Comparing the Similarity of Responses Received from Studies in Amazon’s Mechanical Turk to Studies Conducted Online and with Direct Recruitment

Computer and internet based questionnaires have become a standard tool in Human-Computer Interaction research and other related fields, such as psychology and sociology. Amazon’s Mechanical Turk (AMT) service is a new method of recruiting participants and conducting certain types of experiments. This study compares whether participants recruited through AMT give different responses than participants recruited through an online forum or recruited directly on a university campus. Moreover, we compare whether a study conducted within AMT results in different responses compared to a study for which participants are recruited through AMT but which is conducted using an external online questionnaire service. The results of this study show that there is a statistical difference between results obtained from participants recruited through AMT compared to the results from the participant recruited on campus or through online forums. We do, however, argue that this difference is so small that it has no practical consequence. There was no significant difference between running the study within AMT compared to running it with an online questionnaire service. There was no significant difference between results obtained directly from within AMT compared to results obtained in the campus and online forum condition. This may suggest that AMT is a viable and economical option for recruiting participants and for conducting studies as setting up and running a study with AMT generally requires less effort and time compared to other frequently used methods. We discuss our findings as well as limitations of using AMT for empirical studies.     

Searching for the origins of musicality across species

In the introduction to this theme issue, Honing et al. suggest that the origins of musicality—the capacity that makes it possible for us to perceive, appreciate and produce music—can be pursued productively by searching for components of musicality in other species. Recent studies have highlighted that the behavioural relevance of stimuli to animals and the relation of experimental procedures to their natural behaviour can have a large impact on the type of results that can be obtained for a given species. Through reviewing laboratory findings on animal auditory perception and behaviour, as well as relevant findings on natural behaviour, we provide evidence that both traditional laboratory studies and studies relating to natural behaviour are needed to answer the problem of musicality. Traditional laboratory studies use synthetic stimuli that provide more control than more naturalistic studies, and are in many ways suitable to test the perceptual abilities of animals. However, naturalistic studies are essential to inform us as to what might constitute relevant stimuli and parameters to test with laboratory studies, or why we may or may not expect certain stimulus manipulations to be relevant. These two approaches are both vital in the comparative study of musicality.     

Evaluating Amazon's Mechanical Turk as a Tool for Experimental Behavioral Research

Amazon Mechanical Turk (AMT) is an online crowdsourcing service where anonymous online workers complete web-based tasks for small sums of money. The service has attracted attention from experimental psychologists interested in gathering human subject data more efficiently. However, relative to traditional laboratory studies, many aspects of the testing environment are not under the experimenter''s control. In this paper, we attempt to empirically evaluate the fidelity of the AMT system for use in cognitive behavioral experiments. These types of experiment differ from simple surveys in that they require multiple trials, sustained attention from participants, comprehension of complex instructions, and millisecond accuracy for response recording and stimulus presentation. We replicate a diverse body of tasks from experimental psychology including the Stroop, Switching, Flanker, Simon, Posner Cuing, attentional blink, subliminal priming, and category learning tasks using participants recruited using AMT. While most of replications were qualitatively successful and validated the approach of collecting data anonymously online using a web-browser, others revealed disparity between laboratory results and online results. A number of important lessons were encountered in the process of conducting these replications that should be of value to other researchers.     

Science vs Conspiracy: Collective Narratives in the Age of Misinformation

The large availability of user provided contents on online social media facilitates people aggregation around shared beliefs, interests, worldviews and narratives. In spite of the enthusiastic rhetoric about the so called collective intelligence unsubstantiated rumors and conspiracy theories—e.g., chemtrails, reptilians or the Illuminati—are pervasive in online social networks (OSN). In this work we study, on a sample of 1.2 million of individuals, how information related to very distinct narratives—i.e. main stream scientific and conspiracy news—are consumed and shape communities on Facebook. Our results show that polarized communities emerge around distinct types of contents and usual consumers of conspiracy news result to be more focused and self-contained on their specific contents. To test potential biases induced by the continued exposure to unsubstantiated rumors on users’ content selection, we conclude our analysis measuring how users respond to 4,709 troll information—i.e. parodistic and sarcastic imitation of conspiracy theories. We find that 77.92% of likes and 80.86% of comments are from users usually interacting with conspiracy stories.     

