Replicability and reproducibility of computational models has been somewhat understudied by “the replication movement.” In this paper, we draw on methodological studies into the replicability of psychological experiments and on the mechanistic account of explanation to analyze the functions of model replications and model reproductions in computational neuroscience. We contend that model replicability, or independent researchers' ability to obtain the same output using original code and data, and model reproducibility, or independent researchers' ability to recreate a model (...) without original code, serve different functions and fail for different reasons. This means that measures designed to improve model replicability may not enhance (and, in some cases, may actually damage) model reproducibility. We claim that although both are undesirable, low model reproducibility poses more of a threat to long-term scientific progress than low model replicability. In our opinion, low model reproducibility stems mostly from authors' omitting to provide crucial information in scientific papers and we stress that sharing all computer code and data is not a solution. Reports of computational studies should remain selective and include all and only relevant bits of code. (shrink)

Wigner's quantum mechanical formulation of the problem of biological replication is examined with special reference to DNA. His necessary condition for replication is that the number of independent equations in his formulation should not exceed the number of unknowns. Explicit hypotheses concerning the relevant collision matrix are proposed without assuming biotonic modifications of quantum mechanics. Schrödinger's description of the gene as a low-temperature solid, combined with the concept of template, is given mathematical expression which fails to satisfy (...) Wigner's necessary condition. The condition is satisfied by a further specialization of the collision matrix, which also implies metabolic stability of the replicating unit. Such metabolic stability is in fact a distinguishing feature of the DNA molecule. (shrink)

One of the most important characteristics of modern science is its replicability and objectivity. This means that a scientific result is taken as such only when it has been reproduced by other scientists. Indeed, the replicability of a scientific result in an objective and independent way by members of a scientific community is the cornerstone of science. Experimental laser physics is an example of “normal” science, where it is no doubt that the phenomenon could be replicated; however, the (...) class='Hi'>replication process may not be straightforward since it requires a good understanding of the physics behind it, as well as good technical skills. In this article, two laboratory cases of experiments on laser physics are presented: the first one deals with a Nitrogen N2 laser with a Polloni excitation circuit, and the second one deals with a transversally excited TEA carbon dioxide laser. For the nitrogen laser, it will be shown that reproducibility failed, and therefore, the reported experiment cannot be taken as a valid contribution to the advancement and understanding of nitrogen laser physics and technology. On the other hand, for the case of the TEA carbon dioxide laser, several comments are presented on the development of this finally successful experiment. Both cases show the importance of being technically up-dated in order to reproduce or improve the results reported by other researchers. Finally, a discussion about: What can we learn about the research practice from these two cases? It is presented, as well as the conclusions about the case studies; we hope they may be useful to philosophers of science and young scientists alike. (shrink)

A published simulation model Riolo et al. 2001 ) was replicated in two independent implementations so that the results as well as the conceptual design align. This double replication allowed the original to be analysed and critiqued with confidence. In this case, the replication revealed some weaknesses in the original model, which otherwise might not have come to light. This shows that unreplicated simulation models and their results can not be trusted - as with other kinds of (...) experiment, simulations need to be independently replicated. (shrink)

A growing body of cross-cultural survey research shows high percentages of clinicians report using placebos in clinical settings. One motivation for clinicians using placebos is to help patients by capitalising on the placebo effect’s reported health benefits. This is not surprising, given that placebo studies are burgeoning, with increasing calls by researchers to ethically harness placebo effects among patients. These calls propose placebos/placebo effects offer clinically significant benefits to patients. In this paper, we argue many findings in this highly cited (...) and ‘hot’ field have not been independently replicated. Evaluating the ethicality of placebo use in clinical practice involves first understanding whether placebos are efficacious clinically. Therefore, it is crucial to consider placebo research in the context of the replication crisis and what can be learnt to advance evidence-based knowledge of placebos/placebo effects and their clinical relevance (or lack thereof). In doing so, our goal in this paper is to motivate both increased awareness of replication issues and to help pave the way for advances in scientific research in the field of placebo studies to better inform ethical evidence-based practice. We argue that, only by developing a rigorous evidence base can we better understand how, if at all, placebos/placebo effects can be harnessed ethically in clinical settings. (shrink)

An analysis of biological selection aimed at deriving a mechanism-independent definition removes Hull et al.'s obligatory requirement for replication of the carriers of information, under conditions, such as those obtaining in the nervous system, where the information content of a carrier can be modified without duplication by an amount controlled by the outcome of interactions with the environment.

