The meaning of an experimental result depends on the experiment's conceptual backdrop, particularly its null hypothesis. This observation provides the basis for a functional interpretation of belief in the base rate fallacy. On this interpretation, if the base rate fallacy is to be labelled a “myth,” then it should be recognized that this label is not necessarily a disparaging one.

Ever since ecology's inception, the concept of competition has generated discussion. Recent discussions have focused on the role of interspecific competition in shaping the structure of ecological communities. More in particular, ecologists are split up over the validity of a method that is currently in vogue to discredit explanations of community structure in terms of competition theory. An analysis of this controversy is presented which attempts to show that the discussions so far have focused on the wrong issues. Not the (...) method's ability to generate alternative explanations should be questioned, but its ability to generate superior explanations. The impact of Popperian philosophy of science on the dispute is briefly discussed. (shrink)

We evaluate a common reasoning strategy used in community ecology and comparative psychology for selecting between competing hypotheses. This strategy labels one hypothesis as a “null” on the grounds of its simplicity and epistemically privileges it as accepted until rejected. We argue that this strategy is unjustified. The asymmetrical treatment of statistical null hypotheses is justified through the experimental and mathematical contexts in which they are used, but these contexts are missing in the case of the (...) “pseudo-null hypotheses” found in our case studies. Moreover, statistical nulls are often not epistemically privileged in practice over their alternatives because failing to reject the null is usually a negative result about the alternative, experimental hypothesis. Scientists should eschew the appeal to pseudo-nulls. It is a rhetorical strategy that glosses over a commitment to valuing simplicity over other epistemic virtues in the name of good scientific and statistical methodology. (shrink)

In present day ecology, competition is a subject typically generating controversies that pervade the whole field. Ecology is concerned with relations between organisms and their environment. As the environment of any organism has biotic besides physical components, relations between organisms are obviously important. Competition is one of them. According to many ecologists it crucially affects the fate of populations and species. Precisely this assumption has led to vigorous debates (cf. Lewin 1984).I intend to show that elementary methodological analysis could easily (...) dissolve the controversy. Methodology, indeed, has not always been brought to bear on biology as it should. This point is elaborated at the end of the paper.Ecologists use a variety of descriptive units, beside individual organisms. Here the population - a group of individual organisms of the same species and the community - a group of populations are of special importance. (shrink)

Neanderthal extinction is a matter of intense debate. It has been suggested that demography (as opposed to environment or competition) could alone provide a sufficient explanation for the phenomenon. We argue that demography cannot be a ‘stand-alone’ or ‘alternative’ explanation of token extinctions as demographic features are entangled with competitive and environmental factors, and further because demography should not be conflated with neutrality.

In this article I give a critical evaluation of the use and limitations of null-model-based hypothesis testing as a research strategy in the biological sciences. According to this strategy, the null model based on a randomization procedure provides an appropriate null hypothesis stating that the existence of a pattern is the result of random processes or can be expected by chance alone, and proponents of other hypotheses should first try to reject this null hypothesis in (...) order to demonstrate their own hypotheses. Using as an example the controversy over the use of null hypotheses and null models in species co-occurrence studies, I argue that null-model-based hypothesis testing fails to work as a proper analog to traditional statistical null-hypothesis testing as used in well-controlled experimental research, and that the random process hypothesis should not be privileged as a null hypothesis. Instead, the possible use of the null model resides in its role of providing a way to challenge scientists’ commonsense judgments about how a seemingly unusual pattern could have come to be. Despite this possible use, null-model-based hypothesis testing still carries certain limitations, and it should not be regarded as an obligation for biologists who are interested in explaining patterns in nature to first conduct such a test before pursuing their own hypotheses. (shrink)

Evidence-based medicine frequently uses statistical hypothesis testing. In this paradigm, data can only disconfirm a research hypothesis’ competitors: One tests the negation of a statistical hypothesis that is supposed to correspond to the research hypothesis. In practice, these hypotheses are often misaligned. For instance, directional research hypotheses are often paired with non-directional statistical hypotheses. Prima facie, one cannot gain proper evidence for one’s research hypothesis employing a misaligned statistical hypothesis. This paper sheds lights on the nature of (...) and the reasons for such misalignments and it provides a thorough analysis of whether they pose a threat to evidence-based medicine. The upshots are that the misalignments are often hidden for clinicians and that although some cases of misalignments can be partially counterbalanced, the overall threat is non-negligible. The counterbalances either lead to methodological inadequacy, loss of statistical power, or involve a lack of information that could be crucial for decision making. This result casts doubt on various findings of medical studies in addition to issues associated with under-powered studies or the replication crisis. (shrink)

Entertaining diverse assumptions about empirical research, commentators give a wide range of verdicts on the NHSTP defence in Statistical significance. The null-hypothesis significance- test procedure is defended in a framework in which deductive and inductive rules are deployed in theory corroboration in the spirit of Popper's Conjectures and refutations. The defensible hypothetico-deductive structure of the framework is used to make explicit the distinctions between substantive and statistical hypotheses, statistical alternative and conceptual alternative hypotheses, and making statistical decisions (...) and drawing theoretical conclusions. These distinctions make it easier to show that H0 can be true, the effect size is irrelevant to theory corroboration, and “strong” hypotheses make no difference to NHSTP. Reservations about statistical power, meta-analysis, and the Bayesian approach are still warranted. (shrink)

