The Predication of the Individual in Anthropological Interactionism

In Memory of Max Gluckman
Theories of strategic interaction have been offered as a cure for the failings of structural functionalism and currently enjoy considerable influence in social anthropology. Employing in illustration Barth's Models of Social Organization, this essay argues that interactionism's focus on the individual, rather than on the group, issues from the presupposition of physicalism and makes it impossible to account for values and socioculture as such. A dialectical approach is urged . [transactional analysis, theory, dialectical approach, the "individual"]     

Cognizing "Cognized Models"

In his later work Rappaport acknowledged that his earlier efforts had overemphasized organic and ecological functions in the explanation of cultural phenomena. He then distanced himself from both idealism and reductive materialism and set out to understand the complexities of cultural understandings and ritual. Specifically, he shifted from functionalism to formalism in an effort to understand ritual and its language in relation to cultural norms. Ultimately his analysis was implicitly structural, understanding the part as a constituent of an overarching arrangement and in terms of what Althusser would have called "structural causality." Although his work benefited from this shift from function to structure, Rappaport did not use it to explore the political dimension. However, a holistic ecology such as the one Rappaport essayed must ultimately embrace both political ecology and historical ecology, [cognized models, ritual, political ecology, structural causality-]     

'Common sense' and 'governmentality': local government in southeastern Ireland, 1850-1922

Early paradigms in political anthropology identified formal government councils as a subject for cross-cultural comparison (structural functionalism) or as a political resource for goal-orientated actors (transactionalism). Recent concerns with power and regulation can also profit from a focus on local-level government councils by using them to explore the conceptual and empirical linkages between 'common sense' and 'governmentality'. In this article, as a point of entry, we highlight a key moment in the history of Britain's colonial and hegemonic project in Ireland, namely the orderly administrative transition from colony to state which occurred in Ireland after 1919. By constructing a historical narrative of a local government council in the southeast after 1850, and of its material and discursive bases, we show how the actions and ideologies of elite farmers were implicated in this orderly administrative transition and, therefore, how the concepts of governmentality, hegemony, and common sense might be linked.     

A critical approach to the definition of Darwinian units of selection

What are the biological units of selection? In fact, the notion of "unit of selection" (UOS) is blurred by ambiguity and controversy. To further evaluate the biological entities that are the objects of natural selection, three novel conceptual criteria (holism, minimalism, functionalism) are critically applied; they reveal, in addition to the self-evident case of the "individual," at least six distinct types of UOSs. These UOSs do not always have a defined structural organization; they can be parts of a living organism, a cohesive group of conspecifics, a multiunit entity, a totipotent cell, a DNA fragment, or a whole organism. UOS types diversify by amalgamation or parcelation processes of apparent entities. Therefore, previous attempts to characterize the UOSs solely on some morphological levels (gene, individual, group) without applying stringent criteria have failed to cope with the structural variations of natural phenomena and have led to the ambiguity of terms used.     

L’éclairage biologique des activités mentales: réduction ou mise en perspective ?

The relationship between the human psychological faculties and their underlying biological foundation is traditionally addressed within the mind-matter philosophical framework and its ethical extension regarding freedom and determinism. Neurobiology represents a new method, reflective of our times, to articulate the relationships between biological and psychological phenomena. The various points of view in this field are often based on implicit ontological presuppositions and, at least sometimes, unconscious epistemological assumptions: monism vs dualism, functionalism, reductionism, eliminativism, type identity and other more or less sophisticated variations. Bearing in mind the pitfalls these create, we can try to determine structural analogies across the different levels of the living being and the mind: the energy imbalance maintained for cell survival; the dynamic and complementary relationship between homeostatic and allostatic functions in living organisms; the tension between essential and complementary cognitive brain processes, such as the processes used to represent an object and those used to locate an object in space. Those phenomena all bear structural analogies, even though they work at different levels.     