Language Universals Engage Broca's Area

It is well known that natural languages share certain aspects of their design. For example, across languages, syllables like blif are preferred to lbif. But whether language universals are myths or mentally active constraints—linguistic or otherwise—remains controversial. To address this question, we used fMRI to investigate brain response to four syllable types, arrayed on their linguistic well-formedness (e.g., blif≻bnif≻bdif≻lbif, where ≻ indicates preference). Results showed that syllable structure monotonically modulated hemodynamic response in Broca''s area, and its pattern mirrored participants'' behavioral preferences. In contrast, ill-formed syllables did not systematically tax sensorimotor regions—while such syllables engaged primary auditory cortex, they tended to deactivate (rather than engage) articulatory motor regions. The convergence between the cross-linguistic preferences and English participants'' hemodynamic and behavioral responses is remarkable given that most of these syllables are unattested in their language. We conclude that human brains encode broad restrictions on syllable structure.     

Effects of Edge Directions on the Structural Controllability of Complex Networks

Recent advances indicate that assigning or reversing edge direction can significantly improve the structural controllability of complex networks. For directed networks, approaching the optimal structural controllability can be achieved by detecting and reversing certain “inappropriate” edge directions. However, the existence of multiple sets of “inappropriate” edge directions suggests that different edges have different effects on optimal controllability—that is, different combinations of edges can be reversed to achieve the same structural controllability. Therefore, we classify edges into three categories based on their direction: critical, redundant and intermittent. We then investigate the effects of changing these edge directions on network controllability, and demonstrate that the existence of more critical edge directions implies not only a lower cost of modifying inappropriate edges but also better controllability. Motivated by this finding, we present a simple edge orientation method aimed at producing more critical edge directions—utilizing only local information—which achieves near optimal controllability. Furthermore, we explore the effects of edge direction on the controllability of several real networks.     

SARS-CoV-2 S2P spike ages through distinct states with altered immunogenicity

The SARS-CoV-2 spike is the primary target of virus-neutralizing antibodies and critical to the development of effective vaccines against COVID-19. Here, we demonstrate that the prefusion-stabilized two-proline “S2P” spike—widely employed for laboratory work and clinical studies—unfolds when stored at 4 °C, physiological pH, as observed by electron microscopy (EM) and differential scanning calorimetry, but that its trimeric, native-like conformation can be reacquired by low pH treatment. When stored for approximately 1 week, this unfolding does not significantly alter antigenic characteristics; however, longer storage diminishes antibody binding, and month-old spike elicits virtually no neutralization in mice despite inducing high ELISA-binding titers. Cryo-EM structures reveal the folded fraction of spike to decrease with aging; however, its structure remains largely similar, although with varying mobility of the receptor-binding domain. Thus, the SARS-CoV-2 spike is susceptible to unfolding, which affects immunogenicity, highlighting the need to monitor its integrity.     

