Grid Support for Collaborative Control Room in Fusion Science

The National Fusion Collaboratory project seeks to enable fusion scientists to exploit Grid capabilities in support of experimental science. To this end we are exploring the concept of a collaborative control room that harnesses Grid and collaborative technologies to provide an environment in which remote experimental devices, codes, and expertise can interact in real time during an experiment. This concept has the potential to make fusion experiments more efficient by enabling researchers to perform more analysis and by engaging more expertise from a geographically distributed team of scientists and resources. As the realities of software development, talent distribution, and budgets increasingly encourage pooling resources and specialization, we see such environments as a necessary tool for future science. In this paper, we describe an experimental mock-up of a remote interaction with the DIII-D control room. The collaborative control room was demonstrated at SC03 and later reviewed at an international ITER Grid Workshop. We describe how the combined effect of various technologies—collaborative, visualization, and Grid—can be used effectively in experimental science. Specifically, we describe the Access Grid, experimental data presentation tools, and agreement-based resource management and workflow systems enabling time-bounded end-to-end application execution. We also report on FusionGrid services whose use during the fusion experimental cycle became possible for the first time thanks to this technology, and we discuss its potential use in future fusion experiments.     

What history tells us

The history of science was long considered to be something peripheral to science itself. By supplying interesting stories and gossip, it seemed, at best, to provide material for enlivening lectures. In general, it was deemed a suitable activity for retired scientists. This view has been revised considerably in the past years and indeed, today seems hopelessly out of date. History and philosophy of science are increasingly held to be an essential component of the education of scientists. By becoming acquainted with these areas, practicing scientists — and in particular biologists — can better appreciate the significance of the models and theories that underpin their research, especially with the accelerating succession of one idea by the next. The present series, of which the article that follows is the first, aims to give historical glimpses that bear on contemporary biology. The hope is that these glimpses will be both a source of inspiration and of help in resisting useless fashions.     

Evolution of postmating isolation: comparison of three models based on possible genetic mechanisms

In this study, we simulated the process of the evolution of postmating isolation using three models in which postmating isolation is caused by (1) genetic divergence through collaborative coevolution, (2) genetic divergence through antagonistic coevolution resulting from sexual conflict, and (3) genetic divergence through combinational incompatibility. The collaborative coevolution model and the combinational incompatibility model showed a similar decreasing pattern of hybrid compatibility over generations depending on population size and mutation rates. The antagonistic coevolution model showed that reproductive isolation can evolve rapidly depending on the intensity of selection. In the combinational incompatibility model, the increasing number of loci that interact and result in incompatibility would have both promoting and inhibiting effects on the formation of hybrid incompatibility in the earlier stage of isolation. Mutation rates for genes causing incompatibility significantly affect the number of generations required for postmating isolation, which indicates that models assuming high mutation rates (e.g., μ = 10⁻⁴) might predict much faster evolution for reproductive isolation than those observed in real populations. Received: January 29, 2001 / Accepted: July 4, 2001     

Model of development of science by the example of limnology

Limnology—the science about lakes—is the young and relatively closed area of studies; its existence is owing to several hundreds of scientists. The International Society of Limnologists holds its meetings since 1922. We used materials of these meetings to find out the main stages of development of this science; among these stages there were both fast and relatively calm periods. Based on analysis of these data, we constructed a model of development of the science, the same data being used for tuning and verification of the model. We have suggested that the main regularities and mechanisms of development of limnology can be extrapolated to other sciences. The main “acting person” in the model is population of scientists. Each scientist, with some probability, can propose new ideas as well as use in his studies some particular complex of the already accumulated knowledge and ideas. The model also takes into consideration how the scientific information is spreading, as well as some individual peculiarities of model scientists, such as age, experience, communicability. After the model parameters had been chosen in such a way that is described adequately development of limnology, we performed a series of experiments by changing some of the characteristics and obtained rather unexpected results published preliminary in the short work (Levchenko, V.F. and Menshutkin, V.V., Int. J. Comput. Anticip. Syst., 2008, vol. 22, pp. 63–75) and discussed here in the greater detail. It is revealed that development of science occurs irregularly and is sharply decelerated at low level of communication between scientists and the absence of scientific schools, while the age of “scientific youth” of scientist usually begins only after 40 years.     

