alkylpyrazole. In both topological analyses van der Waals surfaces and molecular electrostatic potential van der Waals surface interrelations) graphical representations and analytical methods were used. A good correlation between the shape codes and the inhibitory activity is found for the linear derivatives. For branched pyrazoles, a tendency in their inhibitory power is predicted. Isopentylpyrazole is suggested to have the same inhibitory profile as 4-butylpyrazole, the linear derivative with one less carbon atom.     

Effects of errors in range maps on estimates of historical species richness of mammals in Canadian national parks

Aim Tests for faunal relaxation in reserves, particularly for mammals, have relied on comparisons of current species richness with estimates of species richness derived from historical range maps. However, any range map reflects the extent of occurrence of species and not necessarily the area of occupancy. Thus, estimates of historical species richness might be prone to error introduced by ‘false positives’, that is, a species might be considered to have been present in locations where it actually was not. The effect of such ‘false positives’ could bias statistical tests of faunal relaxation to type I error, and result in estimates of the extent of faunal relaxation in reserves greater than was actually the case. We evaluated the potential for errors in historical range maps to generate inflated estimates of historical species richness of mammals at sites that are reserves today. Location Canadian national parks in the Canadian portion of the Alleghenian‐‐Illinoian mammal province in south‐eastern Canada (the maritime region and parts of southern Québec, Ontario and Manitoba). Methods The effect of varying levels of error in range maps on estimates of historical species richness was tested using geographical information systems (GIS)‐based statistical sampling of simulated historical ranges. Species’ areas of occupancy were simulated to be only 25%, 75% and 95% of published historical species ranges. For each reserve, estimates of historical species richness from these simulated species ranges were then compared with similar, previously published estimates of richness based on published historical species ranges. Results Previous estimates of historical species richness for reserves were inversely and linearly related to the degree of inaccuracy of species ranges. If species ranges were, on average, 5% smaller than the accepted ranges, then estimates of historical species richness agreed with previous estimates in c. 90% of cases. However, if historical ranges were, on average, 25% smaller than those used in previous analyses, then previous historical estimates of species richness may be overestimates in c. 40% of cases. Main conclusions Estimates of the extent of faunal relaxation in reserves that use historical range maps to quantify past species richness appear to be sensitive to even small errors in the degree to which range maps may overestimate ‘area of occupancy’.     

An investigation of electrical breakdown of bimolecular lipid membranes

The investigation is concerned with the irreversible electrical breakdown of bimolecular lipid membranes, depending on the velocity of linear voltage scanning. It was found that the membrane breakdown potential depended on the velocity of electric field variation. For instance, at voltage scanning velocities of up to 0.1 V/s, the rupture of membrane from glycerol monooleate occurs at 0.20–0.25 V and, at velocities higher than 1 V/s, at 0.5–0.6 V. Then the film breakdown depending on lipid phase transition was studied. At high velocities of imposed voltage scanning, the disruption of the bimolecular lipid membranes was shown not to depend on their phase states; at the same time, at low velocities, one could note a slight difference in the stability of the films at temperatures higher and lower than those of the phase transition. Whereas transition from gel to liquid-crystalline state involves transition from an ordered to a less ordered membrane structure with a sharp increase in the number of defects in the membrane, the authors, conclude that the film breakdown in the second case occurs by the ‘defect’ mechanism suggested earlier. It was also assumed that, in certain cases involving low velocities of voltage scanning, membrane breakdown may occur because of variation in the interfacial tension and in the contact angle between the film and torus. Possible mechanisms of the membrane irreversible electrical breakdown at high velocities of voltage variation are discussed. It was shown that breakdown should occur as a result of membrane compression in an electric field by a mechanism previously examined. The elastic moduli of a number of membranes were calculated by the breakdown criterion suggested earlier. They were found to coincide with the results of other investigators and, depending on the type of lipid, to equal 10⁵–10⁶ Pa.     

