https://rosa.uniroma1.it/rosa04/organisms/issue/feed Organisms. Journal of Biological Sciences 2024-07-23T08:49:50+00:00 Editorial Board Andras.Paldi@ephe.psl.eu Open Journal Systems <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> https://rosa.uniroma1.it/rosa04/organisms/article/view/18555 Single Cell Sequencing Techniques and Biological Explanation 2024-06-13T13:21:42+00:00 Caroline Angleraux caroline@angleraux.com <p>The aim of this paper is to examine the type of biological explanation implied by single-cell sequencing, using established frameworks in the philosophy of biology, particularly those of new mechanical and systems biology. While investigating the extent to which new mechanistic philosophy or systems biology represent theoretical frameworks that align with single-cell sequencing, a part of -omics sequencing techniques, I claim that the objective of single-cell sequencing corresponds with the <em>zeitgeist </em>in theoretical philosophies of biology. The <em>zeitgeist</em> is a stance that advocates for a broader perspective on living organisms and that rejects reductionism. However, there remains a disparity between the scientific narrative and the practical capabilities of single-cell sequencing. Consequently, the conclusion drawn in this paper is that while single-cell sequencing aligns with the <em>zeitgeist </em>in certain theoretical philosophies of biology, it also acknowledges their theoretical limitations.</p> 2024-07-23T00:00:00+00:00 Copyright (c) 2024 Caroline Angleraux https://rosa.uniroma1.it/rosa04/organisms/article/view/18152 Polyploidization, Gene Duplication, and the Origin of Variability: Where is the Evidence? 2024-06-12T16:09:00+00:00 Milton H. Gallardo stefanonikolaevic@gmail.com Elkin Y. Suárez-Villota esuarezv@gmail.com <p>The origin of molecular complexity and its bearings on organismal novelty by duplication of primordial, ancestral states replaced the <em>ab initio</em> modelling to solve the dilemma of protein structure and precedes by far the advent of genome research. The insights of Margaret O. Dayhoff (1966) let her to conclude that ferrodoxins and other proteins were derived by doubling of short peptides and that proteins´ first folded domains arose by duplication, fusion, and diversification of shorter, ancestral peptides. Here, recent genetic, cytogenetic, and genomic data on protein evolution, genome size, and Hox genes patterns are critically analyzed, and the evolutionary importance of polyploidy and its mega cytogenetic effects are stressed. The empirical results from synthetic allopolyploids serve as fundamental knowledge to contend that interlineage crossings are the causal phenomena underlying the origin of macroevolutionary variation. Patterns of gene/genome duplications, the origin of complex proteins and the duplicated Hox gene clusters are signatures of ancient polyploidization, not derived massive events of unequal crossing over or polymerase slippage. Allopolyploidy and ancient gene transfers among the three domains of life generate such a variation that mutation rates based on common descend loose preponderance and the notion of tree of life gets suffocated in an entangled genomic bush. In short, we contend that duplications constitute the resulting outcome; not the source phenomenon that explains protein´s evolutionary complexity and macro phenotypic innovations. Metonymy should be avoided every time that allopolyploidization, not its consequential pattern of genome duplication, is causal of phenotypic variation leading to macroevolutionary innovations.</p> 2024-07-23T00:00:00+00:00 Copyright (c) 2024 Milton H. Gallardo, Elkin Y. Suárez-Villota https://rosa.uniroma1.it/rosa04/organisms/article/view/18136 Cancer, Cytologism and the Kinase Inhibitors Saga 2024-06-13T16:37:25+00:00 Carlos Sonnenschein carlos.sonnenschein@tufts.edu Andras Paldi Andras.paldi@ephe.psl.eu <p>The role of kinases in the cell cycle of unicellular eukaryotes and cells of multicellular organisms has been the object of numerous studies involving normal and cancer cells. These studies described in detail how two daughter cells are generated from a single normal or cancer mother cell. Among the thousands of participants in the cell cycle, kinases play a crucial role in the dynamic aspects of the cell cycle thanks to the phosphorylation of substrates with which they react. Inhibitors of these kinases have figured prominently among the strategies to treat cancers. However, evidence shows that the benefits that cancer patients accrued from this therapeutic approach have been of a limited degree. In this article, we review the rationale for adopting such a strategy and the factors that contribute to its shortcomings.