bluuebunny/crossref_metadata_2025 huggingface dataset:
13 Explaining Economic Change: The Relations of Institutions, Politics, and Culture
Authors: Harriss John
Published: September 2008

This chapter examines the role of politics, power, and culture in the explanation of institutional change. It criticizes the rational choice framework of the new institutional economics for its apparent limitations in theorizing on these issues. It underlines the analytical advantages of historical institutionalism. The conflict among social classes and the institutional substance of power structures are of particular analytical significance. They are interrelated factors in the evolution of cultural values, as exemplified by the case of Indian economic development and its socio-political underpinnings.
14 Polanyian, Regulationist, and Autopoieticist Reflections on States and Markets and their Implications for the Knowledge‐Based Economy
Authors: Jessop Bob
Published: September 2008

This chapter examines Polanyi's substantive institutionalist analysis of market economies, market societies, and state intervention in the light of two later schools: the Parisian regulation approach to contemporary capitalism and systems-theoretical accounts of the market economy as an autopoietic system. All three regard the modern economy as an operationally autonomous system that is nonetheless socially embedded and needful of complex forms of social regulation. For each, an adequate account of economic activities should explore how they are related to the wider social environment; how they are embedded in a wider nexus of social institutions; how the latter assist in reproducing the capitalist (or market) economy; and how their development is coupled to these and other environing institutions. The chapter presents their respective accounts of economic institutedness and embeddedness, and then discusses the stability and reproducibility of the capitalist economy, paying particular attention to governance and meta-governance.
15 Pierre Bourdieu, a Theoretician of Change? The View fromRégulationTheory
Authors: Boyer Robert
Published: September 2008

This chapter examines the relationship between regulation theory and Bourdieu's sociology. Bourdieu's detractors have often taken the titles of his works at face value. While these titles may effectively underline the permanent nature of the reproduction of social roles, Bourdieu's argument is not an attempt to reduce each field's logic to the purely economic level. Bourdieu's defenders have not given sufficient attention to the profoundly dynamic character of his research that effectively forms a totality: from his studies of the Béarn and Kabylia, to his analysis of the market for the single-family house, moving through similar analyses of literature, art, and state nobility. The chapter develops a theme that régulation theory and Bourdieu's sociology are related. On the one hand, regulationist research has turned to the concept of habitus, a term borrowed from Bourdieu, as an alternative to the theory of rational choice as found in economics and the social sciences. On the other hand, both programmes of research can be added to those analyses of contemporary society that set out from a critical evaluation of Marxian insights. They also share this basic hypothesis: that life in society is made possible by the way in which institutions are constructed, just as economic activity is organized by the mode of régulation.
A Modish Name
Authors: Scholar Richard
Published: September 2008

This chapter traces the word history of the je-ne-sais-quoi by examining its precursors and cognates in Latin and Romance languages, the various non-substantival French phrases to which it is closely related, and its rise to the height of linguistic fashion in 17th-century France and England. It adopts a ‘mentalist’ rather than a rigorously ‘nominalist’ approach to the je-ne-sais-quoi, using it as a lexical tracer of a particular movement of the mind. It sketches a semantic definition (or ‘ideal-type’) of the je-ne-sais-quoi, arguing that the word comes above all to designate a certain something experienced by individual human subjects that cannot be explained. The first surviving treatment of the je-ne-sais-quoi as a topic — by the lexicographer and writer of polite prose, Dominique Bouhours, in 1671 — is offered along with evidence from early modern dictionaries in support of this claim.
A Secret of Nature? Descartes and the Philosophers
Authors: Scholar Richard
Published: September 2008

It is commonly said in the early modern period that elusive qualities draw natural bodies together. This chapter offers a critical history of attempts to explain such preternatural forces in natural philosophy. It argues that the je-ne-sais-quoi appears as a key term in the vernacular debate about occult qualities and other secrets of nature, and that it becomes a site of lexical conflict between traditionalists (especially Jesuit natural philosophers) and so-called ‘new’ philosophers (Bacon, Descartes, Leibniz, and Newton). Its appearance in this context is best understood as a symptom of the crisis that besets scholastic natural philosophy in the 17th century. The je-ne-sais-quoi offers in this way a point of entry into central debates of the period known as the ‘Scientific Revolution’. Not only does the word help articulate philosophical discussions about preternatural phenomena, but those discussions also offer access to the nature of the je-ne-sais-quoi itself.
The Stroke of Passion: Pascal and the Poets
Authors: Scholar Richard
Published: September 2008

