Analogical Mapping Research Articles

Using descriptions of biological phenomena for idea generation

Biomimetic design uses biological phenomena to inspire solutions to engineering problems. While many examples of biomimetic design involved detailed understanding of a particular biological phenomenon, the level of understanding required for idea generation is unclear. This paper reports on a study of how descriptions of biological phenomena are used to develop concepts for a simple problem. This study is a continuation of past work on the use of biological analogies for concept generation. Since previous studies had revealed difficulties with fixation and mapping, participants in this study were provided with support for analogical mapping. While participants were observed to extract strategies consistent with the biological phenomena presented, they persisted in applying strategies to specific attributes of the example problem. Since concepts generated varied with attributes chosen, applying the strategy to each possible attribute of the example problem may result in a larger variety of solutions.

Genetic mapping of disease resistance gene analogs from the Italian ryegrass (Lolium multiflorum Lam.) genome

Genomic DNA sequences homologous to the nucleotide binding site (NBS)-leucine-rich repeat (LRR) genes were mapped for Italian ryegrass (Lolium multiflorum Lam.) by using previously published disease resistance gene analogs (RGAs). The RGAs were cloned by means of a nested polymerase chain reaction (PCR) approach with degenerate primers designed from conserved regions of the NBS domain of plant disease resistance genes (R-genes), and primer pairs for specific sequence-tagged sites (STS) were subsequently designed for efficient generation of the RGA fragments. To map the RGA clones on the Italian ryegrass genetic map, an F1 mapping family was used for the detection of restriction-site polymorphisms of the RGA fragments. Out of 50 RGA fragments, 11 detected genetic polymorphism in the F1 family. Polymorphic marker loci data were used for linkage analysis with JoinMap version 3.0. The linkage analysis revealed that 10 of the 11 RGAs were mapped in seven linkage groups constructed with amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR), and expressed sequence tag (EST)-derived cleaved amplified polymorphic sequence (CAPS) markers. This information will be useful for the development of new genetic markers linked to genes associated with disease resistance.

Daily summer monsoon rainfall over northeast India due to synoptic scale systems

The summer monsoon rainfall over northeast India mostly depends on the synoptic systems over the region and neighbourhood and the convection due to the interaction of orography with the synoptic and sub-synoptic scale systems. Hence, an attempt is made to analyse the mean daily rainfall distribution over northeast India due to different synoptic systems like Low Pressure Systems (LPS) and cyclonic circulations (cycir) extending upto lower/middle tropospheric levels over different regions. The mean daily rainfall due to monsoon trough over various locations in northeast India is also analysed. For the above purpose, the rainfall data over 50 uniformly distributed stations in northeast India during summer monsoon season (June-September) for a period of 10 years (1991-2000) are considered. The principal objective of the study is to find out the contribution of the different synoptic systems to the spatial variability of monsoon rainfall over northeast India.
 
 The developed synoptic analog maps may be useful to the forecasters for 24 hours rainfall forecast with the knowledge of location, intensity and movement of the synoptic systems. Based on larger data set, the results confirm the earlier findings (Srinivasan et al., 1972) with respect to rainfall due to monsoon trough and LPS. The Low Level Cycir (LLC) also plays significant role on the rainfall variability over northeast India, as the number of LLC days is significantly higher over the region, contrary to the days of occurrence of LPS. The study finds out the regions of excess/deficient rainfall and active/weak monsoon conditions due to different synoptic systems.

Bootstrapping Processes in the Development of Students' Commonsense Matter Theories: Using Analogical Mappings, Thought Experiments, and Learning to Measure to Promote Conceptual Restructuring

This study explores whether the development of students' understanding of matter as something that occupies space and has weight involves conceptual change and restructuring rather than only simple belief revision. Based on an analysis of how the concepts in students' initial matter theory (henceforth MT1) may differ from the concepts in the matter theory that is a target of middle school instruction (MT2), I propose ways that concepts in a given theory cohere with each other and identify the sources of the new ideas in MT2 and the learning processes by which those new ideas can be acquired. I test implications of these analyses by designing a curriculum unit that exploits these learning mechanisms, by using the curriculum with 4 classes of eighth-grade Earth Science students, and by assessing 42 students' thinking about matter, object size, and weight (via individual interviews and written tests) before and after the teaching unit. Consistent with the hypothesis of conceptual restructuring, the data not only show coherencies in students' thinking about matter, size, and weight before and after teaching, but also coordinated patterns of change. The implications for the design of science instruction are discussed.