. Scientists, for the most part, want to get it right. However, the social structures that govern their work undermine that aim, and this leads to nonreplicable findings in many fields. Because the social structure of science is a decentralized system, it is difficult to intervene. In this article, I discuss how we might do so, focusing on self-corrective-labor schemes. First, I argue that we need to implement a scheme that makes replication work outcome independent, systematic, and sustainable. (...) Second, I use these three criteria to evaluate extant proposals, which place the responsibility for replication on original researchers, consumers of their research, students, or many labs. Third, on the basis of a philosophical analysis of the reward system of science and the benefits of the division of cognitive labor, I propose a scheme that satisfies the criteria better: the professional scheme. This scheme has two main components. First, the scientific community is organized into two groups: discovery researchers, who produce new findings, and confirmation researchers, whose primary function is to do confirmation work. Second, a distinct reward system is established for confirmation researchers so that their career advancement is separated from whether they obtain positive experimental results. (shrink)

The dream-lag effect refers to there being, after the frequent incorporation of memory elements from the previous day into dreams , a lower incorporation of memory elements from 2 to 4 days before the dream, but then an increased incorporation of memory elements from 5 to 7 days before the dream. Participants kept a daily diary and a dream diary for 14 days and then rated the level of matching between every dream report and every daily diary record. Baseline matching (...) was assessed by comparing all dream reports to all diary records for days that occurred after the dream. A significant dream-lag effect for the 5–7 day period, compared to baseline and compared to the 2–4 day period, was found. This may indicate a memory processing function for sleep, which the dream content may reflect. Participants’ and three independent judges’ mean ratings also confirmed a significant day-residue effect. (shrink)

Building on Nozick's invariantism about objectivity, I propose to define scientific objectivity in terms of counterfactual independence. I will argue that such a counterfactual independence account is (a) able to overcome the decisive shortcomings of Nozick's original invariantism and (b) applicable to three paradigmatic kinds of scientific objectivity (that is, objectivity as replication, objectivity as robustness, and objectivity as Mertonian universalism).

Building on Nozick's invariantism about objectivity, I propose to define scientific objectivity in terms of counterfactual independence. I will argue that such a counterfactual independence account is (a) able to overcome the decisive shortcomings of Nozick's original invariantism and (b) applicable to three paradigmatic kinds of scientific objectivity (that is, objectivity as replication, objectivity as robustness, and objectivity as Mertonian universalism).

Diverse living systems possess the capacity for regeneration; that is, they can under some circumstances repair, re-produce, and maintain themselves in the face of disturbance or damage. Think of systems as diverse as forests, microbial biofilms, corals, salamanders, hydra, and human skin cells. This capacity is fundamental to life—without it, many biological systems would be too fragile to cope with stress and would frequently collapse—but because it is multiply realized in wildly different living systems at many scales, finding a common (...) understanding may seem futile, and in fact research has proceeded along independent lines. For example, the sciences of organismal regeneration and ecological regeneration appear to have little more than a nominal relationship. Progress towards unification can be made, we think, by turning to evolutionary theory, specifically by synthesizing recent discussions of the evolution of individuals versus collectives with older literature about replicators versus interactors. This allows us to provide a partial answer in response to MacCord and Maienschein’s call for “basic units and mechanisms” of regeneration, relevant when that process is “adaptive.” We argue that the basics of adaptive regeneration can be understood and generalized through a modification of David Hull’s replicator-interactor framework. (shrink)

Central sensitization refers to the increased responsiveness of nociceptive neurons in the central nervous system after repeated or sustained peripheral nociceptor activation. It is hypothesized to play a key role in the development of chronic pain. A hallmark of central sensitization is an increased sensitivity to noxious mechanical stimuli extending beyond the injured location, known as secondary hyperalgesia. For its ability to modulate the transmission and the processing of nociceptive inputs, attention could constitute a promising target to prevent central sensitization (...) and the development of chronic pain. It was recently shown that the experimental induction of central sensitization at both forearms of healthy volunteers using bilateral high-frequency electrocutaneous stimulation (HFS), can be modulated by encouraging participants to selectively focus their attention to one arm, to the detriment of the other arm, resulting in a greater secondary hyperalgesia on the attended arm as compared to the unattended one. Given the potential value of the question being addressed, we conducted a preregistered replication study in a well-powered independent sample to assess the robustness of the effect, i.e., the modulatory role of spatial attention on the induction of central sensitization. This hypothesis was tested using a double-blind, within-subject design. Sixty-seven healthy volunteers performed a task that required focusing attention toward one forearm to discriminate innocuous vibrotactile stimuli while HFS was applied on both forearms simultaneously. Our results showed a significant increase in mechanical sensitivity directly and 20 min after HFS. However, in contrast to the previous study, we did not find a significant difference in the development of secondary hyperalgesia between the attended vs. unattended arms. Our results question whether spatial selective attention affects the development of secondary hyperalgesia. Alternatively, the non-replication could be because the bottom-up capture of attention caused by the HFS-mediated sensation was too strong in comparison to the top-down modulation exerted by the attentional task. In other words, the task was not engaging enough and the HFS pulses, including those on the unattended arm, were too salient to allow a selective focus on one arm and modulate nociceptive processing. (shrink)