It is commonly said that elusive forces draw individual human beings into passionate relations with one another. This chapter identifies three tendencies towards the je-ne-sais-quoi in the realm of the passions, and argues that these three tendencies correspond loosely to the term's history. The first part deals with Descartes and other philosophers who attempt to draw the je-ne-sais-quoi into, or to exclude it from, a systematic theory. The second part of the chapter is devoted to those early modern writers (Corneille, Pascal, La Rochefoucauld, Molière, Racine, and others) who describe a strange sympathy that springs not from any rational choice but from an inexplicable mutual passion. This falls upon the subject at one stroke and, or so the poets say at the term's moment of lexical currency, as a certain je-ne-sais-quoi. The third part of the chapter looks at those writers (Regnard among others) who come to exploit the term as a fashionable instrument of persuasion.
A Sign of Quality: Bouhours and the Polite Circle
Authors: Scholar Richard
Published: September 2008

This chapter examines uses of the je-ne-sais-quoi in polite literature, particularly Bouhours and his contemporary the Chevalier de Méré, to refer to an imperceptible sign of social quality and distinction. It argues that the ruling class under Louis XIV in the third quarter of the 17th-century comes to cultivate ever subtler signs of cultural quality in order to distinguish itself from those it wishes to exclude, and that the je-ne-sais-quoi encapsulates this élitist process. The polite circle makes and distributes the je-ne-sais-quoi as an inherent quality among its members and their works. The term settles in late 17th-century culture, neither as a force of nature nor as a stroke of passion, but as a collective fabrication. It lends itself, as a result, to ridicule and satire in Congreve, Fielding, and other English authors of the late 17th and early 18th centuries, as well as their French contemporaries.
Beyond Pre-History: The Case of Shakespeare
Authors: Scholar Richard
Published: September 2008

This chapter ends the book by suggesting that the je-ne-sais-quoi might be developed into a critical method for the comparative analysis of literary texts. It offers, as one example of what such an approach might yield, a close reading of Shakespeare's A Midsummer Night's Dream (c. 1595). Shakespeare stands outside the history of the je-ne-sais-quoi, a stranger on its threshold, while effortlessly revealing his mastery of its themes and forms. A Midsummer Night's Dream exemplifies that mastery. Bottom's dream is a bottomless comic encounter with a certain something in human relations that cannot be explained and that leaves Bottom stammering for words. It is suggested that the play itself has itself the quality of the je-ne-sais-quoi, moving away from the term's history in order to remain faithful to the thing itself.
Pre-Aryan India1
Authors: Lal Deepak
Published: September 2008

This chapter begins with a discussion of the geographical environment of Pre-Aryan India. It then discusses the emergence of pastoralism and agriculture, this is followed by a look at the development of the Indus valley civilization. This was the first urban civilization on the subcontinent, which was based on the agriculture and animal husbandry of the Indus flood-plain which appears to have been similar to that of recent centuries in the Indus valley.
Hindu India
Authors: Lal Deepak
Published: September 2008

This chapter outlines the historical evolution of the caste system as well as its major features. It then examines its probable rationale, continuing relevance, and possible economic effects. It argues that the institution of caste — independent of the government and with social ostracism as its most severe sanction — was a powerful factor in the survival of Hinduism.
An Economic Rationale for the Hindu Social System
Authors: Lal Deepak
Published: September 2008

This chapter sketches an economic theory which might be able to explain both the origins and the resilience of the Hindu social system as expressed in its twin pillars: the caste system and the village “community”. It considers another novel aspect of Hindu customs — its ban on cow slaughter. It focuses on the north, in particular on the Indo-Gangetic plain, which was the crucible of Hinduism, and its social expression in the caste system. The chapter also outlines the variant of the Hindu social system that was established in the southern peninsula by about the 6th to 9th centuries AD, and the reasons for the form it took.
Muslim India
Authors: Lal Deepak
Published: September 2008

Muslim India dates from the establishment of the first Turkish sultanate in AD 1206 in northern India, ending with the decline of the Moghul empire after the death of Aurangzeb in 1707. This chapter is divided into three parts, covering the polity, society, and economy under Muslim India. It argues that Islam failed to alter the underlying parameters of the economy, society, and polity established in ancient India. Although there were some changes in institutions, these for the most part reinforced the conditions yielding the so-called “Hindu equilibrium” on the subcontinent.
Polity and Society in British India
Authors: Lal Deepak
Published: September 2008

This chapter addresses the question of whether the British succeeded in altering the living conditions of the mass of the Indian people, and whether this latest foreign assault on the Hindu equilibrium established at the beginning of the Christian era was any more successful in altering the basic parameters of India's polity, society, and economy than its predecessor. The British conquest of India was virtually completed by 1818. Acquired by a band of foreign merchants, Britain's Indian empire at that date ran along the coast from Bengal to Gujarat except for the territorial pockets of Portuguese Goa and French Pondicherry, which were in the hands of the other two European powers who had established footholds in India's coastal economies.
The Economy under the Raj, I:Overall Trends
Authors: Lal Deepak
Published: September 2008