Numerous scenarios explain the origin of the eukaryote cell by fusion or endosymbiosis between an archaeon and a bacterium (and sometimes a third partner). We evaluate these hypotheses using the following three criteria. Can the data be explained by the null hypothesis that new features arise sequentially along a stem lineage? Second, hypotheses involving an archaeon and a bacterium should undergo standard phylogenetic tests of gene distribution. Third, accounting for past events by processes observed in modern cells (...) is preferable to postulating unknown processes that have never been observed. For example, there are many eukaryote examples of bacteria as endosymbionts or endoparasites, but none known in archaea. Strictly post‐hoc hypotheses that ignore this third criterion should be avoided. Applying these three criteria significantly narrows the number of plausible hypotheses. Given current knowledge, our conclusion is that the eukaryote lineage must have diverged from an ancestor of archaea well prior to the origin of the mitochondrion. Significantly, the absence of ancestrally amitochondriate eukaryotes (archezoa) among extant eukaryotes is neither evidence for an archaeal host for the ancestor of mitochondria, nor evidence against a eukaryotic host. BioEssays 29: 74–84, 2007. © 2006 Wiley Periodicals, Inc. (shrink)

Chow's defense of NHSTP ignores the fact that in psychology it is used to test substantive hypotheses in theory-corroborating research. In this role, NHSTP is not only inadequate, but damaging to the progress of psychology as a science. NHSTP does not fulfill the Popperian requirement that theories be tested severely. It also encourages nonspecific predictions and feeble theoretical formulations.

This commentary advocates an alternative to null-hypothesis testing that was originally represented by Rozeboom over three decades ago yet is not considered by Chow (1996). The central distinguishing feature of this approach is that it allows the scientist to conclude that the data are much better fit by those hypotheses whose values fall inside the interval than by those outside.

L’enseignement de la méthodologie scientifique en Psychologie confère un rôle paradigmatique à l’opérationnalisation des « hypothèses générales » : une idée sans rapport précis à l’observation concrète se traduit par la tentative de rejeter une hypothèse statistique nulle au profit d’une hypothèse alternative, dite de recherche, qui opérationnalise l’idée générale. Cette démarche s’avère particulièrement inadaptée à la découverte de lois empiriques. Une loi empirique est définie comme un trou nomothétique émergeant d’un référentiel de la forme Ω x M(X) x M(Y), (...) où Ω est un ensemble d’événements ou d’objets datés dont certains états dans l’ensemble M(Y) sont par hypothèse impossibles étant données certaines conditions initiales décrites dans l’ensemble M(X). Cette approche permet de préciser le regard que l’historien des connaissances peut porter sur les avancées descriptives et nomothétiques de la Psychologie empirique contemporaine. (shrink)

L’enseignement de la méthodologie scientifique en Psychologie confère un rôle paradigmatique à l’opérationnalisation des « hypothèses générales » : une idée sans rapport précis à l’observation concrète se traduit par la tentative de rejeter une hypothèse statistique nulle au profit d’une hypothèse alternative, dite de recherche, qui opérationnalise l’idée générale. Cette démarche s’avère particulièrement inadaptée à la découverte de lois empiriques. Une loi empirique est définie comme un trou nomothétique émergeant d’un référentiel de la forme Ω x M(X) x M(Y), (...) où Ω est un ensemble d’événements ou d’objets datés dont certains états dans l’ensemble M(Y) sont par hypothèse impossibles étant données certaines conditions initiales décrites dans l’ensemble M(X). Cette approche permet de préciser le regard que l’historien des connaissances peut porter sur les avancées descriptives et nomothétiques de la Psychologie empirique contemporaine. (shrink)

The full Bayesian signi/cance test (FBST) for precise hypotheses is presented, with some illustrative applications. In the FBST we compute the evidence against the precise hypothesis. We discuss some of the theoretical properties of the FBST, and provide an invariant formulation for coordinate transformations, provided a reference density has been established. This evidence is the probability of the highest relative surprise set, “tangential” to the sub-manifold (of the parameter space) that defines the null hypothesis.

Background: Prior research has explored reasons why health care providers may or may not choose to seek an ethics consultation. Although low-quality communication is evident in many ethics consultations, it is unknown whether poor communication in clinical settings is related to health care providers' requests for ethics involvement. Objective: To assess the relationship between self-reported ratings of health care providers' inter- and intraprofessional communication and ethics consultation requests. Method: This cross-sectional survey was conducted using a self-administered questionnaire of physicians and (...) nurses in six intensive care units at one academic medical center in the United States. The questionnaire assessed perceptions about requesting ethics consultations and how health care providers perceive communication. Results: Two hundred sixty-two participants (228 nurses and 34 physicians) responded to the survey (response rate 55%; 59% for nurses and 41% for physicians). Requests for an ethics consult were positively associated with perceived quality of interprofessional communication (r =.13, p <.05), but perceptions of the number of ethical dilemmas that occur on participants' units each month were negatively associated with the perceived quality of intra-professional communication (r = −.17, p <.01). Conclusion: The relationship that was hypothesized between perceived poor communication and increased number of ethics consultations was not borne out by these data. Indeed, we found the opposite; these finding suggests that good inter- and intraprofessional communication may promote the use of outside resources, such as ethics, when they are needed. (shrink)

A Bayesian measure of evidence for precise hypotheses is presented. The intention is to give a Bayesian alternative to significance tests or, equivalently, to p-values. In fact, a set is defined in the parameter space and the posterior probability, its credibility, is evaluated. This set is the “Highest Posterior Density Region” that is “tangent” to the set that defines the null hypothesis. Our measure of evidence is the complement of the credibility of the “tangent” region.