On Metre in the Rondo of Brahms’s Op. 25

ABSTRACTThe rondo from Brahms's Piano Quartet Op. 25 projects a number of different metres which may be organised into various metric spaces modelled on those of David Lewin and Richard Cohn. Although this organisation does not yield the multiple pitch‐time analogical mappings proposed by Lewin and Cohn, it may be fruitfully applied to many works of Brahms and other composers. I argue that a movement's centrally located metre (the work's ‘logical’ metric tonic) tends also to be its primary metre (the work's ‘rhetorical’ metric tonic), and outline a new method for hearing contiguities in certain metric spaces. I conclude by designing a metric space tailored for the metres of the Op. 25 rondo, in which the refrain's ‘tonic’ metre is centrally located in three dimensions.

Global-scale mapping of economic benefits from agricultural lands: Implications for conservation priorities

Research in systematic conservation planning has focused heavily on biological considerations, even though a growing number of studies demonstrate that integrating economic costs into the planning process markedly increases the efficiency of resulting plans. At the global scale, the availability of biodiversity maps is increasing, but analogous maps for economic factors that affect biodiversity conservation are rare, and no study has examined global conservation planning at high resolution using both biodiversity and cost information. Here, we integrate spatial information on crop productivity, livestock density, and prices to produce a global map of the gross economic rents from agricultural lands. We then illustrate the importance of including such opportunity costs in global planning for the conservation of endemic vertebrate species. Plans that consider costs represent endemic species at 10–33% of the opportunity cost of plans that do not, and produce priority sets that diverge from existing schemes. Given scarce resources and the great cost-effectiveness of plans that consider both biodiversity and costs, mapping of the economic costs of conservation should receive similar levels of research attention as mapping of biodiversity.

Mapping of genome-wide resistance gene analogs (RGAs) in maize (Zea mays L.)

Isolation and mapping of genome-wide resistance (R) gene analogs (RGAs) is of importance in identifying candidate(s) for a particular resistance gene/QTL. Here we reported our result in mapping totally 228 genome-wide RGAs in maize. By developing RGA-tagged markers and subsequent genotyping a population consisting of 294 recombinant inbred lines (RILs), 67 RGAs were genetically mapped on maize genome. Meanwhile, in silico mapping was conducted to anchor 113 RGAs by comparing all 228 RGAs to those anchored EST and BAC/BAC-end sequences via tblastx search (E-value < 10(-20)). All RGAs from different mapping efforts were integrated into the existing SSR linkage map. After accounting for redundancy, the resultant RGA linkage map was composed of 153 RGAs that were mapped onto 172 loci on maize genome, and the mapped RGAs accounted for approximate three quarters of the genome-wide RGAs in maize. The extensive co-localizations were observed between mapped RGAs and resistance gene/QTL loci, implying the usefulness of this RGA linkage map in R gene cloning via candidate gene approach.

The Micro-Category account of analogy

Here, we investigate how activation of mental representations of categories during analogical reasoning influences subsequent cognitive processing. Specifically, we present and test the central predictions of the “Micro-Category” account of analogy. This account emphasizes the role of categories in aligning terms for analogical mapping. In a semantic priming paradigm, a four-word analogy task was compared to two other four-word tasks. Stimuli were identical in all tasks; only the instructions given to participants differed. Participants were instructed to identify analogy relations, category relations, or conventionalized semantic relations in the four-word sets. After each four-word set, a single target word appeared and participants named this word aloud. Target words that referred to category relations in the preceding four-word sets were primed as strongly when participants identified analogies as when participants identified categories, suggesting that activation of category concepts plays an important role in analogical thinking. In addition, priming of category-referent words in the analogy and category tasks was significantly greater than priming of these words when participants identified conventionalized semantic relations. Since identical stimuli were used in all conditions, this finding indicates that it is the activation of category relations, distinct from any effect of basic semantic association, that causes analogical reasoning to prime category-referent words. We delineate how the “Micro-Category” account of analogy predicts these phenomena and unifies findings from diverse areas of research concerning analogical reasoning.

