From Notebooks to Institutions: The Case for Symbiotic Cognition.
ABSTRACT: Cognition is claimed to be extended by a wide array of items, ranging from notebooks to social institutions. Although the connection between individuals and these items is usually referred to as "coupling," the difference between notebooks and social institutions is so vast that the meaning of "coupling" is bound to be different in each of these cases. In this paper I argue that the radical difference between "artifact-extended cognition" and "socially extended cognition" is not sufficiently highlighted in the literature. I argue that there are two different senses of "cognitive extension" at play, that I shall label, respectively, "implementation extension" and "impact extension." Whereas implementation extension is a causal-functional notion, impact-extension hinges on social normativity that is connected with organization and action coordination. I will argue that the two kinds of cognitive extension are different enough to warrant separate labels. Because the most salient form of social extension of cognition involves the reciprocal co-constitution of cognitive capacities, I will propose to set it apart from other types of extended cognition by using the label "symbiotic cognition."
Project description:Every professional doing active research in the life sciences is required to keep a laboratory notebook. However, while science has changed dramatically over the last centuries, laboratory notebooks have remained essentially unchanged since pre-modern science. We argue that the implementation of electronic laboratory notebooks (eLN) in academic research is overdue, and we provide researchers and their institutions with the background and practical knowledge to select and initiate the implementation of an eLN in their laboratories. In addition, we present data from surveying biomedical researchers and technicians regarding which hypothetical features and functionalities they hope to see implemented in an eLN, and which ones they regard as less important. We also present data on acceptance and satisfaction of those who have recently switched from paper laboratory notebook to an eLN. We thus provide answers to the following questions: What does an electronic laboratory notebook afford a biomedical researcher, what does it require, and how should one go about implementing it?
Project description:Objective:Bioinformatics publications typically include complex software workflows that are difficult to describe in a manuscript. We describe and demonstrate the use of interactive software notebooks to document and distribute bioinformatics research. We provide a user-friendly tool, BiocImageBuilder, that allows users to easily distribute their bioinformatics protocols through interactive notebooks uploaded to either a GitHub repository or a private server. Materials and methods:We present four different interactive Jupyter notebooks using R and Bioconductor workflows to infer differential gene expression, analyze cross-platform datasets, process RNA-seq data and KinomeScan data. These interactive notebooks are available on GitHub. The analytical results can be viewed in a browser. Most importantly, the software contents can be executed and modified. This is accomplished using Binder, which runs the notebook inside software containers, thus avoiding the need to install any software and ensuring reproducibility. All the notebooks were produced using custom files generated by BiocImageBuilder. Results:BiocImageBuilder facilitates the publication of workflows with a point-and-click user interface. We demonstrate that interactive notebooks can be used to disseminate a wide range of bioinformatics analyses. The use of software containers to mirror the original software environment ensures reproducibility of results. Parameters and code can be dynamically modified, allowing for robust verification of published results and encouraging rapid adoption of new methods. Conclusion:Given the increasing complexity of bioinformatics workflows, we anticipate that these interactive software notebooks will become as necessary for documenting software methods as traditional laboratory notebooks have been for documenting bench protocols, and as ubiquitous.
Project description:Gender studies (GS) has been challenged on epistemological grounds. Here, we compare samples of peer-reviewed academic journal publications written by GS authors and authors from closely related disciplines in the social sciences. The material consisted of 2805 statements from 36 peer-reviewed journal articles, sampled from the Swedish Gender Studies List, which covers >12,000 publications. Each statement was coded as expressing a lack of any of three aspects of objectivity: Bias, Normativity, or Political activism, or as considering any of four realms of explanation for the behaviours or phenomena under study: Biology/genetics, Individual/group differences, Environment/culture, or Societal institutions. Statements in GS publications did to a greater extent express bias and normativity, but not political activism. They did also to a greater extent consider cultural, environmental, social, and societal realms of explanation, and to a lesser extent biological and individual differences explanations.
Project description:BioJupies is a web application that enables the automated creation, storage, and deployment of Jupyter Notebooks containing RNA-seq data analyses. Through an intuitive interface, novice users can rapidly generate tailored reports to analyze and visualize their own raw sequencing files, gene expression tables, or fetch data from >9,000 published studies containing >300,000 preprocessed RNA-seq samples. Generated notebooks have the executable code of the entire pipeline, rich narrative text, interactive data visualizations, differential expression, and enrichment analyses. The notebooks are permanently stored in the cloud and made available online through a persistent URL. The notebooks are downloadable, customizable, and can run within a Docker container. By providing an intuitive user interface for notebook generation for RNA-seq data analysis, starting from the raw reads all the way to a complete interactive and reproducible report, BioJupies is a useful resource for experimental and computational biologists. BioJupies is freely available as a web-based application from http://biojupies.cloud.
Project description:In this paper, we argue that several recent 'wide' perspectives on cognition (embodied, embedded, extended, enactive, and distributed) are only partially relevant to the study of cognition. While these wide accounts override traditional methodological individualism, the study of cognition has already progressed beyond these proposed perspectives toward building integrated explanations of the mechanisms involved, including not only internal submechanisms but also interactions with others, groups, cognitive artifacts, and their environment. Wide perspectives are essentially research heuristics for building mechanistic explanations. The claim is substantiated with reference to recent developments in the study of "mindreading" and debates on emotions. We argue that the current practice in cognitive (neuro)science has undergone, in effect, a silent mechanistic revolution, and has turned from initial binary oppositions and abstract proposals toward the integration of wide perspectives with the rest of the cognitive (neuro)sciences.