Phylogenetic, functional, and structural components of variation in bone growth rate of amniotes

SUMMARY The biological features observed in every living organism are the outcome of three sets of factors: historical (inherited by homology), functional (biological adaptation), and structural (properties inherent to the materials with which organs are constructed, and the morphogenetic rules by which they grow). Integrating them should bring satisfactory causal explanations of empirical data. However, little progress has been accomplished in practice toward this goal, because a methodologically efficient tool was lacking. Here we use a new statistical method of variation partitioning to analyze bone growth in amniotes. (1) Historical component . The variation of bone growth rates contains a significant phylogenetic signal, suggesting that the observed patterns are partly the outcome of shared ancestry. (2) Functional causation . High growth rates, although energy costly, may be adaptive (i.e., they may increase survival rates) in taxa showing short growth periods (e.g., birds). In ectothermic amniotes, low resting metabolic rates may limit the maximum possible growth rates. (3) Structural constraint . Whereas soft tissues grow through a multiplicative process, growth of mineralized tissues is accretionary (additive, i.e., mineralization fronts occur only at free surfaces). Bone growth of many amniotes partially circumvents this constraint: it is achieved not only at the external surface of the bone shaft, but also within cavities included in the bone cortex as it grows centrifugally. Our approach contributes to the unification of historicism, functionalism, and structuralism toward a more integrated evolutionary biology.     

Re-reading Ronald Berndt: Exploring the Depths of his Yolngu Ethnography

The title of this essay sets its dialogic structure. Ronald Berndt's writing at times obscured the core insights that he had about Yolngu society, and partly as a consequence Australian anthropology has not yet made the best use of the immense richness of his ethnographic legacy. In retrospect, in many areas of their research the Berndts were pioneers addressing themes and topics that had been for too long ignored. They opened up new fields of study and redressed some of the imbalances associated with functionalism, the dominant paradigm of their early years as anthropologists. In this essay I examine two areas of Ronald Berndt's writings in which he had insights that were not fully appreciated at the time: the analysis of Yolngu social organisation and the analysis of Yolngu sexual symbolism. In both cases, his absorption in Yolngu ethnography made him aware that his predecessors had overlooked important themes of Yolngu society, yet in both cases his analysis was less convincing than it might have been.     

A Durkheimian critique of contemporary multiculturalism

Multiculturalism has been under scrutiny and subject to heated debates by politicians, commentators, and academics over the past two decades. Behind these debates lie concerns about the erosion of social cohesion, national security, and economic problems. This article frames and explains the debates over cultural diversity from the perspective of Durkheimian functionalism. This article presents a systematic review of Durkheim's theory and debunks (mis)interpretations that transpose his notion of division of labour to cultural diversity. It is argued that the competitive nature of the global nation-state system poses challenges for sustaining cultural diversity within national borders. After contrasting the Durkheimian functionalist perspective on multiculturalism with contemporary social justice perspectives, the article highlights and analyses the pressure point between multiculturalism within and the competitive global nation-state system without.     

Explaining Religion without Explaining It Away: Trust, Truth, and the Evolution of Cooperation in Roy A. Rappaport's "The Obvious Aspects of Ritual"

Moving beyond the ecological functionalism of Pigs for the Ancestors, Roy Rappaport's subsequent work on ritual explored how the "obvious aspects" of ritual's formalism and the need to perform it literally embody in its performers expressions of sanctity and truth that counter the threats of lying and alternative inherent in symbolic communication. He recognized that symbolic meaning and truth presuppose social cooperation and trust between individuals, and ritual serves uniquely to reaffirm this mutuality at the level of both individual behavior and conventional meaning. Through a study of male greetings among olive baboons (Papio cynocephalus anubis), this paper illustrates how ritual in Rappaport's sense may indeed intensify cooperation in socially complex but nonlinguistic contexts by establishing a behaviorally transparent means of certifying otherwise opaque individual intentions. Thus, not only may ritual sanctify symbolic communication, but it also may have played a crucial role in its evolution, [ritual, sociocultural evolution, religion and society, symbolic communication, olive baboons, primate social behavior]     

Comparative neurochemical profile of 3,4-methylenedioxymethamphetamine and its metabolite alpha-methyldopamine on key targets of MDMA neurotoxicity

