1
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Newman SA. Form, function, mind: What doesn't compute (and what might). Biochem Biophys Res Commun 2024; 721:150141. [PMID: 38781663 DOI: 10.1016/j.bbrc.2024.150141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/07/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing animal (metazoan) tissues, a non-computational modality, but cell differentiation, which utilizes chromatin-based revisable memory banks and program-like function-calling, via the developmental gene co-expression system unique to the metazoans, has a quasi-computational basis. Multi-attractor dynamical models are argued to be misapplied to global properties of development, and it is suggested that along with computationalism, classic forms of dynamicism are similarly unsuitable to accounting for cognitive phenomena. Proposals are made for treating brains and other nervous tissues as novel forms of excitable matter with inherent properties which enable the intensification of cell-based basal cognition capabilities present throughout the tree of life. Finally, some connections are drawn between the viewpoint described here and active inference models of cognition, such as the Free Energy Principle.
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2
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Watson R. Agency, Goal-Directed Behavior, and Part-Whole Relationships in Biological Systems. BIOLOGICAL THEORY 2023; 19:22-36. [PMID: 38463532 PMCID: PMC10920425 DOI: 10.1007/s13752-023-00447-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/17/2023] [Indexed: 03/12/2024]
Abstract
In this essay we aim to present some considerations regarding a minimal but concrete notion of agency and goal-directed behavior that are useful for characterizing biological systems at different scales. These considerations are a particular perspective, bringing together concepts from dynamical systems, combinatorial problem-solving, and connectionist learning with an emphasis on the relationship between parts and wholes. This perspective affords some ways to think about agents that are concrete and quantifiable, and relevant to some important biological issues. Instead of advocating for a strict definition of minimally agential characteristics, we focus on how (even for a modest notion of agency) the agency of a system can be more than the sum of the agency of its parts. We quantify this in terms of the problem-solving competency of a system with respect to resolution of the frustrations between its parts. This requires goal-directed behavior in the sense of delayed gratification, i.e., taking dynamical trajectories that forego short-term gains (or sustain short-term stress or frustration) in favor of long-term gains. In order for this competency to belong to the system (rather than to its parts or given by its construction or design), it can involve distributed systemic knowledge that is acquired through experience, i.e., changes in the organization of the relationships among its parts (without presupposing a system-level reward function for such changes). This conception of agency helps us think about the ways in which cells, organisms, and perhaps other biological scales, can be agential (i.e., more agential than their parts) in a quantifiable sense, without denying that the behavior of the whole depends on the behaviors of the parts in their current organization.
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Affiliation(s)
- Richard Watson
- Institute for Life Sciences/Electronics and Computer Science, University of Southampton, Southampton, UK
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3
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Silva A, Barcessat AR, Gonçalves R, Landre C, Brandão L, Nunes L, Feitosa H, Costa L, Silva R, de Lima E, Monteiro ES, Rinaldi A, Fontani V, Rinaldi S. REAC Neurobiological Modulation as a Precision Medicine Treatment for Fibromyalgia. J Pers Med 2023; 13:902. [PMID: 37373891 DOI: 10.3390/jpm13060902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/11/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Fibromyalgia syndrome (FS) is a disorder characterized by widespread musculoskeletal pain and psychopathological symptoms, often associated with central pain modulation failure and dysfunctional adaptive responses to environmental stress. The Radio Electric Asymmetric Conveyer (REAC) technology is a neuromodulation technology. The aim of this study was to evaluate the effects of some REAC treatments on psychomotor responses and quality of life in 37 patients with FS. Tests were conducted before and after a single session of Neuro Postural Optimization and after a cycle of 18 sessions of Neuro Psycho Physical Optimization (NPPO), using evaluation of the functional dysmetria (FD) phenomenon, Sitting and Standing (SS), Time Up and Go (TUG) tests for motor evaluation, Fibromyalgia Impact Questionnaire (FIQ) for quality of life. The data were statistically analyzed, and the results showed a statistically significant improvement in motor response and quality of life parameters, including pain, as well as reduced FD measures in all participants. The study concludes that the neurobiological balance established by the REAC therapeutic protocols NPO and NPPO improved the dysfunctional adaptive state caused by environmental and exposomal stress in FS patients, leading to an improvement in psychomotor responses and quality of life. The findings suggest that REAC treatments could be an effective approach for FS patients, reducing the excessive use of analgesic drugs and improving daily activities.
