A general definition of interpretation and its application to origin of life research

We draw on Short’s work on Peirce’s theory of signs to propose a new general definition of interpretation. Short argues that Peirce’s semiotics rests on his naturalised teleology. Our proposal extends Short’s work by modifying his definition of interpretation so as to make it more generally applicable to putatively interpretative processes in biological systems. We use our definition as the basis of an account of different kinds of misinterpretation and we discuss some questions raised by the definition by reference to parallel problems in the field of teleosemantics. We propose that interpretative responses fulfilling the criteria of our definition may be made by relatively simple molecular entities and we suggest two specific empirical applications of the definition to experimental work in the field of origin of life research. Our wider aim is to suggest that a well formulated naturalistic definition of interpretation will allow a re-evaluation of the role of semiotic phenomena in biological systems, including the generation of empirically testable hypotheses.     

Novel application of a quantitative spatial comparison tool to species distribution data

Comparing geographically referenced maps has become an important aspect of spatial ecology (e.g. assessing change in distribution over time). Whilst humans are adept at recognising and extracting structure from maps (i.e. identifying spatial patterns), quantifying these structures can be difficult. Here, we show how the Structural Similarity (SSIM) index, a spatial comparison method adapted from techniques developed in computer science to determine the quality of image compression, can be used to extract additional information from spatial ecological data. We enhance the SSIM index to incorporate uncertainty from the underlying spatial models, and provide a software algorithm to correct for internal edge effects so that loss of spatial information from the map comparison is limited. The SSIM index uses a spatially-local window to calculate statistics based on local mean, variance, and covariance between the maps being compared. A number of statistics can be calculated using the SSIM index, ranging from a single summary statistic to quantify similarities between two maps, to maps of similarities in mean, variance, and covariance that can provide additional insight into underlying biological processes. We demonstrate the applicability of the SSIM approach using a case study of sperm whales in the Mediterranean Sea and identify areas where local-scale differences in space-use between groups and singleton whales occur. We show how novel insights into spatial structure can be extracted, which could not be obtained by visual inspection or cell-by-cell subtraction. As an approach, SSIM is applicable to a broad range of spatial ecological data, providing a novel, implementable tool for map comparison.     

连续性空间分布型模型与应用研究

本文对Pearson-Ⅲ分布与指数分布的空间分布型特征进行了探讨,发现它们的精确性高于经典的频次分布。导出Pearson-Ⅲ分布与指数分布的空间分布型判定指标和抽样量公式,并对赤霉病菌源的分布型和抽样量进行分析,最后指出连续性空间分布型模型的优越性。     

Hierarchy of the interaction energy distribution in the spatial structure of globular proteins and the problem of domain definition.

An algorithm for determining of protein domain structure is proposed. Domain structures resulted from the algorithm application have been obtained and compared with available data. The method is based on entirely physical model of van der Waals interactions that reflects as illustrated in this work the distribution of electron density. Various levels of hierarchy in the protein spatial structure are discerned by analysis of the energy interaction between structural units of different scales. Thus the level of energy hierarchy plays role of sole parameter, and the method obviates the use of complicated geometrical criteria with numerous fitting parameters. The algorithm readily and accurately locates domains formed by continuous segments of the protein chain as well as those comprising non-sequential segments, sets no limit to the number of segments in a domain. We have analyzed 309 protein structures. Among 277 structures for which our results could be compared with the domain definitions made in other works, 243 showed complete or partial coincidence, and only in 34 cases the domain structures proved substantially different. The domains delineated with our approach may coincide with reference definition at different levels of the globule hierarchy. Along with defining the domain structure, our approach allows one to consider the protein spatial structure in terms of the spatial distribution of the interaction energy in order to establish the correspondence between the hierarchy of energy distribution and the hierarchy of structural elements.     