The Generalized Poisson Distribution (GPD) adds an extra parameter to the usual Poisson distribution. This parameter induces a loss of homogeneity in the stochastic processes modeled by the distribution. Thus, the generalized distribution becomes an useful model for counting processes where the occurrence of events is not homogeneous. This model creates the need for an inferential procedure, to test for the value of this extra parameter. The FBST (Full Bayesian Significance Test) is a Bayesian hypotheses test procedure, capable of (...) providing an evidence measure on sharp hypotheses (where the dimension of the parametric space under the null hypotheses is smaller than that of the full parametric space). The goal of this work is study the empirical properties of the FBST for testing the nullity of extra parameter of the generalized Poisson distribution. Numerical experiments show a better performance of FBST with respect to the classical likelihood ratio test, and suggest that FBST is an efficient and robust tool for this application. (shrink)

The replication crisis has caused researchers to distinguish between exact replications, which duplicate all aspects of a study that could potentially affect the results, and direct replications, which duplicate only those aspects of the study that are thought to be theoretically essential to reproduce the original effect. The replication crisis has also prompted researchers to think more carefully about the possibility of making Type I errors when rejecting null hypotheses. In this context, the present article considers the utility (...) of two types of Type I error probability: the Neyman–Pearson long run Type I error rate and the Fisherian sample-specific Type I error probability. It is argued that the Neyman–Pearson Type I error rate is inapplicable in social science because it refers to a long run of exact replications, and social science deals with irreversible units that make exact replications impossible. Instead, the Fisherian sample-specific Type I error probability is recommended as a more meaningful way to conceptualize false positive results in social science because it can be applied to each sample-specific decision about rejecting the same substantive null hypothesis in a series of direct replications. It is concluded that the replication crisis may be partly due to researchers’ unrealistic expectations about replicability based on their consideration of the Neyman–Pearson Type I error rate across a long run of exact replications. (shrink)

The use of power to infer null hypotheses from negative results has recently come under severe attack. In this article, I show that the power of a test can justify accepting the null hypothesis. This argument also gives us a new powerful reason for not treating p-values and power as measures of the strength of evidence.

This chapter focuses on evidence from functional magnetic resonance imaging data, and discusses the application of neuroimaging techniques to various fields, including cognitive sciences. It considers the role of neuroimaging data in providing informative evidence regarding hypotheses in cognitive science, and explains differences in data, high-level null hypotheses, and ways to accommodate null hypotheses. Finally, the chapter looks into the scope of neuroimaging data in the cognitive sciences.

Within the literature on emotion and behavioral action, studies on approach-avoidance take up a prominent place. Several experimental paradigms feature successful conceptual replications but many original studies have not yet been replicated directly. We present such a direct replication attempt of two seminal experiments originally conducted by Chen and Bargh (1999). In their first experiment, participants affectively evaluated attitude objects by pulling or pushing a lever. Participants who had to pull the lever with positively valenced attitude objects and push the (...) lever with negatively valenced attitude objects (i.e., congruent instruction) did so faster than participants who had to follow the reverse (i.e., incongruent) instruction. In Chen and Bargh's second experiment, the explicit evaluative instructions were absent and participants merely responded to the attitude objects by either always pushing or always pulling the lever. Similar results were obtained as in Experiment 1. Based on these findings, Chen and Bargh concluded that (1) attitude objects are evaluated automatically; and (2) attitude objects automatically trigger a behavioral tendency to approach or avoid. We attempted to replicate both experiments and failed to find the effects reported by Chen and Bargh as indicated by our pre-registered Bayesian data analyses; nevertheless, the evidence in favor of the null hypotheses was only anecdotal, and definitive conclusions await further study. (shrink)

Mainstream social psychology focuses on how people characteristically violate norms of action through social misbehaviors such as conformity with false majority judgments, destructive obedience, and failures to help those in need. Likewise, they are seen to violate norms of reasoning through cognitive errors such as misuse of social information, self-enhancement, and an over-readiness to attribute dispositional characteristics. The causes of this negative research emphasis include the apparent informativeness of norm violation, the status of good behavior and judgment as unconfirmable (...) class='Hi'>null hypotheses, and the allure of counter-intuitive findings. The shortcomings of this orientation include frequently erroneous imputations of error, findings of mutually contradictory errors, incoherent interpretations of error, an inability to explain the sources of behavioral or cognitive achievement, and the inhibition of generalized theory. Possible remedies include increased attention to the complete range of behavior and judgmental accomplishment, analytic reforms emphasizing effect sizes and Bayesian inference, and a theoretical paradigm able to account for both the sources of accomplishment and of error. A more balanced social psychology would yield not only a more positive view of human nature, but also an improved understanding of the bases of good behavior and accurate judgment, coherent explanations of occasional lapses, and theoretically grounded suggestions for improvement. Key Words: Bayesian inference; biases; normative models; personality; positive psychology; rationality; reasoning; social behavior; social judgment; social psychology. (shrink)

The term adaptive radiation has been recurrently used to describe evolutionary patterns of several lineages, and has been proposed as the main driver of biological diversification. Different definitions and criteria have been proposed to distinguish an adaptive radiation, and the current literature shows disagreements as to how radiating lineages should be circumscribed. Inconsistencies increase when authors try to differentiate a clade under adaptive radiation from clades evolving under ‘regular’ speciation with adaptation, a pattern anticipated and predicted by the evolutionary theory (...) in any lineage. The most important disagreement is as to which evolutionary rate authors analyze to characterize a radiation; a discussion embedded in a prevailing inability to provide mechanistic explanations of the relationship among evolutionary rates. The union of pattern and process in the same term, the inadequacy of reported null hypotheses, and the frequent use of ad hoc comparisons between lineages have also contributed to the lack of consensus. A rigorous use of available terms and the articulation of solid criteria with objective methodologies in distinguishing evolutionary patterns are imperative. Given the difficulties in detecting adaptation, the use of the ‘adaptive’ term to qualify a radiation should be avoided unless methodologically tested. As an unambiguous method to distinguish radiating lineages, the statistical detection of significant increases in taxonomic diversification rates on monophyletic lineages can be considered a distinctive signature of a radiation. After recognizing this pattern, causal hypotheses explaining them can be stated, as well as correlates with other rates of evolution. (shrink)

