Organisms. Journal of Biological Sciences https://rosa.uniroma1.it/rosa04/organisms <p>ORGANISMS is an open access, peer-reviewed, online journal publishing articles of the highest quality pertaining to the fields of basic, translational, theoretical and clinical research.</p> <p><strong><em>FOREWORD</em></strong></p> <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> <br />(Leonardo da Vinci)</p> <p>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. <strong><em><span style="text-decoration: underline;"><a title="Foreword" href="https://rosa.uniroma1.it/rosaXXX04_3214/organisms/management/settings/context//index.php/Organisms/about/editorialPolicies#custom-3" target="_self">read more</a></span></em></strong></p> <p><em><span style="text-decoration: underline;"><strong> </strong></span></em></p> <p><strong><em>NEW CALL<br /></em></strong></p> <p>The impact of publications in the sciences at large and in biology in particular is subject to a number of variables that depend on whether they are noticed, evaluated and/or interpreted correctly, or just ignored. Perhaps Gregor Mendel’s paper in 1865 is the most dramatic example of such an outcome. It was only 35 years later that its significance was “rediscovered”. <strong><span style="text-decoration: underline;"><em><a title="Announcement" href="https://rosa.uniroma1.it/rosaXXX04_3214/organisms/management/settings/context//index.php/Organisms/announcement" target="_self">read more</a></em></span></strong></p> 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="https://www.dropbox.com/s/ask2aqyyebns7sh/publishing_contract.doc?dl=0">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="http://i.creativecommons.org/l/by/3.0/88x31.png" 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="http://creativecommons.org/licenses/by/3.0/">Licence scheme</a> | <a href="http://creativecommons.org/licenses/by/3.0/legalcode">Legal code</a></p> Where is Science Going? The Main Road Overlaps Disciplines and Crosses Reductionism https://rosa.uniroma1.it/rosa04/organisms/article/view/17751 <p>Guest Editors' Preface to the Special Issue: Where is Science Going? Scenarios and Perspectives of Contemporary Technoscience</p> Dario Altobelli Jacopo Parravicini Nicola Schiavone Copyright (c) 2022 Dario Altobelli, Jacopo Parravicini, Nicola Schiavone https://creativecommons.org/licenses/by/3.0/legalcode 2022-05-05 2022-05-05 5 2 19 20 10.13133/2532-5876/17751 Popper's Nightmare https://rosa.uniroma1.it/rosa04/organisms/article/view/17640 <p>Epistemological relativism and authoritarianism are compressing political and intellectual freedoms by replacing facts with interpretations, as Karl Popper predicted several decades ago. Some suggestions to cope with this situation in science are provided.</p> Jacopo Parravicini Copyright (c) 2022 Jacopo Parravicini https://creativecommons.org/licenses/by/3.0/legalcode 2022-05-14 2022-05-14 5 2 10.13133/2532-5876/17640 Non-locality in the Science of the Millennium https://rosa.uniroma1.it/rosa04/organisms/article/view/17635 <p>The most recent experimental evidences of Quantum Physics and the new theoretical considerations connected to them have paradoxically questioned the basic founding principle of the scientific method, called the local realism principle. The main consequence of this cultural revolution is the need for a different approach to complexity in the world view through a phenomenon that I have called quantum synchronicity.<br />Quantum synchronicity is a phenomenon that is associated with the principle of cause-effect and tells us that in the quantum world there is an intrinsic correlation between systems, not attributable to a recognizable and expressible physical interaction, which means that a quantum system, and in general the entire universe, cannot be traced back even in principle to a set of separable parts, which can be defined locally and interacting only according to causality. The non-local quantum vision has its laws, potentials and limits, which we are learning to know and use for our evolution. The possibilities are largely yet to be explored, and range from technological applications, such as the quantum computer that is almost ready to be commercialized with immense implications in information management, to a revolution in looking at our essence and the world that contains us as inseparable elements.</p> Paolo Silvestrini Copyright (c) 2022 Paolo Silvestrini https://creativecommons.org/licenses/by/3.0/legalcode 2022-05-05 2022-05-05 5 2 27 40 10.13133/2532-5876/17635 The Synchronic Principle for a New Scientific Method https://rosa.uniroma1.it/rosa04/organisms/article/view/17633 <p>Local realism has been superseded by recent theoretical and experimental developments in quantum physics, which show a synchronic connection between the parts. In contrast to the principle of local realism, which is the basis of classical reductionism, I have called the principle of non-locality, “synchronic principle”. In a synchronic paradigm, evolution is characterized by a certain intrinsic freedom of choice that we associate with awareness. Considerations based on the evolution of the universe towards the emergence of life lead us to think that this “awareness” also exists in the vacuum state. In the model, I proposed a definition