Parsimonious Assumption Research Articles

The BTF Vision of Unfolding Rule Worlds

A Behavioral Theory of the Firm (Cyert & March, 1963) is a multifaceted collection of “little ideas” that has the potential to evolve into multiple and potentially revolutionary directions. In my first encounters with the BTF (the book and the theoretical research program), I was intrigued by its predominant focus on models of dynamic processes. BTF employs a distinctive style of theory construction that proceeds through articulation of models of behavior in organizations, and that builds on relatively parsimonious and realistic assumptions about underlying organizational processes (of decision making, information processing, expectation formation, etc.) and their limitations (arising from bounded rationality of organizational actors and processes). It is a bold approach of modeling the organizational processes that shape action in and of organizations, and it has been a persistent source of inspiration for many students of organizations since then. At the same time, BTF models tend to be dynamic (often incorporate computer programs that simulate dynamic processes) and can reveal the surprising implications of organizational processes and structures (e.g., competency traps, superstitious learning, garbage cans, etc.) and their unfolding in time. In particular, dynamic models of organizational learning and organizational rules appear to offer unusual potential for the future elaboration of the BTF.

THE CASE FOR AN EMERGENTIST APPROACH

This paper sets out an argument in favour of emergentism as an alternative theoretical paradigm to nativism, arguing that it offers a coherent, evidence-based account of language structure, language acquisition, language evolution, and language change. A number of key tenets of the nativist approach are summarised first, including the nature of the presumed complexity of language, the poverty of the input argument against the learnability of language, the assumption of parsimony, the view of language as an innate, biological faculty, and the view of the primary function of language as cognitive representation rather than communication. This is followed by a presentation of the emergentist alternative, which hinges on the notion of the grammatical construction as the central unit in the emergentist approach. The properties of constructions, and how they can come into being with recourse to only domain-general cognitive processes, are presented, before the implications of this view for the structure, acquisition, evolution and change of language are discussed. Additional points of difference with the nativist position are highlighted, including the assumptions of non-parsimonious storage and the centrality of communicative interaction in the ontogenetic and phylogenetic development of language. Throughout the presentation, arguments are illustrated with reference to aspects of complementation in Germanic languages. The article concludes with a detailed case study of the wh-extraction construction, drawing on an analysis of corpus data from Afrikaans, to demonstrate how the construction-based, emergentist approach leads to an insightful analysis of a well-known construction, without having to make extensive assumptions about the underlying linguistic complexity and the need for innate mechanisms to enable the acquisition of such a complex construction.

PERSPECTIVES ON INTRACLUSTER ENRICHMENT AND THE STELLAR INITIAL MASS FUNCTION IN ELLIPTICAL GALAXIES

Stars formed in galaxy cluster potential wells must be responsible for the high level of enrichment measured in the intracluster medium (ICM); however, there is increasing tension between this truism and the parsimonious assumption that the stars in the generally old population studied optically in cluster galaxies emerged from the same formation sites at the same epochs. We construct a phenomenological cluster enrichment model to demonstrate that ICM elemental abundances are underestimated by a factor >2 for standard assumptions about the stellar population -- a discrepancy we term the "cluster elemental abundance paradox". Recent evidence of an elliptical galaxy IMF skewed to low masses deepens the paradox. We quantify the adjustments to the star formation efficiency and initial mass function (IMF), and SNIa production efficiency, required to resolve this while being consistent with the observed ICM abundance pattern. The necessary enhancement in metal enrichment may, in principle, originate in the observed stellar population if a larger fraction of stars in the supernova-progenitor mass range form from an initial mass function (IMF) that is either bottom-light or top-heavy, with the latter in some conflict with observed ICM abundance ratios. Other alternatives that imply more modest revisions to the IMF, mass return and remnant fractions, and primordial fraction, posit an increase in the fraction of 3-8 solar mass stars that explode as SNIa or assume that there are more stars than conventionally thought -- although the latter implies a high star formation efficiency. We discuss the feasibility of these various solutions and the implications for the diversity of star formation in the universe, the process of elliptical galaxy formation, and the origin of this "hidden" source of ICM metal enrichment.