This chapter surveys economic trends from 1857 to 1947 of fully-fledged British rule. Topics covered include population, per capita income, sectoral output growth, urbanization, literacy, and infant mortality.
The Economy under the Raj, II: Rural Development
Authors: Lal Deepak
Published: September 2008

This chapter discusses rural development under the century of British rule. Topics covered include the Boserup process; the role of the “leading inputs” required to transform traditional agriculture — irrigation and the complex of complementary inputs represented by fertilizers, new seeds, and pesticides; irrigation, and the commercialization of agriculture.
The Economy under the Raj, III: Trade and Industry
Authors: Lal Deepak
Published: September 2008

This chapter begins with an examination of why the commercialization of agriculture and the integration of the Indian economy into the world economy did not lead to a greater spurt in the development of cash crop agriculture and exports in India as compared with other colonial tropical countries. It then considers the record of Indian industry under the Raj. It discusses the damage done by the policy of protection — from the 1920s onwards — to the prospects of growth of Indian manufactured exports, and the exchange rate policy followed by the Raj.
The Effects and Legacy of the Raj
Authors: Lal Deepak
Published: September 2008

British rule left legacies which have profoundly molded the perceptions and actions of the Indian political and bureaucratic elite concerning Indian economic problems. This chapter summarizes conclusions on these aspects. It then assesses the impact of the Raj on Indian society and politics.
The Economy under Planning and After
Authors: Lal Deepak
Published: September 2008

This chapter examines the ideas that shaped independent India's economic policy. Topics covered include Gandhi and Hind Swaraj, the rise of planning, agricultural growth, savings, capital inflows, investment, public sector growth, and industrial development.
Contemporary Controversies: Population, Poverty, and Regulation
Authors: Lal Deepak
Published: September 2008

This chapter examines the Indian economy since its independence. Topics discussed include the fiscal crisis resulting from the creation of a “rent-seeking” society through the microeconomic distortions introduced by public policy in the planning era, population growth, poverty and income distribution, and the new dirigisme.
On Policy: From a Revenue to a Market Economy
Authors: Lal Deepak
Published: September 2008

This chapter outlines the major policy changes that are required to develop India and shatter the age-old Hindu equilibrium. It explains why the natural propensities of Indian rulers have made the adoption of these policies so difficult. The chapter then provides a more explicit statement of the general theoretical perspective which underlies this book in a formal model of the predatory state.
Media and the Making of Modern Germany
Authors: Ross Corey
Published: September 2008

Few developments in the industrial era have had a greater impact on everyday social life than the explosion of the mass media and commercial entertainments. Few developments have more profoundly shaped the nature of modern politics. Nowhere in Europe were the tensions and controversies surrounding the rise of mass culture more politically charged than in Germany — debates that fatefully played into the hands of the radical right. This book provides an account of the expansion of the mass media in Germany up to the Second World War. In essence, it provides a social history of mass culture by investigating the role and impact of film, radio, recorded music, popular press, and advertising on everyday leisure as well as on shifting patterns of social distinction. Furthermore, it also analyses the political implications of these changes as part of a radically altered public sphere. Straddling the Imperial, Weimar, and Nazi periods, it shows how the social effects and meaning of mass culture were by no means straightforward or ‘standardizing’, but rather changed under different political and economic circumstances. By locating the rapid expansion of communications and commercial entertainments firmly within their broader historical context, it sheds light on the relationship between mass media, social change, and political culture during this tumultuous period in German history.
The Rise of the Mass Media: Modern Communications and Cultural Traditions in the Late Nineteenth and Early Twentieth Centuries
Authors: Ross Corey
Published: September 2008

This chapter offers an overview of the rise of the commercial media in the late 19th and early 20th centuries and their complex inter-relationship with existing cultural traditions in Germany. After briefly surveying the social and economic pre-conditions underlying the growth of the new media, it analyses how they intermingled with existing cultural forms and practices, and how media producers sought to identify with perceived audiences. Though this process entailed a number of innovations, the need to build on older, ‘safe’ traditions drawn from the theatre or music hall profoundly shaped how the media and commercial entertainments were perceived by both producers and consumers alike. Arguing that the new media did not so much displace these traditions as reconfigure them, this section then briefly considers the threat this reconfiguration posed to cultural authority, and the various arguments of articulate critics that were advanced against it.
Technology and Purchasing Power: Media Availability and Audiences
Authors: Ross Corey
Published: September 2008