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Affiliation(s)
- Analízia Silva
- Department of Biological and Health Sciences, Federal University of Amapá-UNIFAP, Macapá 68903-419, Brazil
| | - Ana Rita Barcessat
- Department of Biological and Health Sciences, Federal University of Amapá-UNIFAP, Macapá 68903-419, Brazil
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Rebeca Gonçalves
- Department of Biological and Health Sciences, Federal University of Amapá-UNIFAP, Macapá 68903-419, Brazil
| | - Cleuton Landre
- Department of Biological and Health Sciences, Federal University of Amapá-UNIFAP, Macapá 68903-419, Brazil
| | - Lethícia Brandão
- Department of Biological and Health Sciences, Federal University of Amapá-UNIFAP, Macapá 68903-419, Brazil
| | - Lucas Nunes
- Department of Biological and Health Sciences, Federal University of Amapá-UNIFAP, Macapá 68903-419, Brazil
| | - Hyan Feitosa
- Department of Biological and Health Sciences, Federal University of Amapá-UNIFAP, Macapá 68903-419, Brazil
| | - Leonardo Costa
- Department of Biological and Health Sciences, Federal University of Amapá-UNIFAP, Macapá 68903-419, Brazil
| | - Raquel Silva
- Department of Biological and Health Sciences, Federal University of Amapá-UNIFAP, Macapá 68903-419, Brazil
| | - Emanuel de Lima
- Department of Biological and Health Sciences, Federal University of Amapá-UNIFAP, Macapá 68903-419, Brazil
| | - Ester Suane Monteiro
- Department of Biological and Health Sciences, Federal University of Amapá-UNIFAP, Macapá 68903-419, Brazil
| | - Arianna Rinaldi
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Department of Adaptive Neuro Psycho Physio Pathology and Neuro Psycho Physical Optimization, Rinaldi Fontani Institute, 50144 Florence, Italy
- Department of Regenerative Medicine, Rinaldi Fontani Institute, 50144 Florence, Italy
| | - Vania Fontani
- Department of Adaptive Neuro Psycho Physio Pathology and Neuro Psycho Physical Optimization, Rinaldi Fontani Institute, 50144 Florence, Italy
- Department of Regenerative Medicine, Rinaldi Fontani Institute, 50144 Florence, Italy
- Research Department, Rinaldi Fontani Foundation, 50144 Florence, Italy
| | - Salvatore Rinaldi
- Department of Adaptive Neuro Psycho Physio Pathology and Neuro Psycho Physical Optimization, Rinaldi Fontani Institute, 50144 Florence, Italy
- Department of Regenerative Medicine, Rinaldi Fontani Institute, 50144 Florence, Italy
- Research Department, Rinaldi Fontani Foundation, 50144 Florence, Italy
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4
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Caianiello S, Bertolaso M, Militello G. Thinking in 3 dimensions: philosophies of the microenvironment in organoids and organs-on-chip. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2023; 45:14. [PMID: 36949354 DOI: 10.1007/s40656-023-00560-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Organoids and organs-on-a-chip are currently the two major families of 3D advanced organotypic in vitro culture systems, aimed at reconstituting miniaturized models of physiological and pathological states of human organs. Both share the tenets of the so-called "three-dimensional thinking", a Systems Physiology approach focused on recapitulating the dynamic interactions between cells and their microenvironment. We first review the arguments underlying the "paradigm shift" toward three-dimensional thinking in the in vitro culture community. Then, through a historically informed account of the technical affordances and the epistemic commitments of these two approaches, we highlight how they embody two distinct experimental cultures. We finally argue that the current systematic effort for their integration requires not only innovative "synergistic" engineering solutions, but also conceptual integration between different perspectives on biological causality.
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Affiliation(s)
- Silvia Caianiello
- Institute for the History of Philosophy and Science in the Modern Age (ISPF), Consiglio Nazionale delle Ricerche, Naples, Italy.
- Stazione Zoologica "Anton Dohrn", Naples, Italy.
| | - Marta Bertolaso
- Faculty of Science and Technology for Sustainable Development and One Health, Universitá Campus Bio-Medico di Roma, Rome, Italy
| | - Guglielmo Militello
- Faculty of Science and Technology for Sustainable Development and One Health, Universitá Campus Bio-Medico di Roma, Rome, Italy
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5
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Funk RHW, Scholkmann F. The significance of bioelectricity on all levels of organization of an organism. Part 1: From the subcellular level to cells. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 177:185-201. [PMID: 36481271 DOI: 10.1016/j.pbiomolbio.2022.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/24/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022]
Abstract
Bioelectricity plays an essential role in the structural and functional organization of biological organisms. In this first article of our three-part series, we summarize the importance of bioelectricity for the basic structural level of biological organization, i.e. from the subcellular level (charges, ion channels, molecules and cell organelles) to cells.
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Affiliation(s)
- Richard H W Funk
- Institute of Anatomy, Center for Theoretical Medicine, TU-Dresden, 01307, Dresden, Germany; Dresden International University, 01067, Dresden, Germany.
| | - Felix Scholkmann
- Biomedical Optics Research Laboratory, Department of Neonatology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland.
