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Open research questions in Philosophy of Biology and Scientific Explanation

563 gap statements mined from Philosophy of Biology and Scientific Explanation papers in our 7.9M-paper local library, which holds 5,453 papers on the topic — drawn mostly from each paper's own stated research gap, future-work, challenge and limitation notes, and its abstract. The ones listed below are a selection still marked open; each names the study that raised it, with a DOI link where the paper has one.

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What the literature leaves open

  • Missing-model problems arise when there is a target phenomenon that is not directly accessible, and very little is known about it antecedently. Because, in these cases, very little is known antecedently about the target phenomena, measurement models may be constructed even when there is very little evidence for their validity.

    The Problem of the Missing Model · 2026 · DOI

  • Yet little is known about the epistemology of KBs: how these players’ incentives affect knowledge flow from its origin in scientific research to its end point in use by society, especially in the decisions of policymakers.

    How Knowledge Brokers Shape the Evidence-Based Policy Landscape · 2026 · DOI

  • It explores the relation between the pregnant organism and the gestated one, motivating the further study of pregnancy from a philosophical perspective (§1, §2).

    The Metaphysics of Pregnancy · 2025 · DOI

  • In the present article, the apologiaof “Strong Program” consists in precise interpretation of the principle of causality and social nature of knowledge, but the most controversial and relativistic consequence of the program appears from its rejection of logical and ontological necessity, which remains an open question in philosophy.

    Apologia of “Strong Program” · 2026 · DOI

  • The article suggests that further testing is needed to establish the broad generality of the proposed architecture. The study recommends exploring the application of the proposed architecture to other domains. The paper implies that future research should focus on developing more advanced architectures that can handle a wider range of tasks.

    THE MODAL DISCIPLINE OF SYMBOLIC DISCOVERY: PIR-JEPA, GRAMMAR COVERAGE, PHYSICS MANIFOLD PRIOR, AND CONFRONTATION WITH THE THEORY OF OBJECTIVITY · 2026 · DOI

  • The paper suggests that future research should explore the implications of emergent gravitational dynamics. The paper suggests that future research should investigate the compatibility of emergent gravitational dynamics with the Theory of Objectivity.

    EMERGENT GRAVITATION: a critical-propositional reading of the article Emergent gravitational dynamics from a photon action with an effective refractive index, by Vicente Cotrino Bautista, in confrontation with the Theory of Objectivity · 2026 · DOI

  • The paper identifies a need for a framework that can provide ontological grounding for emergent gravitational dynamics.

    EMERGENT GRAVITATION: a critical-propositional reading of the article Emergent gravitational dynamics from a photon action with an effective refractive index, by Vicente Cotrino Bautista, in confrontation with the Theory of Objectivity · 2026 · DOI

  • The paper suggests that future research should focus on the development of Codex Alpha as a theory. It notes that the theory requires maturation and empirical confrontation. The paper does not provide a comprehensive list of future research directions.

    THE INFORMATIONAL CODE OF THE COSMOS: a critical–propositional analysis of Codex Alpha 3.0 English Version ICONOCLAST, by Davide Cadelano, in confrontation with the Theory of Objectivity · 2026 · DOI

  • The paper notes that Cui's proposal lacks an explicit modal origin. The paper notes that Cui's use of metaphors may weaken the scientific status of the argument. The paper notes that the extension of the model to consciousness, biodiversity, and spiritual wisdom requires further development.

    SUBSTANTIAL SPACETIME, MODAL ONTOLOGY, AND TRANSCENDENT INFORMATION: a critical–propositional analysis of Hugang Cui's article in confrontation with the Theory of Objectivity · 2026 · DOI

  • The paper identifies a gap in Cui's proposal regarding the lack of an explicit modal origin. The paper identifies a gap in the development of new physical theories that can account for the relationship between spacetime and consciousness, biodiversity, and spiritual wisdom.

    SUBSTANTIAL SPACETIME, MODAL ONTOLOGY, AND TRANSCENDENT INFORMATION: a critical–propositional analysis of Hugang Cui's article in confrontation with the Theory of Objectivity · 2026 · DOI

  • Future research can build on the paper's findings to develop new theories and models. Future research can explore the implications of the paper's results for model-building in particle physics. Future research can investigate the application of Bayesian inference to other areas of theoretical physics.

    It’s all in your head—naturalness arguments do not require aleatoric uncertainty · 2026 · DOI

  • The paper recognizes that recent evaluations of naturalness have been unclear and misleading.

    It’s all in your head—naturalness arguments do not require aleatoric uncertainty · 2026 · DOI

  • The gap between what is claimed and what is warranted by the evidence. The lack of a methodological response to assess the proportionality of scientific claims to the strength of the evidence.

    The Bayesian audit: evaluating the proportionality of scientific claims to evidence — a case study on social priming and walking speed · 2026 · DOI

  • The paper identifies the lack of understanding of the relationship between convergence and consilience as a research gap. It identifies the need for a systematic analysis of convergence and consilience as concepts.