The questions and methods of molecular biology and evolutionary biology are clearly distinct, yet a unified approach can lead to deep insights. Unfortunately, attempts to unify these approaches are fraught with pitfalls. In this informal series of questions and answers, we offer the mechanistically oriented biologist a set of steps to come up with evolutionarily reasonable and meaningful hypotheses. We emphasize the critical power and importance of carefully constructed null hypotheses, and we illustrate our ideas with examples (...) representing a range of topics, from the biology of aging, to protein structure, to speciation, and more. We also stress the importance of mathematics as the lingua franca for biologists of all stripes, and encourage mechanistic biologists to seek out quantitative collaborators to build explicit mathematical models, making their assumptions explicit, and their logic clear and testable. Biologists in all realms of inquiry stand to gain from strong bridges between our disciplines. (shrink)

Research in ecology and evolutionary biology (evo-eco) often tries to emulate the “hard” sciences such as physics and chemistry, but to many of its practitioners feels more like the “soft” sciences of psychology and sociology. I argue that this schizophrenic attitude is the result of lack of appreciation of the full consequences of the peculiarity of the evo-eco sciences as lying in between a-historical disciplines such as physics and completely historical ones as like paleontology. Furthermore, evo-eco researchers have gotten stuck (...) on mathematically appealing but philosophi- cally simplistic concepts such as null hypotheses and p-values defined according to the frequentist approach in statistics, with the consequence of having been unable to fully embrace the complexity and subtlety of the problems with which ecologists and evolutionary biologists deal with. I review and discuss some literature in ecology, philosophy of science and psychology to show that a more critical methodological attitude can be liberating for the evo-eco scientist and can lead to a more fecund and enjoyable practice of ecology and evolutionary biology. With this aim, I briefly cover concepts such as the method of multiple hypotheses, Bayesian analysis, and strong inference. (shrink)

Mind is seen as a collection of abilities to take decisions in biologically relevant situations. Mind shaping means to form habits and decision rules of how to proceed in a given situation. Problem-specific decision rules constitute a modular mind; adaptive mind-shaping is likely to be module-specific. We present examples from different behaviour ‘faculties’ throughout the animal kingdom, grouped according to important mind-shaping factors to illustrate three basically different mind-shaping processes: external stimuli guide the differentiation of a nervous structure that controls (...) a given behaviour; information comes in to direct a fixed behaviour pattern to its biological goal, or to complete an inherited behaviour program; specific stimuli activate or inactivate a pre-programmed behaviour. Mind-shaping phenomena found in the animal kingdom are suggested as ‘null-hypotheses’ when looking at how human minds might be shaped. (shrink)

The null-hypothesis significance-test procedure (NHSTP) is defended in the context of the theory-corroboration experiment, as well as the following contrasts: (a) substantive hypotheses versus statistical hypotheses, (b) theory corroboration versus statistical hypothesis testing, (c) theoretical inference versus statistical decision, (d) experiments versus nonexperimental studies, and (e) theory corroboration versus treatment assessment. The null hypothesis can be true because it is the hypothesis that errors are randomly distributed in data. Moreover, the null hypothesis is never used (...) as a categorical proposition. Statistical significance means only that chance influences can be excluded as an explanation of data; it does not identify the nonchance factor responsible. The experimental conclusion is drawn with the inductive principle underlying the experimental design. A chain of deductive arguments gives rise to the theoretical conclusion via the experimental conclusion. The anomalous relationship between statistical significance and the effect size often used to criticize NHSTP is more apparent than real. The absolute size of the effect is not an index of evidential support for the substantive hypothesis. Nor is the effect size, by itself, informative as to the practical importance of the research result. Being a conditional probability, statistical power cannot be the apriori probability of statistical significance. The validity of statistical power is debatable because statistical significance is determined with a single sampling distribution of the test statistic based on H0, whereas it takes two distributions to represent statistical power or effect size. Sample size should not be determined in the mechanical manner envisaged in power analysis. It is inappropriate to criticize NHSTP for nonstatistical reasons. At the same time, neither effect size, nor confidence interval estimate, nor posterior probability can be used to exclude chance as an explanation of data. Neither can any of them fulfill the nonstatistical functions expected of them by critics. (shrink)

The unit root problem plays a central role in empirical applications in the time series econometric literature. However, significance tests developed under the frequentist tradition present various conceptual problems that jeopardize the power of these tests, especially for small samples. Bayesian alternatives, although having interesting interpretations and being precisely defined, experience problems due to the fact that that the hypothesis of interest in this case is sharp or precise. The Bayesian significance test used in this article, for the unit root (...) hypothesis, is based solely on the posterior density function, without the need of imposing positive probabilities to sets of zero Lebesgue measure. Furthermore, it is conducted under strict observance of the likelihood principle. It was designed mainly for testing sharp null hypotheses and it is called FBST for Full Bayesian Significance Test. (shrink)