Molecular Phylogenies Support Homoplasy of Multiple Morphological Characters Used in the Taxonomy of Heteroscleromorpha (Porifera: Demospongiae)

Sponge classification has long been based mainly on morphocladistic analyses but is now being greatly challenged by more than 12 years of accumulated analyses of molecular data analyses. The current study used phylogenetic hypotheses based on sequence data from 18S rRNA, 28S rRNA, and the CO1 barcoding fragment, combined with morphology to justify the resurrection of the order Axinellida Lévi, 1953. Axinellida occupies a key position in different morphologically derived topologies. The abandonment of Axinellida and the establishment of Halichondrida Vosmaer, 1887 sensu lato to contain Halichondriidae Gray, 1867, Axinellidae Carter, 1875, Bubaridae Topsent, 1894, Heteroxyidae Dendy, 1905, and a new family Dictyonellidae van Soest et al., 1990 was based on the conclusion that an axially condensed skeleton evolved independently in separate lineages in preference to the less parsimonious assumption that asters (star-shaped spicules), acanthostyles (club-shaped spicules with spines), and sigmata (C-shaped spicules) each evolved more than once. Our new molecular trees are congruent and contrast with the earlier, morphologically based, trees. The results show that axially condensed skeletons, asters, acanthostyles, and sigmata are all homoplasious characters. The unrecognized homoplasious nature of these characters explains much of the incongruence between molecular-based and morphology-based phylogenies. We use the molecular trees presented here as a basis for re-interpreting the morphological characters within Heteroscleromorpha. The implications for the classification of Heteroscleromorpha are discussed and a new order Biemnida ord. nov. is erected.

Novel Activation of Voltage-gated K+ Channels by Sevoflurane

Halogenated inhaled anesthetics modulate voltage-gated ion channels by unknown mechanisms. Biophysical analyses revealed novel activation of K(v) channels by the inhaled anesthetic sevoflurane. K(v) channel activation by sevoflurane results from the positive allosteric modulation of activation gating. The unique activation of K(v) channels by sevoflurane demonstrates novel anesthetic specificity and offers new insights into allosteric modulation of channel gating. Voltage-gated ion channels are modulated by halogenated inhaled general anesthetics, but the underlying molecular mechanisms are not understood. Alkanols and halogenated inhaled anesthetics such as halothane and isoflurane inhibit the archetypical voltage-gated Kv3 channel homolog K-Shaw2 by stabilizing the resting/closed states. By contrast, sevoflurane, a more heavily fluorinated ether commonly used in general anesthesia, specifically activates K-Shaw2 currents at relevant concentrations (0.05-1 mM) in a rapid and reversible manner. The concentration dependence of this modulation is consistent with the presence of high and low affinity interactions (K(D) = 0.06 and 4 mM, respectively). Sevoflurane (<1 mM) induces a negative shift in the conductance-voltage relation and increases the maximum conductance. Furthermore, suggesting possible roles in general anesthesia, mammalian Kv1.2 and Kv1.5 channels display similar changes. Quantitative description of the observations by an economical allosteric model indicates that sevoflurane binding favors activation gating and eliminates an unstable inactivated state outside the activation pathway. This study casts light on the mechanism of the novel sevoflurane-dependent activation of Kv channels, which helps explain how closely related inhaled anesthetics achieve specific actions and suggests strategies to develop novel Kv channel activators.

Inferring domain-domain interactions from protein-protein interactions in the complex network conformation

