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> Review of Thomas McCabe (ed.) 2021, Descent and Logic in Biosystematics. Juneau: Perseverant Publishing https://rosa.uniroma1.it/rosa04/organisms/article/view/17541 <p>Review of: Thomas McCabe (ed.) 2021, Descent and Logic in Biosystematics. Juneaus: Pereseverant Publishing</p> Alessandro Giuliani Copyright (c) 2021 Alessandro Giuliani https://creativecommons.org/licenses/by/3.0/legalcode 2021-08-10 2021-08-10 87 88 10.13133/2532-5876/17541 Genetics and Epigenetics of Immortality from Bacteria to Humans https://rosa.uniroma1.it/rosa04/organisms/article/view/17508 <p>In humans the search for immortality became concretized by 6,000 B.C. leading to the building of large tombs and statues to <br>immortalize the dead. This refusal to accept death is not limited to Homo sapiens. It occurs already in bacteria, extends to invertebrates and vertebrates, and includes even plants which avoid death by activating defense genes. <br>It turns out that consciousness is an obligatory prerequisite of death refusal. Experiments in single cell organisms (protozoa) <br>revealed that a minimal memory of a previous attack was a prerequisite to initiate active defense. Already in plants consciousness <br>is directly connected with the expectation of danger. They get advanced information from volatile compounds released from other plants that elicit their defense against insects. Consciousness is also not connected with larger brains, as disclosed by a comparison of the number of neurons in birds and apes.<br>Cloning is a natural form of ensuring immortality, which has been used by plants and animals before humans appeared on the <br>planet. Cloning in humans was considered in the 1930s suggesting the cloning of Einstein. This procedure is not ethical and irrelevant. Besides such an individual would not have easily survived the harassment of the mass media.<br>More significant is that epigenetic effects disrupt and diminish the perpetuation of immortality by changing the genome. The <br>evidence on epigenetics is now overwhelming extending from the simple eukaryotes (yeast) to plants and humans. RNAs have an <br>important role in modifying gene function during development and they can even be incorporated into the genome creating novel gene constellations. Immortality is becoming more difficult to achieve than expected.</p> Antonio Lima-de-Faria Copyright (c) 2021 Antonio Lima-de-Faria https://creativecommons.org/licenses/by/3.0/legalcode 2021-08-10 2021-08-10 17 31 10.13133/2532-5876/17508 Control of Cell Proliferation: Is the Default State of Cells Quiescence or Proliferation? https://rosa.uniroma1.it/rosa04/organisms/article/view/17338 <p>The control of cell proliferation in multicellular organisms remains a perennially controversial subject in experimental biology. In this essay, we examine the historical background and the rationale adopted by diverse theoretical and experimental research programs aimed at explaining <em>how</em> and <em>why</em> cells proliferate. We examine the premises that favor the notion that cells in multicellular organisms require direct stimulation from the outside (a task attributed to alleged growth factors) or from the inside (through the elusive action of oncogenes). Our analysis suggests that neither growth factors nor oncogenes directly stimulate the proliferation of cells. Based on evolutionary precedents, theoretical considerations and empirical data we posit instead that proliferation is the default state of all cells; thus, a search for extra- and intra-cellular inhibitory constraints promises to be productive when explaining this basic property of cells within the context of normal and abnormal developmental biology.</p> Carlos Sonnenschein Ana M Soto Copyright (c) 2021 Carlos Sonnenschein, Ana M Soto https://creativecommons.org/licenses/by/3.0/legalcode 2021-08-10 2021-08-10 33 42 10.13133/2532-5876/17338 What is the Value of Science? https://rosa.uniroma1.it/rosa04/organisms/article/view/17390 <p>In our time, scientific research is positively valued as long as, and to the extent that, it has fruitful implications for the development of technology. This is what we may call “the technological assessment of science”, or “technologism”, for short. I contend that this assessment, so widespread today, stems from a serious error of appreciation, both historically and epistemologically, in ignoring the genuine nature of science—a mistake that can lead, and indeed has been leading for a few decades, to the impoverishment of the scientific spirit and of culture in general.