A field-study of inducible molecular defenses,ultraviolet radiation,and melanomagenesis in natural <Emphasis Type="Italic">Xiphophorus</Emphasis> hybrids

Ultraviolet radiation—the primary natural pollutant affecting melanomagenesis—may represent a widespread ecological stressor for many fishes, and yet the relationship between UV-exposure and stress has not been investigated in natural fish populations. Recent lab-based studies have sought to characterize the relationship between tumorigenesis and the induction of molecular defenses, such as heat shock proteins. Here we show that ultraviolet radiation and heat shock protein gene expression explain a significant amount of the variation in hyper-melanization—the phenotypic precursor to melanoma—in wild hybrids of Xiphophorus, laboratory models in cancer research. Our results suggest exposure to UV radiation causes stress which induces molecular defense mechanisms, which in turn may facilitate tumorigenesis in natural fish populations. Studies of laboratory-based model organisms in natural settings, like this one, may provide important insights into ecological and evolutionary relationships obscured in controlled laboratory environments. We hope that ours is only the first of many studies to investigate the such relationships between environmental stress, stress-induced molecular defenses, and cancer in fishes.     

The Role of Teleological Thinking in Learning the Darwinian Model of Evolution

Human beings are predisposed to think of evolution as teleological—i.e., having a purpose or directive principle—and the ways scientists talk about natural selection can feed this predisposition. This work examines the suggestion that students’ teleological thinking operates as an obstacle when the natural selection evolution model is taught. What we mean by obstacle is an established way of thinking that resists change due to its explanatory power. In light of this approach, the challenges of teaching evolution in biology education have been revised, and improved methodological strategies aimed at a better comprehension of the Darwinian evolution model are suggested.     

An EcoHealth Forum in London: Young Researchers Fill a Training Gap

Despite an increasing recognition that addressing complex problems requires transdisciplinary research, the shortage of formal training for how to conduct such research is a major bottleneck to future progress. In response to this training gap, a group of early career scientists in London created the London EcoHealth Forum. Now in its second year, the Forum has matured into a small but dedicated group that cultivates thought and learning about ecosystem approaches to health. This paper discusses the key challenges faced while setting up the group and how they were overcome. The paper also outlines the main activity of the group, a seminar series devoted to a specific topic—the overconsumption of meat in London—and suggests that this format may be a useful tool for others who wish to set up a similar organization or teaching program.     

Maximizing biodiversity, information and sustainability

Numerous global changes—notably anthropogenic extinction—force reconsideration of our management practices and the ways we regulate human influence in today’s world. Here, I define management to maximize biodiversity and illustrate the science that provides information to set goals for such management. Maximizing biodiversity simultaneously achieves sustainability and systemic health by avoiding the abnormal or pathological. The normal or sustainable are determined through the use of empirical integrative patterns to objectively account for the complexity of systems within which we find ourselves as a species. The science that reveals these integrative patterns provides measures of problems that can be solved by maximizing biodiversity—problems heretofore recognized only qualitatively. I use the Shannon-Weiner information index to test, and, with no surprise, reject the null hypothesis that there is no direct anthropogenic effect on biodiversity. The results of this science serve as examples of the kind of information most useful for guiding management and illustrate maximized biodiversity as a standard for management. Reference points based on maximized biodiversity are preferable to statistical parameters in meeting the objective of avoiding the abnormal or pathological in our interactions with other species, ecosystems and the biosphere. Management to maximize biodiversity is implemented by modifying human interactions with other biotic systems to achieve consistency in such interactions by mimicking natural role models of sustainability. Human influence is a significant factor in today’s world and the magnitude of such influence is illustrated by comparing humans with other species.     

A personal retrospective on the second half of the 20th century

During the Second World War scientists and engineers were involved as never before in all technical phases of the war effort. It included intelligence, logistics and large scale automated computation. Much of this required team work which led to the adoption of interdisciplinary perspectives and found expression after the war in new fields of enquiry such as cybernetics, biophysics and artificial intelligence.     