Polycomb group (PcG) proteins maintain the expression state of PcG‐responsive genes during development of multicellular organisms. Recent observations suggest that “the H3K27me3 modification” acts to maintain Polycomb repressive complex (PRC) 2, the enzyme that creates this modification, on replicating chromatin. This could in turn promote propagation of H3K27me3 on newly replicated daughter chromatin, and promote recruitment of PRC1. Other work suggests that PRC1‐class complexes can be maintained on replicating chromatin, at least in vitro, independently of H3K27me3. Thus, histone modifications and (...) PcG proteins themselves may both be maintained through replication. (shrink)

The dominant assumption about the causal architecture of the mind is, that it is composed of a stable set of components that contribute independently to relevant observables that are employed to measure cognitive activity. This view has been called component-dominant dynamics. An alternative has been proposed, according to which the different components are not independent, but fundamentally interdependent, and are not stable basic properties of the mind, but rather an emergent feature of the mind given a particular task context. (...) This view has been called interaction-dominant dynamics. In this paper, we review evidence for interaction-dominant dynamics as the causal architecture of the mind. We point out, that such an architecture is consistent with problems of convergence in research on the level of results and theorizing. Moreover, we point out that if interaction-dominant dynamics as the causal architecture of the mind were to be true, this would naturally lead to problems with generalization and replicability in sciences of the mind and brain, and would probably warrant changes in the scientific practice with regard to study-design and data analysis. (shrink)

Unlike the most well‐characterized prokaryotic polymerase, E. Coli DNA pol I, none of the eukaryotic polymerases have their own 5′ to 3′ exonuclease domain for nick translation and Okazaki fragment processing. In eukaryotes, FEN‐1 is an endo‐and exonuclease that carries out this function independently of the polymerase molecules. Only seven nucleases have been cloned from multicellular eukaryotic cells. Among these, FEN‐1 is intriguing because it has complex structural preferences; specifically, it cleaves at branched DNA structures. The cloning of FEN‐1 permitted (...) establishment of the first eukaryotic nuclease family, predicting that S. cerevisiae RAD2 (S. pombe Rad13) and its mammalian homolog, XPG, would have similar structural specficity. The FEN‐1 nuclease family includes several similar enzymes encoded by bacteriophages. The crystal structures of two enzymes in the FEN‐1 nuclease family have been solved and they provide a structural basis for the interesting steric requirements of FEN‐1 substrates. Because of their unique structural specificities, FEN‐1 and its family members have important roles in DNA replication, repair and, potentially, recombination. Recently, FEN‐1 was found to specifically associate with PCNA, explaining some aspects of FEN‐1 function during DNA replication and potentially in DNA repair. (shrink)

Past research has found a strong and positive association between the independent self-construal and life satisfaction, mediated through self-esteem, in both individualistic and collectivistic cultures. In Study 1, we collected data from four countries and replicated these findings in cultures which have received little attention in past research. In Study 2, we treated independence as a multifaceted construct and further examined its relationship with self-esteem and life satisfaction using samples from the United States and Romania. Different ways of being (...) independent are associated with self-esteem and life satisfaction in the two cultures, suggesting that it is not independence as a global concept that predicts self-esteem and life satisfaction, but rather, feeling independent in culturally appropriate ways is a signal that one’s way of being fits in and is valued in one’s context. (shrink)

Humans preferentially remember information processed for their survival relevance, a memorial benefit known as the survival processing effect. Memory is also biased towards information associated with the prospect of reward. Given the adaptiveness of these effects, they may depend on similar mechanisms. We tested whether motivation drives both effects, with reward incentives that are known to boost extrinsic motivation and survival processing perhaps stimulating intrinsic motivation. Accordingly, we manipulated survival processing and reward incentive independently during an incidental-encoding task in which (...) participants chose between pairs of words concerning their relevance for a scenario, and examined the effects on encoding event-related potentials activity and later performance on a surprise recall test. We hypothesized that if survival processing fosters intrinsic motivation, it should reduce the beneficial effects of extrinsic motivation. In contrast to this prediction, we found that reward incentive and survival processing independently improved memory and that the P300, a measure of lower-level cognitive resource allocation, was increased by reward incentive independent of survival processing. Further, survival processing and reward incentive independently increased the frontal slow wave, a measure of higher-level elaboration. These findings suggest that while survival processing and reward incentive may both increase encoding elaboration, the memory-enhancing effect of survival processing does not depend on increased intrinsic motivation. Additionally, we replicated a recent finding whereby the survival processing effect generalizes to a choice-based encoding task and further showed that the beneficial effect of choice on memory likely does not interact with either survival processing or reward. (shrink)

