Organisms. Journal of Biological Sciences <div id="custom-3"> <h3>FOREWORD</h3> <p><em>“He who loves practice without theory is like the sailor who boards ship without a rudder and compass and never knows where he is going”.</em> </p> <p>(Leonardo da Vinci)</p> <p style="text-indent: 40px;" align="justify">At the beginning of the 21st century, biology is facing an epistemological crisis which anticipates a paradigm change. Reductionism and the molecular analysis it favors have failed to bring about an understanding of complex phenomena in biology. This will require a reappraisal of old research concepts. The dominant view during the last fifty years has been that development is merely the unfolding of a genetic program.</p> <p style="text-indent: 40px;" align="justify">This perception is now being challenged by the resurgence of the once prominent fields of biological inquiry, namely, ecological and evolutionary developmental biology. However, these efforts remain few and far between because they are diluted by a sea of publications still based on reductionist interpretations. Meanwhile, there is no source explicitly committed to a perspective centered on organisms. Thus, there is a need for a journal dedicated to high quality theoretical and experimental work while promoting an interdisciplinary approach to the main topics in biology. We expect that “ORGANISMS” will fill this gap by addressing biological questions from perspectives different from the currently prevalent one.</p> <p style="text-indent: 40px;" align="justify">The philosopher Kant stated that in organisms "every part is thought as owing its presence to the agency of all the remaining parts, and also as existing for the sake of the others and of the whole". This conception of organisms is as central to biology today as it was when it inspired generations of embryologists, the ones invoked when referring to Müllerian ducts, germ layers, and notochord. From this perspective, the causal determination of biological phenomena is not exclusively bottom-up; the agency of each part implies a complex and reciprocal structure of determination. Research programs based on the ideas advanced by those who favored the molecular biology revolution have unintentionally shown that organisms cannot be analyzed only in terms of genes and molecules. This statement will not surprise physicists, because they do not intend to reduce one theory onto another, say classical or relativistic physics to quantum mechanics. Instead, they strive for unifications, that is, for a new theory encompassing two or more theoretical frames. And yet, mainstream biologists are still committed to uncovering the molecular mechanisms that according to reductionism will provide an explanation to every biological phenomenon. The technological improvements conceived to address mechanisms have generated an avalanche of data but biologists neither have the theoretical bases nor an adequate language to make sense of them, particularly when trying to explain the advent of new functions, the generation of shapes (morphogenesis), or the ability of the organism to create its own rules. We acknowledge that the language generated by the molecular biology revolution, namely the concepts of information, program, signal, is theoretically laden forcing causal analysis toward molecules supposed to carry information, such as genes and their products. This structure of determination is inimical to the study of organisms. Consequently, a change of theoretical frame will also require that biologists elaborate a different language, free of these connotations.</p> <p style="text-indent: 40px;" align="justify">Finally, this journal is neither married to a theory nor does it represent the view of a particular group. Its purpose is to encourage researchers to submit manuscripts that a) make explicit the postulates, principles and perspectives that form the conceptual framework of their research subjects, b) foster theoretical and experimental work in the vast field of biology, and c) promote the salutary effect of “friction” between theory and experiment.</p> </div> <div id="custom-4"> <h3>Ahead of Printing</h3> <p>Organisms publishes Ahead of Printing articles, that come online before they appear in a regular issue of the journal. Ahead of Printing articles are copy edited, typeset and approved by the author before being published.</p> <p>Each Ahead of Printing article has a unique Digital Object Identifier (DOI). This should be included in all citations.