BackgroundAs protein domains are functional and structural units of proteins, a large proportion of protein-protein interactions (PPIs) are achieved by domain-domain interactions (DDIs), many computational efforts have been made to identify DDIs from experimental PPIs since high throughput technologies have produced a large number of PPIs for different species. These methods can be separated into two categories: deterministic and probabilistic. In deterministic methods, parsimony assumption has been utilized. Parsimony principle has been widely used in computational biology as the evolution of the nature is considered as a continuous optimization process. In the context of identifying DDIs, parsimony methods try to find a minimal set of DDIs that can explain the observed PPIs. This category of methods are promising since they can be formulated and solved easily. Besides, researches have shown that they can detect specific DDIs, which is often hard for many probabilistic methods. We notice that existing methods just view PPI networks as simply assembled by single interactions, but there is now ample evidence that PPI networks should be considered in a global (systematic) point of view for it exhibits general properties of complex networks, such as 'scale-free' and 'small-world'.ResultsIn this work, we integrate this global point of view into the parsimony-based model. Particularly, prior knowledge is extracted from these global properties by plausible reasoning and then taken as input. We investigate the role of the added information extensively through numerical experiments. Results show that the proposed method has improved performance, which confirms the biological meanings of the extracted prior knowledge.ConclusionsThis work provides us some clues for using these properties of complex networks in computational models and to some extent reveals the biological meanings underlying these general network properties.

Phylogeny- and parsimony-based haplotype inference with constraints

Haplotyping, also known as haplotype phase prediction, is the problem of predicting likely haplotypes based on genotype data. One fast computational haplotyping method is based on an evolutionary model where a perfect phylogenetic tree is sought that explains the observed data. An extension of this approach tries to incorporate prior knowledge in the form of a set of candidate haplotypes from which the right haplotypes must be chosen. The objective is to increase the accuracy of haplotyping methods, but it was conjectured that the resulting formal problem constrained perfect phylogeny haplotyping might be NP-complete. In the paper at hand we present a polynomial-time algorithm for it. Our algorithmic ideas also yield new fixed-parameter algorithms for related haplotyping problems based on the maximum parsimony assumption.

MATE CHOICE FOR OPTIMAL (K)INBREEDING

Mating between related individuals results in inbreeding depression, and this has been thought to select against incestuous matings. However, theory predicts that inbreeding can also be adaptive if it increases the representation of genes identical by descent in future generations. Here, I recapitulate the theory of inclusive fitness benefits of incest, and extend the existing theory by deriving the stable level of inbreeding in populations practicing mate choice for optimal inbreeding. The parsimonious assumptions of the model are that selection maximizes inclusive fitness, and that inbreeding depression is a linear function of homozygosity of offspring. The stable level of inbreeding that maximizes inclusive fitness, and is expected to evolve by natural selection, is shown to be less than previous theory suggests. For wide range of realistic inbreeding depression strengths, mating with intermediately related individuals maximizes inclusive fitness. The predicted preference for intermediately related individuals as reproductive partners is in qualitative agreement with empirical evidence from mate choice experiments and reproductive patterns in nature.

Haplotype Inference by Pure Parsimony: A Survey

Given a set of genotypes from a population, the process of recovering the haplotypes that explain the genotypes is called haplotype inference. The haplotype inference problem under the assumption of pure parsimony consists in finding the smallest number of haplotypes that explain a given set of genotypes. This problem is NP-hard. The original formulations for solving the Haplotype Inference by Pure Parsimony (HIPP) problem were based on integer linear programming and branch-and-bound techniques. More recently, solutions based on Boolean satisfiability, pseudo-Boolean optimization, and answer set programming have been shown to be remarkably more efficient. HIPP can now be regarded as a feasible approach for haplotype inference, which can be competitive with other different approaches. This article provides an overview of the methods for solving the HIPP problem, including preprocessing, bounding techniques, and heuristic approaches. The article also presents an empirical evaluation of exact HIPP solvers on a comprehensive set of synthetic and real problem instances. Moreover, the bounding techniques to the exact problem are evaluated. The final section compares and discusses the HIPP approach with a well-established statistical method that represents the reference algorithm for this problem.

How money got its tail (not too light; not too heavy; but “just so”)

PurposeThe purpose of this paper is to explore the theoretical basis for heavy‐tailed asset‐return distributions.Design/methodology/approachThrough a simple model of asset‐price formation, one can formulate the asset‐return random variable, ln (Pt/Pt−1), as a constant plus the natural log of a ratio of Bernoulli proportions. This random variable admits of different approximations, whose distributions may be studied analytically.FindingsThe paper finds that for two reasonable approximations to the asset‐return random variable, the tails are approximately exponential. This suggests that the Gaussian assumption provides a poor “starting point” for asset‐pricing models, and empirically validated heavy‐tailed behavior is likely the result of time‐dependent components in the tail parameters.Originality/valueThe editorial offers a theoretical analysis of asset‐return distributions using parsimonious modeling assumptions.