The ecologist today finds scarce ground safe from controversy. Decisions must be made about what combination of data, goals, methods, and theories offers them the foundations and tools they need to construct and defend their research. When push comes to shove, ecologists often turn to philosophy to justify why it is their approach that is scientific. Karl Popper’s image of science as bold conjectures and heroic refutations is routinely enlisted to justify testing hypotheses over merely confirming them. One of (...) the most controversial theories in contemporary science is the Neutral Theory of Ecology. Its chief developer and proponent, Stephen Hubbell, presents the neutral theory as a bold conjecture that has so far escaped refutation. Critics of the neutral theory claim that it already stands refuted, despite what the dogmatic neutralists say. We see the controversy through a Popperian lens. But Popper’s is an impoverished philosophy of science that distorts contemporary ecology. -/- The controversy surrounding the neutral theory actually rests on a methodological fault. There is a strong but messy historical link between the concepts of being neutral and being null in biology, and Hubbell perpetuates this when he claims that the neutral theory is supplies the appropriate null for testing alternative theories. What method is being followed here? There are three contenders: -/- Null hypothesis testing tests for whether a there is a pattern to be explained. Null modeling tests for whether a process is causally relevant to a pattern. Baseline modeling apportions relative responsibility to multiple processes each relevant to a pattern. -/- Whether the neutral theory supplies an appropriate “null” depends upon whether null hypothesis, null modeling, or baseline model is intended. These methods prescribe distinct inference patterns. If they are null hypothesis testing or null modeling, the neutralists’s reasoning is invalid. If they are baseline modeling, the justification of a crucial assumption remains opaque. Either way, the neutral-null connection is being exploited rhetorically to privilege the neutral theory over its rivals. Clarifying the reasoning immunizes us against the rhetoric and foregrounds the underlying virtues of the neutralist approach to ecology. -/- The Popperian lens distorts theoretical development as dogmatism. Lakatos’s view of science as the development of research programmes clarifies the epistemology of the neutral theory. Focusing philosophical attention on the neutralist research programme illuminates (1) the synchronic uses of the neutral theory to make predictions and give descriptions and explanations; (2) its diachronic development in response to theoretical innovation and confrontation with data; (3) its complex relationships to alternative theories. For example, baseline modeling is now seen to be its primary explanatory heuristic. The justification for baseline modeling with the neutral theory, previously hidden from view, is seen in the logic of in the neutralist research programme. (shrink)

The Full Bayesian Significance Test (FBST) for precise hypotheses is presented, with some applications relevant to reliability theory. The FBST is an alternative to significance tests or, equivalently, to p-ualue.s. In the FBST we compute the evidence of the precise hypothesis. This evidence is the probability of the complement of a credible set "tangent" to the sub-manifold (of the para,rreter space) that defines the null hypothesis. We use the FBST in an application requiring a quality control of used (...) components, based on remaining life statistics. (shrink)

Several researchers have recently argued that p values lose their meaning in exploratory analyses due to an unknown inflation of the alpha level (e.g., Nosek & Lakens, 2014; Wagenmakers, 2016). For this argument to be tenable, the familywise error rate must be defined in relation to the number of hypotheses that are tested in the same study or article. Under this conceptualization, the familywise error rate is usually unknowable in exploratory analyses because it is usually unclear how many (...) class='Hi'>hypotheses have been tested on a spontaneous basis and then omitted from the final research report. In the present article, I argue that it is inappropriate to conceptualize the familywise error rate in relation to the number of hypotheses that are tested. Instead, it is more appropriate to conceptualize familywise error in relation to the number of different tests that are conducted on the same null hypothesis in the same study. Under this conceptualization, alpha level adjustments in exploratory analyses are (a) less necessary and (b) objectively verifiable. As a result, p values do not lose their meaning in exploratory analyses. (shrink)

The replication (replicability, reproducibility) crisis in social psychology and clinical medicine arises from the fact that many apparently well-confirmed experimental results are subsequently overturned by studies that aim to replicate the original study. The culprit is widely held to be poor science: questionable research practices, failure to publish negative results, bad incentives, and even fraud. In this article I argue that the high rate of failed replications is consistent with high-quality science. We would expect this outcome if the field of (...) science in question produces a high proportion of false hypotheses prior to testing. If most of the hypotheses under test are false, then there will be many false hypotheses that are apparently supported by the outcomes of well conducted experiments and null hypothesis significance tests with a type-I error rate (α) of 5%. Failure to recognize this is to commit the fallacy of ignoring the base rate. I argue that this is a plausible diagnosis of the replication crisis and examine what lessons we thereby learn for the future conduct of science. (shrink)

The zone of latent solutions hypothesis provides an alternative approach to explaining cultural patterns in primates and many other animals. According to the ZLS hypothesis, non-human great ape cultures consist largely or solely of latent solutions. The current competing hypothesis for ape culture argues instead that at least some of their behavioural or artefact forms are copied through specific social learning mechanisms and that their forms may depend on copying. In contrast, the ape ZLS hypothesis does not require these forms (...) to be copied. Instead, it suggests that several social learning mechanisms help determine the frequency of these behaviours and artefacts within connected individuals. The ZLS hypothesis thus suggests that increases and stabilisations of a particular behaviour’s or artefact’s frequency can derive from socially-mediated form reinnovations. Therefore, and while genes and ecology play important roles as well, according to the ape ZLS hypothesis, apes typically acquire the forms of their behaviours and artefacts individually, but are usually socially induced to do so. The ZLS approach is often criticized—perhaps also because it challenges the current null hypothesis, which instead assumes a requirement of form-copying social learning mechanisms to explain many ape behavioural forms. However, as the ZLS hypothesis is a new approach, with less accumulated literature compared to the current null hypothesis, some confusion is to be expected. Here, we clarify the ZLS approach—also in relation to other competing hypotheses—and address misconceptions and objections. We believe that these clarifications will provide researchers with a coherent theoretical approach and an experimental methodology to examine the necessity of form-copying variants of social learning in apes, humans and other species. (shrink)