</p> <p>Please, use this citation format:</p> <p><strong>Before the article has appeared in an issue</strong><br />Lazebnik, Y, 2018, “Who is Dr. Frankenstein? Or, what Professor Hayek and his friends have done to science”, Organisms. Journal of Biological Sciences, Ahead of Printing (November 2018), DOI: 10.13133/2532-5876_XXX<br /><br /><br /></p> <p><strong>After the article has appeared in an issue</strong><br />Lazebnik, Y, 2018, “Who is Dr. Frankenstein? Or, what Professor Hayek and his friends have done to science”, Organisms. Journal of Biological Sciences, Vol.2, No.2, pp. xx_xx, DOI: 10.13133/2532-5876_XXX</p> </div> Department of Experimental Medicine en-US Organisms. Journal of Biological Sciences 2532-5876 <h4>Copyright Agreement with Authors</h4><p>Before publication, after the acceptance of the manuscript, authors have to sign a <strong><a href="">Publication Agreement</a></strong> with <em><strong>Organisms</strong></em>. The authors retain all rights to the original work without any restrictions.</p><h4>License for Published Contents</h4><p><img src="" alt="Licenza Creative Commons" /><br />You are free to copy, distribute and transmit the work, and to adapt the work. You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work).</p><p><a href="">Licence scheme</a> | <a href="">Legal code</a></p> Single-cell Molecular Analysis: When an Experimental Technique Generates Conceptual Controversies <p>The last decade has witnessed a rapid evolution of highly sensitive single-cell molecular analysis techniques. These techniques allow the simultaneous detection and quantification of mRNA and protein molecules in a large number of individual cells. Some of these methods are already commercialized, making them readily available to any interested lab. While the pitfalls concerning the experimental extraction of biocomponents (mRNA and protein) and analytical bioinformatic methods are widely discussed in the literature, little is known regarding the conceptual difficulties raised by single-cell methodologies. Considered and treated as pure technical difficulties, these issues are rarely discussed explicitly. This is a problem as conceptual difficulties precede technical ones and contribute, to a large extent, to the failure of techniques. Consequently, a new theoretical framework is urgently needed to make sense of the ever-increasing amount of data.</p> Andras Paldi Laëtitia Racine Copyright (c) 2023 Andras Paldi, Racine Laëtitia 2023-11-14 2023-11-14 6 2 25 30 10.13133/2532-5876/18129 Do Single-cell Experiments Challenge the Concept of Cell Type? <p>Recent debates among biologists have highlighted problems with the traditional concept of cell type, which is considered vague and subjective. Single-cell technologies reveal the limitations of the current concept by exposing a high degree of heterogeneity in cell populations. At the same time, some biologists believe that these technologies provide the basis for a more objective and precise concept of cell type that is not dependent on prior theoretical assumptions. In this paper, I explore the impact that single-cell experiments and analyses will have on the concept of cell type. Drawing on the practices of biologists using these methods, but also on more principled arguments, I argue that the idea of a purely theory-free classification is unlikely to be realized. However, single-cell technology may affect the concept of cell type in more subtle ways.</p> Fridolin Gross Copyright (c) 2023 Fridolin Gross 2023-11-14 2023-11-14 6 2 10.13133/2532-5876/18131 The Contrasting Role of Single-cell Studies in the Theoretical Debate on Determinism in Molecular Biology <p>In experimental biology, the last three decades have seen a flood of techniques dedicated to study biological phenomena at the single-cell level, and this article aims to reflect on how these technical advances can contribute to the renewal of theoretical perspectives in biology. The case studied here is that of the critique of the genetic determinism of molecular biology. The demonstration of unpredictability in gene expression at the single-cell level, a phenomenon known as stochastic gene expression, even in clonal populations, initially appeared to be a decisive indication that cells do not actually behave as predicted by deterministic frameworks. However, single-cell techniques have also revealed other sources of genetic variation that nuance this picture. The role of single-cell studies thus appears contrasted, and can be used to support or challenge the paradigm of genetic determinism (GDP). This opens up a more general debate on the practical ability of molecular biologists to criticize their own paradigms.