Beyond the Shadow

This paper attempts to probe into the philosophical foundations of organizational theories. By reflecting upon several lofty philosophies and ideas, this paper argues that the convention of functionalism, primarily rests on analogical mapping, possesses inadequate grounding about omitting human issues. By contrast, humanism overstresses non-determinist property of the human mind, and ignores the objective constraints of lifeless entities. Grounded on these arguments, this paper proposes multiple perspectives to complement diverse convictions. The proposed idea seeks to increase the variety of a management system, and an effective intervention in organizational problems.

Commentary on Le Corre & Carey

The experiments reported by Le Corre and Carey were designed to test a form of the analog mapping hypothesis, but not to test the hypothesis advanced by Gallistel and Gelman (1992). Our hypothesis is that very early in the prolonged process of learning verbal counting children recognize 2 that the structure and function of verbal counting are the same as the structure and function of their pre-verbal counting system. Both processes honor the one-one, stable order, and cardinal principles, and both processes deliver symbols that are subject to arithmetic processing. Gelman and her coauthors (Gelman, 1998; Gelman & Lucariello, 2002; Gelman & Williams, 1998) have argued that this recognition of common structure and function is mediated by a more general process that she calls structure mapping, which plays an important role in many other aspects of cognitive development. The Gallistel and Gelman (1992) hypothesis is that it is the early recognition that there is a mapping of both structure and function that drives the long, slow process of learning the bidirectional maps – the mapping from the mental magnitudes to the corresponding count words and the mapping from the count words to the corresponding mental magnitudes. The process of learning these two mappings never goes to completion in that count words like ‘million’, ‘billion’, and ‘trillion’ probably do not map to useable mental magnitudes in most adults. On our hypothesis, counting is a numerically meaningful activity even in children who are very bad counters. They already understand that counting yields a word that represents cardinality and that words representing cardinality are principal players in talk about arithmetic operations, such as addition and subtraction. Thus, we take

Response to Spackman's comment onOn the calculation of the electrostatic potential, electric field and electric field gradient from the aspherical pseudoatom model