Mitochondrial DNA (mtDNA) mutations escalate with increasing age in higher organisms. However, it has so far been difficult to experimentally determine whether mtDNA mutation merely correlates with age or directly limits lifespan. A recent study shows that budding yeast can also lose functional mtDNA late in life. Interestingly, independent studies of replicative lifespan (RLS) and of mtDNA‐deficient cells show that the same mutations can increase both RLS and the division rate of yeast lacking the mitochondrial genome. These exciting, parallel (...) findings imply a potential causal relationship between mtDNA mutation and replicative senescence. Furthermore, these results suggest more efficient methods for discovering genes that determine lifespan. (shrink)

ObjectiveEfforts to understand why some marriages thrive while others falter are not well integrated conceptually and rely heavily on data collected from White middle-class samples. The Vulnerability-Stress-Adaptation Model is used here to integrate prior efforts and is tested using data collected from couples living with low incomes.BackgroundThe VSA Model assumes that enduring vulnerabilities, stress, and couple communication account for unique variance in relationship satisfaction, that communication mediates the effects of vulnerabilities and stress on satisfaction, and that the predictors of satisfaction (...) generalize across socioeconomic levels. To date, these assumptions remain untested.Materials and methodsWith 388 couples from diverse backgrounds, we used latent variable structural equation models to examine enduring vulnerabilities, chronic stress, and observed communication as predictors of 4-wave, 27-month satisfaction trajectories, first as main effects and then interacting with a validated 10-item index of sociodemographic risk.Results The three variable sets independently predict satisfaction trajectories; couple communication does not mediate the effects of enduring vulnerabilities or stress on satisfaction; and in 19% of tests, effects were stronger among couples with higher sociodemographic risk.ConclusionEffects of established predictor domains on satisfaction replicate in a diverse sample of newlywed couples, and most findings generalize across levels of sociodemographic risk. The failure of couple communication to mediate effects of enduring personal vulnerabilities and stress raises new questions about how these two domains undermine committed partnerships. (shrink)

In postmitotic neurons, nucleosomal turnover was long considered to be a static process that is inconsequential to transcription. However, our recent studies in human and rodent brain indicate that replication‐independent (RI) nucleosomal turnover, which requires the histone variant H3.3, is dynamic throughout life and is necessary for activity‐dependent gene expression, synaptic connectivity, and cognition. H3.3 turnover also facilitates cellular lineage specification and plays a role in suppressing the expression of heterochromatic repetitive elements, including mutagenic transposable sequences, in mouse (...) embryonic stem cells. In this essay, we review mechanisms and functions for RI nucleosomal turnover in brain and present the hypothesis that defects in histone dynamics may represent a common mechanism underlying neurological aging and disease. -/- . (shrink)

In many species the mutation rate is higher in males than in females, a phenomenon denoted as male mutation bias. This is often observed in animals where males produce many more sperm than females produce eggs, and is thought to result from differences in the number of replication‐associated mutations accumulated in each sex. Thus, studies of male mutation bias have the capacity to reveal information about the replication‐dependent or replication‐independent nature of different mutations. The availability of (...) whole genome sequences for many species, as well as for multiple individuals within a species, has opened the door to studying factors, both sequence‐specific and those acting on the genome globally, that affect differences in mutation rates between males and females. Here, we assess the advantages that genomic sequences provide for studies of male mutation bias and general mutation mechanisms, discuss major challenges left unresolved, and speculate about the direction of future studies. (shrink)

Histone H3.3 turnover displays distinct dynamics at various genomic elements such as promoters, enhancers, gene bodies, and heterochromatic regions, suggesting that it is differentially regulated according to chromatin context. Incorporation of variant histones into chromatin provides a mechanism to modulate chromatin states in addition to histone modifications. The replication‐independent deposition and replacement of histone variant H3.3, i.e. H3.3 turnover, is mainly associated with transcriptional activity. H3.3 or H3.3‐like histone turnover has been studied in various organisms from yeast to (...) mammals. Here, we review the recent progress on this topic. The diversified turnover profiles of H3.3, and their corresponding underlying mechanisms, may reflect distinct requirements for chromatin accessibility in different biological events. (shrink)

This chapter examines five emulation methods, drawing a distinction between structure replication and reconstruction (SR) methods, and reverse brain engineering (RBE) methods. It argues that we need reasons to claim a particular procedure does or does not maintain identity, independently of whether the procedure is destructive or nondestructive. The chapter proposes that whole brain emulation (WBE) research be aimed primarily at cybernetics and possibility of replacing a biological brain in steps that involve very small parts with no psychologically relevant (...) structure. It also argues that methods reliant on structure replication and reconstruction will not preserve personal identity, based on a neo‐Lockean definition of personal identity according to which the self is a relatively autonomous self‐perpetuating substance whose psychological continuity through time is ensured primarily by immanent causation. All SR methods involve too much transeunt causation. (shrink)