Scientists often adjust their significance threshold during null hypothesis significance testing in order to take into account multiple testing and multiple comparisons. This alpha adjustment has become particularly relevant in the context of the replication crisis in science. The present article considers the conditions in which this alpha adjustment is appropriate and the conditions in which it is inappropriate. A distinction is drawn between three types of multiple testing: disjunction testing, conjunction testing, and individual testing. It is argued that (...) alpha adjustment is only appropriate in the case of disjunction testing, in which at least one test result must be significant in order to reject the associated joint null hypothesis. Alpha adjustment is inappropriate in the case of conjunction testing, in which all relevant results must be significant in order to reject the joint null hypothesis. Alpha adjustment is also inappropriate in the case of individual testing, in which each individual result must be significant in order to reject each associated individual null hypothesis. The conditions under which each of these three types of multiple testing is warranted are examined. It is concluded that researchers should not automatically assume that alpha adjustment is necessary during multiple testing. Illustrations are provided in relation to joint studywise hypotheses and joint multiway ANOVAwise hypotheses. (shrink)

Microscopy has revealed tremendous diversity of bacterial and eukaryotic forms. Recent molecular analyses show discordance in estimates of biodiversity between morphological and molecular analyses. Moreover, phylogenetic analyses of the diversity of microbial forms reveal evidence of convergence at scales as deep as interdomain: morphologies shared between bacteria and eukaryotes. Here, we highlight examples of such discordance, focusing on exemplary lineages such as testate amoebae, ciliates, and cyanobacteria. These have long histories of morphological study, enabling deeper analyses on both the molecular (...) and morphological sides. We discuss examples in two main categories: (i) morphologically identical (or highly similar) individuals that are genetically distinct and (ii) morphologically distinct individuals that are genetically the same. We argue that hypotheses about discordance can be tested using the concept of neutral morphologies, or more broadly neutral phenotypes, as a null hypothesis. -/- . (shrink)

Dans plusieurs passages, Épicure mentionne des durées infraperceptibles saisies par la raison, ce qui conduit à envisager un atomisme du temps, c’est-à-dire l’existence de durées indivisibles ou quanta de temps. Cette hypothèse, nulle part explicite chez Épicure et Lucrèce, a été évoquée par quelques doxographes. L’objet de cet article est de l’étayer et de la préciser, en lisant les textes épicuriens sur le temps à la lumière des trois grandes objections antiatomistes de la Physique. Notre analyse conclut que l’atomisme du (...) temps permet de répondre aux objections d’Aristote, mais doit être limité au seul niveau des atomes, par opposition à celui des agrégats. Il permet alors en effet de justifier l’isotachie des atomes, de rendre concevable la communauté de structure de la grandeur, du mouvement et du temps, et de garantir le caractère fini de la vitesse atomique. Deux lignes argumentatives se superposent : une conception proprement atomiste du mouvement et une reprise des termes de la physique aristotélicienne destinée à mieux en réfuter les objections. (shrink)

Many recent evolutionary psychology and human behavioral ecology studies have tested hypotheses by examining correlations between variables measured at a group level (e.g., state, country, continent). In such analyses, variables collected for each aggregation are often taken to be representative of the individuals present within them, and relationships between such variables are presumed to reflect individual-level processes. There are multiple reasons to exercise caution when doing so, including: (1) the ecological fallacy, whereby relationships observed at the aggregate level do (...) not accurately represent individual-level processes; (2) non-independence of data points, which violates assumptions of the inferential techniques used in null hypothesis testing; and (3) cross-cultural non-equivalence of measurement (differences in construct validity between groups). We provide examples of how each of these gives rise to problems in the context of testing evolutionary hypotheses about human behavior, and we offer some suggestions for future research. (shrink)

The introduction of computer simulation to paleobiology ushered in a new, experimental style of reasoning. Rather than starting with observed fossil patterns and hypothesizing causal processes that may have produced them, it became possible to start with a process model, and from it to simulate a range of possible patterns. ;The MBL Model is a stochastic model of phylogenetic evolution . Computer simulations conducted with the MBL Model served as thought experiments in stochastic evolution. In the MBL work, similarities between (...) empirical and stochastically simulated clades mounted a visual argument that stochastic processes potentially explained large fluctuations in diversity. Stanley and others countered that the similarities were an artifact of scaling. The scaling problem may have been obscured by visual bias: measures of clade shape are scale-invariant, but diversification itself is highly scale-dependent. ;Null and neutral models are frequently conflated. Null models generate hypothetical data distributions under conditions that exclude some process of interest to test whether patterns in an actual data distribution provide statistical evidence for that process. A neutral model assumes selective equivalence among all units at a specified hierarchical level in the evolving system. Neutral models are often inappropriate as null models. Pattern recognition presupposes a null model, but tacit null models are subject to persistent cognitive biases, necessitating explicit formulation of null models. Nonetheless, failure to reject the null model should not preclude further investigation of a pattern. ;Often, models are not candidates for falsification, but serve to simulate data for testing concepts or methods. Sepkoski and Kendrick , and Robeck, Maley, and Donoghue used the MBL Model to test whether mass extinction periodicity is an artifact of paraphyly in taxonomic data. Such numerical experiments, which make all assumptions explicit, can serve as templates for localizing points of disagreement. Models may fall into lineages, each generation providing lessons for the next, but often sharing operational assumptions. Artifacts of shared operational assumptions are often a threat to the validity of inferences. Results holding across models should not be accepted unless they withstand rigorous robustness analysis. (shrink)