This chapter shifts the focus away from elites and their concerns about the mass media towards the actual distribution and patterns of usage among media audiences. It shows that the availability of the different media and the constitution of their audiences were profoundly shaped by technological limitations, commercial considerations, cultural attitudes, and household budgets. Focusing above all on the Weimar era, it briefly reconstructs the social topography of cinema and radio audiences, and how they changed over this period. By highlighting the limited extent of radio usage and the many divides within the cinema audience, it demonstrates that the rise of the mass media did not necessarily signal an inexorable trend towards a more universal ‘mass culture’ that bulldozed class boundaries and flattened cultural distinctions in German society.
Meeting Demand: Consumer Preference and Social Difference
Authors: Ross Corey
Published: September 2008

This chapter moves beyond the question of availability to consider how patterns of uptake, different programme offerings, and different audience preferences reflected the social distinctions in Weimar society. By focusing on the highly fragmented press landscape in Germany, the problems of popularizing the radio programme, and the disparate fare on offer in different types of cinema, it demonstrates that audiences were certainly not the passive and amorphous entity many contemporary reformers had in mind when they devised their schemes to uplift popular tastes. Rather, ‘mass culture’ during the 1920s was mediated through older structures of region, class, neighbourhood, and gender, and how people partook in it was powerfully moulded by these social factors.
Media Publics Between Fragmentation and Integration
Authors: Ross Corey
Published: September 2008

This chapter argues that the potential of the mass media to open a more universal public sphere was by no means linear or straightforward, but was accompanied by a simultaneous process of differentiation that reflected the highly variegated market for entertainment and information. Rather, these processes had a wide range of possible social implications, including the potential to unite or to divide audiences, to weaken or reproduce existing social distinctions and, of course, to create new ones. In addition, it shows that different media exerted quite different effects within the rapidly changing public sphere. In sum, the modern media and commercial entertainment, despite their underlying ‘democratic’ logic, were not the culturally ‘standardizing’ and socially ‘levelling’ forces so often conjured by contemporaries and historians alike.
Propaganda and the Modern Public
Authors: Ross Corey
Published: September 2008

This chapter focuses on the relationship between the expansion of modern media and the changing nature of popular politics. Even before the First World War, the gradual emergence of new patterns of perception and expectation promoted by the media had profound implications for processes of popular political mobilization. How political elites sought to adapt to these developments, and how their efforts were related to evolving currents within the realm of commercial advertising, is the central subject. The chapter surveys the wide-ranging German discourse on public opinion, propaganda and the nature of political leadership during and after the First World War, which strongly influenced conceptions of political mobilization.
Republicans, Radicals, and the Battle of Images
Authors: Ross Corey
Published: September 2008

This chapter investigates how republican political elites participated in the discourse discussed in Chapter 7, and how they attempted to devise a more democratic form of public relations distinct from the negative connotations of ‘propaganda’ reverberating after the excesses of the war. The attempt to devise a rational form of democratic ‘instruction’ is discussed. The chapter then analyses the challenge posed by the aggressive and in many ways cutting-edge image campaigns of the radical anti-republican movements, especially the National Socialists, and how both the deepening crisis of the early 1930s and the ‘lessons’ of the wider discourse on propaganda eventually led to a hesitant yet fateful process of re-thinking on these issues within government and democratic circles.
Entertaining the National Community
Authors: Ross Corey
Published: September 2008

This chapter shows that the processes of political control and commercial concentration outlined in Chapter 9 dovetailed with Nazi efforts to satisfy audiences with popular, if somewhat circumscribed, entertainment. It goes beyond existing interpretations of Nazi mass culture as a form of political propaganda to consider also the extent to which it matched audience expectations and helped transcend older audience segmentations. Overall, it argues that the reconfiguration of the media and popular entertainment in the Third Reich — though in many ways merely an acceleration of existing trends and at base more destructive than creative — contributed to the increasing convergence of the media and their audiences in the 1930s, and ultimately to a more common cultural frame of reference shared by wider range of social groups.
The Media and the Second World War: From Integration to Disintegration
Authors: Ross Corey
Published: September 2008

This chapter shows how the war years witnessed a dramatic intensification of the ongoing tension between the integrative and disaggregating social potential of the mass media. On the one hand, the overall trend towards a more ‘common culture’ saw its apogee during the early years of the war as popular demand for film, radio, and the press soared. On the other hand, after 1942/3 the socially divisive potential of the media once again came to the fore in terms of content as well as the radical shifts in the wider societal context and how the media were consumed by audiences. Whereas the early war years witnessed an unprecedented social integration of audiences, after 1942 patterns of leisure and media consumption reflected the multiplying signs of social disintegration on the German home front.
Conclusion
Authors: Ross Corey
Published: September 2008

This concluding chapter draws out a number of themes that run throughout the book. Only by approaching the rise of the media within a longer-term framework and considering what was unique about Germany in international perspective can one adequately appreciate their social role. It advances a number of arguments: that the social and political impact of the media were powerfully influenced by local conditions; that they supported both processes of democratization and populist dictatorship; that their social impact depended on the precise nature of production and consumption; and that the major turning points in the story tended to be periods of upheaval and depression. In many respects mass culture under the Nazis was very much a part of broader trends; what most distinguished it was the violent and racist context in which it operated.
The early days of paleogenetics: connecting molecules to the planet
Authors: Benner Steven A.
Published: September 2008