A new paradigm for graduate research and training in the biomedical sciences and engineering

98Emphasis on the individual investigator has fostered discovery for centuries, yet it is now recognized that the complexity of problems in the biomedical sciences and engineering requires collaborative efforts from individuals having diverse training and expertise. Various approaches can facilitate interdisciplinary interactions, but we submit that there is a critical need for a new educational paradigm for the way that we train biomedical engineers, life scientists, and mathematicians. We cannot continue to train graduate students in isolation within single disciplines, nor can we ask any one individual to learn all the essentials of biology, engineering, and mathematics. We must transform how students are trained and incorporate how real-world research and development are done-in diverse, interdisciplinary teams. Our fundamental vision is to create an innovative paradigm for graduate research and training that yields a new generation of biomedical engineers, life scientists, and mathematicians that is more diverse and that embraces and actively pursues a truly interdisciplinary, team-based approach to research based on a known benefit and mutual respect. In this paper, we describe our attempt to accomplish this via focused training in biomechanics, biomedical optics, mathematics, mechanobiology, and physiology. The overall approach is applicable, however, to most areas of biomedical research.     

Craniodental Characters in the Taxonomy of Propithecus

The indriid genus Propithecus comprises the sifakas, medium-sized lemurs endemic to the forests of Madagascar. Traditionally, scientists divided the genus into only 2 or 3 species —Propithecus diadema, P. verreauxi, and, since 1988, P. tattersalli— with 4 or 5 subspecies in each of the first 2 taxa, but recent authors have suggested that many more distinct species should be recognized. We draw from quantitative and qualitative studies of craniodental traits to evaluate further the phenetic distinctiveness and taxonomic status of each named form of Propithecus. We recognize 9–10 species in the genus. The 4 or 5 species of the Propithecus diadema group —P. diadema, P. candidus, P. perrieri, P. edwardsi, and perhaps P. holomelas, if distinct— share several derived features, including large average body size and a mandible specialized for rotational chewing, and clearly comprise a closely related complex. The 5 species of the Propithecus verreauxi group —P. verreauxi, P. coquereli, P. deckenii, P. coronatus, P. tattersalli— are each highly distinctive morphologically and likely do not comprise a monophyletic group. In particular, we point out the highly distinctive cranial features of Propithecus coronatus, which researchers have traditionally largely overlooked.     

Biosynthesis of the branched-chain amino acids in the cyanobacterium Synechocystis PCC6803: existence of compensatory pathways

Complementation of an E. coli mutant auxotrophic for the branched-chain amino acids (BCAA)—valine, leucine, and isoleucine—by the ilvG gene (slr2088) of the cyanobacterium Synechocystis PCC6803 indicates that this gene encodes an active α-acetohydroxy acid synthase. Differences of response of the recombinants to the addition of the essential amino acids suggested a lower specificity for the initial reaction of the valine/leucine chain than for the isoleucine one. Inactivation of ilvG in Synechocystis led to a leaky phenotype, suggesting a capacity to compensate the auxotrophies by other processes. This observation is discussed in view of the general difficulty of obtaining auxotrophs in cyanobacteria. Received: 16 October 2001 / Accepted: 26 November 2001     

The Quantum Co-Evolution Unit: An Example of ‘Awa (Kava—<Emphasis Type="Italic">Piper methysticum</Emphasis> G. Foster) in Hawaiian Culture

The Quantum Co-Evolution Unit: An Example of ‘Awa (Kava— Piper methysticum G. Foster) in Hawaiian Culture. The process of co-evolution occurs in many kinds of relationships and on various scales. One example of a co-evolutionary relationship is that of a plant and a culture with which it interacts. Such relationships are dynamic and ever changing. Researchers have discussed this concept and its implications for decades, yet no quantifiable unit or standardized scale has been accepted with which to measure this change. The theoretical “quantum co-evolution unit” (QCU) is proposed as the smallest measurable scale of interactions between plants and people. A collection of QCUs for a linked plant and human population would be its “ethnobotanical population.” This could be measured at various points in time to quantify the changing relationships between plants and people. These models set up a structure to discuss methodologies for quantifying co-evolutionary relationships such as are seen in the evolution of ethnobotanical populations. The co-evolving relationship between ‘awa (kava—Piper methysticum) and Hawaiian culture is used as an example to illustrate this idea.     