We fully agree with Spackman’s tribute to the considerable contribution of R. F. Stewart to the field of charge-density analysis and will restrict our comments to the second half of his letter which discusses a number of issues relevant to the results presented in our paper (Volkov, King et al., 2006). Mark Spackman (MS) states that ‘it is worth noting that the map presented by VKCF is based on a direct-space summation of contributions from only the eight nearest neighbours in the crystal’, implying that the figure presented will change significantly if more neighbouring molecules are included in the calculation. In Fig. 1 below, we present analogous maps obtained by taking into account the contributions of pseudoatoms within several unit cells (this option was available in the latest version of XD2006 at the time our original paper was published). Only small changes are observed on the periphery of the map, which do not in any way change any of the conclusions presented in our paper. For the calculation of the electrostatic potential (ESP), electric field (EF) and electric field gradient (EFG), we use the same EPMM approach (Volkov et al., 2004) developed for calculation of the electrostatic interaction energy. Exact formulae are used for atoms located within a certain distance (typically ~6 A for the ESP, EF and EFG in organic systems) from the point at which the properties are calculated. Beyond that distance, approximate formulae, based on the expansion of the ESP, EF and EFG in atomic multipole moments, are used. Table 1 includes a comparison between exact and EPMM methods, demonstrating the satisfactory accuracy of the much faster (Table 2) EPMM method. Table 3 shows the convergence of the x and y components of the EF vector in the plane of the map versus the number of unit cells included in the calculation. An excellent convergence is achieved when including atoms with fractional coordinates of 1 < x, y, z < 2, while the inclusion of eight neighbouring cells is also quite satisfactory, i.e. the r.m.s. deviation is only 0.02–0.03 e A , which is less than 1% of the r.m.s. values of the Ex (~5.4 e A ) and Ey (~6.5 e A ) components of the EF vector in the plane of the map. Note that a similar direct-space approach is used for the calculation of the electrostatic binding energy in the crystal (Volkov et al., 2007), which has also been implemented in XD2006 (Volkov, Macchi et al., 2006). The efficient combination of the exact formulae and the multipole moment approximation eliminates the convergence problems inferred by MS. MS quotes Cummins et al. (1976) that ‘computation of the EF in the crystal due to point dipoles is well known to require lattice summation techniques to achieve convergence’ and adds that ‘these combined approaches are entirely analogous to the Ewald approach used to achieve rapid convergence of lattice sums.’ We are of course well aware of the existence of the Ewald summation techniques which we used previously in the calculation of the lattice energy of ionic (Su & Coppens, 1995) and molecular (Abramov, Volkov, Wu & Coppens, 2000a,b; Abramov, Volkov & Coppens, 2000) crystals. However, the direct-space summation was found to be advantageous in terms of both speed and ease of implementation when combined with the new EPMM method (Volkov et al., 2007). MS states that we misunderstand the purpose of the methods described by Brown & Spackman (1994) as several algorithms published in this paper were used only for debugging of the VALRAY code and should not be considered of practical importance. Table 1 Root-mean-squared differences in electric field components Ex and Ey (e A ) in the plane of the map between exact and EPMM calculations .

Nonintentional analogical inference in text comprehension

We present findings suggesting that analogical inference processes can play a role in fluent comprehension and interpretation. Participants were found to use information from a prior relationally similar example in understanding the content of a later example, but they reported that they were not aware of having done so. These inference processes were sensitive to structural mappings between the two instances, ruling out explanations based solely on more general kinds of activation, such as priming. Reading speed measures were consistent with the possibility that these inferences had taken place during encoding of the target rather than during the later recognition test. These findings suggest that analogical mapping, though often viewed as an explicit deliberative process, can sometimes operate without intent or even awareness.

Evaluating Flood Hazard for Land-Use Planning in Greater Dhaka of Bangladesh Using Remote Sensing and GIS Techniques

Floods are a common feature in rapidly urbanizing Dhaka and its adjoining areas. Though Greater Dhaka experiences flood almost in every year, flood management policies are mostly based on structural options including flood walls, dykes, embankments etc. Many shortcomings of the existing flood management systems are reported in numerous literatures. The objective of this paper is to assess flood hazard in Greater Dhaka for the historical flood event of 1998 using Synthetic Aperture Radar (SAR) data with GIS data. Flood-affected frequency and flood depth calculated from the multi-date SAR imageries were used as hydrologic parameters. Elevation heights, land cover classification, geomorphic division and drainage network data generated from optical remote sensing and analogue maps were used through GIS approach. Using a ranking matrix in three dimensional multiplication mode, flood hazard was assessed. All possible combination of flood hazard maps was prepared using land-cover, geomorphology and elevation heights for flood-affected frequency and floodwater depth. Using two hazard maps which produced the highest congruence for flood frequency and flood depth, a new flood hazard map was developed by considering the interactive effect of flood-affected frequency and floodwater depth, simultaneously. This new hazard map can provide more safety for flood countermeasures because pixels belonging to higher hazard degrees were increased due to the consideration of higher degrees of ranks. The estimation of flood hazard areas revealed that a major portion of Greater Dhaka comprised moderate to very high hazard zone. Only a little portion (8.04%) was found to be the least vulnerable to potential flood hazard. Conversely, 28.70% of Greater Dhaka was found within very high hazard zone. Based on this study, comprehensive flood hazard management strategies for land use planning decision were proposed for the efficient management of future flood disasters.