Project description:The fundamental goal of the growing open science movement is to increase the efficiency of the global scientific community and accelerate progress and discoveries for the common good. Central to this principle is the rapid disclosure of research outputs in open-access peer-reviewed journals and on pre-print servers. The next bold step in this direction is open laboratory notebooks, where research scientists share their research - including detailed protocols, negative and positive results - online and in near-real-time to synergize with their peers. Here, we highlight the benefits of open lab notebooks to science, society and scientists, and discuss the challenges that this nascent movement is facing. We also present the implementation and progress of our own initiative at openlabnotebooks.org, with more than 20 active contributors after one year of operation.
Project description:Traditional attempts to understand the evolution of human cognition compare humans with other primates. This research showed that relative brain size covaries with cognitive skills, while adaptations that buffer the developmental and energetic costs of large brains (e.g. allomaternal care), and ecological or social benefits of cognitive abilities, are critical for their evolution. To understand the drivers of cognitive adaptations, it is profitable to consider distant lineages with convergently evolved cognitions. Here, we examine the facilitators of cognitive evolution in corvid birds, where some species display cultural learning, with an emphasis on family life. We propose that extended parenting (protracted parent-offspring association) is pivotal in the evolution of cognition: it combines critical life-history, social and ecological conditions allowing for the development and maintenance of cognitive skillsets that confer fitness benefits to individuals. This novel hypothesis complements the extended childhood idea by considering the parents' role in juvenile development. Using phylogenetic comparative analyses, we show that corvids have larger body sizes, longer development times, extended parenting and larger relative brain sizes than other passerines. Case studies from two corvid species with different ecologies and social systems highlight the critical role of life-history features on juveniles' cognitive development: extended parenting provides a safe haven, access to tolerant role models, reliable learning opportunities and food, resulting in higher survival. The benefits of extended juvenile learning periods, over evolutionary time, lead to selection for expanded cognitive skillsets. Similarly, in our ancestors, cooperative breeding and increased group sizes facilitated learning and teaching. Our analyses highlight the critical role of life-history, ecological and social factors that underlie both extended parenting and expanded cognitive skillsets. This article is part of the theme issue 'Life history and learning: how childhood, caregiving and old age shape cognition and culture in humans and other animals'.
Project description:This article illustrates and discusses the idea of 'implicit normativity', and specifically its relevance to the management of ethical uncertainty. In particular I consider (i) the role implicit normativity plays in masking and containing potential ethical uncertainty and (ii) the contrast and boundary between implicit normativity and 'overt ethics' where ethical contestation - as well as particular processes and agents - are highlighted as salient. Using examples I show how the idea of implicit normativity can be applied not only to specific practices but also to whole fields of practice. The notion of 'moral settlements' - along with the explanatory role of the threat of 'chaos' - is introduced and elucidated to develop these points. I argue that attention to the management of ethical uncertainty shows the critically important contribution that an ambitious sociology of ethics can make to clinical ethics, including by helping to formulate and drive home questions about the 'ethics of ethics'. The account presented here has resonances with work that seeks to use sociological lenses to move beyond conventional bioethics, including Petersen's (2013) call for a 'normative sociology'.
Project description:Social engineering cyberattacks are a major threat because they often prelude sophisticated and devastating cyberattacks. Social engineering cyberattacks are a kind of psychological attack that exploits weaknesses in human cognitive functions. Adequate defense against social engineering cyberattacks requires a deeper understanding of what aspects of human cognition are exploited by these cyberattacks, why humans are susceptible to these cyberattacks, and how we can minimize or at least mitigate their damage. These questions have received some amount of attention, but the state-of-the-art understanding is superficial and scattered in the literature. In this paper, we review human cognition through the lens of social engineering cyberattacks. Then, we propose an extended framework of human cognitive functions to accommodate social engineering cyberattacks. We cast existing studies on various aspects of social engineering cyberattacks into the extended framework, while drawing a number of insights that represent the current understanding and shed light on future research directions. The extended framework might inspire future research endeavor toward a new sub-field that can be called Cybersecurity Cognitive Psychology, which tailors or adapts principles of Cognitive Psychology to the cybersecurity domain while embracing new notions and concepts that are unique to the cybersecurity domain.
Project description:Understanding the spread of false or dangerous beliefs-often called misinformation or disinformation-through a population has never seemed so urgent. Network science researchers have often taken a page from epidemiologists, and modeled the spread of false beliefs as similar to how a disease spreads through a social network. However, absent from those disease-inspired models is an internal model of an individual's set of current beliefs, where cognitive science has increasingly documented how the interaction between mental models and incoming messages seems to be crucially important for their adoption or rejection. Some computational social science modelers analyze agent-based models where individuals do have simulated cognition, but they often lack the strengths of network science, namely in empirically-driven network structures. We introduce a cognitive cascade model that combines a network science belief cascade approach with an internal cognitive model of the individual agents as in opinion diffusion models as a public opinion diffusion (POD) model, adding media institutions as agents which begin opinion cascades. We show that the model, even with a very simplistic belief function to capture cognitive effects cited in disinformation study (dissonance and exposure), adds expressive power over existing cascade models. We conduct an analysis of the cognitive cascade model with our simple cognitive function across various graph topologies and institutional messaging patterns. We argue from our results that population-level aggregate outcomes of the model qualitatively match what has been reported in COVID-related public opinion polls, and that the model dynamics lend insights as to how to address the spread of problematic beliefs. The overall model sets up a framework with which social science misinformation researchers and computational opinion diffusion modelers can join forces to understand, and hopefully learn how to best counter, the spread of disinformation and "alternative facts."