Organisms. Journal of Biological Sciences 2023-01-17T00:00:00+00:00 Editorial Board 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> The Pandemic and the 'Techno-fix' 2022-02-09T10:04:08+00:00 Caroline Petit Giuseppe Longo <p>The current pandemic was an announced possibility. Its potential causes were known: destroyed ecosystem niches, declining biological diversity, intensive farming, abuse of genetics, and biological manipulations. This paper deals with some aspects of the biological (and social) history of the ongoing COVID-19 pandemic but also with the history of previous epidemics, including the AIDS epidemics, which all have in common to be highly linked, enhanced or even the result of human activities. But now, the myth is setting in that an innovative technique for fast production of vaccines is the only <em>and sufficient</em> response to the crisis in the ecosystem and in health structures, of which this pandemic is a symptom. The reductionist and mechanistic approaches to the ecosystem and human biology are feeding the idea that the natural world may be fully manipulated and controlled (“the power to control Evolution” as in a recent book by a Nobel Award winner). This article calls for a critical thinking about the interfaces between the technosphere and the biosphere, their limits as well as for new frameworks for biology and medicine.</p> 2023-01-17T00:00:00+00:00 Copyright (c) 2023 Petit, Longo Georges Canguilhem, the Health-Disease Transition and the Return of Organicism 2022-10-03T19:25:42+00:00 Ana Soto Carlos Sonnenschein <p><em>The Normal and the Pathological</em> is a remarkable book by Georges Canguilhem, originally published almost 80 years ago. It should play a much more important role in medical education and in the study and praxis of biology because of its rich and relevant approach to the knowledge of organisms. Indeed, only organisms can go through sickness and health; these states are axiological categories as they represent values. However, when it was published, the molecular biology revolution introduced the idea of genetic program and that organisms would be a kind of machine or computer. This concept combined the naive 19th-century physicalism with the metaphor of programs and signals borrowed from mathematical theories of information. As a consequence, the main concepts of biology, such as teleology, agency and normativity—the latter, a central concept in Canguilhem’s thought—were abandoned by biologists and medical doctors. <br />Over the last 20 years, the failure of ideas guiding the molecular biology revolution allowed for the growth of organicism, a tradition committed to the autonomy of biology and its irreducibility to physics and chemistry. These developments encouraged theoretical biologists and philosophers to re-examine the aforementioned biological concepts rejected by reductionism. Their critical work produced versions of these concepts that are now compatible with notions of scientific causality, and therefore, an opportunity to present Canguilhem’s work to new generations of biologists and physicians. <br />Canguilhem’s work advances the understanding of biological entities by introducing the axiological notion of individuality, the concept of organismal “normativity” (i.e. the capacity of organisms to create their own norms) and, related to these two concepts, the organism’s propensity to make mistakes—an exclusive property of biological systems.</p> 2023-01-17T00:00:00+00:00 Copyright (c) 2023 Ana Soto, Carlos Sonnenschein On the Meaning of Averages in Genome-wide Association Studies: What Should Come Next? 2022-07-15T15:58:26+00:00 Cyril Rauch Jonathan Wattis Sian Bray <p>Identifying the association between phenotypes and genotypes is the fundamental basis of genetic analyses.<br />Although genomic technologies used to generate data have rapidly advanced within the last 20 years, the statistical models used in genome-wide associations studies (GWAS) to analyze these data are still predominantly based on the model developed by Fisher more than 100 years ago. The question is, does Fisher’s theory need to be replaced or improved, and if so, what should come next? The theory developed by Fisher was inspired by the<br />field of probability. To make use of probability not only did Fisher have to assume valid a number of questionable<br />hypotheses, but he also had to conceptually frame genotype-phenotype associations in a specific way giving<br />primordial importance to the notion of average. However, the “average” in probability results from the notions<br />of “imprecision” or “ignorance”. After reviewing the historical emergence and societal impact of probability as<br />a method, it is clear what is needed now is a new method acknowledging precision in measurements. That is, a<br />method that does not rely on categorizing or binning data.</p> 2023-01-17T00:00:00+00:00 Copyright (c) 2023 Cyril Rauch Old Ideas Die Hard, Particularly in Cancer Biology 2022-10-03T19:22:53+00:00 Andras Paldi <p>-</p> 2023-01-17T00:00:00+00:00 Copyright (c) 2023 Andras Paldi What Happens with the Mind when the Brain Dies? 2022-12-13T16:19:17+00:00 Alex Gomez-Marin <p>A neuroscientist reflects on his near-death experience to ponder the nature of the human mind and the survival of consciousness after death. Ancient traditions, manifold personal experiences, nuanced philosophical views, and recent scientific evidence, all point to the brain as a filter (or receiver) of consciousness rather than its fanciful producer. No doubt, good-old-fashioned materialists —nowadays rebranded as physicalists, crypto-dualists, or illusionists wearing virtual reality goggles— insist that minds are “nothing but” what brains do. Nevertheless, a trans-materialist science can expand the scope and depth of the answers (and the questions) that really matter not only to science but also to human flourishing.</p> 2023-01-17T00:00:00+00:00 Copyright (c) 2023 Alex Gomez-Marin The Hallmarks of Failures in Cancer Research 2022-10-21T15:33:42+00:00 <p>.</p> 2023-01-17T00:00:00+00:00 Copyright (c) 2022 Carlos Sonnenschein