Professor Meehl [2] has pointed out a very significant problem in the methodology of psychological research, indicating that statistical tests of psychological hypotheses against a null hypothesis are loaded in favor of eventual success at rejecting the null hypothesis. In my opinion this is not, however, a contrast between physics and psychology, but rather between the method of parameter estimation and that of the null hypothesis in the tradition of Fisher. A physicist could use the (...) class='Hi'>null hypothesis method as well as the psychologist. The fact that he doesn't is probably related to the more advanced state of his measurement techniques and theoretical constructs. (shrink)

The existence of superstition and religious beliefs in most, if not all, human societies is puzzling for behavioral ecology. These phenomena bring about various fitness costs ranging from burial objects to celibacy, and these costs are not outweighed by any obvious benefits. In an attempt to resolve this problem, we present a verbal model describing how humans and other organisms learn from the observation of coincidence (associative learning). As in statistical analysis, learning organisms need rules to distinguish between real patterns (...) and randomness. These rules, which we argue are equivalent to setting the level of α for rejection of the null hypothesis in statistics, are governed by risk management as well as by comparison to previous experiences. Risk management means that the cost of a possible type I error (superstition) has to be traded off against the cost of a possible type II error (ignorance). This trade-off implies that the occurrence of superstitious beliefs is an inevitable consequence of an organism’s ability to learn from observation of coincidence. Comparison with previous experiences (as in Bayesian statistics) improves the chances of making the right decision. While this Bayesian approach is found in most learning organisms, humans have evolved a unique ability to judge from experiences whether a candidate subject has the power to mechanistically cause the observed effect. Such “strong” causal thinking evolved because it allowed humans to understand and manipulate their environment. Strong causal thinking, however, involves the generation of hypotheses about underlying mechanisms (i.e., beliefs). Assuming that natural selection has favored individuals that learn quicker and more successfully than others owing to (1) active search to detect patterns and (2) the desire to explain these patterns mechanistically, we suggest that superstition has evolved as a by-product of the first, and that belief has evolved as a by-product of the second. (shrink)

The ongoing incidence of schizophrenia is considered a paradox, as the disorder has genetic basis yet confers survival handicaps. Researchers have not reached consensus regarding theories explaining this contradiction. Major evolutionary theories hypothesize that schizophrenia is: a byproduct of other evolutionary processes, linked to survival advantages that counteract disadvantages, associated with processes such as shamanism conferring advantages to groups, a consequence of modern environments, a result of random processes, such as mutations. A null hypothesis argues that philosophical or methodological (...) problems render evolutionary paradigms inappropriate. These arguments are reviewed in light of an experience-centered approach, which regards experiential accounts as data. A ritual healing theory, derived from this orientation, has bearing on evolutionary theories pertaining to schizophrenia. This theory explains the nature of shamanism, which has features coinciding with schizophrenia. The ritual healing theory is supported by folklore, medical, and anthropological evidence, is amenable to empirical evaluation, and has clinical applications. (shrink)

This paper analyses the broad methodological structure of population-biological theorising. In it, I show that the distinction between initial exploratory, hypothesis-generating research and the subsequent process-reconstructing, hypothesis-testing type of research is not being made. Rather, the hypotheses generated in population biology are elaborated in such detail that students confound the initial research phase with the subsequent hypotheses-testing phase of research. In this context, I therefore analyse some testing procedures within the exploration phase and show that, as an extreme (...) form of confusion, statistical null-models are mistakenly given the status of causal population-biological theory. (shrink)

Chow's (1996) Statistical significance is a defence of null-hypothesis significance testing (NHSTP). The most common and straightforward use of significance testing is for the statistical corroboration of general hypotheses. In this case, criticisms of NHSTP, at least those mentioned in the book, are unfounded or misdirected. This point is driven home by the author a bit too forcefully and meticulously. The awkward and cumbersome organisation and argumentation of the book makes it even harder to read.

Sleep strengthens memories by repeatedly reactivating associated neuron ensembles. Our studies show that although long-term memory for a medium number of word-pairs benefits from sleep, a large number does not. This suggests an upper limit to the amount of information that has access to sleep-dependent declarative memory consolidation, which is possibly linked to the availability of reactivation opportunities. Due to competing processes of global forgetting that are active during sleep, we hypothesized that even larger amounts of information would enhance the (...) proportion of information that is actively forgotten during sleep. In the present study, we aimed to induce such forgetting by challenging the sleeping brain with vast amounts of to be remembered information. For this, 78 participants learned a very large number of 640 word-pairs interspersed with periods of quiet awake rest over the course of an entire day and then either slept or stayed awake during the night. Recall was tested after another night of regular sleep. Results revealed comparable retention rates between the sleep and wake groups. Although this null-effect can be reconciled with the concept of limited capacities available for sleep-dependent consolidation, it contradicts our hypothesis that sleep would increase forgetting compared to the wake group. Additional exploratory analyses relying on equivalence testing and Bayesian statistics reveal that there is evidence against sleep having a detrimental effect on the retention of declarative memory at high information loads. We argue that forgetting occurs in both wake and sleep states through different mechanisms, i.e., through increased interference and through global synaptic downscaling, respectively. Both of these processes might scale similarly with information load. (shrink)