Conventional sacrificial moral dilemmas propose directly causing some harm to prevent greater harm. Theory suggests that accepting such actions (consistent with utilitarian philosophy) involves more reflective reasoning than rejecting such actions (consistent with deontological philosophy). However, past findings do not always replicate, confound different kinds of reflection, and employ conventional sacrificial dilemmas that treat utilitarian and deontological considerations as opposite. In two studies, we examined whether past findings would replicate when employing process dissociation to assess deontological and utilitarian inclinations independently. (...) Findings suggested two categorically different impacts of reflection: measures of arithmetic reflection, such as the Cognitive Reflection Test, predicted only utilitarian, not deontological, response tendencies. However, measures of logical reflection, such as performance on logical syllogisms, positively predicted both utilitarian and deontological tendencies. These studies replicate some findings, clarify others, and reveal opportunity for additional nuance in dual process theorist’s claims about the link between reflection and dilemma judgments. (shrink)

Transcription and replication of genes in mammalian cells always requires a promoter or replication origin, respectively, but the ability of enhancers to stimulate these regulatory elements and the interactions that mediate this stimulation are developmentally acquired. The primary function of enhancers is to prevent repression, which appears to result from particular components of chromatin structure. Factors responsible for this repression are present in the maternal nucleus of oocytes and its descendant, the maternal pronucleus of mouse 1‐cell embryos and (...) in mouse 2‐cell embryos, but are absent in the paternal pronucleus. Thus, enhancers are not needed to achieve efficient transcription and replication in paternal pronuclei. However, enhancers, even in the presence of their specific activation protein, are inactive prior to formation of a 2‐cell embryo, suggesting that a coactivator essential for enhancer function is not available until zygotic gene expression begins. Furthermore, enhancer stimulation of transcription appears to be mediated through a promoter transcription factor, but this interaction can change as cells undergo differentiation, switching from a TATA‐box independent to a TATA‐box dependent mode. (shrink)

In the context of discovery-oriented hypothesis testing research, behavioral scientists widely accept a convention for false positive (α) and false negative error rates (β) proposed by Jacob Cohen, who deemed the general relative seriousness of the antecedently accepted α = 0.05 to be matched by β = 0.20. Cohen’s convention not only ignores contexts of hypothesis testing where the more serious error is the β-error. Cohen’s convention also implies for discovery-oriented hypothesis testing research that a statistically significant observed effect is (...) four times more probable to be a mistaken discovery than for a statistically significant true observed effect to be independently replicable. In the long run, Cohen’s convention thus is epistemically harmful to the development of a progressive science of human behavior, making its acceptance crucial in explaining the replication crisis in behavioral science. The balance between α- and β-errors generally ought to be struck using both epistemic and practical considerations. Yet epistemic considerations alone imply that making a genuine contribution to the body of knowledge in behavioral science requires error rates that are not only small but also symmetrical. (shrink)

The visual attention (VA) span is defined as the amount of distinct visual elements which can be processed in parallel in a multi-element array. Both recent empirical data and theoretical accounts suggest that a VA span deficit might contribute to developmental dyslexia, independently of a phonological disorder. In this study, this hypothesis was assessed in two large samples of French and British dyslexic children whose performance was compared to that of chronological-age matched control children. Results of the French study show (...) that the VA span capacities account for a substantial amount of unique variance in reading, as do phonological skills. The British study replicates this finding and further reveals that the contribution of the VA span to reading performance remains even after controlling IQ, verbal fluency, vocabulary and single letter identification skills, in addition to phoneme awareness. In both studies, most dyslexic children exhibit a selective phonological or VA span disorder. Overall, these findings support a multi-factorial view of developmental dyslexia. In many cases, developmental reading disorders do not seem to be due to phonological disorders. We propose that a VA span deficit is a likely alternative underlying cognitive deficit in dyslexia. (shrink)

Observational learning can enhance the acquisition and performance quality of complex motor skills. While an extensive body of research has focused on the benefits of synchronous (i.e., concurrent physical practice) and non-synchronous (i.e., delayed physical practice) observational learning strategies, the question remains as to whether these approaches differentially influence performance outcomes. Accordingly, we investigate the differential outcomes of synchronous and non-synchronous observational training contexts using a novel dance sequence. Using multidimensional cross-recurrence quantification analysis, movement time-series were recorded for novice dancers (...) who either synchronised with (n = 22) or observed and then imitated (n = 20) an expert dancer. Participants performed a 16-count choreographed dance sequence for 20 trials assisted by the expert, followed by one final, unassisted performance trial. Although end-state performance did not significantly differ between synchronous and non-synchronous learners, a significant decline in performance quality from imitation to independent replication was shown for synchronous learners. A non-significant positive trend in performance accuracy was shown for non-synchronous learners. For all participants, better imitative performance across training trials led to better end-state performance, but only for the accuracy (and not timing) of movement reproduction. Collectively, the results suggest that synchronous learners came to rely on a realtime mapping process between visual input from the expert and their own visual and proprioceptive intrinsic feedback, to the detriment of learning. Thus, the act of synchronising alone does not ensure an appropriate training context for advanced sequence learning. (shrink)

