Pub Date : 2025-11-03DOI: 10.1016/j.plrev.2025.11.002
Christopher J. Whyte , Andrew W. Corcoran , Jonathan Robinson , Ryan Smith , Rosalyn J. Moran , Thomas Parr , Karl J. Friston , Anil K. Seth , Jakob Hohwy
The multifaceted nature of subjective experience poses a challenge to the study of consciousness. Traditional neuroscientific approaches often concentrate on isolated facets, such as perceptual awareness or the global state of consciousness and construct a theory around the relevant empirical paradigms and findings. Theories of consciousness are, therefore, often difficult to compare; indeed, there might be little overlap in the phenomena such theories aim to explain. Here, we take a different approach: starting with active inference, a first principles framework for modelling behaviour as (approximate) Bayesian inference, and building up to a minimal theory of consciousness, which emerges from the shared features of computational models derived under active inference. We review a body of work applying active inference models to the study of consciousness and argue that there is implicit in all these models a small set of theoretical commitments that point to a minimal (and testable) theory of consciousness.
{"title":"On the minimal theory of consciousness implicit in active inference","authors":"Christopher J. Whyte , Andrew W. Corcoran , Jonathan Robinson , Ryan Smith , Rosalyn J. Moran , Thomas Parr , Karl J. Friston , Anil K. Seth , Jakob Hohwy","doi":"10.1016/j.plrev.2025.11.002","DOIUrl":"10.1016/j.plrev.2025.11.002","url":null,"abstract":"<div><div>The multifaceted nature of subjective experience poses a challenge to the study of consciousness. Traditional neuroscientific approaches often concentrate on isolated facets, such as perceptual awareness or the global state of consciousness and construct a theory around the relevant empirical paradigms and findings. Theories of consciousness are, therefore, often difficult to compare; indeed, there might be little overlap in the phenomena such theories aim to explain. Here, we take a different approach: starting with active inference, a first principles framework for modelling behaviour as (approximate) Bayesian inference, and building up to a minimal theory of consciousness, which emerges from the shared features of computational models derived under active inference. We review a body of work applying active inference models to the study of consciousness and argue that there is implicit in all these models a small set of theoretical commitments that point to a minimal (and testable) theory of consciousness.</div></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"56 ","pages":"Pages 4-28"},"PeriodicalIF":14.3,"publicationDate":"2025-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145601636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-01DOI: 10.1016/j.plrev.2025.11.001
Fenfang Li
{"title":"The dynamic duo: Calcium signaling and ultrasound modulation of cellular viscoelasticity: Comment on “Viscoelastic mechanics of living cells” by Zhou et al.","authors":"Fenfang Li","doi":"10.1016/j.plrev.2025.11.001","DOIUrl":"10.1016/j.plrev.2025.11.001","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"55 ","pages":"Pages 232-234"},"PeriodicalIF":14.3,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145457103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-31DOI: 10.1016/j.plrev.2025.10.008
Frédérique de Vignemont
{"title":"Time in peripersonal space. Comment on \"computational models of peripersonal space representation\" by Tommaso Bertoni, Ishan-Singh J. Chauhan, Jean-Paul Noel, Andrea Serino","authors":"Frédérique de Vignemont","doi":"10.1016/j.plrev.2025.10.008","DOIUrl":"10.1016/j.plrev.2025.10.008","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"55 ","pages":"Pages 253-254"},"PeriodicalIF":14.3,"publicationDate":"2025-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145511455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-28DOI: 10.1016/j.plrev.2025.10.005
Friedemann Pulvermüller , Michael Pauen
Recent discussions about the nature of meaning and concepts focus on abstract semantic knowledge including key information about inner states of the individual. Classic cognitive approaches anchor the meaning of words in universal concepts, semantic networks or semantic features encapsulated in the individual’s own mind. However, this does not explain how symbols become interpretable during language development. Embodiment theorists acknowledge the relevance of semantic grounding of concrete referential symbols in perceptions and actions during learning, but, similar to classic cognitivism, assume internal anchoring of mental terms in introspection, thus once again implicating a main role of privileged access to ‘private’ inner states in language learning. This raises the basic question as to how a public language can be founded in private inner access.
Here, we argue that, in semantic learning, a purely introspection-based classification of inner states is neither possible nor required, and even less so a first-person privilege in accessing these states. Rather, classification and semantic learning of symbols for mentalistic concepts is an interactive process between the learner and an external observer who can employ contextual knowledge and behavioral information for recognizing and categorizing the learner’s mental states. In support of this ‘extrospective’ mental grounding account, we review observations that, in case of doubt about internal states, third-person evidence can play a decisive role. We also highlight supporting empirical studies showing that individuals in whom the link between first-person experience and externally observable behavior is broken may suffer from deficits in processing and understanding the related mentalistic vocabulary.