“ The Origins of Genome Architecture ” by Michael Lynch (2007) may not immediately sound like a book that someone interested in the philosophy of biology would grab off the shelf. But there are three important reasons why you should read this book. Firstly, if you want to understand biological evolution, you should have at least a passing familiarity with evolutionary change at the level of the genome. This is not to say that everyone interested in evolution should be a (...) geneticist or a bioinformatician, but that a working knowledge of genetic change is an essential part of the intellectual toolkit of modern evolutionary biology, even if your primary focus is the evolution of behaviour or the diversity of communities. Secondly, this book provides excellent examples of another important tool in the biologist’s intellectual toolkit, but one that is rarely explained or illustrated to such an extent: null (or neutral) models. The role null models play in testing hypotheses in evolution is a central focus of this book. Thirdly, as an accomplished work of advocacy for a strictly microevolutionary view of evolution, this book provides grist for the mill for the important debate about whether population genetic processes are the sine qua non of evolutionary explanations. (shrink)

Dans cet article nous avons essayé d'examiner la valeur de l'attribution traditionelle du commentaire De Anima à Simplicius. En comparant ce traité aux grands commentaires de Simplicius (sur les Catégories, la Physique et le De Caelo d'Aristote), nous avons été en effet frappés par les divergences de style, et de langue, ainsi que par la différente manière de commenter. Dans la première partie nous démontrons que l'auteur de l'In D.A. a écrit également la Metaphrasis in Theophrastum, qui nous a été (...) transmise sous le nom de Priscien le Lydien. 1° Dans le In D.A. l'auteur renvoie à une de ses œuvres, qu'il appelle „Epitomé de la Physique de Théophraste". En réalité, cette référence se rapporte à un passage de la Métaphrase de Priscien, où la même problématique est exposée dans des termes identiques. — 2° Une comparaison détaillée, qui porte sur l'ensemble des deux œuvres, nous révèle une telle ressemblance de style et de pensée — il y a même des phrases à peu près identiques — qu'elle ne peut s'expliquer que par l'hypothèse de l'identité de l'auteur. Dans la deuxième partie nous essayons d'identifier l'auteur de ces deux œuvres qui pourtant nous ont été transmises sous deux noms différents. L'étude de la tradition directe et indirecte n'apporte guère de solution, puisque l'attribution des deux textes, l'un à Simplicius, l'autre à Priscien, y paraît très solide. Ce n'est donc que par une critique interne de l'In D.A., notamment par la confrontation avec les commentaires de Simplicius, dont l'attribution est certaine, que la question pourra être tranchée. 1° Dans l'In D.A. l'auteur renvoie trois fois à son commentaire sur la Physique. Pourtant, il est bien difficile de retrouver dans le grand commentaire de Simplicius trois passages dont le contenu et surtout le vocabulaire prouvent que l'auteur s'y réfère. — 2° Dans l'In D.A. on ne retrouve pas les traits caractéristiques de la méthode de commenter de Simplicius, ni l'approche du texte par la documentation historique, ni les longues discussions avec les exégètes antérieurs, ni l'exposé prolixe et bien structuré; d'autre part aucun des commentaires de Simplicius ne témoigne de la phraséologie tortueuse de notre oeuvre, ni de ses formules stéréotypées. — 3° La différence doctrinale est encore plus importante. Nulle part chez Simplicius n'apparaît la théorie de l'âme comme όριστική, qui est si fondamentale dans l'In D.A. (όρίζω y est un concept-clé). Les rares digressions de l'In D.A. à propos de questions physiques et logiques ne correspondent pas aux exposés de Simplicius sur les mêmes problèmes. Ainsi nous avons confronté la doctrine de la ‚physis', de l'âme et de son ‚automotion’ et enfin le rapport entre le ‚genre’ et les différences ‚constitutives’ et ‚diérétiques’. De tout cela se dégage une telle divergence entre l'In D. A. et les autres commentaires qu'elle ne peut s'expliquer par une évolution chez Simplicius lui-même. L'in D.A. lui est donc faussement attribué; et puisque nous avons établi que ce commentaire est du même auteur que la Métaphrase, nous pouvons conclure qu'il a été vraisemblablement écrit par Priscien le Lydien, un philosophe néoplatonicien dont nous savons seulement qu'il a accompagné Damascius et Simplicius en exil en Perse. (shrink)

Comparative psychology experiments typically test a null statistical hypothesis against an alternative. Coupled with Morgan’s canon, this is often taken to imply that the model positing the simpler psychological capacity should be treated as a ‘default’ that must be ruled out before any other model can be accepted. It has been posited that this practice neglects evidence. I argue that the problem is deeper, including the way it structures the evaluation of evidence that is considered; it frames model choice (...) around the acceptance or rejection of a default. I oppose this default framing in all its forms and develop an evidentialist alternative. Default framing fails to respect the difference between experimental statistical hypotheses and substantive hypotheses such as models. It is not actually supported by the use of null hypothesis significance testing (which I retain), it distorts the weighting of evidence, and it systematically biases practice. (shrink)

We consider several variants of Keisler’s isomorphism theorem. We separate these variants by showing implications between them and cardinal invariants hypotheses. We characterize saturation hypotheses that are stronger than Keisler’s theorem with respect to models of size $\aleph _1$ and $\aleph _0$ by $\mathrm {CH}$ and $\operatorname {cov}(\mathsf {meager}) = \mathfrak {c} \land 2^{<\mathfrak {c}} = \mathfrak {c}$ respectively. We prove that Keisler’s theorem for models of size $\aleph _1$ and $\aleph _0$ implies $\mathfrak {b} = \aleph _1$ (...) and $\operatorname {cov}(\mathsf {null}) \le \mathfrak {d}$ respectively. As a consequence, Keisler’s theorem for models of size $\aleph _0$ fails in the random model. We also show that for Keisler’s theorem for models of size $\aleph _1$ to hold it is not necessary that $\operatorname {cov}(\mathsf {meager})$ equals $\mathfrak {c}$. (shrink)