Communicative and Integrative Biology最新文献

{"title":"Oscillators and servomechanisms in navigation and orientation.","authors":"Ken Cheng","doi":"10.1080/19420889.2023.2293268","DOIUrl":"10.1080/19420889.2023.2293268","url":null,"abstract":"<p><p>I summarize my recent theorizing on orientation and navigation across life. Organisms use navigational servomechanisms working with oscillators to get to goals. Navigational servomechanisms track errors from the best direction of travel and initiate action to correct the error. They work with endogenously generated action patterns, oscillations produced by oscillators, to adjust the course of travel. The theme applies to all scales of life from micrometers to thousands of kilometers. Servomechanisms and oscillators also characterize some other domains of cognition.</p>","PeriodicalId":39647,"journal":{"name":"Communicative and Integrative Biology","volume":"17 1","pages":"2293268"},"PeriodicalIF":0.0,"publicationDate":"2023-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10761010/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139088953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The feelings of knowing - fundamental interoceptive patterns (FoK-FIP) system: connecting consciousness to physics.","authors":"Holly Pollard-Wright","doi":"10.1080/19420889.2023.2260682","DOIUrl":"https://doi.org/10.1080/19420889.2023.2260682","url":null,"abstract":"<p><p>The feelings of knowing - fundamental interoceptive patterns (FoK-FIP) theory is both a theory of the mind and a unification theory. It includes cosmological and cellular frameworks. The cellular frameworks occur through the cosmological frameworks. This framework within a framework approach allows the connection between physics and consciousness to be envisioned in new ways, expanding current understanding and definitions. The cosmological frameworks refer to the astrophysics and theoretical physics constructs (e.g., string theory) that, without the use of mathematical language, conceptually expand the theory. In contrast, the cellular frameworks are the constructs represented by living organism models with DNA. In this way, the FoK-FIP theory represents an efficient framework for understanding consciousness and its phenomena. The transdisciplinary modeling of the FoK-FIP theory creates contextual bridging between classical theory and quantum theory as well as a broad range of empirical research so that biology and information connect, creating new avenues for disease diagnosis, intervention, and prevention. This article intends to render the FoK-FIP theory more robust and accessible for practical application by introducing the FoK-FIP system, which includes figures to promote clarity. Further, the theory aims to stimulate reasoning that challenges current notions about 'life' and the concept of 'self.' Through this process, the theory might contribute to the transdisciplinary collaboration needed to address some of the world's complex issues. It is suggested that a significant contributor to the current complex matters in the world is the lack of understanding of how things are and how they appear.</p>","PeriodicalId":39647,"journal":{"name":"Communicative and Integrative Biology","volume":"16 1","pages":"2260682"},"PeriodicalIF":0.0,"publicationDate":"2023-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10538454/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41153384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cellular and Natural Viral Engineering in Cognition-Based Evolution.","authors":"Miller W B, Reber A S, Marshall P, Baluška F","doi":"10.1080/19420889.2023.2196145","DOIUrl":"10.1080/19420889.2023.2196145","url":null,"abstract":"<p><p>Neo-Darwinism conceptualizes evolution as the continuous succession of predominately random genetic variations disciplined by natural selection. In that frame, the primary interaction between cells and the virome is relegated to host-parasite dynamics governed by selective influences. Cognition-Based Evolution regards biological and evolutionary development as a reciprocating cognition-based informational interactome for the protection of self-referential cells. To sustain cellular homeorhesis, cognitive cells collaborate to assess the validity of ambiguous biological information. That collective interaction involves coordinate measurement, communication, and active deployment of resources as Natural Cellular Engineering. These coordinated activities drive multicellularity, biological development, and evolutionary change. The virome participates as the vital intercessory among the cellular domains to ensure their shared permanent perpetuation. The interactions between the virome and the cellular domains represent active virocellular cross-communications for the continual exchange of resources. Modular genetic transfers between viruses and cells carry bioactive potentials. Those exchanges are deployed as nonrandom flexible tools among the domains in their continuous confrontation with environmental stresses. This alternative framework fundamentally shifts our perspective on viral-cellular interactions, strengthening established principles of viral symbiogenesis. Pathogenesis can now be properly appraised as one expression of a range of outcomes between cells and viruses within a larger conceptual framework of Natural Viral Engineering as a co-engineering participant with cells. It is proposed that Natural Viral Engineering should be viewed as a co-existent facet of Natural Cellular Engineering within Cognition-Based Evolution.