This paper examines the available United States data on academic
research and development (R&D) expenditures and the number of papers
published and the number of citations to these papers as possible
measures of “output” of this enterprise. We look at these numbers
for science and engineering as a whole, for five selected major fields,
and at the individual university field level. The published data in
Science and Engineering Indicators imply sharply
diminishing returns to academic R&D using published papers as an
“output” measure. These data are quite problematic. Using a newer
set of data on papers and citations, based on an “expanding” set
of journals and the newly released Bureau of Economic Analysis R&D
deflators, changes the picture drastically, eliminating the appearance
of diminishing returns but raising the question of why the input prices
of academic R&D are rising so much faster than either the gross
domestic product deflator or the implicit R&D deflator in industry. A
production function analysis of such data at the individual field level
follows. It indicates significant diminishing returns to “own”
R&D, with the R&D coefficients hovering around 0.5 for estimates with
paper numbers as the dependent variable and around 0.6 if total
citations are used as the dependent variable. When we substitute
scientists and engineers in place of R&D as the right-hand side
A review of data mining and analysis techniques that can be used for the mapping of knowledge domains is given. Literature mapping techniques can be based on authors, documents, journals, words, and/or indicators. Most mapping questions are related to research assessment or to the structure and dynamics of disciplines or networks. Several mapping techniques are demonstrated on a data set comprising 20 years of papers published in PNAS. Data from a variety of sources are merged to provide unique indicators of the domain bounded by PNAS. By using funding source information and citation counts, it is shown that, on an aggregate basis, papers funded jointly by the U.S. Public Health Service (which includes the National Institutes of Health) and non-U.S. government sources outperform papers funded by other sources, including by the U.S. Public Health Service alone. Grant data from the National Institute on Aging show that, on average, papers from large grants are cited more than those from small grants, with performance increasing with grant amount. A map of the highest performing papers over the 20-year period was generated by using citation analysis. Changes and trends in the subjects of highest impact within the PNAS domain are described. Interactions between topics over the most recent 5-year period are also detailed.
By using data from three bibliographic databases in biology, physics, and mathematics, respectively, networks are constructed in which the nodes are scientists, and two scientists are connected if they have coauthored a paper. We use these networks to answer a broad variety of questions about collaboration patterns, such as the numbers of papers authors write, how many people they write them with, what the typical distance between scientists is through the network, and how patterns of collaboration vary between subjects and over time. We also summarize a number of recent results by other authors on coauthorship patterns.
We are interested in tracking changes in large-scale data by periodically creating an agglomerative clustering and examining the evolution of clusters (communities) over time. We examine a large real-world data set: the NEC CiteSeer database, a linked network of >250,000 papers. Tracking changes over time requires a clustering algorithm that produces clusters stable under small perturbations of the input data. However, small perturbations of the CiteSeer data lead to significant changes to most of the clusters. One reason for this is that the order in which papers within communities are combined is somewhat arbitrary. However, certain subsets of papers, called natural communities, correspond to real structure in the CiteSeer database and thus appear in any clustering. By identifying the subset of clusters that remain stable under multiple clustering runs, we get the set of natural communities that we can track over time. We demonstrate that such natural communities allow us to identify emerging communities and track temporal changes in the underlying structure of our network data.
A crossmapping technique is introduced for visualizing multiple and overlapping relations among entity types in collections of journal articles. Groups of entities from two entity types are crossplotted to show correspondence of relations. For example, author collaboration groups are plotted on the x axis against groups of papers (research fronts) on the y axis. At the intersection of each pair of author group/research front pairs a circular symbol is plotted whose size is proportional to the number of times that authors in the group appear as authors in papers in the research front. Entity groups are found by agglomerative hierarchical clustering using conventional similarity measures. Crossmaps comprise a simple technique that is particularly suited to showing overlap in relations among entity groups. Particularly useful crossmaps are: research fronts against base reference clusters, research fronts against author collaboration groups, and research fronts against term co-occurrence clusters. When exploring the knowledge domain of a collection of journal papers, it is useful to have several crossmaps of different entity pairs, complemented by research front timelines and base reference cluster timelines.
Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define “functional information,” I(Ex), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA–GTP binding energy), I(Ex) = −log2[F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function ≥ Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree. In each case we observe evidence for several distinct solutions with different maximum degrees of function, features that lead to steps in plots of information versus degree of function.
