Associational-Metaphorical Activity: Another View of Language and Mind

This paper extends Sapir's idea that language embodies intertwined and isolable patterns of two distinct orders—patterns of reference (in my terms, communication) and patterns of expression (associational-metaphorical activity). Viewing language as a continuum of usages ranging from schizophrenic usage, at one extreme, to objective, representational usage at the other, associational-metaphorical activity is seen as variously operative throughout. There are illustrations of how this dimension is woven into normal communication. Finally, there is speculation on the source of associational-metaphorical activity and the light it throws on human mentality as projected in language.     

Camelot at Yale: The Construction and Dismantling of the Sapirian Synthesis, 1931-39

For a brief shining moment in the 1930s, Edward Sapir stood at the forefront of a new synthesis of Boasian ethnology and linguistics. But his call to Yale in 1931 was a mandate taken up against formidable odds, and the grand synthesis soon began to unravel. George Peter Murdock, who became chairman in 1939, moved the department toward science and "verified theory." In the period immediately following World War II, Sapir's program was not revived, but its legacies have come to us by way of the Yale ethnoscience and linguistic anthropology of the 1960s, and his synthesis remains a viable option for Americanist anthropology at the millennium.     

Distributive Models of Culture: A Sapirian Alternative to Essentialism

The Boasian conception of culture has been roundly criticized in recent years for its essentialist, or even racist, implications. Yet an alternative model that avoids these implications was proposed in the 1930s by Boas student Edward Sapir. Having long survived on the margins of anthropological theory, Sapir's "distributive" concept of culture is now entering the theoretical mainstream through recent developments in both psychological and "postmodernist" anthropology.
By emphasizing the full range of variation within any so-called culture, anthropologists have begun to apply the same style of population thinking that helped launch the Darwinian revolution in biology.     

Protein cross-linking analysis using mass spectrometry, isotope-coded cross-linkers, and integrated computational data processing

Distance constraints in proteins and protein complexes provide invaluable information for calculation of 3D structures, identification of protein binding partners and localization of protein-protein contact sites. We have developed an integrative approach to identify and characterize such sites through the analysis of proteolytic products derived from proteins chemically cross-linked by isotopically coded cross-linkers using LC-MALDI tandem mass spectrometry and computer software. This method is specifically tailored toward the rapid analysis of low microgram amounts of proteins or multimeric protein complexes cross-linked with nonlabeled and deuterium-labeled bis-NHS ester cross-linking reagents (both commercially available and readily synthesized). Through labeling with [18O]water solvent and LC-MALDI analysis, the method further allows the possible distinction between Type 0 and Type 1 or Type 2 modified peptides (monolinks and looplinks or cross-links), although such a distinction is more readily made from analysis of tandem mass spectrometry data. When applied to the bacterial Colicin E7 DNAse/Im7 heterodimeric protein complex, 23 cross-links were identified including six intersubunit cross-links, all between residues that are close in space when examined in the context of the X-ray structure of the heterodimer. In addition, cross-links were successfully identified in five single subunit proteins, beta-lactoglobulin, cytochrome c, lysozyme, myoglobin, and ribonuclease A, establishing the generality of the approach.     

Body size, energy metabolism, and the lungs

The theoretical basis for applying the power function y = aMb to the study of structure-function relationships is discussed. Dimensional analysis and the distinction between intensive and extensive properties of animals show that the mass coefficient a represents the effect of intensive or qualitative factors on the considered function or structure. The theoretical mass exponent is a criterion for the constancy of a and the qualitative sameness of the compared structure or function. Examples from respiratory and metabolic physiology are given.     

Culture,Context, and Maternal Self-Efficacy in Latina Mothers

Youth civic engagement occupies a central space in applied developmental science. However, understanding of the processes and contexts in which early adolescents become civically engaged is still limited. This study draws on a sample of approximately 4,000 students from 11 urban middle schools in Tennessee to address several gaps in the civic engagement literature. First, we use latent class analysis to identify types of civic engagement in early adolescence. Second, we explore associations between types of engagement and youth behavioral and academic outcomes. Third, we focus on urban youth. A latent class analysis using survey items suggests a three-class structure for civic engagement in urban middle schools. One distinction is between students who are engaged and those who are not. Another distinction is that, among the engaged groups, one is engaged both behaviorally and attitudinally (social justice actors), whereas another has strong civic attitudes but infrequent civic behaviors (social justice sympathizers).     