Using Remote Sensing and GIS Techniques for Quick Estimation of the URBAN Growth in the North Region of Khartoum State

Satellite imagery acquired by IKONOS imaging system in 2003 and the analog map of the study area at scale 1:25000 (1984) have been used to estimate the urban growth taken place in the study area during the period 1984-2003. Remote sensing, digital image processing and GIS techniques were used to map this growth. Different procedures have been applied to the test data to achieve the objectives of this study. Image restoration as well as map projection and rectification operations were adopted to bring the test data at a common geo-reference coordinate system (UTM). Image enhancement and spatial topology processes have been applied and constructed to achieve the virtual representation of the real world. Analysis and overlay process were applied to the test data to model the urban growth in the study area between the year 1984 and the year 2003. The estimated amount of the urban growth was found to be approximately 3.249 Km2. The experimental test, carried throughout this study, proved that integrated remote sensing and GIS techniques have great impact on detecting environmental changes and man-made features variations through time.

Visual analogy: Viewing analogical retrieval and mapping as constraint satisfaction problems

The core issue of analogical reasoning is the transfer of relational knowledge from a source case to a target problem. Visual analogical reasoning pertains to problems containing only visual knowledge. Holyoak and Thagard proposed that the retrieval and mapping tasks of analogy in general can be productively viewed as constraint satisfaction problems, and provided connectionist implementations of their proposal. In this paper, we reexamine the retrieval and mapping tasks of analogy in the context of diagrammatic cases, representing the spatial structure of source and target diagrams as semantic networks in which the nodes represent spatial elements and the links represent spatial relations. We use a method of constraint satisfaction with backtracking for the retrieval and mapping tasks, with subgraph isomorphism over a particular domain language as the similarity measure. Results in the domain of 2D line drawings suggest that at least for this domain the above method is quite promising.

Epac1 and cAMP-dependent Protein Kinase Holoenzyme Have Similar cAMP Affinity, but Their cAMP Domains Have Distinct Structural Features and Cyclic Nucleotide Recognition

The cAMP-dependent protein kinase (PKA I and II) and the cAMP-stimulated GDP exchange factors (Epac1 and -2) are major cAMP effectors. The cAMP affinity of the PKA holoenzyme has not been determined previously. We found that cAMP bound to PKA I with a K(d) value (2.9 microM) similar to that of Epac1. In contrast, the free regulatory subunit of PKA type I (RI) had K(d) values in the low nanomolar range. The cAMP sites of RI therefore appear engineered to respond to physiological cAMP concentrations only when in the holoenzyme form, whereas Epac can respond in its free form. Epac is phylogenetically younger than PKA, and its functional cAMP site has presumably evolved from site B of PKA. A striking feature is the replacement of a conserved Glu in PKA by Gln (Epac1) or Lys (Epac2). We found that such a switch (E326Q) in site B of human RIalpha led to a 280-fold decreased cAMP affinity. A similar single switch early in Epac evolution could therefore have decreased the high cAMP affinity of the free regulatory subunit sufficiently to allow Epac to respond to physiologically relevant cAMP levels. Molecular dynamics simulations and cAMP analog mapping indicated that the E326Q switch led to flipping of Tyr-373, which normally stacks with the adenine ring of cAMP. Combined molecular dynamics simulation, GRID analysis, and cAMP analog mapping of wild-type and mutated BI and Epac1 revealed additional differences, independent of the Glu/Gln switch, between the binding sites, regarding space (roominess), hydrophobicity/polarity, and side chain flexibility. This helped explain the specificity of current cAMP analogs and, more importantly, lays a foundation for the generation of even more discriminative analogs.