of the agents of consciousness in terms of arrays of correlated qu-bit, from the simplest one, which consists of 6 qu-bits of the quantum vacuum (a superposition of 64 base states), up to the most complex organisms consisting of a very large number of correlated quantum bits. Some of the fundamental vacuum states of consciousness can be related to known elementary particles (leptons and quarks) and to fundamental interactions. The rest constitutes purely non-local elements of consciousness with no counterpart in terms of wave or particle within the local observation limit. In this model, consciousness processes quantum information through logic gates and collapses as a result of observations, like a quantum computer does. Synchronicity does not deny the conclusions reached by traditional science. It can work at the local level, but opens scientific knowledge to new possibilities, and invites us to look at the world through a different, non-local awareness.</p> Paolo Silvestrini Copyright (c) 2022 Paolo Silvestrini https://creativecommons.org/licenses/by/3.0/legalcode 2022-05-05 2022-05-05 5 2 10.13133/2532-5876/17633 Einstein Classical Program Revived https://rosa.uniroma1.it/rosa04/organisms/article/view/17626 <p style="margin-bottom: 0cm; line-height: 0.35cm;" align="justify">The Einstein Classical Program is well known: to prove that, at least in the domain of atomic physics, quantum mechanics can be recovered from a theory presenting some “realistic character’’. Here we address an extreme form of the program in which the realistic theory is just classical electrodynamics of point charges, and give concrete examples in which typical “quantum phenomena’’ are explained. Namely, spectral lines (in the case of ionic crystals) and chemical bond (in the case of the H2+ ion of the Hydrogen molecule). Additionally, an explanation is given of a phenomenon (existence of polaritons in ionic crystals), for which a quantum explanation is still lacking. Concerning the general objection that a classical theory would be impossible because of radiative collapse (radiation emission by accelerated charges), we illustrate how it is removed for charges in a medium, in virtue of the Wheeler-Feynman cancellation. The impact of such results for the general reductionistic program is also commented.</p> Andrea Carati Luigi Galgani Copyright (c) 2022 andrea carati, Luigi Galgani https://creativecommons.org/licenses/by/3.0/legalcode 2022-05-05 2022-05-05 5 2 53 61 10.13133/2532-5876/17626 Data, Knowledge, and Theory: A Biostatistician’s Perspective https://rosa.uniroma1.it/rosa04/organisms/article/view/17620 <p>This commentary, inspired by a recent opinion piece of noted biologist Paul Nurse, overviews the interplay between data and various types of scientific knowledge within the realms of prediction, data patterns, causal inference, and scientific theory.</p> Stuart Glenn Baker Copyright (c) 2022 Stuart Glenn Baker https://creativecommons.org/licenses/by/3.0/legalcode 2022-05-05 2022-05-05 5 2 10.13133/2532-5876/17620 The Enigma of cancer resistance to treatment https://rosa.uniroma1.it/rosa04/organisms/article/view/17613 <p>Polyploid giant cancer cells (PGCC) are evaluated by histopathologists for cancer diagnosis, yet their role in cancer is poorly understood. In this essay, we highlight a particular aspect of these cells in relation to genomic self-organisation and transcriptional networks with relevance to treatment resistance. Embodying dynamic restructuring of the genomic network, epigenome and microenvironment, through explorative adaptation in response to sublethal challenge these cells operate at the edge of chaos and order. This state is manifested through oscillations in opposing cell fate pathways, with accelerated senescence coupled to reprogramming and an atavistic shift towards phylogenetically ancient unicellular genetic programmes accessed through bivalent mediator genes. It recapitulates certain unicellular life-cycles in a cancer “life-cycle” which reciprocally connects the somatic &nbsp;mitotic cell cycle with the germline cycle of the PGCC.</p> Jekaterina Erenpreisa Kristine Salmina Olga Anatskaya Alexander Vinogradov Mark Cragg Copyright (c) 2022 Dr. Jekaterina Erenpreisa, Dr. Kristine Salmina, Dr. Olga Anatskaya, Dr. Alexander Vinogradov, Dr. Mark Steven Cragg https://creativecommons.org/licenses/by/3.0/legalcode 2022-05-05 2022-05-05 5 2 71 75 10.13133/2532-5876/17613 Complexity: the Role of Information in Organizing Chance https://rosa.uniroma1.it/rosa04/organisms/article/view/17651 <p>A review on some of the more relevant results arising from the crisis of reductionism in different contexts of sciences, starting from the late XIX century until our days, leading to complexity theory and the problem of foundations is presented. Relation between complexity and mathematical non-linearity is emphasized. A mention of Chaitin’s compressibie/incompressibie strings to be compared to the philosophical notion of universal is suggested. A comparison of today’s notion of information, especially in its algorithmic version, and the Aristotelian-Thomisitc notion of form, is suggested. In particular we show, by the aid of pictures and animations, how chance can generate stable order and organization only if some information drives the dynamics of the process. Starting from random initial conditions, suitable information leads the evolution trajectories of each cell (element) of some system (either simple or complex) towards a precise attractor. Examples of fractals, galaxies and models of a biological organ in a living system, like a human heart, generated by stem cells are proposed. Ancient Aristotelian-Thomistic logic/ontology appears to be more close to contemporary science than in the past centuries; a result which may contribute constructively even to philosophy, beside science.