Combined electron transfer dissociation-collision-induced dissociation fragmentation in the mass spectrometric distinction of leucine, isoleucine, and hydroxyproline residues in Peptide natural products

Distinctions between isobaric residues have been a major challenge in mass spectrometric peptide sequencing. Here, we propose a methodology for distinction among isobaric leucine, isoleucine, and hydroxyproline, a commonly found post-translationally modified amino acid with a nominal mass of 113 Da, through a combined electron transfer dissociation-collision-induced dissociation approach. While the absence of c and z(?) ions, corresponding to the Yyy-Xxx (Xxx = Leu, Ile, or Hyp) segment, is indicative of the presence of hydroxyproline, loss of isopropyl (Δm = 43 Da) or ethyl radicals (Δm = 29 Da), through collisional activation of z radical ions, are characteristic of leucine or isoleucine, respectively. Radical migration processes permit distinctions even in cases where the specific z(?) ions, corresponding to the Yyy-Leu or -Ile segments, are absent or of low intensity. This tandem mass spectrometric (MS(n)) method has been successfully implemented in a liquid chromatography-MS(n) platform to determine the identity of 23 different isobaric residues from a mixture of five different peptides. The approach is convenient for distinction of isobaric residues from any crude peptide mixture, typically encountered in natural peptide libraries or proteomic analysis.     

Microbiome Structure and Function: A New Framework for Interpreting Data

A distinction between different notions of “structure” and “function” is suggested for interpreting the overwhelming amount of data on microbiome structure and function. Sequence data, biochemical agents, interaction networks, taxonomic communities, and their dynamics can be linked to potential or actual biochemical activities, causal roles, and selected effects, respectively. This conceptual clarification has important methodological consequences for how to interpret existing data and approach open questions in contemporary microbiome research practice. In particular, the field will have to start thinking about notions of function more directly. Also see the video abstract here https://youtu.be/j5pq5uGld1k .     

Causal specificity and the instructive–permissive distinction

I use some recent formal work on measuring causation to explore a suggestion by James Woodward: that the notion of causal specificity can clarify the distinction in biology between permissive and instructive causes. This distinction arises when a complex developmental process, such as the formation of an entire body part, can be triggered by a simple switch, such as the presence of particular protein. In such cases, the protein is said to merely induce or "permit" the developmental process, whilst the causal "instructions" for guiding that process are already prefigured within the cells. I construct a novel model that expresses in a simple and tractable way the relevant causal structure of biological development and then use a measure of causal specificity to analyse the model. I show that the permissive-instructive distinction cannot be captured by simply contrasting the specificity of two causes as Woodward proposes, and instead introduce an alternative, hierarchical approach to analysing the interaction between two causes. The resulting analysis highlights the importance of focusing on gene regulation, rather than just the coding regions, when analysing the distinctive causal power of genes.     

The R(Pi-mcd1) locus from Solanum microdontum involved in resistance to Phytophthora infestans, causing a delay in infection, maps on potato chromosome 4 in a cluster of NBS-LRR genes

The distinction between field resistance and resistance based on resistance (R) genes has been proven valid for many plant-pathogen interactions. This distinction does not seem to be valid for the interaction between potato and late blight. In this study, a locus involved in late blight resistance, derived from Solanum microdontum, provides additional evidence for this lack of distinction. The resistance is associated with a hypersensitive response and results in a delay of infection of approximately 1 to 2 weeks. Both a quantitative as well as a qualitative genetic approach were used, based on data from a field assay. Quantitative trait locus (QTL) analysis identified a QTL on chromosome 4 after correction of the resistance data for plant maturity. A qualitative genetic analysis resulted in the positioning of this locus on the short arm of chromosome 4 in between amplified fragment length polymorphism marker pCTmACG_310 and cleaved amplified polymorphic sequence markers TG339 and T0703. This position coincides with a conserved Phytophthora R gene cluster which includes R2, R(2-like), R(Pi-blb3), and R(Pi-abpt). This implies that R(Pi-mcd1) is the fifth R gene of this nucleotide-binding site leucine-rich repeat cluster. The implications of our results on R-gene-based and field resistance are discussed.     

Tracking of nanoscale structural variations on a single amyloid fibril with tip‐enhanced Raman scattering

Amyloid fibrils are known to be responsible for diseases such as Alzheimer's disease. A detailed insight into the structure of amyloid fibrils is fundamental since it is not yet understood what triggers the misfolding of proteins to the fiber like structures. The molecular structure of fibril surfaces on a single amino acid level has not been revealed so far but would present a valuable contribution to this question. Here we demonstrate the direct molecular distinction of selected amino acids on insulin fibril surfaces with a lateral resolution better than 2 nm by applying tip‐enhanced Raman spectroscopy (TERS). This approach provides simultaneously a way to directly reveal conformational changes in the secondary structure, namely α‐helix, β‐sheet, on the fibril surface with nanometer resolution. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