</p> 2024-07-23T00:00:00+00:00 Copyright (c) 2024 Carlos Sonnenschein, Andras Paldi https://rosa.uniroma1.it/rosa04/organisms/article/view/18466 The Role of Biological Plasticity in Model-based Translational Research 2024-06-13T14:49:19+00:00 Jessica Bolker jbolker@unh.edu <div> <p class="AbstractBodyOrganisms"><span class="normaltextrun"><span lang="IT">Reports of low replicability and translatability of biomedical research have called the value of animal models into question. The problems are real, but abandoning animal research is not the solution. Rather, improving the translatability of model-based research requires attention to relevant differences between humans and models, and to attributes of the models themselves that are essential to both robust science and effective translation. One is biological plasticity, the responsiveness of individual organisms to complex and variable environments. Though under-represented in model systems (for both historical and practical reasons), plasticity is central to human biology. While there are good reasons to minimize environmentally-induced variation in model-based research, doing so may undermine its translatability by eliding the kinds of external influences that are critical to human development, health, and disease. Accounting for plasticity can strengthen both the replicability and the translatability of model-based studies; this paper identifies strategies for doing so at each stage of the research process. </span></span></p> </div> 2024-07-23T00:00:00+00:00 Copyright (c) 2024 Jessica Bolker https://rosa.uniroma1.it/rosa04/organisms/article/view/18557 Science Across the Abyss: Knitting Bridges with Butterflies 2024-06-13T16:16:21+00:00 Caroline Nicole Bacquet Perez caroline.bacquet@ikiam.edu.ec Jorge Batres jorgebatres@jorge.it <p>Science is built on the pursuit of answers to fundamental questions and the constant expansion of our understanding of the world around us. However, this effort has not been without challenges and inequalities. This article critically examines the issue of diversity in science and the notable disparities that persist in global scientific knowledge. Throughout history, the contributions of scientists from diverse regions and cultures have been pivotal to scientific advancement. Nevertheless, significant gaps in terms of access, funding, and recognition in the global scientific community still endure. We use the concept of the "abyss," as a metaphor for the disparities in scientific practices across diverse regions of the world within the context of globalization. We seek to shed light on how the abyss influences the very essence of scientific inquiry, ranging from disparities in access to knowledge to the limitations imposed by technology and resources. This article addresses how socioeconomic, gender, and geographical disparities impact who has the opportunity to engage in and lead scientific research. The decolonization of science and the incorporation of indigenous and local perspectives in research are highlighted as crucial ways to address these disparities. Additionally, the concept of participative science is explored as an inclusive approach that allows diverse communities to take part in scientific research. Ultimately, this exploration of diversity in science and disparities in scientific knowledge seeks to inspire deeper reflection on how we can work together to ensure that science becomes a truly global and representative endeavor, enriched by a multitude of perspectives and the collaboration of people from all corners of the world.</p> 2024-07-23T00:00:00+00:00 Copyright (c) 2024 Caroline Nicole Bacquet Perez https://rosa.uniroma1.it/rosa04/organisms/article/view/18556 Organicist Perspectives in Newly Published Biology Textbooks 2024-06-13T15:36:47+00:00 Carlos Sonnenschein carlos.sonnenschein@tufts.edu <p>Review of Bernd Rosslenbroich (2023). Propertiesof Life: Toward a Theory of Organismic Biology. Vienna Series in Theoretical Biology. Boston: The MIT Press.</p> <h2>&nbsp;</h2> 2024-07-23T00:00:00+00:00 Copyright (c) 2024 Carlos Sonnenschein