</p>","PeriodicalId":39647,"journal":{"name":"Communicative and Integrative Biology","volume":"16 1","pages":"2196145"},"PeriodicalIF":0.0,"publicationDate":"2023-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10155641/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9431726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational and cellular exploration of the protein-protein interaction between <i>Vibrio fischeri</i> STAS domain protein SypA and serine kinase SypE.","authors":"Morgan E Milton, Karen L Visick","doi":"10.1080/19420889.2023.2203626","DOIUrl":"10.1080/19420889.2023.2203626","url":null,"abstract":"<p><p>Anti-sigma factor antagonists SpoIIAA and RsbV from <i>Bacillus subtilis</i> are the archetypes for single-domain STAS proteins in bacteria. The structures and mechanisms of these proteins along with their cognate anti-sigma factors have been well studied. SpoIIAA and RsbV utilize a partner-switching mechanism to regulate gene expression through protein-protein interactions to control the activity of their downstream anti-sigma factor partners. The <i>Vibrio fischeri</i> STAS domain protein SypA is also proposed to employ a partner-switching mechanism with its partner SypE, a serine kinase/phosphatase that controls SypA's phosphorylation state. However, this regulation appears opposite to the canonical pathway, with SypA being the more downstream component rather than SypE. Here we explore the commonalities and differences between SypA and the canonical single-domain STAS proteins SpoIIAA and RsbV. We use a combination of AlphaFold 2 structure predictions and computational modeling to investigate the SypA-SypE binding interface. We then test a subset of our predictions in <i>V.fischeri</i> by generating and expressing SypA variants. Our findings suggest that, while SypA shares many sequence and structural traits with anti-sigma factor antagonist STAS domain proteins, there are significant differences that may account for SypA's distinct regulatory output.</p>","PeriodicalId":39647,"journal":{"name":"Communicative and Integrative Biology","volume":"16 1","pages":"2203626"},"PeriodicalIF":0.0,"publicationDate":"2023-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10120452/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9758056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Towards a unifying theory of linguistic meaning.","authors":"Prakash Mondal","doi":"10.1080/19420889.2023.2200666","DOIUrl":"https://doi.org/10.1080/19420889.2023.2200666","url":null,"abstract":"<p><p>Fundamental tensions exist between formal-logical approaches and cognitive approaches to linguistic meaning. The divergence arises from the fundamental differences in nature and form between formal/mathematical structures of natural language meaning and their cognitive representations. While the former are abstract and logical categories of representations, the latter are ultimately embodied and grounded in sensory-motor systems of the brain. This article aims to motivate a unifying theory/formalism of linguistic meaning from a general biologically integrative perspective in the context of current theorizing in linguistics, neurobiology and cognitive sciences on human language meaning within which two divergent approaches for the mathematical and cognitive aspects of linguistic meaning exist. The tensions can be somewhat neutralized if formal-mathematical structures and cognitive representations of natural language meaning can be shown to have representational duality and unity in brain dynamics. This work shows a broad outline of one, if not the only one, path toward this vision.</p>","PeriodicalId":39647,"journal":{"name":"Communicative and Integrative Biology","volume":"16 1","pages":"2200666"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10134947/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9392324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A scale-free universal relational information matrix (N-space) reconciles the information problem: N-space as the fabric of reality.","authors":"William B Miller","doi":"10.1080/19420889.2023.2193006","DOIUrl":"https://doi.org/10.1080/19420889.2023.2193006","url":null,"abstract":"<p><p>Cellular measurement is a crucial faculty in living systems, and exaptations are acknowledged as a significant source of evolutionary innovation. However, the possibility that the origin of biological order is predicated on an exaptation of the measurement of information from the abiotic realm has not been previously explored. To support this hypothesis, the existence of a universal holographic relational information space-time matrix is proposed as a scale-free unification of abiotic and biotic information systems. In this framework, information is a universal property representing the interactions between matter and energy that can be subject to observation. Since observers are also universally distributed, information can be deemed the fundamental fabric of the universe. The novel concept of compartmentalizing this universal N-space information matrix into separate N-space partitions as nodes of informational density defined by Markov blankets and boundaries is introduced, permitting their applicability to both abiotic and biotic systems. Based on these N-space partitions, abiotic systems can derive meaningful information from the conditional settlement of quantum entanglement asymmetries and coherences between separately bounded quantum informational reference frames sufficient to be construed as a form of measurement. These conditional relationships are the precursor of the reiterating nested architecture of the N-space-derived information fields that characterize life and account for biological order. Accordingly, biotic measurement and biological N-space partitioning are exaptations of preexisting information processes within abiotic systems. Abiotic and biotic states thereby reconcile as differing forms of measurement of fundamental universal information. The essential difference between abiotic and biotic states lies within the attributes of the specific observer/detectors, thereby clarifying several contentious aspects of self-referential consciousness.</p>","PeriodicalId":39647,"journal":{"name":"Communicative and Integrative Biology","volume":"16 1","pages":"2193006"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10177686/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10194067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"On power and its corrupting effects: the effects of power on human behavior and the limits of accountability systems.","authors":"Tobore Onojighofia Tobore","doi":"10.1080/19420889.2023.2246793","DOIUrl":"https://doi.org/10.1080/19420889.2023.2246793","url":null,"abstract":"<p><p>Power is an all-pervasive, and fundamental force in human relationships and plays a valuable role in social, political, and economic interactions. Power differences are important in social groups in enhancing group functioning. Most people want to have power and there are many benefits to having power. However, power is a corrupting force and this has been a topic of interest for centuries to scholars from Plato to Lord Acton. Even with increased knowledge of power's corrupting effect and safeguards put in place to counteract such tendencies, power abuse remains rampant in society suggesting that the full extent of this effect is not well understood. In this paper, an effort is made to improve understanding of power's corrupting effects on human behavior through an integrated and comprehensive synthesis of the neurological, sociological, physiological, and psychological literature on power. The structural limits of justice systems' capability to hold powerful people accountable are also discussed.