The intensity of competition versus its importance: an overlooked distinction and some implications

The intensity of competition is a physiological concept, related directly to the well-being of individual organisms but only indirectly and conditionally to their fitness, and even more indirectly to the evolution of populations and the structure of communities. The importance of competition is primarily an ecological and evolutionary concept, related directly to the ecology and fitness of individuals but only indirectly to their physiological states. The intensity of competition is not necessarily correlated with the intensities of predation, disturbance, abiotic stress, or other ecological processes. The importance of competition is necessarily relative to the importances of other processes. Intensity refers primarily to the process of present competition, whereas importance refers primarily to the products of past competition. The distinction between the intensity and the importance of competition clarifies two long-standing ecological debates. Some ecologists have proposed that competition is greater in more stressful habitats, others the opposite, and still others that no such relationship exists. Evidence cited to refute or support these positions often confuses intensity and importance. Distinguishing between them focuses questions more sharply and indicates what sorts of new evidence should be sought. The more widely known debate over the prevalence of competition as an agent of community structure is a debate about the importance of competition, but evidence about the intensity of competition has often been used by both sides. We argue that intensity and importance need not be correlated, and so measurements of the intensity of competition are not directly relevant to this debate. This distinction also generates testable hypotheses and suggests directions for research. For example, we hypothesize that competition can be unimportant even if it is very intense: no such hypothesis is possible unless importance is distinguished from intensity. We discuss the application of these ideas to methods and theories used to study competition, ecological communities, and the evolution of competitive ability. We advocate a research approach that presumes multiple, interacting causes, including competition, affecting community structure, and we show how the distinction between intensity and importance helps to make this feasible.     

Comparison of two fingerprinting techniques, terminal restriction fragment length polymorphism and automated ribosomal intergenic spacer analysis, for determination of bacterial diversity in aquatic environments

We investigated bacterial diversity in different aquatic environments (including marine and lagoon sediments, coastal seawater, and groundwater), and we compared two fingerprinting techniques (terminal restriction fragment length polymorphism [T-RFLP] and automated ribosomal intergenic spacer analysis [ARISA]) which are currently utilized for estimating richness and community composition. Bacterial diversity ranged from 27 to 99 phylotypes (on average, 56) using the T-RFLP approach and from 62 to 101 genotypes (on average, 81) when the same samples were analyzed using ARISA. The total diversity encountered in all matrices analyzed was 144 phylotypes for T-RFLP and 200 genotypes for ARISA. Although the two techniques provided similar results in the analysis of community structure, bacterial richness and diversity estimates were significantly higher using ARISA. These findings suggest that ARISA is more effective than T-RFLP in detecting the presence of bacterial taxa accounting for <5% of total amplified product. ARISA enabled also distinction among aquatic bacterial isolates of Pseudomonas spp. which were indistinguishable using T-RFLP analysis. Overall, the results of this study show that ARISA is more accurate than T-RFLP analysis on the 16S rRNA gene for estimating the biodiversity of aquatic bacterial assemblages.     

Comparison of Two Fingerprinting Techniques, Terminal Restriction Fragment Length Polymorphism and Automated Ribosomal Intergenic Spacer Analysis, for Determination of Bacterial Diversity in Aquatic Environments

We investigated bacterial diversity in different aquatic environments (including marine and lagoon sediments, coastal seawater, and groundwater), and we compared two fingerprinting techniques (terminal restriction fragment length polymorphism [T-RFLP] and automated ribosomal intergenic spacer analysis [ARISA]) which are currently utilized for estimating richness and community composition. Bacterial diversity ranged from 27 to 99 phylotypes (on average, 56) using the T-RFLP approach and from 62 to 101 genotypes (on average, 81) when the same samples were analyzed using ARISA. The total diversity encountered in all matrices analyzed was 144 phylotypes for T-RFLP and 200 genotypes for ARISA. Although the two techniques provided similar results in the analysis of community structure, bacterial richness and diversity estimates were significantly higher using ARISA. These findings suggest that ARISA is more effective than T-RFLP in detecting the presence of bacterial taxa accounting for <5% of total amplified product. ARISA enabled also distinction among aquatic bacterial isolates of Pseudomonas spp. which were indistinguishable using T-RFLP analysis. Overall, the results of this study show that ARISA is more accurate than T-RFLP analysis on the 16S rRNA gene for estimating the biodiversity of aquatic bacterial assemblages.     