Managing the Human–Ecological Interface: Marine Resources as Example and Laboratory

The field of resource management integrates human and ecological systems. It is currently undergoing a difficult transition as it broadens to accommodate new values and interests. Some of the problems associated with this transition are evident in marine ecosystems, where the management of the ecological–human interface has been hindered by a lack of basic understanding. Using marine fisheries as examples, this paper describes the proximate and underlying causes of the human–ecological problem. It identifies areas in which basic research is needed on the behavioral dynamics of marine resource use, including incentives, feedbacks, management scale, monitoring and evaluation, alternative management approaches, the role of history, and human capital. It discusses the cost of failing to invest in social science research and identifies barriers to interdisciplinary research. Priorities for interdisciplinary research are listed. Received 30 November 2000; accepted 20 April 2001.     

Ancestor or Adapiform? Darwinius and the Search for Our Early Primate Ancestors

On May 19, 2009, an international team of scientists claimed to have found one of our early primate ancestors. Dubbed Darwinius masillae, the 47 million-year-old primate was presented as “the link” that bridged a gap between early primates and our anthropoid progenitors through a major media campaign, yet details about the way the fossil was acquired, the role media companies played in the presentation of the fossil, and disagreements about the fossil’s interpretation generated a controversy in which scientists, journalists, and science bloggers all played important roles. These debates were reinvigorated in the fall of 2009 when an independent team of researchers described a related fossil primate named Afradapis longicristatus, the study of which suggested that Darwinius was much further removed from our ancestry than had been initially proposed. The discussion of these fossils will no doubt continue, but the “Darwinius debates” of 2009 are significant in that they precipitated a long-awaited analysis of early primate relationships, illustrated the benefits and pitfalls of “going broad” with new discoveries, and exhibited how science blogs can work with traditional media outlets to counter exaggerated claims.     

Commentaries on field‐laboratory collaborations in primatology: Introduction to a special section of the American Journal of Primatology

Finding better approaches to bridge field and laboratory primate research was identified as an important goal in a recent (2017) member survey of the American Society of Primatologists. Collaborative field‐captive research was identified by >60% of respondents as somewhat or very underrepresented in the Society. In this introductory essay for a special section of American Journal of Primatology, I review commonalities and differences in the papers that were requested from field‐captive primate collaborative teams. Each team approached important primate biology or welfare problems from different perspectives. The five commentaries in this section addressed how the collaborations began, scientific benefits that accrued, and insights or challenges that researchers faced in the collaboration. Despite the fact that the specific fields of inquiry were different (conservation genetics, chimpanzee captive welfare, environmental physiology, feeding biology, and reproductive physiology), the commentaries converged on the concept that an intentional, interdisciplinary approach, that included field observations and experiments informed by laboratory expertise, were essential to achieving innovative results.     

New Analytic Results for Speciation Times in Neutral Models

In this paper, we investigate the standard Yule model, and a recently studied model of speciation and extinction, the “critical branching process.” We develop an analytic way—as opposed to the common simulation approach—for calculating the speciation times in a reconstructed phylogenetic tree. Simple expressions for the density and the moments of the speciation times are obtained. Methods for dating a speciation event become valuable, if for the reconstructed phylogenetic trees, no time scale is available. A missing time scale could be due to supertree methods, morphological data, or molecular data which violates the molecular clock. Our analytic approach is, in particular, useful for the model with extinction, since simulations of birth-death processes which are conditioned on obtaining n extant species today are quite delicate. Further, simulations are very time consuming for big n under both models.     