</p> Carlos Ulises Moulines Copyright (c) 2021 Carlos Ulises Moulines https://creativecommons.org/licenses/by/3.0/legalcode 2021-08-10 2021-08-10 43 56 10.13133/2532-5876/17390 Epidemiology, Ecology, and Evolution of Human-Virus Interaction: An Overview of the Relevance to Human Health and Disease https://rosa.uniroma1.it/rosa04/organisms/article/view/17539 <p>Acquiring a systemic perspective on epidemic events is mandatory in an age in which such events are rapidly growing in both number and spatial distribution. In this work we describe the human/virus interaction through the ‘deep time’ of evolution. We show how ancient epidemics shaped animal and human biology influencing basic traits like multi-cellularity, immunity and cancer. Furthermore, on a much shorter time scale, we focus on the role played by globalization and anthropogenic environmental deterioration in the growing menace of recurring pandemics.</p> Carlo Modonesi Alessandro Giuliani Copyright (c) 2021 Carlo Modonesi, Alessandro Giuliani https://creativecommons.org/licenses/by/3.0/legalcode 2021-08-10 2021-08-10 10.13133/2532-5876/17539 The concept of nature between Heraclitus and Prigogine https://rosa.uniroma1.it/rosa04/organisms/article/view/17540 <p>In the Greek tradition, “physis” denotes both the “nature” (the “essence”) of an entity and its accomplishment, that is to say, its “development”. For example, the embryo is the “essence” of the unfolding organism and, at the same time, the process leading to it. The egg is a symbol of wholeness, but this totality cannot be perceived out of its self-organizing process. In this way, according to Heraclitus, the living being “hides.” Essentially, the Self can only be recognized as an outcome rather than a starting point. This stance, endorsed by Heraclitus and Aristotle, has been left aside by modern scientific research since Bacon’s time when the less noble Stoic inheritance was tacitly assumed. In Stoics’ belief, physis means power (God or otherwise), i.e. the causal principle (causa prima), which is involved in generating any natural process. Having emphasized the “cause”—even in absence of a clear definition of such a concept—the “real process” lost its relevance and its intelligibility was impaired. The description of the process began to be confused with the description of the “entity” (the thing-in-itself), and this representation eventually ended up identifying the “essence” with its (presumed) “primary” causes. This way, natural things and/or processes were re-absorbed into their presumptive causes, missing the true complexity of the natural system.</p> Mariano Bizzarri Copyright (c) 2021 Mariano Bizzarri https://creativecommons.org/licenses/by/3.0/legalcode 2021-08-10 2021-08-10 67 71 10.13133/2532-5876/17540 Programming Evolution: A Crack in Science https://rosa.uniroma1.it/rosa04/organisms/article/view/17538 <p>Nobel Prize winner, Jennifer Doudna, and Samuel Sternberg survey recent advances in a pioneering area of molecular biology. In an accessible and elegant style, the authors present the successes and challenges of a new DNA-modifying technique: CRISPR. They transmit their emotions of discovery, passion for research, and intellectual audacity. While greatly admiring the technical skills of the authors, who are among the best researchers in the field, this review critically stresses the limits of their experimental practices, namely: a vague or incomplete theoretical frame; often unreachable genetic targets; off-target effects; prior failures to deliver by other forms of genetic manipulation, and, finally, the intrinsic unpredictability of many phenotypic consequences of such a powerful technique. Due to these concerns, the authors’ approach to organisms and Evolution is questioned with the purpose to generate an open debate.</p> Giuseppe Longo Copyright (c) 2021 Giuseppe Longo https://creativecommons.org/licenses/by/3.0/legalcode 2021-08-10 2021-08-10 10.13133/2532-5876/17538