Taking species abundance distributions beyond individuals

The species abundance distribution (SAD) is one of the few universal patterns in ecology. Research on this fundamental distribution has primarily focused on the study of numerical counts, irrespective of the traits of individuals. Here we show that considering a set of Generalized Species Abundance Distributions (GSADs) encompassing several abundance measures, such as numerical abundance, biomass and resource use, can provide novel insights into the structure of ecological communities and the forces that organize them. We use a taxonomically diverse combination of macroecological data sets to investigate the similarities and differences between GSADs. We then use probability theory to explore, under parsimonious assumptions, theoretical linkages among them. Our study suggests that examining different GSADs simultaneously in natural systems may help with assessing determinants of community structure. Broadening SADs to encompass multiple abundance measures opens novel perspectives in biodiversity research and warrants future empirical and theoretical developments.

Science without (parametric) models: the case of bootstrap resampling

Scientific and statistical inferences build heavily on explicit, parametric models, and often with good reasons. However, the limited scope of parametric models and the increasing complexity of the studied systems in modern science raise the risk of model misspecification. Therefore, I examine alternative, data-based inference techniques, such as bootstrap resampling. I argue that their neglect in the philosophical literature is unjustified: they suit some contexts of inquiry much better and use a more direct approach to scientific inference. Moreover, they make more parsimonious assumptions and often replace theoretical understanding and knowledge about mechanisms by careful experimental design. Thus, it is worthwhile to study in detail how nonparametric models serve as inferential engines in science.

Portfolio choice when relative income matters

This paper derives conditions under which concerns about relative income produce rational herding—the shift of individuals’ portfolios into the same direction as others’. To endure the generality of results, the model makes parsimonious behavioral assumptions and no assumption about the functional form of utility. The two most critical conditions are substitutability between one's own income and relative income and diminishing marginal utility of relative income. The keeping-up-with-the-Joneses (KUJ) motive unambiguously contributes to rational herding. When relative income is viewed as a measure of status, however, the KUJ motive is neither a necessary nor a sufficient condition.

Context-Dependent Mutation Rates May Cause Spurious Signatures of a Fixation Bias Favoring Higher GC-Content in Humans

Understanding the proximate and ultimate causes underlying the evolution of nucleotide composition in mammalian genomes is of fundamental interest to the study of molecular evolution. Comparative genomics studies have revealed that many more substitutions occur from G and C nucleotides to A and T nucleotides than the reverse, suggesting that mammalian genomes are not at equilibrium for base composition. Analysis of human polymorphism data suggests that mutations that increase GC-content tend to be at much higher frequencies than those that decrease or preserve GC-content when the ancestral allele is inferred via parsimony using the chimpanzee genome. These observations have been interpreted as evidence for a fixation bias in favor of G and C alleles due to either positive natural selection or biased gene conversion. Here, we test the robustness of this interpretation to violations of the parsimony assumption using a data set of 21,488 noncoding single nucleotide polymorphisms (SNPs) discovered by the National Institute of Environmental Health Sciences (NIEHS) SNPs project via direct resequencing of n = 95 individuals. Applying standard nonparametric and parametric population genetic approaches, we replicate the signatures of a fixation bias in favor of G and C alleles when the ancestral base is assumed to be the base found in the chimpanzee outgroup. However, upon taking into account the probability of misidentifying the ancestral state of each SNP using a context-dependent mutation model, the corrected distribution of SNP frequencies for GC-content increasing SNPs are nearly indistinguishable from the patterns observed for other types of mutations, suggesting that the signature of fixation bias is a spurious artifact of the parsimony assumption.