Paleogenetics was actualized in the 1980s to permit the experimental test of ‘just so stories’ emerging from molecular evolution. Paleogenetics has since grown to support the development of interconnected models for life, from the molecule to the ecosystem. This chapter reviews tools to manage ambiguities in paleogenetics, and how paleogenetics was applied to understand the emerging role of alcohol in the Cretaceous.
Linking sequence to function in drug design with ancestral sequence reconstruction
Authors: Kodra Janos T. , Skovgaard Marie , Madsen Dennis , Liberles David A.
Published: September 2008

Many bioactive peptides and proteins of pharmaceutical interest are found in animal venoms. Nature often reuses scaffolds within protein frameworks to develop new properties. The binding core of the peptide from venomous animals is conserved through species (built on a small number of permissive scaffolds). The same scaffolds are often found in nature in protein, performing other non-toxic functions, and it is likely that such conserved motifs are the result of divergent evolution from a common ancestor protein framework via gene duplication. This chapter describes the use of ancestral sequence reconstruction to identify and reconstruct the evolutionary history of important physiological protein and peptide and to connect their common ancestor to certain venom peptides and proteins. This process helps with identifying which amino acids are important for functioning and which ultimately can be used to engineer new bioactive peptide with tailor made properties.
Probabilistic models and their impact on the accuracy of reconstructed ancestral protein sequences
Authors: Pupko Tal , Doron-Faigenboim Adi , Liberles David A. , Cannarozzi Gina M.
Published: September 2008

Modeling of sequence evolution is fundamental to ancestral sequence reconstruction. Care must be taken in choosing a model, however, as the use of unrealistic models can lead to erroneous conclusions. The choice of model and the effects of assumptions inherent within are discussed in this chapter in terms of their effects on probabilistic ancestral sequence reconstruction. This chapter discusses standard probabilistic models, site rate variation to these models, and deviations from the standard (homogeneous, stationary, reversible) models. Model selection, selecting one model from many, given data, and the comparison of different models are included as well as covarion models, the use of outside information when modeling, and the treatment of gaps.
Probabilistic ancestral sequences based on the Markovian model of evolution: algorithms and applications
Authors: Cannarozzi Gina M. , Schneider Adrian , Gonnet Gaston H.
Published: September 2008

A probabilistic sequence (PS) is a sequence in which each position instead of having a single character (amino acid, nucleotide, or codon), has a vector describing the probability of each symbol being the character at that position. A probabilistic ancestral sequence (PAS) is a reconstructed PS for the common ancestor of several sequences. This chapter presents a formalism to compute the probabilities of each character at each position of the biological sequence for the internal nodes in a given phylogenetic tree using a Markov model of evolution. From this model, the probability of an evolutionary configuration can be computed. In addition, efficient algorithms for computing the likelihood score of aligning a character with a character, a character with a probabilistic character, or two probabilistic characters are derived. These scores can then be used in direct string matching or dynamic programming alignments of probabilistic sequences with insertions and deletions. Applications for these alignments, including long-distance homology searching and multiple sequence alignment construction, are shown.
Coarse projections of the protein-mutational fitness landscape
Authors: Braun F. Nicholas
Published: September 2008

The extant phylogenetic variability of a given protein contains information about its underlying sequence-fitness landscape, potentially of value to ancestral reconstruction. In extracting such information, it is pertinent to focus on coarse-grained traits of sequence with strong physicochemical bearing on the protein's phenotype. This chapter uses phylogenetic data to stake out roughly the landscape for a protein component of spider silk.
Dealing with uncertainty in ancestral sequence reconstruction: sampling from the posterior distribution
Authors: Pollock David D. , Chang Belinda S.W.
Published: September 2008

The goal of ancestral inference is to have as accurate a picture of ancestral function as possible. Thus, it is worthwhile to try to understand the nature and cause of the sequence and functional bias, and how to overcome this bias. This chapter argues that the bias inherent in in the choice to reconstruct the ancestral sequence with the highest posterior probability, along with the optimization bias due to site-specific model inaccuracy, may have biased the frequencies with which certain amino acids are inferred. Amino acids that tend to have consistently low posterior probabilities are most probably undersampled. A simple strategy to address amino acid sampling bias when reconstructing ancestral proteins in the laboratory is discussed.
Evolutionary properties of sequences and ancestral state reconstruction
Authors: Collins Lesley J. , Lockhart Peter J.
Published: September 2008