The extent to which “developmental constraints” in complex organisms restrict evolutionary directions remains contentious. Yet, other forms of internal constraint, which have received less attention, may also exist. It will be argued here that a set of partial constraints below the level of phenotypes, those involving genes and molecules, influences and channels the set of possible evolutionary trajectories. At the top-most organizational level there are the genetic network modules, whose operations directly underlie complex morphological traits. The properties of these network modules, however, have themselves been set by the evolutionary history of the component genes and their interactions. Characterization of the components, structures, and operational dynamics of specific genetic networks should lead to a better understanding not only of the morphological traits they underlie but of the biases that influence the directions of evolutionary change. Furthermore, such knowledge may permit assessment of the relative degrees of probability of short evolutionary trajectories, those on the microevolutionary scale. In effect, a “network perspective” may help transform evolutionary biology into a scientific enterprise with greater predictive capability than it has hitherto possessed.
The vast majority of biologists engaged in evolutionary studies interpret virtually every aspect of biodiversity in adaptive terms. This narrow view of evolution has become untenable in light of recent observations from genomic sequencing and population-genetic theory. Numerous aspects of genomic architecture, gene structure, and developmental pathways are difficult to explain without invoking the nonadaptive forces of genetic drift and mutation. In addition, emergent biological features such as complexity, modularity, and evolvability, all of which are current targets of considerable speculation, may be nothing more than indirect by-products of processes operating at lower levels of organization. These issues are examined in the context of the view that the origins of many aspects of biological diversity, from gene-structural embellishments to novelties at the phenotypic level, have roots in nonadaptive processes, with the population-genetic environment imposing strong directionality on the paths that are open to evolutionary exploitation.
Individuality is a complex trait, yet a series of stages each advantageous in itself can be shown to exist allowing evolution to get from unicellular individuals to multicellular individuals. We consider several of the key stages involved in this transition: the initial advantage of group formation, the origin of reproductive altruism within the group, and the further specialization of cell types as groups increase in size. How do groups become individuals? This is the central question we address. Our hypothesis is that fitness tradeoffs drive the transition of a cell group into a multicellular individual through the evolution of cells specialized at reproductive and vegetative functions of the group. We have modeled this hypothesis and have tested our models in two ways. We have studied the origin of the genetic basis for reproductive altruism (somatic cells specialized at vegetative functions) in the multicellular Volvox carteri by showing how an altruistic gene may have originated through cooption of a life-history tradeoff gene present in a unicellular ancestor. Second, we ask why reproductive altruism and individuality arise only in the larger members of the volvocine group (recognizing that high levels of kinship are present in all volvocine algae groups). Our answer is that the selective pressures leading to reproductive altruism stem from the increasing cost of reproduction with increasing group size. Concepts from population genetics and evolutionary biology appear to be sufficient to explain complexity...
Genomics has revealed that inheritance systems of separate species are often not well segregated: genes and capabilities that evolve in one lineage are often stably acquired by another lineage. Although direct gene transfer between species has occurred at some level in all major groups, it appears to be far more frequent in prokaryotes than in multicellular eukaryotes. An alternative to incorporating novel genes into a recipient genome is acquiring a stable, possibly heritable, symbiotic association and thus enjoying benefits of complementary metabolic capabilities. These kinds of symbioses have arisen frequently in animals; for example, many insect groups have diversified on the basis of symbiotic associations acquired early in their evolutionary histories. The resulting associations are highly complex, often involving specialized cell types and organs, developmental mechanisms that ensure transfer of symbionts between generations, and mechanisms for controlling symbiont proliferation and location. The genomes of long-term obligate symbionts often undergo irreversible gene loss and deterioration even as hosts evolve dependence on them. In some cases, animal genomes may have acquired genes from symbionts, mirroring the gene uptake from mitochondrial and plastid genomes. Multiple symbionts often coexist in the same host...
Butterflies and primates are interesting for comparative color vision studies, because both have evolved middle- (M) and long-wavelength- (L) sensitive photopigments with overlapping absorbance spectrum maxima (λmax values). Although positive selection is important for the maintenance of spectral variation within the primate pigments, it remains an open question whether it contributes similarly to the diversification of butterfly pigments. To examine this issue, we performed epimicrospectrophotometry on the eyes of five Limenitis butterfly species and found a 31-nm range of variation in the λmax values of the L-sensitive photopigments (514–545 nm). We cloned partial Limenitis L opsin gene sequences and found a significant excess of replacement substitutions relative to polymorphisms among species. Mapping of these L photopigment λmax values onto a phylogeny revealed two instances within Lepidoptera of convergently evolved L photopigment lineages whose λmax values were blue-shifted. A codon-based maximum-likelihood analysis indicated that, associated with the two blue spectral shifts, four amino acid sites (Ile17Met, Ala64Ser, Asn70Ser, and Ser137Ala) have evolved substitutions in parallel and exhibit significant dN/dS >1. Homology modeling of the full-length Limenitis arthemis astyanax L opsin placed all four substitutions within the chromophore-binding pocket. Strikingly...