</p>","PeriodicalId":39647,"journal":{"name":"Communicative and Integrative Biology","volume":"16 1","pages":"2246793"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10461512/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10195996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prostaglandin production in brain endothelial cells during the initiation of fever.","authors":"Anna Eskilsson,&nbsp;Kiseko Shionoya,&nbsp;Anders Blomqvist","doi":"10.1080/19420889.2023.2166237","DOIUrl":"https://doi.org/10.1080/19420889.2023.2166237","url":null,"abstract":"<p><p>The initiation of fever has been a matter of controversy. Based on observations of little or no induction of prostaglandin synthesizing enzymes in the brain during the first phase of fever it was suggested that fever is initiated by prostaglandin released into the circulation from cells in the liver and lungs. Here we show in the mouse that prostaglandin synthesis is rapidly induced in the brain after immune challenge. These data are consistent with our recent findings in functional experiments that prostaglandin production in brain endothelial cells is both necessary and sufficient for the generation of all phases of fever.</p>","PeriodicalId":39647,"journal":{"name":"Communicative and Integrative Biology","volume":"16 1","pages":"2166237"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9839369/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10536352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Construction and analysis of protein-protein interaction networks based on nuclear proteomics data of the desiccation-tolerant <i>Xerophyta schlechteri</i> leaves subjected to dehydration stress.","authors":"Ryman Shoko,&nbsp;Babra Magogo,&nbsp;Jessica Pullen,&nbsp;Reagan Mudziwapasi,&nbsp;Joice Ndlovu","doi":"10.1080/19420889.2023.2193000","DOIUrl":"https://doi.org/10.1080/19420889.2023.2193000","url":null,"abstract":"<p><p>In order to understand the mechanism of desiccation tolerance in <i>Xerophyta schlechteri</i>, we carried out an <i>in silico</i> study to identify hub proteins and functional modules in the nuclear proteome of the leaves. Protein-protein interaction networks were constructed and analyzed from proteome data obtained from Abdalla and Rafudeen. We constructed networks in Cytoscape using the GeneMania software and analyzed them using a Network Analyzer. Functional enrichment analysis of key proteins in the respective networks was done using GeneMania network enrichment analysis, and GO (Gene Ontology) terms were summarized using REViGO. Also, community analysis of differentially expressed proteins was conducted using the Cytoscape Apps, GeneMania and ClusterMaker. Functional modules associated with the communities were identified using an online tool, ShinyGO. We identified HSP 70-2 as the super-hub protein among the up-regulated proteins. On the other hand, 40S ribosomal protein S2-3 (a protein added by GeneMANIA) was identified as a super-hub protein associated with the down-regulated proteins. For up-regulated proteins, the enriched biological process terms were those associated with chromatin organization and negative regulation of transcription. In the down-regulated protein-set, terms associated with protein synthesis were significantly enriched. Community analysis identified three functional modules that can be categorized as chromatin organization, anti-oxidant activity and metabolic processes.</p>","PeriodicalId":39647,"journal":{"name":"Communicative and Integrative Biology","volume":"16 1","pages":"2193000"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10038031/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9187346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A correlational study investigating whether semantic knowledge facilitates face identity processing.","authors":"Yue Qiu,&nbsp;Yuanzhe Li","doi":"10.1080/19420889.2023.2206203","DOIUrl":"https://doi.org/10.1080/19420889.2023.2206203","url":null,"abstract":"<p><p>The ability to recognize faces is a fundamental skill in human social interaction. While much research has focused on the recognition of familiar faces, there is growing interest in understanding the cognitive processes underlying the recognition of unfamiliar faces. Previous studies have suggested that both semantic knowledge and physical features play a role in unfamiliar face recognition, but the nature of their relationship is not well understood. This study examines the relationship between unfamiliar face recognition ability and the encoding abilities of semantic knowledge and physical features for famous faces. Using the Gorilla platform, a large group of participants (<i>N</i> = 66) with a broad age range completed three tasks: a challenging unfamiliar face matching task and Famous People Recognition Tests 1 and 2 to evaluate semantic and physical feature encoding abilities, respectively. Results indicate positive correlations between encoding abilities for both semantic knowledge and physical features of familiar faces with Model Face Matching Task scores. Additionally, the encoding ability for semantic knowledge was found to be positively associated with that of physical features.</p>","PeriodicalId":39647,"journal":{"name":"Communicative and Integrative Biology","volume":"16 1","pages":"2206203"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/cb/45/KCIB_16_2206203.PMC10150614.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9416812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}