</p> Thomas Heams Copyright (c) 2023 Thomas Heams 2023-11-14 2023-11-14 6 2 31 42 10.13133/2532-5876/18306 The Common Origin of Multicellularity and Cancer: Lessons from the Fossil Record <p>Despite the methodological limitations in the study of fossil record and some confusion in the literature about the diagnostic distinction between real neoplasia and other types of proliferation or even malformations in species very distant from mammals, paleopathological studies have revealed many cases of bona fide benign as well as malignant neoplasms in animals and land plants since Paleozoic Era onwards. Further, almost all types of modern neoplastic diseases have been documented in ancient Homo sapiens bone remains. It is worth to note that, despite the major changes in the structure of animal populations, the prevalence of malignant as well benign neoplasms has remained relatively constant (and in some cases it has even increased), among the different taxa of animals for hundred million years suggesting that malignancies as well as benign neoplasms are rooted quite deeply in the evolutionary life of organisms. This seemingly unremarkably fact represents a remarkable riddle for evolutionary biologists. If natural selection, working on living organisms has been powerful enough to produce complex adaptations, from the eye to the immune system, why has it been unable to eliminate or even reduce the incidence of cancer, even though many apparently less harmful traits have been eliminated during species evolution. Based on the fact that, both today and in the fossil record, cancer seems to occur in organs that have experienced a decline or loss of their regenerative ability we suggested that it may be an ultimate, even futile, reparative attempt. Therefore, the permanence of cancer by hundred million years might be understood if its existence is coupled to the normal regenerative mechanisms of the organisms without which no pluricellular organism could survive. This interpretation, encoded in the so-called hypothesis of the biological sense of cancer, was built within the broad framework of tissue organization field theory (TOFT) by assuming that cancer is primarily a disease of higher levels of organization, that is, an organismic, organ or tissue-based disease rather than a cellular one.</p> Daniela Montagna Raúl Ruggiero Copyright (c) 2023 Raúl Ruggiero, Daniela Montagna 2023-11-14 2023-11-14 6 2 43 69 10.13133/2532-5876/18130 New Genetically Modified Organisms (GMOs): Towards a “scientific precautionary principle” <p>To the ordinary precautionary principle, we should add a more precise “scientific precautionary principle”. In short, we cannot act on nature based on ‘dogmas’ that are either manifestly false or are implicitly adopting an uncritical way of thinking. Science is the invention of a new way of thinking, of new theoretical frameworks, starting from a critical review of the principles mobilized, which are themselves well explained. Without this, technoscience, in all its power, becomes a nightmare, as it is totally unsuited to make us live in an ecosystem with all its complexity. The case of New Genetic Technologies, whose application to agriculture is under discussion in Europe, is paradigmatic and urgent.</p> <p>*A preliminary version of this paper was published in French in Philosophy World Democracy, 1/9/23,</p> Giuseppe Longo Copyright (c) 2023 Giuseppe Longo 2023-11-14 2023-11-14 6 2 77 81 10.13133/2532-5876/18307 Celebrating Evelyn Fox Keller: “The Toronto Statement" <p>With much anticipation, in time and spirit, a group of historians and philosophers of biology, and theoretical and experimental biologists, met at the Institute for the History and Philosophy of Science and Technology at the University of Toronto, Canada, on 22 and 23 September 2023, to pay homage to Evelyn Fox Keller for her contributions to theoretical biology. The conference was supported and sponsored by the Department of Philosophy, Institute for the History and Philosophy of Science and Technology, Faculty of Arts and Science (all at University of Toronto), as well as the Social Sciences and Humanities Research Council of Canada. The workshop was an in-person celebration complementing the publication of a volume celebrating her work (Vicedo &amp; Walsh 2020a, 2020b), which includes the following contributions: (Herrington &amp; Jablonka 2020; Longo &amp; Mossio 2020; Radick 2020; Riskin 2020; Soto &amp; Sonnenschein 2020; Walsh 2020). After introductory remarks by Denis Walsh and a short video in which Evelyn Fox Keller thanked us for this homage and wished us well, we learned of her death.</p> Rasmus Grønfeldt Winther Eva Jablonka Giuseppe Longo Gregory Radick Sarah S. Richardson Jessica Riskin Gregory Rupik Ana M. Soto Carlos Sonnenschein Sonia Sultan Marga Vicedo Denis Walsh Anat Zeligowski Copyright (c) 2023 Rasmus G. Winther, Eva Jablonka, Giuseppe Longo, Gregory Radick, Sarah S. Richardson, Jessica Riskin, Gregory Rupik, Ana M. Soto, Carlos Sonnenschein, Sonia Sultan, Marga Vicedo, Denis Walsh, Anat Zeligowski 2023-11-14 2023-11-14 6 2 71 76 10.13133/2532-5876/18309 Process-philosophical Perspectives on Biology: Intuiting Life (Edited by Spyridon A. Koutroufinis and Arthur Araujo)—Philosophical Intuitions for a New Understanding of Life <p>Book review</p> Mariano Bizzarri Copyright (c) 2023 Mariano Bizzarri 2023-11-14 2023-11-14 6 2 10.13133/2532-5876/18310 Special Issue, “Single-cell Analysis: Epistemological Inquiries” <p>Editorial</p> Caroline Angleraux Matteo Mossio Copyright (c) 2023 Caroline Angleraux, Matteo Mossio 2023-11-14 2023-11-14 6 2 5 9 10.13133/2532-5876/18311