{"title":"Making the private public: external grounding in inner States","authors":"Friedemann Pulvermüller , Michael Pauen","doi":"10.1016/j.plrev.2025.10.005","DOIUrl":"10.1016/j.plrev.2025.10.005","url":null,"abstract":"<div><div>Recent discussions about the nature of meaning and concepts focus on abstract semantic knowledge including key information about inner states of the individual. Classic cognitive approaches anchor the meaning of words in universal concepts, semantic networks or semantic features encapsulated in the individual’s own mind. However, this does not explain how symbols become interpretable during language development. Embodiment theorists acknowledge the relevance of semantic grounding of concrete referential symbols in perceptions and actions during learning, but, similar to classic cognitivism, assume internal anchoring of mental terms in introspection, thus once again implicating a main role of privileged access to ‘private’ inner states in language learning. This raises the basic question as to how a public language can be founded in private inner access.</div><div>Here, we argue that, in semantic learning, a purely introspection-based classification of inner states is neither possible nor required, and even less so a first-person privilege in accessing these states. Rather, classification and semantic learning of symbols for mentalistic concepts is an interactive process between the learner and an external observer who can employ contextual knowledge and behavioral information for recognizing and categorizing the learner’s mental states. In support of this ‘extrospective’ mental grounding account, we review observations that, in case of doubt about internal states, third-person evidence can play a decisive role. We also highlight supporting empirical studies showing that individuals in whom the link between first-person experience and externally observable behavior is broken may suffer from deficits in processing and understanding the related mentalistic vocabulary.</div></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"55 ","pages":"Pages 235-249"},"PeriodicalIF":14.3,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145480496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-28DOI: 10.1016/j.plrev.2025.10.006
Arnaud Messé , Claus C. Hilgetag , Marc-Thorsten Hütt
In a world dominated by large-scale numerical simulations and applications of machine learning to biology, medicine and neuroscience (and complex systems, in general), each driven by the availability of ‘big data’ and decreasing costs of computation, the art form of constructing simple models is no longer in the focus of scientific attention. Yet, the most successful of these ‘minimal models’ have brought about a revolution of our understanding of complex systems, in particular in the life sciences, and are still shaping our view of the world today. It is hard to look at a power-law distribution without thinking of the Bak-Tang-Wiesenfeld sandpile model. And it is near impossible to reflect on synchronization without imagining coupled phase oscillators. Here we have put together a few ideas on how to formulate and analyze simple models and to draw conclusions from them.
{"title":"Simple rules for simple models","authors":"Arnaud Messé , Claus C. Hilgetag , Marc-Thorsten Hütt","doi":"10.1016/j.plrev.2025.10.006","DOIUrl":"10.1016/j.plrev.2025.10.006","url":null,"abstract":"<div><div>In a world dominated by large-scale numerical simulations and applications of machine learning to biology, medicine and neuroscience (and complex systems, in general), each driven by the availability of ‘big data’ and decreasing costs of computation, the art form of constructing simple models is no longer in the focus of scientific attention. Yet, the most successful of these ‘minimal models’ have brought about a revolution of our understanding of complex systems, in particular in the life sciences, and are still shaping our view of the world today. It is hard to look at a power-law distribution without thinking of the Bak-Tang-Wiesenfeld sandpile model. And it is near impossible to reflect on synchronization without imagining coupled phase oscillators. Here we have put together a few ideas on how to formulate and analyze simple models and to draw conclusions from them.</div></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"55 ","pages":"Pages 217-228"},"PeriodicalIF":14.3,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145412381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-27DOI: 10.1016/j.plrev.2025.10.007
Massimo Silvetti , Eliana Vassena
{"title":"Getting surprise under control: Via active inference or meta-reinforcement learning?","authors":"Massimo Silvetti , Eliana Vassena","doi":"10.1016/j.plrev.2025.10.007","DOIUrl":"10.1016/j.plrev.2025.10.007","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"55 ","pages":"Pages 229-231"},"PeriodicalIF":14.3,"publicationDate":"2025-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145443428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-22DOI: 10.1016/j.plrev.2025.10.002
Michael Laakasuo , Paolo Buttazzoni , Marianna Drosinou
{"title":"But does humanity have a choice?: Comment on “To Enhance or not to Enhance” by Grinschgl S., Ninaus, M., Wood. G. & Neubauer, AC (2025)","authors":"Michael Laakasuo , Paolo Buttazzoni , Marianna Drosinou","doi":"10.1016/j.plrev.2025.10.002","DOIUrl":"10.1016/j.plrev.2025.10.002","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"55 ","pages":"Pages 213-214"},"PeriodicalIF":14.3,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145407774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-21DOI: 10.1016/j.plrev.2025.10.003
Sung Hee Baek , Keun Il Kim