The neurotoxicity of MDMA or "Ecstasy" in rats is selectively serotonergic, while in mice it is both dopaminergic and serotonergic. MDMA metabolism may play a key role in this neurotoxicity. The function of serotonin and dopamine transporter and the effect of MDMA and its metabolites on them are essential to understand MDMA neurotoxicity. The aim of the present study was to investigate and compare the effects of MDMA and its metabolite alpha-methyldopamine (MeDA) on several molecular targets, mainly the dopamine and serotonin transporter functionality, to provide evidence for the role of this metabolite in the neurotoxicity of MDMA in rodents. MeDA had no affinity for the serotonin transporter but competed with serotonin for its uptake. It had no persistent effects on the functionalism of the serotonin transporter, in contrast to the effect of MDMA. Moreover, MeDA inhibited the uptake of dopamine into the serotonergic terminal and also MAO(B) activity. MeDA inhibited dopamine uptake with a lower IC(50) value than MDMA. After drug washout, the inhibition by MeDA persisted while that of MDMA was significantly reduced. The effect of MDMA on the dopamine transporter is related with dopamine release from vesicular stores, as this inhibition disappeared in reserpine-treated animals. However, the effect of MeDA seems to be a persistent conformational change of this transporter. Moreover, in contrast with MDMA, MeDA did not show affinity for nicotinic receptors, so no effects of MeDA derived from these interactions can be expected. The metabolite reduced cell viability at lower concentrations than MDMA. Apoptosis plays a key role in MDMA induced cellular toxicity but necrosis is the major process involved in MeDA cytotoxicity. We conclude that MeDA could protect against the serotonergic lesion induced by MDMA but potentiate the dopaminergic lesion as a result of the persistent blockade of the dopamine transporter induced this metabolite.     

Code Biology – A New Science of Life

Systems Biology and the Modern Synthesis are recent versions of two classical biological paradigms that are known as structuralism and functionalism, or internalism and externalism. According to functionalism (or externalism), living matter is a fundamentally passive entity that owes its organization to external forces (functions that shape organs) or to an external organizing agent (natural selection). Structuralism (or internalism), is the view that living matter is an intrinsically active entity that is capable of organizing itself from within, with purely internal processes that are based on mathematical principles and physical laws. At the molecular level, the basic mechanism of the Modern Synthesis is molecular copying, the process that leads in the short run to heredity and in the long run to natural selection. The basic mechanism of Systems Biology, instead, is self-assembly, the process by which many supramolecular structures are formed by the spontaneous aggregation of their components. In addition to molecular copying and self-assembly, however, molecular biology has uncovered also a third great mechanism at the heart of life. The existence of the genetic code and of many other organic codes in Nature tells us that molecular coding is a biological reality and we need therefore a framework that accounts for it. This framework is Code biology, the study of the codes of life, a new field of research that brings to light an entirely new dimension of the living world and gives us a completely new understanding of the origin and the evolution of life.     

Murburn posttranslational modifications of proteins: Cellular redox processes and murzyme-mediated metabolo-proteomics

Murburn concept constitutes the thesis that diffusible reactive species or DRS are obligatorily involved in routine metabolic and physiological activities. Murzymes are defined as biomolecules/proteins that generate/modulate/sustain/utilize DRS. Murburn posttranslational modifications (PTMs) result because murburn/murzyme functionalism is integral to cellular existence. Cells must incorporate the inherently stochastic nature of operations mediated by DRS. Due to the earlier/inertial stigmatic perception that DRS are mere agents of chaos, several such outcomes were either understood as deterministic modulations sponsored by house-keeping enzymes or deemed as unregulated nonenzymatic events resulting out of “oxidative stress”. In the current review, I dispel the myths around DRS-functions, and undertake systematic parsing and analyses of murburn modifications of proteins. Although it is impossible to demarcate all PTMs into the classical or murburn modalities, telltale signs of the latter are evident from the relative inaccessibility of the locus, non-specificities and mechanistic details. It is pointed out that while many murburn PTMs may be harmless, some others could have deleterious or beneficial physiological implications. Some details of reversible/irreversible modifications of amino acid residues and cofactors that may be subjected to phosphorylation, halogenation, glycosylation, alkylation/acetylation, hydroxylation/oxidation, etc. are listed, along with citations of select proteins where such modifications have been reported. The contexts of these modifications and their significance in (patho)physiology/aging and therapy are also presented. With more balanced explorations and statistically verified data, a definitive understanding of normal versus pathological contexts of murburn modifications would be obtainable in the future.     