Characterising the temporal variability of the spatial distribution of animals: an application to seabirds at sea

Understanding the patterns of spatial and temporal variations in animal abundance is a fundamental question in ecology. Here, we propose a method to quantify temporal variations in animal spatial patterns and to determine the spatial scale at which such temporal variability is expressed. The methodology extends from the approach proposed by Taylor (Taylor, L. R. 1961. Aggregation, variance and the mean. Nature 189: 732–735) and relies on models of the relationship between temporal mean and variance in animal abundance. Repeated observations of the spatial distribution of populations are used to construct spatially explicit models of Taylor's power law. The resulting slope parameters of the Taylor power law provide local measures of the temporal variability in animal abundance. We investigate if the value of the slope varies significantly with spatial location and with spatial scale. The method is applied to seabirds distribution in the Bay of Biscay. We study four taxa (northern gannets, large gulls, auks and kittiwakes) that display distinct geographical distribution, spatial structure and foraging strategy. Our results show that the temporal variability associated to the spatial distribution of northern gannets is high and spatially homogeneous. By contrast, kittiwakes present large geographical areas associated with high and low variability. The temporal variability of auk's spatial distribution is strongly scale-dependent: at fine scale high variability is associated to high abundance, but at large scale high variability is associated to the external border of their distribution range. The method provides satisfactory results and useful information on species spatio-temporal distribution.     

Effects of farming practices on spatial behaviour of common voles

This study aimed to reveal changes in spatial behaviour of common voles (Microtus arvalis) after alteration of their habitat by farming practices. Radio-collared common voles were tracked before and after mulching, mowing, harvesting wheat, and ploughing in the flood plain of the river Unstrut in central Germany. Voles undisturbed by agricultural practices were tracked on a mulchland, an abandoned pasture, and a cattle pasture. There was a large decrease in home-range size after harvesting wheat (96%, P<0.001). Changes after mowing (–74%, P=0.06) were almost significant whereas changes after mulching were not (+14%, P=0.60). On the cattle pasture we found a decrease in home-range size (42%, P=0.03) possibly due to increased spatial activity of cattle in autumn. There was a positive correlation of home-range size and vegetation height for plots with and without farming activity but no correlation with vegetation cover, population density, and breeding. Radio-collared common voles did not show evasive movements and farming practices did not cause a shift of centres of activity. Common voles clearly reacted to sudden changes in vegetation height, which may indicate an immediate response to predation risk. Electronic Publication     

The size distribution of potato tubers and its application to grading schemes

The weight, length, breadth and depth were measured for each of 10 000 potato tubers. These were samples over 3 years of the 10 most commonly grown UK maincrop varieties. Volume, square-mesh riddle size and average projected area were also measured in the final 2 years. A multivariate log-normal distribution was found to give a good fit to the data. Illustrations are presented of how this distribution can be used to assess grading schemes.     

中国西南地区石漠化敏感性评价及其空间分析

石漠化是我国西南地区最为严重的生态环境问题之一,识别发生石漠化敏感区域,为岩溶地区石漠化防治提供科学依据显得十分必要。总体分析了目前中国石漠化和有关生态环境研究的资料,将石漠化敏感性影响因子归结为岩性、降水、坡度和植被等4项,并确定了各因素对石漠化敏感性影响等级,综合评价了我国西南五省(市)(包括黔、滇、贵、川、渝)石漠化敏感性及其空间分布格局。结果表明,敏感性评价结果基本反映石漠化现状,石漠化敏感区集中分布在贵州西部、南部,广西西部、东部以及云南东部等地。四川、重庆等地石漠化危害相对较小。     

Molecular phylogenetic diversity of bacteria and its spatial distribution in composts

AIMS: To investigate microbial diversity of swine manure composts in the initial stage and the spatial distribution due to gradient effect. METHODS AND RESULTS: Samples in different locations of a composting pile were taken and analysed by using a culture-independent approach. Total community DNA was extracted and bacterial 16S rRNA genes were subsequently amplified, cloned, restriction fragment length polymorphism-screened and sequenced. Thirty-three unique sequence types were found among the 110 analysed positive clones from superstratum sample; 56 among 122 from middle-level sample and 32 among 114 from substrate sample, respectively. The sequences related to Clostridium sp. were most common in the composts. One hundred and thirteen out of 121 16S rDNA sequence types displayed homology with those in the GenBank database. Seven 16S rDNA sequence types were not closely related to any known species. The middle-level sample had the highest microbial diversity, containing unique sequences related to Lactosphaera pasteurii, Firmicutes sp., Aerococcus sp., Megasphaera sp. and Stenotrophomonas sp. CONCLUSIONS: Pile temperature significantly affected microbial community in the initial stage of the composting. Microbial community in different locations is quite different resulting from gradient effect. SIGNIFICANCE AND IMPACT OF THE STUDY: Results of this study reveal high bacterial diversity in manure composts, and provide molecular evidence to support gradient effect on microbial diversity in initial stage as well.     