A number of authors have recently stressed the importance of understanding the evolution of protein-protein interactions as an underlying cause of covarion-like patterns of evolution in ancestral sequences. Coevolution of interacting partners is seen as important, first in directing the evolution of proteins, and second in explaining why structural constraints may become lineage-specific while function remains the same. Although the concept of heterotachy and covarion evolution in the literature is most often restricted to describing the evolution of orthologs, the same or similar principles of sequence divergence apply to proteins related by gene duplication (paralogs), and which have different functions and functional constraints. This chapter discusses heterotachy and gene finding, gene finding with ancestral sequences, and heterotachy and ancestral state reconstruction.
Reconstructing the ancestral eukaryote: lessons from the past
Authors: O'Connell Mary J. , McInerney James O.
Published: September 2008

Reconstructing ancestral proteins relies heavily on accurate phylogeny reconstruction. This is a challenging area particularly for early eukaryote evolution. Despite decades of extensive studies to resolve the structure of the deepest branches of the Eukaryota, a generally accepted phylogenetic reconstruction has not been achieved. This chapter explores the relationships of the three crown eukaryota and the root of the animal kingdom itself. It describes the methodological developments that have aided the field of early eukaryote evolution and the biases that exist in certain methods and data.
Reconstruction of ancestral proteomes
Authors: Gabaldón Toni , Huynen Martijn A.
Published: September 2008

The process of inferring the set of proteins that was likely encoded in the genome of an extinct organism is called Ancestral Proteome Reconstruction. This process usually involves the comparison of proteomes of extant species and the reconstruction of their ancestors by using different methods that range from parsimonius reconstruction over a species-phylogeny to the reconstruction and analysis of complete phylomes. Although still in its infancy, Ancestral Proteome Reconstruction has proven to be a very useful tool to test hypotheses on extant organisms and past evolutionary events. This chapter provides an overview of the methodology involved and surveys recent studies that deal with the origin and evolution of the Last Universal Common Ancestor (LUCA), and eukaryotic organelles such as mitochondria and peroxisomes.
Computational reconstruction of ancestral genomic regions from evolutionarily conserved gene clusters
Authors: Danchin Etienne G.J. , Gaucher Eric A. , Pontarotti Pierre
Published: September 2008

Gene clusters that are evolutionarily conserved between different species can result from a common ancestral genomic region. By identifying and comparing conserved gene clusters between different taxa, it is possible to infer the gene content of the corresponding putative ancestral region, and hence it is possible to shed light on ancestral genomic organization. From selected genomic region in vertebrates, this chapter identifies evolutionarily conservation in other taxa as evolutionary distant as arthropods (i.e., Drosophila melanogaster and Anopheles gambiae). This is made possible through systematic phylogenetic analysis (for determining homology relationships) and stringent statistical testing (for evaluating the significance of the clusters' conservation). The comparison of these conserved gene clusters means that conceptual ancestral gene clusters in Urbilateria (the last common ancestor of all bilaterian species) can be deciphered. In order to reconstruct ancestral features at a larger genomic scale, it is possible to consider automation of the approach and important concepts are developed in this chapter.
Experimental resurrection of ancient biomolecules: gene synthesis, heterologous protein expression, and functional assays
Authors: Gaucher Eric A.
Published: September 2008

Approximately twenty studies have emerged where specific molecular systems from extinct organisms have been resurrected for study in the laboratory. These include digestive proteins (ribonucleases, proteases, and lysozymes) in ruminants and primates, which are used to illustrate how digestive function arose from non-digestive function in response to a changing global ecosystem; fermentive enzymes from fungi, which are used to illustrate how molecular adaptation supported mammals as they displaced dinosaurs as the dominant large land animals; pigments in the visual system adapting to different environments; steroid hormone receptors adapting to changing function in steroid-based regulation of metazoans; fluorescent proteins from ocean-dwelling invertebrates; enzyme cofactor evolution; and proteins from very ancient bacteria helping to define environments where the earliest forms of bacterial life lived. This chapter summarizes the different approaches exploited by these studies. The chapter outlines the different strategies exploited when building ancient genes in the laboratory, the various systems used to express the encoded proteins of the ancient genes, and the different types of functional assay used to characterize the behaviors of the ancient biomolecules.
Dealing with model uncertainty in reconstructing ancestral proteins in the laboratory: examples from archosaur visual pigments and coralfluorescent proteins
Authors: Chang Belinda S.W. , Matz Mikhail V. , Field Steven F. , Müller Johannes , van Hazel Ilke
Published: September 2008

This chapter discusses efficient experimental strategies to explore variation in ancestral sequence reconstructions. The experimental strategies are illustrated with two examples, ancestral rhodopsins in archosaurs and green fluorescent protein (GFP)-like proteins in corals.
Using ancestral gene resurrection to unravel the evolution of protein function
Authors: Thornton Joseph W. , Bridgham Jamie T.
Published: September 2008

