Thomas Pradeu

Cancers rely on multiple, heterogeneous processes at different scales, pertaining to many biomedical fields. Therefore, understanding cancer is necessarily an interdisciplinary task that requires placing specialised experimental and clinical research into a broader conceptual, theoretical, and methodological framework. Without such a framework, oncology will collect piecemeal results, with scant dialogue between the different scientific communities studying cancer. We argue that one important way forward in service of a more successful dialogue is through greater integration of applied sciences (experimental and clinical) with conceptual and theoretical approaches, informed by philosophical methods. By way of illustration, we explore six central themes: (i) the role of mutations in cancer; (ii) the clonal evolution of cancer cells; (iii) the relationship between cancer and multicellularity; (iv) the tumour microenvironment; (v) the immune system; and (vi) stem cells. In each case, we examine open questions in the scientific literature through a philosophical methodology and show the benefit of such a synergy for the scientific and medical understanding of cancer.

In this article, I address the question of what Developmental Systems Theory aims at explaining. I distinguish two lines of thought in DST, one that deals specifically with development and tries to explain the development of the individual organism, and the other that presents itself as a reconceptualization of evolution and tries to explain the evolution of populations of developmental systems. I emphasize that, despite the claim of the contrary by DST proponents, there are two very different definitions of the “developmental system,” and therefore DST is not a unified theory of evolution and development. I show that DST loses the most interesting aspects of its reconceptualization of development when it tries to reconceptualize evolutionary theory. I suggest that DST is about development per se, and that it fails at offering a new view on evolution

The presence and role of microbes in human cancers has come full circle in the last century. Tumors are no longer considered aseptic, but implications for cancer biology and oncology remain underappreciated. Opportunities to identify and build translational diagnostics, prognostics, and therapeutics that exploit cancer's second genome—the metagenome—are manifold, but require careful consideration of microbial experimental idiosyncrasies that are distinct from host‐centric methods. Furthermore, the discoveries of intracellular and intra‐metastatic cancer bacteria necessitate fundamental changes in describing clonal evolution and selection, reflecting bidirectional interactions with non‐human residents. Reconsidering cancer clonality as a multispecies process similarly holds key implications for understanding metastasis and prognosing therapeutic resistance while providing rational guidance for the next generation of bacterial cancer therapies. Guided by these new findings and challenges, this Review describes opportunities to exploit cancer's metagenome in oncology and proposes an evolutionary framework as a first step towards modeling multispecies cancer clonality. Also see the video abstract here: https://youtu.be/-WDtIRJYZSs.

This volume is the best available tool to compare and appraise the different approaches of today’s biology and their conceptual frameworks, serving as a springboard for new research on a clarified conceptual basis. It is expected to constitute a key reference work for biologists and philosophers of biology, as well as for all scientists interested in understanding what is at stake in the present transformations of biological models and theories. The volume is distinguished by including, for the first time, self-reflections and exchanges of views on practice and theoretical attitudes by important participants in recent biological debates. The questions of how biological models and theories are constructed, how concepts are chosen and how different models can be articulated, are asked. Then the book explores some of these convergences between different models or theoretical frameworks. Confronting views on adaptive complexity are investigated, as well as the role of self-organization in evolution; niche construction meets developmental biology; the promises of the emergent field of ecological-evolutionary-development are examined. In sum, this book is a marvellous account of the dynamism of today’s theoretical biology. Foreword: Carving Nature at its Joints? Richard Lewontin Chapter 1: Introduction Anouk Barberousse, Michel Morange, Thomas Pradeu Chapter 2: Articulating Different Modes of Explanation: The Present Boundary in Biological Research Michel Morange Chapter 3: Compromising Positions: The Minding of Matter Susan Oyama Chapter 4:ions, Idealizations, and Evolutionary Biology Peter Godfrey-Smith Chapter 5: The Adequacy of Model Systems for Evo-Devo: Modeling the Formation Of Organisms / Modeling the Formation Of Society Scott F. Gilbert Chapter 6: Niche Construction in Evolution, Ecosystems and Developmental Biology John Odling-Smee Chapter 7: Novelty, Plasticity and Niche Construction: The Influence of Phenotypic Variation on Evolution Kim Sterelny Chapter 8: The Evolution of Complexity Mark A. Bedau Chapter 9: Self-Organization, Self-Assembly, and the Origin of Life Evelyn Fox Keller Chapter 10: Self-Organization and Complexity in Evolutionary Theory, or, In this Life the Bread Always Falls Jammy Side Down Michael Ruse.

Resident microorganisms, known as the microbiota, are essential for many physiological functions including protection against pathogens. Microbiota is indeed required for proper immune system development and function, and can also host-independently protect against infections. Thus, a co-constructed view of host protection involving both host and microbiota, named ’co-immunity,’ has been proposed, and the idea of an ’immunological holobiont’ has been suggested. Yet this view of co-immunity might be too limited, as experimental work has shown that the immune system is involved in functions other than protection, essentially development and repair. Microbiota, through co-immunity, is thereby most likely involved in these functions, although strong evidence is currently lacking. Moreover, as our point of view is mainly host-centered, we may miss the implications of co-immunity at broader scales, including cellular and population levels. Intriguingly, co-immunity effects could be beneficial for one function and/or one level, while being detrimental for others. All these elements should be taken into consideration for microbiota manipulation, in order to avoid potentially harmful side effects.

