Article
History & Philosophy Of Science
Michal Oleksowicz, Leandro Gaitan
Summary: The new mechanistic philosophy aims to identify and explain the mechanisms of various phenomena, including their organization and interactions between components. This paper argues that near-death experiences can be studied within the new mechanistic framework as part of religious experiences, involving complex cognitive, affective, and behavioral processes. While some scholars highlight the potential of mechanistic explanation for understanding religion, we emphasize its neglected limits and compare it to alternative models proposed by other researchers.
Article
Anthropology
Jan Schulz, Daniel M. Mayerhoffer, Anna Gebhard
Summary: Individual citizens across income groups and countries have significantly incorrect perceptions of economic inequality. These misperceptions can have significant consequences, as they may shape redistributive preferences based on perceived inequality rather than actual inequality. Our proposed explanation of perceived inequality, based on network-based theories, can replicate all observed stylised facts and generate social networks similar to real-world networks.
Article
Cell Biology
Vidya Manian, Jairo Orozco-Sandoval, Victor Diaz-Martinez
Summary: This study successfully identified key gene regulators causing muscle atrophy through mining transcriptomic data and training a graph neural network, and constructed gene-disease and disease-drug knowledge graphs to predict new drugs and suitable drug repurposing candidates for space missions.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
History & Philosophy Of Science
Matthew Inglis, Juan Pablo Mejia-Ramos
Summary: Mathematical explanations are often hard to understand, but the proposal of functional explanation suggests that explanations are things that generate understanding in the right circumstances. By considering a basic model of human cognitive architecture, existing accounts of mathematical explanation can be derived from the proposal of functional explanation. Therefore, explanatory criteria can be seen as features that make it more likely for a mathematical proof to generate understanding.
Article
Engineering, Electrical & Electronic
Jun Xiao, Zhongwei Cai, Ziyu Liang, Buxin She
Summary: This paper proposes a mathematical model for the total supply capability (TSC) curve of a distribution network and reveals the mechanism that determines the shape of the curve. The study finds that the intersection variable in the model causes capability decline and ultimately forms the curve. A mathematical formula is derived to calculate the capability decline and its physical meaning is explained. The proposed model and mechanism are verified using wiring mode cases and the IEEE_RBTS case.
INTERNATIONAL JOURNAL OF ELECTRICAL POWER & ENERGY SYSTEMS
(2022)
Article
Biochemical Research Methods
Haluk Dogan, Zeynep Hakguder, Roland Madadjim, Stephen Scott, Massimiliano Pierobon, Juan Cui
Summary: Powered by advanced genomics discovery tools, recent biomedical research has generated massive genomic data on (post-)transcriptional regulations, and computational modeling has produced promising quantitative models representing complex gene regulatory mechanisms. However, dynamic changes in interactomes in chaotic systems like cancers and the growing heterogeneous data pose challenges in model complexity and scalability. This study introduces a new integrative machine learning approach for inferring multifaceted gene regulations in cancers, with a focus on microRNA regulation, and has identified distinct gene regulatory networks associated with different cancer stages in human breast cancer.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Pharmacology & Pharmacy
Kwang-Il To, Zhen-Xing Zhu, Ya-Ni Wang, Gang-Ao Li, Yu-Meng Sun, Yang Li, Ying-Hua Jin
Summary: This study investigated the drug targets and pathways of Ginsenoside Rh4 (G-Rh4) in treating inflammation using network pharmacology and experimental approaches. The results showed that G-Rh4 may exert anti-inflammatory effects through the JAK-STAT signaling pathway, TNF signaling pathway, NF-kappa B signaling pathway, and PI3K-Akt signaling pathway.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Ecology
Brian MacPherson, Ryan Scott, Robin Gras
Summary: Attempts to resolve the paradox of sexual reproduction in animal species have typically involved single factor explanations, but only a few studies have investigated the potential interaction of multiple factors. This study is the first to examine the potential interaction between purifying selection, the ability to avoid predators, and the ability to cope with fluctuating resources. The results suggest that multiple factors can act integratively, antagonistically, and non-reductively at the same time, providing a significant contribution to the understanding of the effect of multiple factors on the prevalence of sexual reproduction.