The article analyses in detail the Meselson–Stahl experiment, identifying two novel difficulties for the crucial experiment account, namely, the fragility of the experimental results and the fact that the hypotheses under scrutiny were not mutually exclusive. The crucial experiment account is rejected in favour of an experimental-mechanistic account of the historical significance of the experiment, emphasizing that the experiment generated data about the biochemistry of DNA replication that is independent of the testing of the semi-conservative, conservative, and dispersive (...) hypotheses. _1_ Introduction _2_ The Meselson–Stahl Experiment _3_ Some Difficulties for the Crucial Experiment Account _3.1_ Additional experiments were required _3.2_ Simplicity considerations are unconvincing _3.3_ The fragility of the experimental results _3.4_ The problematic interpretation of falsifyng results _3.5_ Not all possible hypotheses considered or tested _3.6_ The tested hypotheses were not mutually exclusive _4_ The Historical and Scientific Significance of the Meselson–Stahl Experiment _4.1_ The challenge for the crucial experiment account _4.2_ A mechanistic perspective on the experiment _4.3_ The experimental design and its independence from theoretical speculations _4.4_ The advantages of a ‘bottom-up’ mechanistic account _5_ Conclusion. (shrink)

The organism is one of the fundamental concepts of biology and has been at the center of many discussions about biological individuality, yet what exactly it is can be confusing. The definition that we find generally useful is that an organism is a unit in which all the subunits have evolved to be highly cooperative, with very little conflict. We focus on how often organisms evolve from two or more formerly independent organisms. Two canonical transitions of this type—replicators clustered (...) in cells and endosymbiotic organelles within host cells—demonstrate the reality of this kind of evolutionary transition and suggest conditions that can favor it. These conditions include co-transmission of the partners across generations and rules that strongly regulate and limit conflict, such as a fair meiosis. Recently, much attention has been given to associations of animals with microbes involved in their nutrition. These range from tight endosymbiotic associations like those between aphids and Buchnera bacteria, to the complex communities in animal intestines. Here, starting with a reflection about identity through time, we consider the distinctions between these kinds of animal–bacteria interactions and describe the criteria by which a few can be considered jointly organismal but most cannot. (shrink)

The ‘psychologist’s green thumb’ refers to the argument that an experimenter needs an indeterminate set of skills to successfully replicate an effect. This argument is sometimes invoked by psychological researchers to explain away failures of independent replication attempts of their work. In this paper, I assess the psychologist’s green thumb as a candidate explanation for individual replication failure and argue that it is potentially costly for psychology as a field. I also present other, more likely reasons for (...) these replication failures. I conclude that appealing to a psychologist’s green thumb is not a convincing explanation for replication failure. (shrink)

Objective Manic and depressive phases of bipolar disorder (BD) show opposite psychomotor symptoms. Neuronally, these may depend on altered relationships between sensorimotor network (SMN) and subcortical structures. The study aimed to investigate the functional relationships of SMN with substantia nigra (SN) and raphe nuclei (RN) via subcortical-cortical loops, and their alteration in bipolar mania and depression, as characterized by psychomotor excitation and inhibition. -/- Method In this resting-state functional magnetic resonance imaging (fMRI) study on healthy (n = 67) and BD (...) patients (n = 100), (1) functional connectivity (FC) between thalamus and SMN was calculated and correlated with FC from SN or RN to basal ganglia (BG)/thalamus in healthy; (2) using an a-priori-driven approach, thalamus-SMN FC, SN-BG/thalamus FC, and RN-BG/thalamus FC were compared between healthy and BD, focusing on manic (n = 34) and inhibited depressed (n = 21) patients. -/- Results (1) In healthy, the thalamus-SMN FC showed a quadratic correlation with SN-BG/thalamus FC and a linear negative correlation with RN-BG/thalamus FC. Accordingly, the SN-related FC appears to enable the thalamus-SMN coupling, while the RN-related FC affects it favoring anti-correlation. (2) In BD, mania showed an increase in thalamus-SMN FC toward positive values (ie, thalamus-SMN abnormal coupling) paralleled by reduction of RN-BG/thalamus FC. By contrast, inhibited depression showed a decrease in thalamus-SMN FC toward around-zero values (ie, thalamus-SMN disconnection) paralleled by reduction of SN-BG/thalamus FC (and RN-BG/thalamus FC). The results were replicated in independent HC and BD datasets. -/- Conclusions These findings suggest an abnormal relationship of SMN with neurotransmitters-related areas via subcortical-cortical loops in mania and inhibited depression, finally resulting in psychomotor alterations. (shrink)