IS GLOBAL ETHICS MORAL NEO‐COLONIALISM? AN INVESTIGATION OF THE ISSUE IN THE CONTEXT OF BIOETHICS

This paper considers the possibility and desirability of global ethics in light of the claim that ‘global ethics’ in any form is not global, but simply the imposition of one form of local ethics – Western ethics – and, as such, a form of moral neo‐colonialism. The claim that any form of global ethics is moral neo‐colonialism is outlined using the work of a group of ‘developing world bioethicists’ who are sceptical of the possibility of global ethics. The work of virtue ethicists is then introduced and compared to the position of the developing world bioethicists in order to show that the divide between ‘Western’ and ‘non‐Western’ ethics is exaggerated. The final section of the paper turns to the practical arena and considers the question of global ethics in light of practical issues in bioethics. The paper concludes that practical necessity is driving the creation of global ethics and thus the pertinent question is no longer ‘Whether global ethics?’, but ‘Why global ethics?’.     

Learning, memory, and the role of neural network architecture

The performance of information processing systems, from artificial neural networks to natural neuronal ensembles, depends heavily on the underlying system architecture. In this study, we compare the performance of parallel and layered network architectures during sequential tasks that require both acquisition and retention of information, thereby identifying tradeoffs between learning and memory processes. During the task of supervised, sequential function approximation, networks produce and adapt representations of external information. Performance is evaluated by statistically analyzing the error in these representations while varying the initial network state, the structure of the external information, and the time given to learn the information. We link performance to complexity in network architecture by characterizing local error landscape curvature. We find that variations in error landscape structure give rise to tradeoffs in performance; these include the ability of the network to maximize accuracy versus minimize inaccuracy and produce specific versus generalizable representations of information. Parallel networks generate smooth error landscapes with deep, narrow minima, enabling them to find highly specific representations given sufficient time. While accurate, however, these representations are difficult to generalize. In contrast, layered networks generate rough error landscapes with a variety of local minima, allowing them to quickly find coarse representations. Although less accurate, these representations are easily adaptable. The presence of measurable performance tradeoffs in both layered and parallel networks has implications for understanding the behavior of a wide variety of natural and artificial learning systems.     

The ecosystem service assessment challenge: Reflections from Flanders-REA

This paper aims to improve ecosystem assessment practice by sharing the lessons learned from the Flanders Regional Ecosystem Assessment. The ‘EU biodiversity strategy to 2020’, requests the EU member states ‘to map and assess the state of ecosystems and their services by 2014’. However, a large number of member states have yet to start this assessment, and depend on assistance from the European Commission and on experiences from ongoing national assessments. In the region of Flanders (Belgium), several ecosystem service projects have since 2009 led the way to the ‘Flanders Regional Ecosystem Assessment’ (Flanders-REA), led by the governments’ leading research institute on biodiversity. To attain high regional requirements on scientific quality, acceptance and effective local policy impact, this assessment has tackled a number of challenges. The challenges discussed in this paper are obtaining conceptual clarity and consensus across disciplines and partners, the integration of multiple sources of information, critical handling of maps and the inclusion of experts and stakeholders. This paper also critically reflects on the definition of EU targets, their implementation, the current EU assistance to the member states, and the alignment with actual local and global policy needs.     

The annual Day of the Dead song contest: musical‐linguistic ideology and practice,piratability, and the challenge of scale

Building on research theorizing scale, this article proposes augmentations to existing frameworks that will help illuminate how localities are linked to ‘stranger collectives’ like nations, ethnicities, and global religious ‘communities’. In this case of ethnic revival from Mexico's Sierra Mazateca, people use new vernacular literacy practices tied to local musical performances as a way of ‘customizing’ modular forms deployed by national and global institutions to manage indigenous difference. People ‘re‐imagine’ locality through a localized indigenous literacy that takes templates provided by the Mexican state and the Catholic Church and places them in productive tension with local context: musical properties of the indigenous language Mazatec, locally valued performance practices, and local musical‐linguistic ideologies. While this revival movement draws on immanently modular forms, once locally embedded they become ‘unpiratable’, and constitute a new resource for inscribing local belonging. This case suggests the importance of considering linguistic and musical aspects of social context often taken for granted in anthropological investigations of scale.     