Populations native to the Tibetan and Andean Plateaus are descended from colonizers who arrived perhaps 25,000 and 11,000 years ago, respectively. Both have been exposed to the opportunity for natural selection for traits that offset the unavoidable environmental stress of severe lifelong high-altitude hypoxia. This paper presents evidence that Tibetan and Andean high-altitude natives have adapted differently, as indicated by large quantitative differences in numerous physiological traits comprising the oxygen delivery process. These findings suggest the hypothesis that evolutionary processes have tinkered differently on the two founding populations and their descendents, with the result that the two followed different routes to the same functional outcome of successful oxygen delivery, long-term persistence and high function. Assessed on the basis of basal and maximal oxygen consumption, both populations avail themselves of essentially the full range of oxygen-using metabolism as populations at sea level, in contrast with the curtailed range available to visitors at high altitudes. Efforts to identify the genetic bases of these traits have included quantitative genetics, genetic admixture, and candidate gene approaches. These reveal generally more genetic variance in the Tibetan population and more potential for natural selection. There is evidence that natural selection is ongoing in the Tibetan population...
Many scarab beetles produce rigid projections from the body called horns. The exaggerated sizes of these structures and the staggering diversity of their forms have impressed biologists for centuries. Recent comparative studies using DNA sequence-based phylogenies have begun to reconstruct the historical patterns of beetle horn evolution. At the same time, developmental genetic experiments have begun to elucidate how beetle horns grow and how horn growth is modulated in response to environmental variables, such as nutrition. We bring together these two perspectives to show that they converge on very similar conclusions regarding beetle evolution. Horns do not appear to be difficult structures to gain or lose, and they can diverge both dramatically and rapidly in form. Although much of this work is still preliminary, we use available information to propose a conceptual developmental model for the major trajectories of beetle horn evolution. We illustrate putative mechanisms underlying the evolutionary origin of horns and the evolution of horn location, shape, allometry, and dimorphism.
The Sackler Colloquium entitled “Nanomaterials in Biology and Medicine: Promises and Perils” was held on April 10–11, 2007. We have been able to assemble a representative sampling of 17 of the invited talks ranging over the topics presented. Any new technology carries with it both a promise of transforming the way we do things and the possibility that there are unforeseen consequences. The papers collected here represent a cross-section of these issues. As an example, we present our own work on nano-upconversion phosphors as an example of this new class of nanomaterials with potential use in medicine and biology.
Industrial ecology is the network of all industrial processes as they may interact with each other and live off each other, not only in the economic sense, but also in the sense of direct use of each other's material and energy wastes and products. This paper, which reflects upon the papers and discussions at the National Academy of Sciences Colloquium on Industrial Ecology on May 20-21, 1991, is structured around 10 questions. Do sociotechnical systems have long-range environmental goals? How is the concept of industrial ecology useful and timely? What are environmental technologies? Is there a systematic way to choose among alternatives for improving the ecology of technologies? What are ways to measure performance with respect to industrial ecology? What are the sources and rates of innovation in environmental technologies? How is the market economy performing with respect to industrial ecology? What will be the effect of the ecological modernization of the developed nations of the North on the developing countries of the South? How can creative interaction on environmental issues be fostered among diverse social groups? How must research and education change?
There has been a long history of research into the structure and evolution of mankind's scientific endeavor. However, recent progress in applying the tools of science to understand science itself has been unprecedented because only recently has there been access to high-volume and high-quality data sets of scientific output (e.g., publications, patents, grants) and computers and algorithms capable of handling this enormous stream of data. This article reviews major work on models that aim to capture and recreate the structure and dynamics of scientific evolution. We then introduce a general process model that simultaneously grows coauthor and paper citation networks. The statistical and dynamic properties of the networks generated by this model are validated against a 20-year data set of articles published in PNAS. Systematic deviations from a power law distribution of citations to papers are well fit by a model that incorporates a partitioning of authors and papers into topics, a bias for authors to cite recent papers, and a tendency for authors to cite papers cited by papers that they have read. In this TARL model (for topics, aging, and recursive linking), the number of topics is linearly related to the clustering coefficient of the simulated paper citation network.