What counts as human rationality: reasoning processes that embody content-independent formal theories, such as propositional logic, or reasoning processes that are well designed for solving important adaptive problems? Most theories of human reasoning have been based on content-independent formal rationality, whereas adaptive reasoning, ecological or evolutionary, has been little explored. We elaborate and test an evolutionary approach, Cosmides' social contract theory, using the Wason selection task. In the first part, we disentangle the theoretical concept of a “social contract” (...) from that of a “cheater-detection algorithm”. We demonstrate that the fact that a rule is perceived as a social contract — or a conditional permission or obligation, as Cheng and Holyoak proposed — is not sufficient to elicit Cosmides' striking results, which we replicated. The crucial issue is not semantic, but pragmatic: whether a person is cued into the perspective of a party who can be cheated. In the second part, we distinguish between social contracts with bilateral and unilateral cheating options. Perspective change in contracts with bilateral cheating options turns P & not-Q responses into not-P & Q responses. The results strongly support social contract theory, contradict availability theory, and cannot be accounted for by pragmatic reasoning schema theory, which lacks the pragmatic concepts of perspectives and cheating detection. (shrink)

This paper examines the process of modelling a complex empirical phenomenon in modern astrophysics: extended extragalactic radio sources. I show that modelling is done piecemeal, addressing selected striking or puzzling features of that phenomenon separately and individually. The result is various independent and separate sub-models concerned only with limited aspects of the same phenomenon. Because the sub-models represent features of the same physical phenomenon, they need to be reasonably consistent with each other - a criterion not always fully adhered (...) to - and there needs to be a way to conceptually `re-unite' the sub-models to form an overall-model. Visualisation, that is, supplying a concrete interpretation of abstract, theoretical sub-models, aids this modelling process. My case study further endorses the view that modelling is `work in progress', i.e. a form of developing knowledge whereby models represent, not replicate, a phenomenon. (shrink)

We present a theoretical rationale and supporting studies revealing how unethical leader behavior fosters an unethical climate within workgroups that increases member turnover intentions and malfeasance. Drawing on the attraction–selection–attrition model of organizational behavior, we propose a selective attrition effect whereby unethical leader behavior results in the retention of group members who are more comfortable with dishonesty and, consequently, more likely to engage in unethical behavior toward their group. In two experiments, exposure to unethical leader behavior increased group members’ likelihood (...) of choosing to leave the group. Members who chose to remain in a group with an unethical leader were more likely than those who chose to leave to cheat their group in a subsequent task. A two time-period survey replicated these findings and identified psychological distress as the mechanism driving group members’ turnover intentions. This research extends our understanding of the complex relationships between unethical leadership and follower turnover intentions, psychological distress, and malfeasance. We contribute to the behavioral ethics literature by identifying a previously underappreciated form of selective attrition that produces internal costs to groups and organizations, independent of reputational consequences and whether the unethicality is publicized. (shrink)

A general case about the insights and oversights of molecular genetics is argued for by considering two specific cases: the first concerns the bearing of molecular genetics on Mendelian genetics, and the second concerns the bearing of molecular genetics on the replicability of the genetic material. As in the first case, it is argued that Mendel's law of segregation cannot be explained wholly in terms of molecular genetics--the law demands evolutionary scrutiny as well. In the second case, it is argued (...) that an account of the replicability of the genetic material in terms of molecular genetics is not entirely independent of evolutionary considerations, in the sense that it raises further evolutionary questions. The limitations of the molecular-genetic approach in these cases point to the limitations of that approach in general. (shrink)

Stable adaptive strategy of Homo sapiens (SASH) is a result of the integration in the three-module fractal adaptations based on three independent processes of generation, replication, and the implementation of adaptations — genetic, socio-cultural and symbolic ones. The evolutionary landscape SASH is a topos of several evolutionary multi-dimensional vectors: 1) extraversional projective-activity behavioral intention (adaptive inversion 1), 2) mimesis (socio-cultural inheritance), 3) social (Machiavellian) intelligence, 4) the extension of inter-individual communication beyond their own social groups and their own (...) species in the rest of the world, 5) the symbolic system of communication (symbolic inheritance), 6) spiritualistic trans- formation of emotionally-shaped components of mentality, 7) the dominance of the rationalist thought mentality (enhancer of adaptive inverse 1), 8) a recursive distribution of projective-activity intentions on the man himself his genome, psyche and culture (Adaptive Inversion 2), 9) introversional reorientation of the vector of cognitive activity (adaptive inversion 3). (shrink)