The carinated denticulates from the Paleolithic site of Isernia La Pineta (Molise,Central Italy): Tools or flaking waste? The results of the 1993 lithic experiments

During 1993 a campaing of lithic experiments was carried out near the National Paleolithic Museum and archaeological park at Isernia La Pineta, with the aim of reproducing the morphologies of the tools found at the Paleolithic site in order to try to understand the techniques used for their manufacture and the possible uses to which they were put. In this article the results of this work are presented. The flint artifacts were faithfully reproduced using the same types of raw material used by the prehistoric artisans, and using a variety of different techniques (anvil technique, direct percussion and bipolar technique), among which the bipolar technique seems to assume a particular importance. Of considerable interest is the fact that in the light of the experiments the denticulates and carinated becs, which at the site of Isernia La Pineta represent more than 90% of what are usually considered “tools” according to the conventional typological schemes, turned out in fact to be the residue of cores, that is flaking waste. Furthermore, flakes of small dimensions, derived from flint tablets or flakecores by means of the bipolar technique, were used as cutting tools in different possible activities and revealed their high degree of functionalism in contrast with the carinated “tools”. The analysis of the traces of wear have shown that the great majority of these are found on the small unretouched flakes rather than on the “tools” such as the denticulates and becs, thereby demonstrating that the latter represent blanks for obtaining real tools, that are the cutting edges of unretouched flakes. The industry from Isernia is thus shown to be very opportunistic, based on an intense exploitation of raw material and practically lacking those which, according to the conventional schemes usually adopted, can be considered as retouched “tools”.     

Structural analysis based on state-space modeling.

A new method has been developed to compute the probability that each amino acid in a protein sequence is in a particular secondary structural element. Each of these probabilities is computed using the entire sequence and a set of predefined structural class models. This set of structural classes is patterned after Jane Richardson''s taxonomy for the domains of globular proteins. For each structural class considered, a mathematical model is constructed to represent constraints on the pattern of secondary structural elements characteristic of that class. These are stochastic models having discrete state spaces (referred to as hidden Markov models by researchers in signal processing and automatic speech recognition). Each model is a mathematical generator of amino acid sequences; the sequence under consideration is modeled as having been generated by one model in the set of candidates. The probability that each model generated the given sequence is computed using a filtering algorithm. The protein is then classified as belonging to the structural class having the most probable model. The secondary structure of the sequence is then analyzed using a "smoothing" algorithm that is optimal for that structural class model. For each residue position in the sequence, the smoother computes the probability that the residue is contained within each of the defined secondary structural elements of the model. This method has two important advantages: (1) the probability of each residue being in each of the modeled secondary structural elements is computed using the totality of the amino acid sequence, and (2) these probabilities are consistent with prior knowledge of realizable domain folds as encoded in each model. As an example of the method''s utility, we present its application to flavodoxin, a prototypical alpha/beta protein having a central beta-sheet, and to thioredoxin, which belongs to a similar structural class but shares no significant sequence similarity.     

Structural trees for proteins containing φ-motifs

In the present study, a novel structural motif of proteins referred to as the phi-motif is considered, and two novel structural trees in which the phi-motif is taken as the root structure have been constructed. The simplest phi-motif is formed by three adjacent beta-strands connected by loops and packed in one beta-sheet so that its overall fold resembles the Greek letter phi. Construction of the structural trees and modeling of folding pathways have shown that all structures of the protein superfamilies can be obtained by stepwise addition of alpha-helices and/or beta-strands to the root phi-motif taking into account a restricted set of rules inferred from known principles of protein structure. The structural trees are a good tool for structure comparison, structural classification of proteins, as well as for searching for all possible protein folds and folding pathways.     

Analysis of Protein Structural Motifs in Terms of Sets of Codes Representing Local Structures

An amino acid sequence pattern conserved among a family of proteins is called motif. It is usually related to the specific function of the family. On the other hand, functions of proteins are realized through their 3D structures. Specific local structures, called structural motifs, are considered as related to their functions. However, searching for common structural motifs in different proteins is much more difficult than for common sequence motifs. We are attempting in this study to convert the information about the structural motifs into a set of one-dimensional digital strings, i.e., a set of codes, to compare them more easily by computer and to investigate their relationship to functions more quantitatively. By applying the Delaunay tessellation to a 3D structure of a protein, we can assign each local structure to a unique code that is defined so as to reflect its structural feature. Since a structural motif is defined as a set of the local structures in this paper, the structural motif is represented by a set of the codes. In order to examine the ability of the set of the codes to distinguish differences among the sets of local structures with a given PROSITE pattern that contain both true and false positives, we clustered them by introducing a similarity measure among the set of the codes. The obtained clustering shows a good agreement with other results by direct structural comparison methods such as a superposition method. The structural motifs in homologous proteins are also properly clustered according to their sources. These results suggest that the structural motifs can be well characterized by these sets of the codes, and that the method can be utilized in comparing structural motifs and relating them with function.     