{"title":"From static catalogs to dynamic regulation: Comment on “Unlocking the brain's code: The crucial role of post-translational modifications in neurodevelopment and neurological function” by Peng Ye et al.","authors":"Sung Hee Baek , Keun Il Kim","doi":"10.1016/j.plrev.2025.10.003","DOIUrl":"10.1016/j.plrev.2025.10.003","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"55 ","pages":"Pages 215-216"},"PeriodicalIF":14.3,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145412382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-21DOI: 10.1016/j.plrev.2025.10.004
Stephan Schleim , Boris B. Quednow
{"title":"What challenges remain after 25 years of the enhancement debate?","authors":"Stephan Schleim , Boris B. Quednow","doi":"10.1016/j.plrev.2025.10.004","DOIUrl":"10.1016/j.plrev.2025.10.004","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"55 ","pages":"Pages 210-212"},"PeriodicalIF":14.3,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145358051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-12DOI: 10.1016/j.plrev.2025.10.001
Haoling Zhang , Qilu Yan , Shuya Jiang , Dan Hu , Ping Lu , Shaowei Li , Doblin Sandai , Haolong Zhang , Wangzheqi Zhang , Chenglong Zhu
Protein post-translational modifications (PTMs), which involve the covalent attachment of specific chemical groups to amino acid residues, significantly reshape protein structure and function. These modifications play a crucial role in fundamental physiological processes such as signal transduction, metabolic regulation, and protein homeostasis. In the context of pan-cancer, various types of PTMs, including phosphorylation, acetylation, glycosylation, and ubiquitination, create an intricate crosstalk network that finely tunes the stability and function of immune checkpoint molecules, directly influencing tumor immune evasion and immune cell recognition. Additionally, PTMs exert multilayered regulation over the functional states of key immune cells, such as T cells, macrophages, and dendritic cells (DCs), thereby determining the intensity and nature of immune responses within the tumor microenvironment (TME). Furthermore, PTMs are pivotal in antigen processing and presentation by influencing antigen diversity and epitope display, which facilitates tumor cell escape from immune surveillance. Dynamic analyses reveal that PTM landscapes exhibit spatiotemporal specificity during tumor initiation, progression, and metastasis, closely correlating with tumor stage and the establishment of an immunosuppressive microenvironment. Based on these findings, immunotherapeutic strategies targeting key PTM-modifying enzymes, such as kinases, deacetylases, and deubiquitinases, are rapidly emerging. However, these approaches still face challenges, including drug specificity, resistance, and off-target effects. The exploration of synergistic effects through the combinational targeting of distinct PTM pathways, along with a deeper understanding of the interactive regulatory networks among PTMs, opens promising avenues for the development of next-generation precision immunotherapies. This review aims to systematically elucidate the multifaceted roles and dynamic regulation of PTMs in tumor immunity, providing a theoretical foundation and research direction for identifying novel immunotherapeutic targets and optimizing therapeutic strategies.
{"title":"Protein post-translational modifications and tumor immunity: A pan-cancer perspective","authors":"Haoling Zhang , Qilu Yan , Shuya Jiang , Dan Hu , Ping Lu , Shaowei Li , Doblin Sandai , Haolong Zhang , Wangzheqi Zhang , Chenglong Zhu","doi":"10.1016/j.plrev.2025.10.001","DOIUrl":"10.1016/j.plrev.2025.10.001","url":null,"abstract":"<div><div>Protein post-translational modifications (PTMs), which involve the covalent attachment of specific chemical groups to amino acid residues, significantly reshape protein structure and function. These modifications play a crucial role in fundamental physiological processes such as signal transduction, metabolic regulation, and protein homeostasis. In the context of pan-cancer, various types of PTMs, including phosphorylation, acetylation, glycosylation, and ubiquitination, create an intricate crosstalk network that finely tunes the stability and function of immune checkpoint molecules, directly influencing tumor immune evasion and immune cell recognition. Additionally, PTMs exert multilayered regulation over the functional states of key immune cells, such as T cells, macrophages, and dendritic cells (DCs), thereby determining the intensity and nature of immune responses within the tumor microenvironment (TME). Furthermore, PTMs are pivotal in antigen processing and presentation by influencing antigen diversity and epitope display, which facilitates tumor cell escape from immune surveillance. Dynamic analyses reveal that PTM landscapes exhibit spatiotemporal specificity during tumor initiation, progression, and metastasis, closely correlating with tumor stage and the establishment of an immunosuppressive microenvironment. Based on these findings, immunotherapeutic strategies targeting key PTM-modifying enzymes, such as kinases, deacetylases, and deubiquitinases, are rapidly emerging. However, these approaches still face challenges, including drug specificity, resistance, and off-target effects. The exploration of synergistic effects through the combinational targeting of distinct PTM pathways, along with a deeper understanding of the interactive regulatory networks among PTMs, opens promising avenues for the development of next-generation precision immunotherapies. This review aims to systematically elucidate the multifaceted roles and dynamic regulation of PTMs in tumor immunity, providing a theoretical foundation and research direction for identifying novel immunotherapeutic targets and optimizing therapeutic strategies.</div></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"55 ","pages":"Pages 142-209"},"PeriodicalIF":14.3,"publicationDate":"2025-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145353327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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