Context Dependence, Ancestral Misidentification, and Spurious Signatures of Natural Selection

Population genetic analyses often use polymorphism data from one species, and orthologous genomic sequences from closely related outgroup species. These outgroup sequences are frequently used to identify ancestral alleles at segregating sites and to compare the patterns of polymorphism and divergence. Inherent in such studies is the assumption of parsimony, which posits that the ancestral state of each single nucleotide polymorphism (SNP) is the allele that matches the orthologous site in the outgroup sequence, and that all nucleotide substitutions between species have been observed. This study tests the effect of violating the parsimony assumption when mutation rates vary across sites and over time. Using a context-dependent mutation model that accounts for elevated mutation rates at CpG dinucleotides, increased propensity for transitional versus transversional mutations, as well as other directional and contextual mutation biases estimated along the human lineage, we show (using both simulations and a theoretical model) that enough unobserved substitutions could have occurred since the divergence of human and chimpanzee to cause many statistical tests to spuriously reject neutrality. Moreover, using both the chimpanzee and rhesus macaque genomes to parsimoniously identify ancestral states causes a large fraction of the data to be removed while not completely alleviating problem. By constructing a novel model of the context-dependent mutation process, we can correct polymorphism data for the effect of ancestral misidentification using a single outgroup.

Gene arrangements and branching orders of gram-positive bacteria

The availability of complete genomic sequence data allows one to develop new methods of reconstructing phylogenetic trees. A simple method of reconstructing branching orders based on gene transposition (or lateral transfer) is presented. It is argued that specific gene arrangements on four different genomes could determine a branching order. A computer search for such gene arrangements was carried out against gene order data of completely sequenced Gram-positive bacteria. Gene arrangements around ribosomal protein S4 gene, murC (UDP- N-acetylmuramate:alanine ligase) gene and dnaE (DNA polymerase III α chain) gene each suggest a branching order in which actinobacteria with a high genomic G+C content first branched off from other Gram-positives with a low G+C content and then a split occurred between Mycoplasma species and a group closely related to Bacillus subtilis. A recently sequenced thermophilic bacterium Thermoanaerobacter tengcongensis is suggested to have branched off from the lineage leading to the low G+C Gram-positives prior to the split between the Mycoplasma and Bacillus groups. By contrast to the indel analysis in which a single evolutionary event of insertion or deletion of a signature sequence is assumed, the present method does not necessarily require such a parsimonious assumption of gene transposition.

Agathiphaga wing vestiture revisited: evidence for complex early evolution of lepidopteran scales (Lepidoptera: Agathiphagidae)

AbstractAgathiphaga moths lack microtrichiation on most of the fore-wing upperside (apart from a basal anterior area), while it well developed on the hind-wing upperside and on the underside of both wing pairs. Scales on the fore-wing upperside largely occur in clusters, which then often comprise one larger, notched/truncate and pigmented 'cover' scale, and one or more smaller, weakly pigmented/unpigmented, smoothly rounded 'ground' scale. The former scale type proved to be hollow and have trabeculae in the inner lumen. However, it has no perforations in the abwing lamella; hence the absence of such perforations (ore even vestiges thereof, in the form of small depressions) from a scale is not necessarily indicative that it is of the solid type. The ground scales, like all hind-wing and underside scales, are of the commonplace solid type which is of general occurrence in non-glossatan moths. Evolutionary aspects of scale morphology in basal moths are discussed. The origin of hollow wing-surface scales cannot have been a single, unreversed event, but independent evolution of this scale types in the Agathiphagidae and the Coelolepida (= Acanthopteroctetidae + Lophocoronidae + Myoglossata) remains the most parsimonious assumption.