Using Bagging classifier to predict protein domain structural class

Classification and prediction of protein domain structural class is one of the important topics in the molecular biology. We introduce the Bagging (Bootstrap aggregating), one of the bootstrap methods, for classifying and predicting protein structural classes. By a bootstrap aggregating procedure, the Bagging can improve a weak classifier, for instance the random tree method, to a significant step towards optimality. In this research, it is demonstrated that the Bagging performed at least as well as LogitBoost and Support vector machines in predicting the structural classes for a given protein domain dataset by 10 cross-validation test, which indicate that the Bagging method is promising and anticipated that it could be potentially further improved on predicting protein structural classes as well as other bio-macromolecular attributes, if the bagging method and other existing methods can be effectively complemented with each other.     

Combining evolutionary and structural information for local protein structure prediction

We study the effects of various factors in representing and combining evolutionary and structural information for local protein structural prediction based on fragment selection. We prepare databases of fragments from a set of non-redundant protein domains. For each fragment, evolutionary information is derived from homologous sequences and represented as estimated effective counts and frequencies of amino acids (evolutionary frequencies) at each position. Position-specific amino acid preferences called structural frequencies are derived from statistical analysis of discrete local structural environments in database structures. Our method for local structure prediction is based on ranking and selecting database fragments that are most similar to a target fragment. Using secondary structure type as a local structural property, we test our method in a number of settings. The major findings are: (1) the COMPASS-type scoring function for fragment similarity comparison gives better prediction accuracy than three other tested scoring functions for profile-profile comparison. We show that the COMPASS-type scoring function can be derived both in the probabilistic framework and in the framework of statistical potentials. (2) Using the evolutionary frequencies of database fragments gives better prediction accuracy than using structural frequencies. (3) Finer definition of local environments, such as including more side-chain solvent accessibility classes and considering the backbone conformations of neighboring residues, gives increasingly better prediction accuracy using structural frequencies. (4) Combining evolutionary and structural frequencies of database fragments, either in a linear fashion or using a pseudocount mixture formula, results in improvement of prediction accuracy. Combination at the log-odds score level is not as effective as combination at the frequency level. This suggests that there might be better ways of combining sequence and structural information than the commonly used linear combination of log-odds scores. Our method of fragment selection and frequency combination gives reasonable results of secondary structure prediction tested on 56 CASP5 targets (average SOV score 0.77), suggesting that it is a valid method for local protein structure prediction. Mixture of predicted structural frequencies and evolutionary frequencies improve the quality of local profile-to-profile alignment by COMPASS.     

Genetic control of lipid transport in mice. II. Genes controlling structure of high density lipoproteins

Genetic factors controlling the structure of high density lipoproteins (HDL) in mice have been examined. Surveys of inbred strains of mice revealed genetic structural variations of the two major apolipoproteins of mouse HDL, apolipoproteins A-I and A-II. The structural variations alter the charge of the proteins as judged by isoelectric focusing of HDL under denaturing conditions. The structural variations are inherited as single Mendelian genes exhibiting co-dominant expression. The structural gene for mouse apolipoprotein A-II, designated Alp-2, resides on mouse chromosome 1, tightly linked to Ly-m20, a lymphocyte alloantigen locus. Previous studies, as well as our results, suggest that the structural gene for mouse apolipoprotein A-I, designated Alp-1, is on mouse chromosome 9. The genetic structural variation for apo-A-I results in a shift in the charge of the entire family of apo-A-I isoforms, indicating that they are all encoded by a common structural gene. The structure of intact HDL, examined primarily by electrophoretic techniques, exhibits numerous and complex phenotypes among different strains of mice. One variation, controlling the density and possibly the size of HDL, has been studied in two sets of recombinant inbred strains of mice. The results indicate that the variation is controlled by a single major gene that is either tightly linked to or identical with the Alp-2 gene on chromosome 1. In addition to structural variation, inbred strains of mice exhibited considerable quantitative variation of plasma HDL. Thus, the mouse provides a useful model system for examining the genetic control of mammalian HDL structure and regulation.