A division between foraging range and territory related to food distribution in the red fox

Spatial organization of the red fox (Vulpes vulpes schrencki) was investigated on the basis of seasonal food distribution in the Shiretoko National Park, Hokkaido from 1992 to 1994. Four periods were recorded pertaining to the distribution of 2 kinds of food resources: human food and spawning salmonid carcasses. The home range utilizations of radio-collared foxes were compared for the periods. In the periods when food was not spatially concentrated, resident foxes were territorial, showing exclusive distribution of home ranges between families, defense against intruding foxes at the edge of home ranges, and site specific dominance over intruding foxes. In contrast, during periods when food distribution was concentrated, home ranges overlapped. In the latter periods, foxes made round trips of up to 8 km from their territories to the localized concentration of food, the distance that foxes can travel within a day. This suggests that red foxes in this area have unique foraging ranges that include some seasonally available food outside their territories, and that these ranges depend on fluctuating food distribution caused by humans.     

An intervened Poisson distribution and its medical application

Among probability distributions that are used to describe a chance mechanism whose observational apparatus becomes active only when at least one event occurs is the zero-truncated Poisson distribution (ZTPD). A modified version of the ZTPD, which we call an intervened Poisson distribution (IPD), is discussed in this paper. We give a genesis of IPD and obtain its statistical properties. A numerical example is included to illustrate the results.     

Chlorophyll content and factors affecting its spatial distribution in the Middle Volga reservoirs

On the basis of the data obtained during field observations in the summer low water period of 2001, the patterns of chlorophyll distribution and its relation to hydrological and hydrochemical factors in two eutrophic reservoirs of the Middle Volga are studied. The hydrological structure of the Gorky Reservoir, where the Volga water mass dominates, is homogeneous, while in the Cheboksary Reservoir along with the eutrophic Volga waters, the mesotrophic Oka water masses can be distinguished keeping their abiotic and biotic features over a long distance. Phytoplankton in the two contiguous reservoirs with different flow regimens and anthropogenic loads responds differently to the external influence. An autotrophic community in the Gorky Reservoir is more stable and depends little on abiotic factors which account for ∼63% of the explained chlorophyll variation. In the Cheboksary Reservoir under maximal for the Volga cascade flow velocity and anthropogenic load, the development and distribution of phytoplankton are almost completely (R ² = 0.93) controlled by these factors. The trophic state of the reservoirs has not changed as compared to the beginning of the 1990s.     

洱海流域湖泊大型底栖动物群落结构及空间分布

2009年5月对洱海及其流域内的海西海、茈碧湖和西湖3个小型湖泊进行底栖动物群落结构调查,以期阐明该流域湖泊底栖动物群落结构现状及其与水环境因子关系.结果表明:洱海底栖动物密度为1556ind·m-2,生物量8.9g·m-2.主要以摇蚊、霍甫水丝蚓和萝卜螺为密度优势种,相对丰度分别为43.5%、39.5%和8.6%;生物量优势种为刻纹蚬、萝卜螺和摇蚊.GIS插值显示,洱海北部密度最高,中部沿岸区生物量最高,南部密度和生物量均较低,Shannon多样性指数以湖岸区较高.其余3个湖泊以线虫、摇蚊科、颤蚓科和幽蚊科为主,其中以茈碧湖的密度和生物量最高(260.8ind·m-2和1.14g·M-2).CCA分析表明:洱海底栖动物主要受水体TP和Ca2+浓度的影响,贡献率分别为34%和27%;西湖与洱海群落组成最相似,主要由水体中较高的TN含量引起.对比历史数据可知,洱海寡毛类和摇蚊科比例继续增加,表明湖泊有机污染进一步加重.     