    Convergence, Consilience, and the Hierarchical Architecture of Reality: A Meta-Analysis with Worked Examples from Interdisciplinary Physics · 2026 · DOI

  • The paper suggests that future research should focus on developing Majority World psychological frameworks. The paper highlights the importance of considering multiple perspectives in the acquisition of reliable knowledge. The paper suggests that future research should aim to increase the reliability of knowledge production in psychology.

    The pursuitworthiness of majority world psychology · 2026 · DOI

  • The paper identifies a gap in the discipline of psychology, namely the lack of alternative perspectives. The paper argues that this gap raises significant concerns for the epistemic integrity of the discipline. The paper suggests that fostering multiple perspectives is a step towards addressing this gap.

    The pursuitworthiness of majority world psychology · 2026 · DOI

  • The need for a clear distinction between scientific and scientists' understanding. The lack of reconciliation between objectualist and explanationist accounts.

    Disentangling scientific and scientists’ understanding · 2026 · DOI

  • The gap in current research is the lack of a clear criterion for distinguishing between productive pluralism and destructive relativism. The gap is the lack of a normative criterion for scientific knowledge that can account for the systematic unity of knowledge.

    SCIENCE AS A SYSTEM: KANT’S ARCHITECTONIC AND THE LIMITS OF EPISTEMIC RELATIVITY · 2026 · DOI

  • The cognitive cost of doubt and the formation of collective dogmas are frequently neglected phenomena. The scientific community lacks a minimal institutional response to allocate a small fraction of research resources to unorthodox projects.

    THE LIMIT OF DOUBT AND CERTAINTY · 2026 · DOI

  • However, my argument for pragmatic pluralism is not limited to the COVID-19 outbreak or moments of crisis.

    Pragmatic pluralism and problem framing: Why pragmatism demands pluralism · 2026 · DOI

  • It notes that the theory may reconfigure the physics of spacetime but does not fully resolve the genesis of the informational principle itself. The paper argues that Cadelano's work does not yet fully satisfy the objectivist demand for modal necessity.

    THE INFORMATIONAL CODE OF THE COSMOS: a critical–propositional analysis of Codex Alpha 3.0 English Version ICONOCLAST, by Davide Cadelano, in confrontation with the Theory of Objectivity · 2026 · DOI

  • To address the problem of demarcation and create an institution dedicated to managing it. To explore the implications of allocating a small fraction of research resources to unorthodox projects on the promotion of epistemic diversity and the generation of conflict between dogmas.

    THE LIMIT OF DOUBT AND CERTAINTY · 2026 · DOI

  • I first collect universally adopted aptness principles into a basic account, flagging open questions and choice points along the way.

    Causal Models and Metaphysics—Part 2: Interpreting Causal Models · 2024 · DOI

  • The paper identifies a gap in the current symbolic regression systems in physics, which lies in the grammatical coverage of the expression space. The study recognizes that the current systems fail structurally whenever the canonical form of the law lies outside the predefined repertoire.

    THE MODAL DISCIPLINE OF SYMBOLIC DISCOVERY: PIR-JEPA, GRAMMAR COVERAGE, PHYSICS MANIFOLD PRIOR, AND CONFRONTATION WITH THE THEORY OF OBJECTIVITY · 2026 · DOI

  • The lack of a history of science literacy component in science education, - The need for a simple and powerful pedagogical tool to apply HPS lessons to current science, - The importance of distinguishing phenomenal claims from explanatory claims in scientific…

    History of Science Literacy as a Core of Science Literacy · 2026 · DOI

Most-cited papers in Philosophy of Biology and Scientific Explanation

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Open questions raised by papers listed on this page include: (1) Missing-model problems arise when there is a target phenomenon that is not directly accessible, and very little is known about it antecedently (“The Problem of the Missing Model”, 2026); (2) Yet little is known about the epistemology of KBs: how these players’ incentives affect knowledge flow from its origin in scientific research to its end point in use by society, especially in the decisions of policymakers (“How Knowledge Brokers Shape the Evidence-Based Policy Landscape”, 2026); (3) The article suggests that further testing is needed to establish the broad generality of the proposed architecture (“THE MODAL DISCIPLINE OF SYMBOLIC DISCOVERY: PIR-JEPA, GRAMMAR COVERAGE, PHYSICS…”, 2026); (4) The paper suggests that future research should explore the implications of emergent gravitational dynamics (“EMERGENT GRAVITATION: a critical-propositional reading of the article Emergent…”, 2026); (5) The paper suggests that future research should focus on the development of Codex Alpha as a theory (“THE INFORMATIONAL CODE OF THE COSMOS: a critical–propositional analysis of…”, 2026). 563 gap statements have been mined from Philosophy of Biology and Scientific Explanation papers in our 7.9M-paper local library, which holds 5,453 papers on the topic; the gaps come from whichever of those papers state one. They are mostly the research gaps the authors state and the papers' abstracts, plus future-work, limitations and challenges passages. The ones listed below are a selection still marked open; each names the study that raised it, with a DOI link where the paper has one, so you can read the original claim in context.

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