Analogy and diagonal argument

In this paper, I try to accomplish two goals. The first is to provide a general characterization of a method of proofs called — in mathematics — the diagonal argument. The second is to establish that analogical thinking plays an important role also in mathematical creativity. Namely, mathematical research make use of analogies regarding general strategies of proof. Some of mathematicians, for example George Polya, argued that deductions is impotent without analogy. What I want to show is that there exists a direct line leading from Cantor’s diagonal argument to constructions that underlies of the proofs of several important theorems of the mathematical logic (in particular, Church’s theorem concerning the undecidability of formal arithmetic, Godel’s theorem concerning the incopleteness of formal arithmetic, Tarski’s theorem concerning truth, and Turing’s theorem concerning the Halting Problem), and that the line could be described as an analogical mapping. In other words, Cantor’s diagonal argument and the proofs of the limitative theorems are structurally the same. Hence they can be represented as instances (or special cases) of the same general scheme.

Cloning, genetic and physical mapping of resistance gene analogs in barley (Hordeum vulgare L.)

AbstractThe majority of verified plant disease resistance genes isolated to date belong to the NBS‐LRR class, encoding proteins with a predicted nucleotide binding site (NBS) and a leucine‐rich repeat (LRR) region. Using degenerate primers, designed from the conserved motifs of the NBS region in tobacco N and Arabidopsis RPS2 genes, we isolated 190 resistance gene analogs (RGA) clones from barley genomic DNA. A total of 13 single‐ and low‐copy RGAs were genetically mapped onto chromosomes 1H–7H (except 5H) using three barley double haploid (DH) mapping populations: Steptoe × Morex, Harrington × TR306 and LUGC × Bowman. Sequence analysis of the RGAs showed that they are members of a diverse group. As a result of BLAST searches, one RGA proved unique as it did not detect any significant hit. Another RGA is putatively functional, because it detected several barley expressed sequence tag (EST) matches. To physically map the RGAs, 13 sequences were used to screen a 6.3 × cv. ‘Morex’ bacterial artificial chromosome (BAC) library. After fingerprint analysis, eight contigs were constructed incorporating 62 BAC clones. These BAC contigs are of great value for positional cloning of disease resistance genes, because they span the regions where various barley R genes have been genetically mapped.

Identification and mapping of resistance gene analogs (RGAs) in Prunus: a resistance map for Prunus

The genetically anchored physical map of peach is a valuable tool for identifying loci controlling economically important traits in Prunus. Breeding for disease resistance is a key component of most breeding programs. The identification of loci for pathogen resistance in peach provides information about resistance loci, the organization of resistance genes throughout the genome, and permits comparison of resistance regions among other genomes in the Rosaceae. This information will facilitate the breeding of resistant species of Prunus. A candidate gene approach was implemented for locating resistance loci in the genome of peach. Candidate genes representing NBS-LRR, kinase, transmembrane domain classes, as well as, pathogen response (PR) proteins and resistance-associated transcription factors were hybridized to a peach BAC library and mapped by using the peach physical map database and the Genome Database for Rosaceae (GDR). A resistance map for Prunus was generated and currently contains 42 map locations for putative resistance regions distributed among 7 of the 8 linkage groups.

Modelling of light pollution in suburban areas using remotely sensed imagery and GIS

This paper describes a methodology for modelling light pollution using geographical information systems (GIS) and remote sensing (RS) technology. The proposed approach attempts to address the issue of environmental assessment in sensitive suburban areas. The modern way of life in developing countries is conductive to environmental degradation in urban and suburban areas. One specific parameter for this degradation is light pollution due to intense artificial night lighting. This paper aims to assess this parameter for the Athens metropolitan area, using modern analytical and data capturing technologies. For this purpose, night-time satellite images and analogue maps have been used in order to create the spatial database of the GIS for the study area. Using GIS advanced analytical functionality, visibility analysis was implemented. The outputs for this analysis are a series of maps reflecting direct and indirect light pollution around the city of Athens. Direct light pollution corresponds to optical contact with artificial night light sources, while indirect light pollution corresponds to optical contact with the sky glow above the city. Additionally, the assessment of light pollution in different periods allows for dynamic evaluation of the phenomenon. The case study demonstrates high levels of light pollution in Athens suburban areas and its increase over the last decade.