Dimensional oscillation. A fast variation of energy embedding gives good results with the AMBER potential energy function.

The structure of the AMBER potential energy surface of the cyclic tetrapeptide cyclotetrasarcosyl is analyzed as a function of the dimensionality of coordinate space. It is found that the number of local energy minima decreases as the dimensionality of the space increases until some limit at which point equipotential subspaces appear. The applicability of energy embedding methods to finding global energy minima in this type of energy-conformation space is explored. Dimensional oscillation, a computationally fast variant of energy embedding is introduced and found to sample conformation space widely and to do a good job of finding global and near-global energy minima.     

Understanding global patterns in amphibian geographic range size: does Rapoport rule?

Aim Species geographic ranges are the ‘fundamental units’ of macroecology. Range size is a major correlate of extinction risk in many groups, and is also critical in studies of biotic responses to climate change. Despite this, there is a lack of studies exploring the role of environmental, historical and anthropogenic processes in determining large‐scale patterns in range size. We perform the first global analysis of putative drivers of range size variation in any group, choosing amphibians as our study taxon. Our aims are to disentangle the many hypothesized causes of range size variation and evaluate support for ‘Rapoport's rule’, the observation that range size correlates with latitude. Location Global. Methods We develop a global map of gridded median range size using the International Union for Conservation of Nature (IUCN) distribution maps. From this we perform spatial and non‐spatial regressions to explore relationships between range size and nine hypothesized variables in six biogeographic realms. We use information‐theoretic model selection to compare multiple competing variables, simultaneously evaluating the relative support for each one. Results Current climate – environmental water and energy, and temperature seasonality – is consistently highly ranked in spatial and non‐spatial analyses. Human impacts and other environmental measures (topographic and landscape complexity, effective area, climate extremes) show mixed support, and glacial history is consistently unimportant. Our findings add further evidence to the view that Rapoport's rule is a regional, not global, phenomenon. Main conclusions The primary importance of temperature seasonality may explain why Rapoport's rule is largely restricted to northern latitudes, as this is where seasonality is most pronounced. More generally, the dominance of contemporary climate in our analyses (even when accounting for space) has stark implications for the future status of amphibians. Changes in climate will almost certainly interact with the anthropogenic processes already threatening a third of amphibians globally, with the effects being most keenly felt by species with a restricted range.     

Conformational analysis of cytokinins and analogs

The conformational energy surfaces of 12 active cytokinins and analogs are studied with the aid of PCILO quantum mechanical calculations. The resulting conformational energy maps indicate that cytokinin activity is associated with the ability of the above molecules to attain a specific conformation, presumably related to their conformation at the active site of cytokinin receptor(s). The calculations locate the conformational energy minima and describe the flexibility of the studied molecules in terms of conformational barriers and transition paths. An approximate relation is found between cytokinin activity and the values of energy barriers to transitions between certain local minima. According to this relation, active compounds should have rotational barriers within 4–12 kcal/mol, besides the known hitherto constitutional requirements for high physiological activity.     

Quantum chemical calculation of the (S)-9-(2,3-dihydroxypropyl)adenine molecule.

Quantum chemical calculations of conformational maps of the molecule of a new virostatic agent (S)-9-(2,3-dihydroxypropyl)adenine were performed. The thermodynamically most advantageous conformation I corresponds, for the D-series, to the alpha-ribo configuration, while the following minima, which are close in energy (II,III), correspond to beta-ribo and beta-xylo configurations.     

Assessing understanding in biology

This paper discusses several new assessment strategies that encourage meaningful learning and conceptual understanding in the biological sciences. Our purpose is to introduce a handful of evaluation and measurement techniques that help students assimilate well-integrated, strongly cohesive frameworks of interrelated concepts as a way of facilitating ‘real understanding’ of natural phenomena. Among these methods are concept maps, V diagrams, SemNet software, image-based test items, clinical interviews, portfolios, written products, performance measures, and conceptual diagnostic tests. Evidence suggests that these methods are most useful at highlighting ‘alternative conceptions’ and assisting students who wish to ‘learn how to learn’.