Cladistic biogeography of the Mexican transition zone

AbstractBiogeographic relationships among nine montane areas of endemism across the transition zone between North and South America are analysed cladistically based on phylogenetic hypotheses of thirty‐three resident monophyletic taxa of insects, fish, reptiles, and plants.Areas of endemism include the Arizona mountains (AZ), Sonoran Desert (SD), Sierra Madre Occidental (OCC), southern Sierra Madre Occidental (SOC), Sierra Madre Oriental (ORI), Sierra Transvolcanica (TRAN), Sierra Madre del Sur (SUR), Chiapan‐Guatemalan Highlands (CGH), and Talamancan Cordillera (TC).Area relationships are summarized using Brooks Parsimony Analysis and Assumption 0, with the former resulting in more defensible biogeographic hypotheses.Areas of endemism are dividable into two monophyletic groups; a northern group including AZ, SD, OCC, and ORI, and a southern group consisting of TC, CGH, TRAN, SUR, and the isolated southern regions of the Sierra Madre Occidental (SOC).The northern set of areas are characterized by recent, probably Pleistocene, isolation and prevalent widespread species, whereas the southerly areas probably diverged after Pliocene closure of the Panamanian isthmus.The southern areas are redundantly represented on many of the taxon‐area cladograms by endemic species, indicative of much higher levels of endemism in the Sierra Transvolcanica and further south.Use of a general area cladogram in such a transition zone permits explicit exploration of biogeographic patterns and establishes a predictive framework for taxonomy and conservation prioritization.

The binding problem.

Both Ghose and Maunsell and Shadlen and Movshon point out what is perhaps the fundamental problem with the binding hypothesis: even supposing that temporal coding is the vehicle for signaling which neural populations should be bound together, the theory does not adequately address how those combinations are computed. In a sense, the binding problem is pushed back one level, for it must be solved at least partially for the necessary temporal correlations to be established. Are neurons with appropriate receptive field properties and anatomical connectivity a sufficient basis for the generation of correlated signals? What is the role of top-down connections in establishing proper synchrony? These questions are difficult to answer and difficult to model with biological realism. A similar problem rests with the output side of the temporal binding hypothesis—if correlations are the signal for binding, how are those signals read out? The readout problem is one of the most puzzling and fundamental problems for systems neuroscience in general: how is the firing of populations of neurons interpreted and transformed by other neurons to result in decision, action, perception, etc? This problem plagues most, if not all, models of brain function, for in modeling it is the modeler that attributes semantics to nodes in a network. One way to potentially avoid that problem would be to close the loop between the model and the world, so that the world impinges upon the network, which then acts upon and affects the world, thus generating semantics through action.This brings me to mention (by virtue of my editorial license) what is perhaps the most mystifying binding problem of all: the problem of consciousness. How does something as simple and mechanistic as neural firing add up to subjectivity, raw feelings, a self? Are the mechanisms that allow us to attribute the correct color and shape to an object the same ones that lead to the unity of phenomenal experience? Will the solution of the binding problem be the solution to the mystery of consciousness? I will not belabor the point, since answers will be long in coming, but although none of the scientists who authored the reviews that follow discuss binding with respect to consciousness, I will wager that the a good part of the interest, excitement, and contentiousness that surrounds the binding debate is attributable to the magnitude of the issues with which it is connected. The following pieces provide a comprehensive review of the status of the binding problem at the dawn of the new millenium. It will be extremely interesting to repeat this exercise in a decade or two, to chart the progress that we as scientists make on one of the most puzzling and fascinating issues that the brain and cognitive sciences have ever faced.*E-mail: aroskies@cell.com.

An empirical test of the Hull-White option pricing model

INTRODUCTIONThe Black-Scholes (1973) option pricing model provides the foundationfor the modern theory of options valuation. In actual applications, how-ever, the model has certain well-known deficiencies. For example, whencalibrated to accurately price at-the-money options the Black-Scholes(1973) model often misprices deep in-the-money and deep out-of-the-money options. This model-anomalous behavior givesrisetowhatoptionsprofessionals call “volatility smiles.” A volatility smile is the skewed pat-tern that results from calculating implied volatilities across a range ofstrike prices for an option series. This phenomenon is not predicted bythe Black-Scholes (1973) model, since volatility is a property of the un-derlying instrument and the same implied volatility value should be ob-served across all options onthatinstrument.Volatilitysmilesaregenerallythought to result from the parsimonious assumptions used to derive theBlack-Scholes model. In particular, the Black-Scholes (1973) model as-sumes that security log prices follow a constant variance diffusion pro-cess. The constant variance assumption has been tested and rejected inearly studies by Beckers (1980), Black and Scholes (1972), Christie