The performance of field sampling for parasite detection in a wild passerine

Parasites can impact the behavior of animals and alter the interplay with ecological factors in their environment. Studying the effects that parasites have on animals thus requires accurate estimates of infections in individuals. However, quantifying parasites can be challenging due to several factors. Laboratory techniques, physiological fluctuations, methodological constraints, and environmental influences can introduce measurement errors, in particular when screening individuals in the wild. These issues are pervasive in ecological studies where it is common to sample study subjects only once. Such factors should be carefully considered when choosing a sampling strategy, yet presently there is little guidance covering the major sources of error. In this study, we estimate the reliability and sensitivity of different sampling practices at detecting two internal parasites—Serratospiculoides amaculata and Isospora sp.—in a model organism, the great tit Parus major. We combine field and captive sampling to assess whether individual parasite infection status and load can be estimated from single field samples, using different laboratory techniques—McMaster and mini‐FLOTAC. We test whether they vary in their performance, and quantify how sample processing affects parasite detection rates. We found that single field samples had elevated rates of false negatives. By contrast, samples collected from captivity over 24 h were highly reliable (few false negatives) and accurate (repeatable in the intensity of infection). In terms of methods, we found that the McMaster technique provided more repeatable estimates than the mini‐FLOTAC for S. amaculata eggs, and both techniques were largely equally suitable for Isospora oocysts. Our study shows that field samples are likely to be unreliable in accurately detecting the presence of parasites and, in particular, for estimating parasite loads in songbirds. We highlight important considerations for those designing host–parasite studies in captive or wild systems giving guidance that can help select suitable methods, minimize biases, and acknowledge possible limitations.     

Diversifying Carotenoid Biosynthetic Pathways by Directed Evolution

Microorganisms and plants synthesize a diverse array of natural products, many of which have proven indispensable to human health and well-being. Although many thousands of these have been characterized, the space of possible natural products—those that could be made biosynthetically—remains largely unexplored. For decades, this space has largely been the domain of chemists, who have synthesized scores of natural product analogs and have found many with improved or novel functions. New natural products have also been made in recombinant organisms, via engineered biosynthetic pathways. Recently, methods inspired by natural evolution have begun to be applied to the search for new natural products. These methods force pathways to evolve in convenient laboratory organisms, where the products of new pathways can be identified and characterized in high-throughput screening programs. Carotenoid biosynthetic pathways have served as a convenient experimental system with which to demonstrate these ideas. Researchers have mixed, matched, and mutated carotenoid biosynthetic enzymes and screened libraries of these “evolved” pathways for the emergence of new carotenoid products. This has led to dozens of new pathway products not previously known to be made by the assembled enzymes. These new products include whole families of carotenoids built from backbones not found in nature. This review details the strategies and specific methods that have been employed to generate new carotenoid biosynthetic pathways in the laboratory. The potential application of laboratory evolution to other biosynthetic pathways is also discussed.     

Drosophila Food-Associated Pheromones: Effect of Experience,Genotype and Antibiotics on Larval Behavior

Animals ubiquitously use chemical signals to communicate many aspects of their social life. These chemical signals often consist of environmental cues mixed with species-specific signals—pheromones—emitted by conspecifics. During their life, insects can use pheromones to aggregate, disperse, choose a mate, or find the most suitable food source on which to lay eggs. Before pupariation, larvae of several Drosophila species migrate to food sources depending on their composition and the presence of pheromones. Some pheromones derive from microbiota gut activity and these food-associated cues can enhance larval attraction or repulsion. To explore the mechanisms underlying the preference (attraction/repulsion) to these cues and clarify their effect, we manipulated factors potentially involved in larval response. In particular, we found that the (i) early exposure to conspecifics, (ii) genotype, and (iii) antibiotic treatment changed D. melanogaster larval behavior. Generally, larvae—tested either individually or in groups—strongly avoided food processed by other larvae. Compared to previous reports on larval attractive pheromones, our data suggest that such attractive effects are largely masked by food-associated compounds eliciting larval aversion. The antagonistic effect of attractive vs. aversive compounds could modulate larval choice of a pupariation site and impact the dispersion of individuals in nature.     

The emergence of consciousness: Research on animals yields insights into how,when and why consciousness evolved

Whether some animal species possess consciousness is no longer the question; rather how their environment and evolution shaped species‐specific forms of self‐awareness Subject Categories: Ecology, Neuroscience