Hearing underlies our ability to locate sound sources in the
environment, our appreciation of music, and our ability to communicate.
Participants in the National Academy of Sciences colloquium on Auditory
Neuroscience: Development, Transduction, and Integration presented
research results bearing on four key issues in auditory research. How
does the complex inner ear develop? How does the cochlea transduce
sounds into electrical signals? How does the brain's ability to
compute the location of a sound source develop? How does the forebrain
analyze complex sounds, particularly species-specific communications?
This article provides an introduction to the papers stemming from the
This volume contains the papers presented at CICLOPS'12: 12th International
Colloquium on Implementation of Constraint and LOgic Programming Systems held
on Tueseday September 4th, 2012 in Budapest.
The program included 1 invited talk, 9 technical presentations and a panel
discussion on Prolog open standards (open.pl). Each programme paper was
reviewed by 3 reviewers.
CICLOPS'12 continues a tradition of successful workshops on Implementations
of Logic Programming Systems, previously held in Budapest (1993) and Ithaca
(1994), the Compulog Net workshops on Parallelism and Implementation
Technologies held in Madrid (1993 and 1994), Utrecht (1995) and Bonn (1996),
the Workshop on Parallelism and Implementation Technology for (Constraint)
Logic Programming Languages held in Port Jefferson (1997), Manchester (1998),
Las Cruces (1999), and London (2000), and more recently the Colloquium on
Implementation of Constraint and LOgic Programming Systems in Paphos (2001),
Copenhagen (2002), Mumbai (2003), Saint Malo (2004), Sitges (2005), Seattle
(2006), Porto (2007), Udine (2008), Pasadena (2009), Edinburgh (2010) -
together with WLPE, Lexington (2011).
We would like to thank all the authors, Tom Schrijvers for his invited talk,
the programme committee members...
This volume contains the proceedings of the 13th International Colloquium on
Implementation of Constraint and LOgic Programming Systems (CICLOPS 2013), held
in Istanbul, Turkey during August 25, 2013. CICLOPS is a well established line
of workshops, traditionally co-located with ICLP, that aims at discussing and
exchanging experience on the design, implementation, and optimization of
constraint and logic programming systems, and other systems based on logic as a
means of expressing computations. This year, CICLOPS received 8 paper
submissions. Each submission was reviewed by at least 3 Program Committee
members and, at the end, 6 papers were accepted for presentation at the
workshop. We would like to thank the ICLP organizers for their support, the
EasyChair conference management system for making the life of the program
chairs easier and arxiv.org for providing permanent hosting. Thanks should go
also to the authors of all submitted papers for their contribution to make
CICLOPS alive and to the participants for making the event a meeting point for
a fruitful exchange of ideas and feedback on recent developments. Finally, we
want to express our gratitude to the Program Committee members, as the
symposium would not have been possible without their dedicated work.; Comment: Proceedings of the 13th International Colloquium on Implementation of
Constraint LOgic Programming Systems (CICLOPS 2013)...
During the month of March 1997 the Facultat de Traducció i d'Interpretació of the Universitat Autònoma de Barcelona held its first on-line international translation colloquium, dedicated to the subject of intercultural transfer. A dedicated Web site was established to house invited position papers on the subject by Doug Robinson and Anthony Pym, and a response by Michael Cronin. An electronic mailing list was established to permit discussion of the position papers, and messages received were also housed at the Web site. Some 160 participants from 35 countries took part in the colloquium. The extracts published here include the position papers and a selection of responses elicited by the discussion.; Al llarg del mes de març de 1997, la Facultat de Traducció i d'Interpretació de la Universitat Autònoma de Barcelona va dur a terme el seu primer col·loqui internacional en línia de traducció, amb la transferència intercultural com a tema principal. Es van publicar en pàgines web les ponències convidades de Doug Robinson i d'Anthony Pym, i una resposta de Michael Cronin. Es va crear una llista electrònica per fomentar el debat, i es van publicar els missatges rebuts al mateix lloc. Hi van participar unes 160 persones de 35 països. Aquí es publiquen les ponències i una selecció de les respostes que es van produir al llarg del debat.