</p> Alberto Strumia Copyright (c) 2022 Alberto Strumia https://creativecommons.org/licenses/by/3.0/legalcode 2022-05-05 2022-05-05 5 2 77 85 10.13133/2532-5876/17651 Science and the Dragon: Redistributing the Treasure of Knowledge https://rosa.uniroma1.it/rosa04/organisms/article/view/17628 <p><span style="font-weight: 400;">We start from an analogy: science can be seen as one of the dragons of Western mythology, described as sitting on their hoard of gold but not using it for any useful purpose. Similarly, scientists seem to be content with accumulating knowledge, doing little or nothing to use it outside their restricted domain of expertise. We argue that this attitude is one of the elements causing the ongoing decline of science as a way to produce innovative knowledge. We propose that the situation could be improved by encouraging scientific communication and the redistribution of the scientific treasure of knowledge in the form of “mind-sized” memes. </span></p> Ugo Bardi Ilaria Perissi Luisella Chiavenuto Alessandro Lavacchi Copyright (c) 2022 Ugo Bardi, Dr. , Ms, Dr. https://creativecommons.org/licenses/by/3.0/legalcode 2022-05-06 2022-05-06 5 2 87 94 10.13133/2532-5876/17628 Habeas Mentem and Neurotechnology: A Brief Introduction to the Ethical Problem of Neurorights Protection https://rosa.uniroma1.it/rosa04/organisms/article/view/17649 <p>Over the last twenty years neuroscience has evolved much more rapidly than the ability to update national and international human rights law. In this regulatory vacuum new and potentially dangerous market niches have been created for more and less invasive devices dedicated to our mental activities. How, and in which contexts, it is still possible to fill this serious gap is a topic that the scientific community and civil society must discuss as soon as possible. Otherwise, dystopian scenarios might open up, in which algocracy and technocracy could converge into a regime of perpetual overpowering of our humanity.</p> Julie Bicocchi Copyright (c) 2022 Julie Bicocchi https://creativecommons.org/licenses/by/3.0/legalcode 2022-05-05 2022-05-05 5 2 95 99 10.13133/2532-5876/17649 RNA-based Vaccines against SARS-CoV-2: A Word of Caution and an Analysis of Potential Long-term Adverse Events https://rosa.uniroma1.it/rosa04/organisms/article/view/17641 <p>This paper briefly discusses the mechanism and potential of still unknown side-effects of RNA-based vaccines against SARS-CoV-2.</p> Carlo Gambacorti-Passerini Andrea Aroldi Copyright (c) 2022 Carlo Gambacorti-Passerini, Andrea Aroldi https://creativecommons.org/licenses/by/3.0/legalcode 2022-05-05 2022-05-05 5 2 10.13133/2532-5876/17641 A Century of Empty Promises? https://rosa.uniroma1.it/rosa04/organisms/article/view/17747 Copyright (c) 2022 Organisms https://creativecommons.org/licenses/by/3.0/legalcode 2022-05-05 2022-05-05 5 2 5 6 10.13133/2532-5876/17747 Upper Limb Structural Anatomic Mechanisms of Protection (SAMPs) https://rosa.uniroma1.it/rosa04/organisms/article/view/17748 <p>Introduction Nature has provided living bodies with extraordinarily effective reparative mechanisms. Furthermore, the biological processes involved in anatomical structures are built-up to protect life against external injuries. A series of these protective systems in the upper limb are herein described. Material and Methods From 2009 to 2017, 864 fresh frozen cadaveric upper limbs were dissected from the axilla to the fingers during the Italian Hand Society surgical anatomy dissection course. Results Arrangement of anatomical structures in the upper limb is able to protect major life supporting organs. Conclusions External injuries affecting the upper limb may cause damage to many important structures resulting in severe functional impairments. The layout of the structures and the relationship between them are organized to preserve arteries integrity first, more than muscles and nerves. This means, in our opinion, that these structures are organized to preserve life even if this has functional cost.</p> <p>Keywords: protection mechanisms, upper limb, anatomy, injury</p> <p>Note: this is a slightly revised version of: Marzella, L, De Vitis, R, Gravina, P, Ricci G, &amp; De Francesco, F, 2021, “Upper Limb Structural Anatomic Mechanisms of Protection (SAMPs)”, Organisms: Journal of Biological Sciences, published online ahead of print December 30 2021. DOI: 10.13133/2532-5876/17506</p> Giulia Ricci Rocco De Vitis Luciana Marzella Pasquale Gravina Francesco De Francesco Copyright (c) 2022 Giulia Ricci, Rocco De Vitis, Luciana Marzella, Pasquale Gravina, Francesco De Francesco https://creativecommons.org/licenses/by/3.0/legalcode 2022-05-05 2022-05-05 5 2 7 17 10.13133/2532-5876/17748