This chapter reviews the use of ancestral gene resurrection to understand how the members of a biologically crucial gene family, the steroid hormone receptors, evolved their diverse and highly specific functions. It also discusses some methodological questions and concerns — particularly related to uncertainty in the reconstruction of ancestral sequences — and point to potential future directions for the budding field of ancestral gene resurrection. Topics covered include the evolution of molecular interactions, steroid hormones and their receptors, evolution of corticoid receptor specificity, and evolution of the MR-aldosterone interaction.
A thermophilic last universal ancestor inferred from its estimated amino acid composition
Authors: Brooks Dawn J. , Gaucher Eric A.
Published: September 2008

The last universal ancestor (LUA) represents a relatively accessible theoretical intermediary between extant cellular organisms and early, precellular ‘life’. In a previous study, the expectation-maximization (EM) approach was used to infer ancestral amino acid frequencies, where in each iteration expected counts were derived from posterior distributions at each site. Applying this approach to estimate the amino acid composition of 65 proteins in the LUA showed that composition was more similar to that of extant thermophiles than mesophiles. This chapter examines whether the previous result is robust with respect to the OGT of the taxa used to infer the amino acid composition of proteins in the LUA. It is shown that even if only mesophilic species are used to derive the estimated ancestral amino acid composition, that composition is most similar to that of thermophiles, as measured by Euclidean distance. The relative mean Euclidean distance between the amino acid composition in any one species and that of a set of mesophiles or thermophiles can be used unequivocally to classify it. Thus, the inferred amino acid composition in the LUA allows its classification as a thermophile.
The resurrection of ribonucleases from mammals: from ecology to medicine
Authors: Sassi Slim O. , Benner Steven A.
Published: September 2008

Ribonucleases, well-known digestive enzymes that supported the development of much of protein science, emerged through an evolutionary history having a rich history of functional recruitment. This chapter reviews paleogenetic studies that explored changing function in this family. Similar approaches promise to be powerful tools to advance medicine in a post-genomic world.
Evolution of specificity and diversity
Authors: Shields Denis C. , Johnston Catriona R. , Wallace Iain M. , Edwards Richard J.
Published: September 2008

The divergence of proteins following gene duplication has long been recognized as an important process in the evolution of both new and specific protein functions. For functional divergence to occur, the duplicated gene has to survive duplication and avoid becoming a pseudogene (gene death). The mechanism by which a gene duplicates survive is still under some debate, but it is thought that maintenance of duplicate pairs can be accomplished by the evolution of novel functions, splitting ancestral functions between duplicate pairs called paralogs, or some combination of both neo- and subfunctionalization. Although no consensus has been reached as to which process plays a more dominant role in the generation and maintenance of duplicates at the genomic or protein level, the distinction is somewhat irrelevant for the bioinformatic prediction of individual specificity-determining sites; that is, those sites that are important for differences in gene function between paralogs. Instead, the evolutionary history and changing selective constraints for individual residues is important for the interpretation of results. This chapter examines the types of substitution that occur at these sites and the phylogenetic signals that they leave.
1 Why Social Sciences Are Not Scientific Enough
Authors: Taagepera Rein
Published: September 2008

Science is not only about the empirical “What is?” but also very much about the conceptual “How should it be on logical grounds?” Statistical approaches are essentially descriptive, while quantitatively formulated logical models are essentially predictive in an explanatory way. Social sciences have overemphasized statistical data analysis, often limiting their logical models to prediction of the direction of effect, oblivious of its quantitative extent. A better balance of methods is possible and will make social sciences more relevant to society. This book is about going beyond regression and other statistical approaches, and also about improving their use.
2 Can Social Science Approaches Find the Law of Gravitation?
Authors: Taagepera Rein
Published: September 2008

When a number of social scientists were given synthetic data that fitted the universal law of gravitation, they all missed the underlying pattern. Yet they found results satisfactory and complete by the current social science norms: high R  2, degree of significance of input factors, and the direction of their impact. The design of this experiment can be criticized, but it still should give us pause. If some social phenomena existed that were of the form most prevalent in physics, then the quantitative methods currently dominant in social sciences might not suffice to discover them.
3 How to Construct Predictive Models: Simplicity and Nonabsurdity
Authors: Taagepera Rein
Published: September 2008

Predictive models should be as simple as one can get away with, and they must not predict absurdities. They join the parsimony of “Occam's razor” to the “Sherlock Holmes principle”: Show how things cannot be connected, and only one acceptable form of relationship may remain – or very few. Conceptual models must not predict absurdities even under extreme circumstances. All too many variables are interdependent rather than “independent” or “dependent,” so it is safer to talk about input and output variables under given conditions.
4 Example of Model Building: Electoral Volatility
Authors: Taagepera Rein
Published: September 2008