Is it possible to explain and predict the development of living things? What is development? Articulate answers to these seemingly innocuous questions are far from straightforward. To date, no systematic, targeted effort has been made to construct a unifying theory of development. This novel work offers a unique exploration of the foundations of ontogeny by asking how the development of living things should be understood. It explores the key concepts of developmental biology, asks whether general principles of development can be discovered, and examines the role of models and theories.The two editors have assembled a team of leading contributors who are representative of the scientific and philosophical community within which a diversity of thoughts are growing, and out of which a theory of development may eventually emerge. They analyse a wealth of approaches to concepts, models and theories of development, such as gene regulatory networks, accounts based on systems biology and on physics of soft matter, the different articulations of evolution and development, symbiont-induced development, as well as the widely discussed concepts of positional information and morphogenetic field, the idea of a

Immunology is central to contemporary biology and medicine, but it also provides novel philosophical insights. Its most significant contribution to philosophy concerns the understanding of biological individuality: what a biological individual is, what makes it unique, how its boundaries are established and what ensures its identity through time. Immunology also offers answers to some of the most interesting philosophical questions. What is the definition of life? How are bodily systems delineated? How do the mind and the body interact? In this Element, Thomas Pradeu considers the ways in which immunology can shed light on these and other important philosophical issues. This title is also available as Open Access on Cambridge Core.

The unexpected roles of the microbiota in cancer challenge explanations of carcinogenesis that focus on tumor-intrinsic properties. Most tumors contain bacteria and viruses, and the host’s proximal and distal microbiota influence both cancer incidence and therapeutic responsiveness. Continuing the history of cancer–microbe research, these findings raise a key question: to what extent is the microbiota relevant for clinical oncology? We approach this by critically evaluating three issues: how the microbiota provides a predictive biomarker of cancer growth and therapeutic responsiveness, the microbiota’s causal role(s) in cancer development, and how therapeutic manipulations of the microbiota improve patient outcomes in cancer. Clarifying the conceptual and empirical aspects of the cancer-associated microbiota can orient future research and guide its implementation in clinical oncology.

Cancer is most commonly viewed as resulting from somatic mutations enhancing proliferation and invasion. Some hypotheses further propose that these new capacities reveal a breakdown of multicellularity allowing cancer cells to escape proliferation and cooperation control mechanisms that were implemented during evolution of multicellularity. Here we critically review one such hypothesis, named “atavism,” which puts forward the idea that cancer results from the re‐expression of normally repressed genes forming a program, or toolbox, inherited from unicellular or simple multicellular ancestors. This hypothesis places cancer in an interesting evolutionary perspective that has not been widely explored and deserves attention. Thinking about cancer within an evolutionary framework, especially the major transitions to multicellularity, offers particularly promising perspectives. It is therefore of the utmost important to analyze why one approach that tries to achieve this aim, the atavism hypothesis, has not so far emerged as a major theory on cancer. We outline the features of the atavism hypothesis that, would benefit from clarification and, if possible, unification.

Le Précis de philosophie des sciences vise à présenter, de manière pédagogique, l'état actuel des grandes questions et des grands domaines de la philosophie des sciences. C'est un ouvrage de niveau "intermédiaire", entre les ouvrages d'initiation et les ouvrages de recherche. Il peut être utilisé comme manuel pour des cours de philosophie des sciences au niveau Master, ainsi que dans le cadre de la préparation aux nouvelles épreuves d'épistémologie des CAPES scientifiques. Il a notamment pour vocation de servir de support de cours pour des enseignements en épistémologie et philosophie des sciences de niveau L3, M1 et M2.

This chapter introduces the main issues and themes of the volume. Approaches to individuality from metaphysics and philosophy of science are contrasted. Recent philosophical developments regarding concepts of biological and physical individuality are exposed. These research trends show how philosophy of physics and philosophy of biology address differently the question of what an individual is. Five main divergences are identified: the centrality of part-whole questions, the issue of identical individuals, the importance of the Principle of the Identity of Indiscernibles and, finally, the importance of structuralist concerns. At the end of the chapter, the structure of the book is explained in detail.

In this contribution, I show that Jean Gayon’s work operates an original synthesis between the history of scienceHistory of science, the philosophy of science and the life sciences. I propose that the philosophy of biology as it has been constructed since the 1970s could usefully draw inspiration from this synthesis to develop a much richer and more open analysis of current biological sciences. While the philosophy of biology is very strongly dominated by the biology of evolution, the history of biologyGayon, Jeanon the history of biology has opened up to practically all the major fields of contemporary biology (for example, cell biology, molecular biologyMolecular biology, or virology, among many others). Perhaps Jean Gayon’s work is an invitation to draw inspiration from this thematic diversity to construct a new philosophy of biology and, beyond that, a new synthesis between philosophy, history, and biology.