Systemic features of immune recognition in the gut

The immune system, to protect the body, must discriminate between the pathogenic and non-pathogenic microbes and respond to them in different ways. How the mucosal immune system manages to make this distinction is poorly understood. We suggest here that the distinction between pathogenic and non-pathogenic microbes is made by an integrated system rather than by single types of cells or single types of receptors; a systems biology approach is needed to understand immune recognition.     

Genetic differences between populations of sardine, Sardina pilchardus, and anchovy, Engraulis encrasicolus, in the Aegean and Ionian seas

Genetic distances based on electrophoretic variation and multivariate analysis of several morpho-metric and meristic characters suggest that populations of sardine and anchovy from the Aegean and Ionian seas do not form one panmictic population. The distinction between these two classes of populations emerges only as a statistical property, and for some characters the within-sea variation is larger than the between-sea variation. Thus, the reproductive isolation between populations inhabiting the two seas appears to be only partial. Our findings do not support the' pure' or' discrete' stock concept. Instead, they provide evidence for the dynamic population structure model according to which physical (e.g., hydrographic) or biological (e.g., predation or behaviour) factors impose a population structure maintained in a semi-equilibrium state under the opposing influences of migration and selection. Such a dynamic state may not be stable in the long run, and it may not allow for the accumulation of genetic divergence necessary for the emergence of higher taxa. It must, nevertheless, be taken into account in the management of exploited natural populations.     

The proximate/ultimate distinction in the multiple careers of Ernst Mayr

Ernst Mayr's distinction between “ultimate” and “proximate” causes is justly considered a major contribution to philosophy of biology. But how did Mayr come to this “philosophical” distinction, and what role did it play in his earlier “scientific” work? I address these issues by dividing Mayr's work into three careers or phases: 1) Mayr the naturalist/researcher, 2) Mayr the representative of and spokesman for evolutionary biology and systematics, and more recently 3) Mayr the historian and philosopher of biology. If we want to understand the role of the proximate/ultimate distinction in Mayr's more recent career as a philosopher and historian, then it helps to consider hisearlier use of the distinction, in the course of his research, and in his promotion of the professions of evolutionary biology and systematics. I believe that this approach would also shed light on some other important “philosophical” positions that Mayr has defended, including the distinction between “essentialism: and “population thinking.”     

Two ways to use imaging: focusing directly on mechanism, or indirectly via behaviour?

Recent developments in mesoscopic imaging--imaging at the level of tissues and organs, rather than the subcellular or molecular scale--are proving to be powerful for developmental biology. At the same time, these developments are also helping to emphasize an important distinction between two quite different approaches of how imaging is used. In the more traditional approach, images provide a direct insight into how a systems works-suggesting a mechanism or part of a mechanism. However an alternative approach is gaining ground, in which imaging is used to quantify the behaviour of a system, rather than directly assessing the mechanism. In this case the causal relationships of a system are inferred in a more indirect way-by comparing quantitative measurements with mathematical models of the system in question. Although indirect, this approach is powerful for addressing more complex biological systems--especially multiscale problems. It is tempting to distinguish the latter approach with the label 'quantitative biology', but this term only emphasizes the use of numbers, and therefore obscures the more fundamental difference, which is the powerful but indirect nature of the approach. Here I will discuss the distinction between the two imaging approaches, particularly in the context of recent improvements to tissue-level imaging techniques.     

Inherent intractability of the ascertainment problem for pedigree data: a general likelihood framework.

The problem of ascertainment in segregation analysis arises when families are selected for study through ascertainment of affected individuals. In this case, ascertainment must be corrected for in data analysis. However, methods for ascertainment correction are not available for many common sampling schemes, e.g., sequential sampling of extended pedigrees (except in the case of "single" selection). Concerns about whether ascertainment correction is even required for large pedigrees, about whether and how multiple probands in the same pedigree can be taken into account properly, and about how to apply sequential sampling strategies have occupied many investigators in recent years. We address these concerns by reconsidering a central issue, namely, how to handle pedigree structure (including size). We introduce a new distinction, between sampling in such a way that observed pedigree structure does not depend on which pedigree members are probands (proband-independent [PI] sampling) and sampling in such a way that observed pedigree structure does depend on who are the probands (proband-dependent [PD] sampling). This distinction corresponds roughly (but not exactly) to the distinction between fixed-structure and sequential sampling. We show that conditioning on observed pedigree structure in ascertained data sets obtained under PD sampling is not in general correct (with the exception of "single" selection), while PI sampling of pedigree structures larger than simple sibships is generally not possible. Yet, in practice one has little choice but to condition on observed pedigree structure. We conclude that the problem of genetic modeling in ascertained data sets is, in most situations, literally intractable. We recommend that future efforts focus on the development of robust approximate approaches to the problem.