A central debate in the cognitive sciences surrounds the nature of adult speakers' linguistic representations: Are they purely syntactic (a traditional and widely held view; e.g., Branigan & Pickering, ), or are they semantically structured? A recent study (Ambridge, Bidgood, Pine, Rowland, & Freudenthal, ) found support for the latter view, showing that adults' acceptability judgments of passive sentences were significantly predicted by independent semantic “affectedness” ratings designed to capture the putative semantics of the construction (e.g., Bob was pushed (...) by Wendy is rated as more acceptable than Bob was liked by Wendy, as Bob is more affected in the former). However, because English lacks a separate topicalization construction which provides an alternative means of highlighting the patient (e.g., BOB, Wendy kicked), these findings have a possible alternative explanation: that highly affected entities are more likely to be topicalized, rather than passivized per se. Here we show that, in fact, Ambridge et al.'s () finding replicates in Indonesian, a language with a topicalization construction. The present study therefore provides particularly compelling evidence that grammatical representations have semantic structure. (shrink)

According to the variety of evidence thesis items of evidence from independent lines of investigation are more confirmatory, ceteris paribus, than, for example, replications of analogous studies. This thesis is known to fail (Bovens and Hartmann; Claveau). However, the results obtained by Bovens and Hartmann only concern instruments whose evidence is either fully random or perfectly reliable; instead, for Claveau, unreliability is modelled as deterministic bias. In both cases, the unreliable instrument delivers totally irrelevant information. We present a model (...) that formalizes both reliability and unreliability differently. Our instruments either are reliable, but affected by random error, or are biased but not deterministically so.Bovens and Hartmann’s results are counter-intuitive in that in their model a long series of consistent reports from the same instrument does not raise suspicion of ‘too-good-to-be-true’ evidence. This happens precisely because they contemplate neither the role of systematic bias, nor unavoidable random error of reliable instruments. In our model, the variety of evidence thesis fails as well, but the area of failure is considerably smaller than for Bovens and Hartmann and Claveau, and holds for (the majority of) realistic cases (that is, where biased instruments are very biased). The essential mechanism that triggers variety of evidence thesis failure is the rate of false to true positives for the two kinds of instruments. Our emphasis is on modelling beliefs about sources of knowledge and their role in hypothesis confirmation in interaction with dimensions of evidence, such as variety and consistency. (shrink)

Stable adaptive strategy of Homo sapiens (SESH) is a superposition of three different adaptive data arrays: biological, socio-cultural and technological modules, based on three independent processes of generation and replication of an adaptive information – genetic, socio-cultural and symbolic transmissions (inheritance). Third component SESH focused equally to the adaptive transformation of the environment and carrier of SESH. With the advent of High Hume technology, risk has reached the existential significance level. The existential level of technical risk is, by (...) definition, an evolutionary risk as possible leads to the genesis of disappearance of humanity as a species. The emergence of bioethics has to consider as a form of modern (transdisciplinary) scientific concept and sociocultural adaptation for regulate human identity in the global-evolutionary transformation and performs the function of self-preservation. (shrink)

Mutation and lateral transfer are two categories of processes generating genetic diversity in prokaryotic genomes. Their relative importance varies between lineages, yet both are complementary rather than independent, separable evolutionary forces. The replication process inevitably merges together their effects on the genome. We develop the concept of “open lineages” to characterize evolutionary lineages that over time accumulate more changes in their genomes by lateral transfer than by mutation. They contrast with “closed lineages,” in which most of the changes (...) are caused by mutation. Open and closed lineages are interspersed along the branches of any tree of prokaryotes. This patchy distribution conflicts with the basic assumptions of traditional phylogenetic approaches. As a result, a tree representation including both open and closed lineages is a misrepresentation. The evolution of all prokaryotic lineages cannot be studied under a single model unless new phylogenetic approaches that are more pluralistic about lineage evolution are designed. (shrink)

Ideals (or ideal values) help people to navigate in social life. They indicate at a very fundamental level what people are concerned about, what they strive for, and what they want to be affiliated with. Transferring this to a leader-follower analysis, our first study (n = 306) confirms that followers' identification and satisfaction with their leaders are stronger, the more leaders match followers' ideal leader values. Study 2 (n = 244) extends the perspective by introducing the novel concept of counterideals (...) (i. e., how an ideal leader should not be) as a second, non-redundant point of reference. Results confirm that a leader's match on ideal and on counter-ideal values have independent effects in that both explain unique variance in followers' identification and satisfaction with their leader. Study 3 (n = 136) replicates the previous results in an experimental scenario study and provides evidence for the proposed causal direction of the underlying process. We conclude that counter-ideal values might be an additional point of reference that people use to triangulate targets above and beyond ideal values and discuss the implications of our findings for value research and management. (shrink)