A comparison of approaches for modelling the occurrence of marine animals

Approaches for modelling the distribution of animals in relation to their environment can be divided into two basic types, those which use records of absence as well as records of presence and those which use only presence records. For terrestrial species, presence–absence approaches have been found to produce models with greater predictive ability than presence-only approaches. This study compared the predictive ability of both approaches for a marine animal, the harbour porpoise (Phoceoena phocoena). Using data on the occurrence of harbour porpoises in the Sea of Hebrides, Scotland, the predictive abilities of one presence–absence approach (generalised linear modelling—GLM) and three presence-only approaches (Principal component analysis—PCA, ecological niche factor analysis—ENFA and genetic algorithm for rule-set prediction—GARP) were compared. When the predictive ability of the models was assessed using receiver operating characteristic (ROC) plots, the presence–absence approach (GLM) was found to have the greatest predictive ability. However, all approaches were found to produce models that predicted occurrence significantly better than a random model and the GLM model did not perform significantly better than ENFA and GARP. The PCA had a significantly lower predictive ability than GLM but not the other approaches. In addition, all models predicted a similar spatial distribution. Therefore, while models constructed using presence–absence approaches are likely to provide the best understanding of species distribution within a surveyed area, presence-only models can perform almost as well. However, careful consideration of the potential limitations and biases in the data, especially with regards to representativeness, is needed if the results of presence-only models are to be used for conservation and/or management purposes. Guest editor: V. D. Valavanis Essential Habitat Mapping in the Mediterranean     

An ecological classification of Central European macromoths: habitat associations and conservation status returned from life history attributes

To be used as a predictive conservation tool, classification of animal habitats should rely on actual resource requirements of individual species. Shreeve et al. (J Insect Conserv 5:145–161, 2001) produced a resource-based habitat classification for British butterflies, obtaining habitat association groups, whose constituent species differed in their distribution extent, distribution change and vulnerability in Britain. To test the utility of this approach for a group with a less-known biology, we produced a resource-based classification of habitats of Central European macromoths. We worked with macrolepidopteran moth families, except for the megadiverse Geometridae and Noctuidae. We produced a matrix of 178 life history attributes describing resource use by 164 species, subjected the matrix to ordination analysis, and compared the resulting moths groupings with external ecological information. Five habitat association groups were distinguished: I—close canopy moths, II—open canopy moths, III—grasslands moths, IV—herb-feeding hawk moths, and V—lichen feeders. The classification sustained deleting attributes related to host plants taxonomy. Groups I–III sustained control for taxonomic positions of the moths, whereas IV and V did not. Members of the groups differed in the representation of externally obtained habitat associations, biogeography elements, threat status, and range size. Endangered species were over-represented in groups II and III and underrepresented in group I, in agreement with recent land cover changes across the continent. Species resources can be used to reconstruct their habitat needs, and it is possible to scale up from life histories through habitat use to range structures.     

Stoichiometry in producer-grazer systems: Linking energy flow with element cycling

All organisms are composed of multiple chemical elements such as carbon, nitrogen and phosphorus. While energy flow and element cycling are two fundamental and unifying principles in ecosystem theory, population models usually ignore the latter. Such models implicitly assume chemical homogeneity of all trophic levels by concentrating on a single constituent, generally an equivalent of energy. In this paper, we examine ramifications of an explicit assumption that both producer and grazer are composed of two essential elements: carbon and phosphorous. Using stoichiometric principles, we construct a two-dimensional Lotka-Volterra type model that incorporates chemical heterogeneity of the first two trophic levels of a food chain. The analysis shows that indirect competition between two populations for phosphorus can shift predator—prey interactions from a (+, −) type to an unusual (−, −) class. This leads to complex dynamics with multiple positive equilibria, where bistability and deterministic extinction of the grazer are possible. We derive simple graphical tests for the local stability of all equilibria and show that system dynamics are confined to a bounded region. Numerical simulations supported by qualitative analysis reveal that Rosenzweig’s paradox of enrichment holds only in the part of the phase plane where the grazer is energy limited; a new phenomenon, the paradox of energy enrichment, arises in the other part, where the grazer is phosphorus limited. A bifurcation diagram shows that energy enrichment of producer—grazer systems differs radically from nutrient enrichment. Hence, expressing producer—grazer interactions in stoichiometrically realistic terms reveals qualitatively new dynamical behavior.