bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractA 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

Abstract
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

AbstractThe 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

AbstractA 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

AbstractReconstructing 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

Abstract
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

Abstract
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

Abstract
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

AbstractThis 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

AbstractThis 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

AbstractThe 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

AbstractRibonucleases, 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

AbstractThe 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

AbstractScience 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

AbstractWhen 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

AbstractPredictive 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

AbstractThe 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

AbstractMost 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

AbstractThe 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

AbstractThe 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

AbstractThe 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

AbstractGeometric 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.
12 Why We Should Shift to Symmetric Regression
Authors: Taagepera Rein 
Published: September 2008

AbstractWhen 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

AbstractModels 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.
14 From Descriptive to Predictive Approaches
Authors: Taagepera Rein 
Published: September 2008

AbstractRoutine statistical approaches are essentially descriptive, giving answers within a narrow range of questions. Quantitatively formulated logical model force us to ask further questions and are predictive in an explanatory way. Descriptive approaches are not conducive to detection of social laws, especially if one simultaneously feeds in variables which actually connect sequentially. Rather than a single sequence of “hypothesis testing,” scientific procedure involves repeat cycles where predictive and descriptive approaches enter intermixed. Directional models and reams of numbers ground out by canned computer programs must make room for quantitative logical models and sparse conceptually grounded constants.
15 Recommendations for Better Regression
Authors: Taagepera Rein 
Published: September 2008

AbstractTake seriously the introductory advice by most introductory texts of statistics: graph the data and look at the graph so as to make sure linear regression makes sense from a statistical viewpoint. Graph more than the data – graph the entire conceptually allowed area and anchor points so as to make sure linear regression makes sense from a substantive viewpoint. If using linear regression, report not only the regression coefficients and the intercept but also the ranges, mean values, and medians of all input variables. While symmetric regression has advantages over OLS, fully reported symmetric regression is still merely regression.
17 Are Electoral Studies a Rosetta Stone for Parts of Social Sciences?
Authors: Taagepera Rein 
Published: September 2008

AbstractSome aspects of social sciences can be made more predictive and, in this sense, more like natural sciences. Electoral studies have many variables with a natural zero (ratio variables), which makes them amenable to certain types of logical model building and sets them apart from other social sciences. Still, plenty of ratio variables occur in other social sciences too, and here electoral studies may offer valuable methodological tips. From temperature to political involvement, looser scales sometimes have a way to turn into ratio scales, if we dare to play with them.
2 Delegation and Commission Leadership in Economic and Monetary Union
Authors: Howarth David 
Published: September 2008

Abstract
Monetary integration through the Maastricht Treaty in European Union was achieved by delegation to the Commission. This was fuelled by the need for centralised expertise to coordinate complex change and the member states' desire to commit themselves to future compliance with the stability and Growth Pact rules that were agreed upon to enforce budgetary discipline. The Commission built political support for the transition to a single currency. To ensure the credibility of member government commitments to the debt and budget deficit convergence criteria, the Excessive Deficit Procedure was devised and implemented by the Commission as was the Early Warning Procedure of the Ecofin finance ministers. The European Central Bank enforced the low inflation target.