Ever since humans acknowledged consciousness in themselves, they speculated whether animals could have a similar sentience or awareness of their internal and external existence. But although human philosophers had pondered on consciousness for centuries, it was not until 1927 when the American psychologist Harvey Carr laid the foundations for research on animal consciousness. He argued that awareness in animals could be only understood and measured when we had developed “an accurate and complete knowledge of its essential conditions in man” (Carr, 1927).This may have provided a springboard for the field, but a definition of the essential conditions of consciousness in Homo sapiens has proved elusive to this day—hence, research on animal consciousness has struggled to achieve a sound basis for formulating and evaluating testable hypotheses. However, there has been some progress in developing correlates of human consciousness that can be applied to study animals, while brain scanning and imaging has recently allowed comparative studies of human and animal neurological activity while performing mental tasks. It has also become possible to observe animal behaviour and communication in much greater depth and identify examples of activities—such as advance planning, or recognition of individuals through their vocalization—that can be associated with human consciousness. Overall, there is a growing consensus that this research has moved beyond merely questioning whether animals can be conscious or aware of themselves to defining different dimensions along which this can be assessed.

… research has moved beyond merely questioning whether animals can be conscious or aware of themselves to defining different dimensions along which this can be assessed.

     

Proportionality: A Valid Alternative to Correlation for Relative Data

In the life sciences, many measurement methods yield only the relative abundances of different components in a sample. With such relative—or compositional—data, differential expression needs careful interpretation, and correlation—a statistical workhorse for analyzing pairwise relationships—is an inappropriate measure of association. Using yeast gene expression data we show how correlation can be misleading and present proportionality as a valid alternative for relative data. We show how the strength of proportionality between two variables can be meaningfully and interpretably described by a new statistic ϕ which can be used instead of correlation as the basis of familiar analyses and visualisation methods, including co-expression networks and clustered heatmaps. While the main aim of this study is to present proportionality as a means to analyse relative data, it also raises intriguing questions about the molecular mechanisms underlying the proportional regulation of a range of yeast genes.     

Eliminating accidental deviations to minimize generalization error and maximize replicability: Applications in connectomics and genomics

Replicability, the ability to replicate scientific findings, is a prerequisite for scientific discovery and clinical utility. Troublingly, we are in the midst of a replicability crisis. A key to replicability is that multiple measurements of the same item (e.g., experimental sample or clinical participant) under fixed experimental constraints are relatively similar to one another. Thus, statistics that quantify the relative contributions of accidental deviations—such as measurement error—as compared to systematic deviations—such as individual differences—are critical. We demonstrate that existing replicability statistics, such as intra-class correlation coefficient and fingerprinting, fail to adequately differentiate between accidental and systematic deviations in very simple settings. We therefore propose a novel statistic, discriminability, which quantifies the degree to which an individual’s samples are relatively similar to one another, without restricting the data to be univariate, Gaussian, or even Euclidean. Using this statistic, we introduce the possibility of optimizing experimental design via increasing discriminability and prove that optimizing discriminability improves performance bounds in subsequent inference tasks. In extensive simulated and real datasets (focusing on brain imaging and demonstrating on genomics), only optimizing data discriminability improves performance on all subsequent inference tasks for each dataset. We therefore suggest that designing experiments and analyses to optimize discriminability may be a crucial step in solving the replicability crisis, and more generally, mitigating accidental measurement error.     

Entrainment of Lemna CO(2) Output Through Phytochrome

The entrainability of Lemna perpusilla CO₂ output by periodic 15 minute red (R) and far red (F) illuminations was tested in low nitrate medium. R every 8 hour, symbolized R/R/R, gives a flat output (no entrainment) as does F/F/F. However, R/—/— (R every 24 hour) entrains rapidly, and F/—/— does so as well, in a similar manner. The effects of R/R/— and F/F/— also resemble each other closely. Entrainment by R/F/F or R/R/F is rapid and indifferent to order of presentation, e.g., R/F/F and F/R/F lead to the same steady state. Typical phytochrome reversals occur, e.g., R,F/F/F holds output flat, while F,R/F/F entrains in the manner of R/F/F. Blue (B) light acts like R in schedules such as B/F/F but like F in schedules such as B/R/R. In all schedules studied, the zeitgeber (primary synchronizer) appears to be the sharpest transition from a low to a high level of far red-absorbing phytochrome that occurs with a 24-hr periodicity. Thus in entrainment, and by inference in photoperiodic timing, the level of far red-absorbing phytochrome at any time may be less significant than the succession of levels of which it is a part, a conclusion that implies the existence of a “scanning” mechanism that compares levels of far red-absorbing phytochrome at various times of day.     