铁杉球蚜的生物学及空间分布

通过对铁杉(Tusga chinensis Pritz)-云杉(Picea retroflexac Mast)、铁杉-华山松(Pinus armardi Franch)、云南铁杉(Tusga domosa Eichler)-槭树(Acer mono Maxim)-桦木(Betula platyphylla Suk)四川主要铁杉林类型中铁杉球蚜Adelges tsugae Annand林间定株、种群随机抽样、室内饲养研究表明,铁杉球蚜在四川1年发生2代(越冬代和第1代),世代重叠,成虫营孤雌生殖。越冬代从4月上旬至第2年的4月下旬,产卵盛期在5月下旬,平均产卵量为15.58粒,1龄若虫具有滞育越夏习性;第1代从12月下旬至8月中旬,产卵盛期在3月下旬,平均产卵量为67.37粒,并可产生有翅成虫,但无转主危害现象。种群的发育与温度有相关性,温度高林分种群发育进度快于温度低林分。该虫的危害与生境有一定相关性,铁杉针阔混交林危害重于铁杉针叶林;同一树冠不同层次之间、不同方位之间危害程度差异不显著;当年受害严重的树株第2年受害不严重。     

Parsimony analysis of the distribution pattern of Japanese primary freshwater fishes, and its application to the distribution of the bagrid catfishes

The geographic distribution of Japanese primary and some secondary freshwater fishes was analyzed using parsimony analysis of endemicity (PAE). Analysis of 73 taxa (species and intraspecific forms) on the four main islands of Japan (divided into 25 geographic areas), produced 44 most parsimonious cladograms. In all of the latter, a total of eight single and compound areas were recognized as endemic areas in nested relationships. The area cladograms showed Japan as comprising a middle-eastern Hokkaido area plus southern areas, the latter containing mainly a northeastern-Honshu endemic area and more heterogeneous southwestern areas, including four endemic areas (western Kyushu, southeastern Chugoku, middle Kinki and Tokai around Ise Bay) and several peripheral areas. Some patterns, e.g., the distinction in fauna across Fossa Magna, noted by previous studies, were supported by these results. Even though the analysis had some problems (e.g., not all geographic ranges of taxa could be included), it provided evidence for the detection of general distribution patterns, because the relationships or similarities among areas were clearly defined by shared taxa. To demonstrate the historical implications of the analysis, the allopatric distribution of, four bagrid catfishes was reconsidered in the area cladogram. The general pattern implied secondary extinction ofPseudobagrus nudiceps around lse Bay, which was in keeping with the fossil record.     

Genetic diversity of the house mouse Mus musculus and geographic distribution of its subspecies-specific RAPD markers on the territory of Russia

Genetic diversity and geographic distribution of taxon-specific RAPD markers was examined in ten local populations of the house mouse Mus musculus (n = 42). The house mice were generally characterized by moderate genetic variation: polymorphism P99 = 60%, P95 = 32.57%; heterozygosity H = 0.12; the observed allele number n(a) = 1.6; the effective allele number n(e) = 1.18; the within-population differentiation Theta = 0.388; and Shannon index I = 0.19. The degree of genetic isolation of individual local populations was greatly variable. The genetic subdivision index G(st) varied from 0.162 to 0.770 at the gene flow of Nm = 2.58-0.149, while the among-population distances D(N) varied from 0.026 to 0.178. of the largest part of the genetic diversity was found among the populations (H(T) = 0.125), while the within-population diversity was twice lower (H(S) = 0.06). The samples examined were well discriminated relative to the sets of RAPD markers. The character distribution pattern provided conditional subdivision of the mice into the "western" and the "eastern" groups with the putative boarder along the Baikal Lake. The first group was characterized by the prevalence of the markers typical of M. m. musculus and M. m. domesticus. The second group was characterized by the prevalence of the markers typical of M. m. musculus, M. m. gansuensis, M. m. castaneus, M. m. domesticus, and m. m. wagneri. The genotype of the nominative subspecies M. m. musculus was background for all populations. In the populations examined some of earlier described subspecies-specific molecular markers were found at different frequencies, pointing to the involvement of several subspecies of M. musculus in the process of hybridization.