The foremost mental roadblocks in predictive model building are refusal to make outrageous simplifications and reluctance to play with means of extreme cases. “Ignorance-based” models focus on conceptual constraints: What do we already know about the situation, even before collecting any data? Eliminate the conceptually forbidden areas where data points could not possibly occur, and locate the conceptual anchor points where the value of x imposes a unique value of y. Once this is done, few options may remain for how y can depend on x–unless you tell yourself “It can't be that simple.” A low R  2 may still confirm a predictive model, and a high one may work to reject it.
5 Physicists Multiply, Social Scientists Add—Even When It Does Not Add Up
Authors: Taagepera Rein
Published: September 2008

Most physics equations include few variables and at most one freely adjustable constant, which multiply or divide. In contrast, regression equations favored in social sciences often have many variables in additive–subtractive strings, with plenty of freely adjustable constants/coefficients. Physics equations are reversible and transitive; standard regression equations are unidirectional and nontransitive. Physics rarely offers alternate equations for the same phenomenon, with a different set of input variables and constants; this is frequent in social science regression analysis. Physics equations are presented with prediction in mind, while tables of regression coefficients in social sciences reflect postdiction and often preclude even that.
6 All Hypotheses Are Not Created Equal
Authors: Taagepera Rein
Published: September 2008

The null hypothesis offers close to null prediction. Directional hypotheses are relatively easy to satisfy and offer correspondingly vague predictions. Quantitative hypotheses (models) are hard to satisfy and offer quantitatively falsifiable predictions. The customary hypothesis-testing recipe in social sciences, “hypothesis → data collection → testing → acceptance/rejection,” is only a single cycle in an ascending spiral. Having “p=.01” does NOT mean confirmation in 99% of replications.
7 Why Most Numbers Published in Social Sciences Are Dead on Arrival
Authors: Taagepera Rein
Published: September 2008

The numbers published in physics are steppingstones for further inquiry, because they are few and other researchers often make use of them. The numbers published in social sciences are endpoints, because they are profligate and, once printed, hardly anyone makes use of them. Astronomy could not develop without overcoming the Ptolemaic syndrome of reducing all motion to circular. Social sciences must overcome their syndrome of reducing all relationships to linear. Physicists, like people in general, start with causal models, while social scientists stand apart by starting with empirical models.
8 Forbidden Areas and Anchor Points
Authors: Taagepera Rein
Published: September 2008

The outcomes of sociopolitical processes often depend on the factor in shortest supply; this makes multiplication of factors superior to their addition. Naïve linear regression may not detect all relationships between physical or social factors, because nonlinear relationships predominate. When x and y can conceptually take only positive values, the simplest conceptually acceptable fit is to connect y to x raised to a power (an exponent). This means that linear regression should be carried out on the logarithms of x and y, not on x and y. Various other constraints, such as forbidden areas and anchor points, lead to exponential, simple logistic, and more complex patterns.
9 Geometric Means and Lognormal Distributions
Authors: Taagepera Rein
Published: September 2008

Geometric means are often more meaningful than arithmetic means, because they are closer to the central figure (median). When x and y can conceptually take only positive values, their distributions cannot be normal and may be lognormal. When running a normal distribution yields a standard deviation larger than one-half of the mean, one should dump the normal fit and try a lognormal fit instead.
10 Example of Interlocking Models: Party Sizes and Cabinet Duration
Authors: Taagepera Rein
Published: September 2008

Interlocking networks of equations, based on logical models, are possible in social sciences. Partial evidence is offered by a sequence of models that ties mean duration of governmental cabinets first to the number of parties and then to the number of seats in the electoral district and the entire representative assembly.
12 Why We Should Shift to Symmetric Regression
Authors: Taagepera Rein
Published: September 2008

When data are scattered, Ordinary Least-Squares (OLS) regression produces two quite distinct regression lines – one for y versus x and another for x versus y – and both may differ appreciably from what your eyes tell you. If data are scattered, OLS regression of y against x will disconfirm a model that actually fits; thus good statistics can be death of good science. Standard OLS equations cannot form a system of interlocking models, because they are unidirectional and nontransitive. Scale-independent symmetric regression avoids these problems of OLS, offering a single reversible and transitive equation.
13 All Indices Are Not Created Equal
Authors: Taagepera Rein
Published: September 2008

Models are tested with data, but also data are tested by agreement with conceptual models. When competing indices exist to measure the same phenomena, one should use the ones that agree with logically supported prediction. These indices need not be philosophically “truer” measures of the underlying concepts, but they are more useful for prediction. The choice between two accepted ways to measure cabinet duration and three ways to measure the number of parties illustrates this advice. Clearest results emerge when symmetric regression is used for testing.