Phase separation by the SARS-CoV-2 nucleocapsid protein: Consensus and open questions

In response to the recent SARS-CoV-2 pandemic, a number of labs across the world have reallocated their time and resources to better our understanding of the virus. For some viruses, including SARS-CoV-2, viral proteins can undergo phase separation: a biophysical process often related to the partitioning of protein and RNA into membraneless organelles in vivo. In this review, we discuss emerging observations of phase separation by the SARS-CoV-2 nucleocapsid (N) protein—an essential viral protein required for viral replication—and the possible in vivo functions that have been proposed for N-protein phase separation, including viral replication, viral genomic RNA packaging, and modulation of host-cell response to infection. Additionally, since a relatively large number of studies examining SARS-CoV-2 N-protein phase separation have been published in a short span of time, we take advantage of this situation to compare results from similar experiments across studies. Our evaluation highlights potential strengths and pitfalls of drawing conclusions from a single set of experiments, as well as the value of publishing overlapping scientific observations performed simultaneously by multiple labs.     

Historical Divergence and Gene Flow in the Genus Zea

Gene flow plays a fundamental role in plant evolutionary history, yet its role in population divergence—and ultimately speciation—remains poorly understood. We investigated gene flow and the modalities of divergence in the domesticate Zea mays ssp. mays and three wild Zea taxa using sequence polymorphism data from 26 nuclear loci. We described diversity across loci and assessed evidence for adaptive and purifying selection at nonsynonymous sites. For each of three divergence events in the history of these taxa, we used approximate Bayesian simulation to estimate population sizes and divergence times and explicitly compare among alternative models of divergence. Our estimates of divergence times are surprisingly consistent with previous data from other markers and suggest rapid diversification of lineages within Zea in the last ~150,000 years. We found widespread evidence of historical gene flow, including evidence for divergence in the face of gene flow. We speculate that cultivated maize may serve as a bridge for gene flow among otherwise allopatric wild taxa.     

The Use of Duplication-Generating Rearrangements for Studying Heterokaryon Incompatibility Genes in Neurospora

Heterokaryon (vegetative) incompatibility, governing the fusion of somatic hyphal filaments to form stable heterokaryons, is of interest because of its widespread occurrence in fungi and its bearing on cellular recognition. Conventional investigations of the genetic basis of heterokaryon incompatibility in N. crassa are difficult because in commonly used stocks differences are present at several het loci, all with similar incompatibility phenotypes. This difficulty is overcome by using duplications (partial diploids) that are unlikely to contain more than one het locus. A phenotypically expressed incompatibility reaction occurs when unlike het alleles are present within the same somatic nucleus, and this parallels the heterokaryon incompatibility reaction that occurs when unlike alleles in different haploid nuclei are introduced into the same somatic hypha by mycelial fusion.—Nontandem duplications were used to confirm that the incompatibility reactions in heterokaryons and in duplications are alternate expressions of the same genes. This was demonstrated for three loci which had previously been established by conventional heterokaryon tests—het-e, het-c and mt. These were each obtained in duplications as recombinant meiotic segregants from crosses heterozygous for duplication-generating chromosome rearrangements. The particular method of producing the duplications is irrelevant so long as the incompatibility alleles are heterozygous.—The duplication technique has made it possible to determine easily the het-e and het-c genotypes of numerous laboratory and wild strains of unknown constitution. In laboratory strains both loci are represented simply by two alleles. Analysis of het-c is more complicated in some wild strains, where differences have been demonstrated at one or more additional het loci within the duplication used and multiple allelism is also possible.—The results show that the duplication method can be used to identify and map additional vegetative incompatibility loci, without the necessity of heterokaryon tests.