ECOLOGICAL MODELLING
(2023)
Article
History & Philosophy Of Science
Gila Sher
Summary: This paper presents a special kind of pluralism called correspondence-pluralism, which argues that truth requires correspondence principles to fulfill its function in knowledge, rather than mere coherence, pragmatism, or deflationism. These correspondence principles do not have to be the traditional naive principles and can vary in different fields of knowledge, allowing for high standards of truth while accommodating the special conditions of each field.
Article
History & Philosophy Of Science
Eric Muszynski, Christophe Malaterre
Summary: The text discusses the various interpretations of pluralism in the philosophy of science, with a focus on behavior science. It presents three main types of pluralism - type pluralism, fragmentation pluralism, and insular pluralism. The article serves as an introduction to a topical collection on explanatory pluralism across the life sciences.
Article
Criminology & Penology
Daniel Wegerhoff, Tony Ward, Louise Dixon
Summary: The impact of gang-related harms has led to diverse definitions and explanations being developed, creating challenges in reaching consensus among stakeholders. Researchers have proposed a unificationist framework, but some advocate for a pluralistic approach to gang research.
AGGRESSION AND VIOLENT BEHAVIOR
(2021)
Article
Biodiversity Conservation
Marcelo Domingos de Santis
Summary: Cladists have sought to make their discipline more scientific by incorporating Karl Popper's philosophy, but their use of the covering law model has been widely criticized by philosophers for lacking practical guidance.
SYSTEMATICS AND BIODIVERSITY
(2021)
Article
Environmental Sciences
Faustino Gomez-Santiz, Maria Perevochtchikova, Driss Ezzine-de-Blas
Summary: The SES analytical framework is widely endorsed for describing complex feedback relationships between social and ecological subsystems, promoting multidisciplinarity and interdisciplinarity. However, there is a wide methodological plurality in actual research, with few studies opting for mixed methods to capture the complexity of SES. Additionally, scientific networks mainly consist of established groups of scientists from the Global North, with peripheral groups in the Global South developing studies primarily in their own regions.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Review
Pharmacology & Pharmacy
Haiyu Xu, Yanqiong Zhang, Ping Wang, Junhong Zhang, Hong Chen, Luoqi Zhang, Xia Du, Chunhui Zhao, Dan Wu, Feng Liu, Hongjun Yang, Changxiao Liu
Summary: TCMIP is an interdisciplinary science that can establish qualitative and quantitative PK-PD correlations and presents research contents and methodologies for studying TCM formulas. Additionally, TCMIP can be applied to improve TCM quality control, clarify molecular mechanisms underlying TCM actions, and discover potential new drugs.
ACTA PHARMACEUTICA SINICA B
(2021)
Article
Computer Science, Artificial Intelligence
Juan M. Duran
Summary: Explanatory AI (XAI) is gaining momentum in the computational community, policymakers, and philosophers, with this article contributing to the debate by distinguishing scientific XAI (sXAI) from other forms of XAI. It discusses the structure of bona fide sXAI, the pragmatics of explanation, and Meaningful Human Explanation, focusing on AI systems used in medicine and healthcare. The article also critically addresses current philosophical and computational approaches to XAI, arguing against the long-standing interpretation of classifications as explanation.
ARTIFICIAL INTELLIGENCE
(2021)
Article
Biology
Javier Suarez, Adrian Stencel
BIOLOGICAL REVIEWS
(2020)
Article
Biochemical Research Methods
Alberto Perez-Cervera, Jaroslav Hlinka
Summary: This study explores how slow-fast models in the epileptic brain respond to perturbations, shedding light on the mechanisms that trigger or delay seizures. The research uses isochrons and phase response curves to analyze the theoretical framework, revealing the role of slow flow components in relaxation oscillators. The findings suggest potential stimulation strategies ranging from mere delaying to complete suppression of seizures.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Book Review
History & Philosophy Of Science
Javier Suarez
HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES
(2021)
Article
History & Philosophy Of Science
Johannes Findl, Javier Suarez
Summary: The COVID-19 pandemic has had a significant impact on our lives in 2020, leading to the development of various epidemiological models. Early statistical models had predictive capacity but lacked causal knowledge, sparking philosophical questions about the relationship between prediction and understanding in these models. The Institute of Health Metrics and Evaluation's model is cited to argue for the existence of descriptive understanding as an alternative to explanatory understanding.
HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES
(2021)
Article
Physics, Multidisciplinary
Alberto Perez-Cervera, Benjamin Lindner, Peter J. Thomas
Summary: Thomas and Lindner defined an asymptotic phase for stochastic oscillators, while we introduced the concept of stochastic isostable coordinate to complete the phase-amplitude description of noisy oscillators. Our results suggest a framework for stochastic limit cycle dynamics that include noise-induced oscillations.
PHYSICAL REVIEW LETTERS
(2021)
Article
Biochemical Research Methods
Gregory Dumont, Alberto Perez-Cervera, Boris Gutkin
Summary: Brain rhythms are generated by synchronized spiking neurons. This study presents a theoretical framework and methodology to compute the phase-resetting curve (PRC) of spiking networks with collective oscillations. The framework captures the network dynamics effectively using a renewal approach and the refractory density equation. The proposed method can link biological properties at the individual neuron scale and the macroscopic oscillatory network properties. It is also applicable to a broad class of systems described by renewal processes.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
History & Philosophy Of Science
Javier Suarez
Summary: I investigate the intrinsic/extrinsic nature of stemness in muscle stem cells (MSC) and argue that the study of quiescence is crucial in establishing the intrinsicness/extrinsicness of stemness in some stem cells. I propose that MSC's stem capacities result from a combination of intrinsic cues and extrinsic factors, making stemness an extrinsic disposition. Additionally, I highlight the role of the stem cell niche in masking the manifestation of stemness, revealing that stemness in MSC is an extrinsically structurally masked disposition.
EUROPEAN JOURNAL FOR PHILOSOPHY OF SCIENCE
(2023)
Article
History & Philosophy Of Science
Javier Suarez
Summary: This paper presents a description of the nature of stem cells based on the concept of disposition. It offers a framework to overcome controversies surrounding stemness and provides insights for interpreting stem cell experiments and guiding interventions. The paper highlights the causal role of different levels and suggests interventions at various levels.
BIOLOGY & PHILOSOPHY
(2023)
Article
History & Philosophy Of Science
Javier Suarez, Federico Boem
Summary: This paper challenges the claim in philosophy of science regarding the appropriateness of objects acting as surrogates. The author argues that knowledge about the type of inference permitted by surrogates is essential to avoid misinterpreting data and hypotheses.
Article
History & Philosophy Of Science
Sophie J. Veigl, Javier Suarez, Adrian Stencel
Summary: This paper introduces the reconstitutor as a comprehensive unit of heredity in evolutionary research. The author justifies the necessity of introducing the reconstitutor by showing the limitations of other evolutionary conceptions, and illustrates how it covers cases of hereditary phenomena not covered by previous accounts.
Article
Computer Science, Cybernetics
Alberto Perez-Cervera, Benjamin Lindner, Peter J. Thomas
Summary: This paper quantitatively compares the definitions of deterministic phase and stochastic phase, and discusses their characteristics and similarities. The research results can be used to explain the behavior of specific systems.
BIOLOGICAL CYBERNETICS
(2022)
Article
History & Philosophy Of Science
Javier Suarez
Summary: The debate on units or levels of selection focuses on which biological systems are stable enough to undergo natural selection, discussing the levels of interaction with the environment and reproduction. Recently, there has been discussion on whether multi-species consortia may act as a unit of selection, but this view has faced criticism.
THEORIA-REVISTA DE TEORIA HISTORIA Y FUNDAMENTOS DE LA CIENCIA
(2021)