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Harrison D, Rorot W, Laukaityte U. Mind the matter: Active matter, soft robotics, and the making of bio-inspired artificial intelligence. Front Neurorobot 2022; 16:880724. [PMID: 36620483 PMCID: PMC9815774 DOI: 10.3389/fnbot.2022.880724] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 10/31/2022] [Indexed: 12/23/2022] Open
Abstract
Philosophical and theoretical debates on the multiple realisability of the cognitive have historically influenced discussions of the possible systems capable of instantiating complex functions like memory, learning, goal-directedness, and decision-making. These debates have had the corollary of undermining, if not altogether neglecting, the materiality and corporeality of cognition-treating material, living processes as "hardware" problems that can be abstracted out and, in principle, implemented in a variety of materials-in particular on digital computers and in the form of state-of-the-art neural networks. In sum, the matter in se has been taken not to matter for cognition. However, in this paper, we argue that the materiality of cognition-and the living, self-organizing processes that it enables-requires a more detailed assessment when understanding the nature of cognition and recreating it in the field of embodied robotics. Or, in slogan form, that the matter matters for cognitive form and function. We pull from the fields of Active Matter Physics, Soft Robotics, and Basal Cognition literature to suggest that the imbrication between material and cognitive processes is closer than standard accounts of multiple realisability suggest. In light of this, we propose upgrading the notion of multiple realisability from the standard version-what we call 1.0-to a more nuanced conception 2.0 to better reflect the recent empirical advancements, while at the same time averting many of the problems that have been raised for it. These fields are actively reshaping the terrain in which we understand materiality and how it enables, mediates, and constrains cognition. We propose that taking the materiality of our embodied, precarious nature seriously furnishes an important research avenue for the development of embodied robots that autonomously value, engage, and interact with the environment in a goal-directed manner, in response to existential needs of survival, persistence, and, ultimately, reproduction. Thus, we argue that by placing further emphasis on the soft, active, and plastic nature of the materials that constitute cognitive embodiment, we can move further in the direction of autonomous embodied robots and Artificial Intelligence.
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Affiliation(s)
- David Harrison
- Department of History and Philosophy of Science, University of Cambridge, Cambridge, United Kingdom,Leverhulme Centre for the Future of Intelligence, Cambridge, United Kingdom,Konrad Lorenz Institute for Evolution and Cognition Research, Vienna, Austria,*Correspondence: David Harrison
| | - Wiktor Rorot
- Human Interactivity and Language Lab, Faculty of Psychology, University of Warsaw, Warsaw, Poland,Wiktor Rorot
| | - Urte Laukaityte
- Department of Philosophy, University of California, Berkeley, Berkeley, CA, United States
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7
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Graphical Representation of the Movements of Motives of Consciousness in Leontyev's Activity Theory. Integr Psychol Behav Sci 2022; 56:1113-1127. [PMID: 34331659 DOI: 10.1007/s12124-021-09629-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2021] [Indexed: 10/20/2022]
Abstract
The present study aims at giving a graphical representation of the movements of motives of consciousness in Leontyev's Activity Theory. In addition, related works concerning "vertical" and "horizontal" in the area of cultural historical activity theory are presented along with demonstrating Leontyev's conceptual distinctions, in a multimodal way, including pastoral psychology and technology. Finally, the last part suggests answers to Vygotsky's and Leontyev's fundamental questions.
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8
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Esmaeili J, Barati A, Charelli LE. Discussing the final size and shape of the reconstructed tissues in tissue engineering. J Artif Organs 2022:10.1007/s10047-022-01360-1. [PMID: 36125581 DOI: 10.1007/s10047-022-01360-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/15/2022] [Indexed: 11/30/2022]
Abstract
Tissue engineering (TE) has made a revolution in repairing, replacing, or regenerating tissues or organs, but it has still a long way ahead. The mechanical properties along with suitable physicochemical and biological characteristics are the initial criteria for scaffolds in TE that should be fulfilled. This research will provide another point of view toward TE challenges concerning the morphological and geometrical aspects of the reconstructed tissue and which parameters may affect it. Based on our survey, there is a high possibility that the final reconstructed tissue may be different in size and shape compared to the original design scaffold. Thereby, the 3D-printed scaffold might not guarantee an accurate tissue reconstruction. The main justification for this is the unpredicted behavior of cells, specifically in the outer layer of the scaffold. It can also be a concern when the scaffold is implanted while cell migration cannot be controlled through the in vivo signaling pathways, which might cause cancer challenges. To sum up, it is concluded that more studies are necessary to focus on the size and geometry of the final reconstructed tissue.
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Affiliation(s)
- Javad Esmaeili
- Department of Chemical Engineering, Faculty of Engineering, Arak University, Arak, 38156-88349, Iran.,Tissue Engineering Department, TISSUEHUB Co., Tehran, Iran
| | - Aboulfazl Barati
- Department of Chemical Engineering, Faculty of Engineering, Arak University, Arak, 38156-88349, Iran.
| | - Letícia Emiliano Charelli
- Nanotechnology Engineering Program, Alberto Luiz Coimbra Institute for Graduate Studies and Research in Engineering, COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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9
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Tassinari R, Cavallini C, Olivi E, Facchin F, Taglioli V, Zannini C, Marcuzzi M, Ventura C. Cell Responsiveness to Physical Energies: Paving the Way to Decipher a Morphogenetic Code. Int J Mol Sci 2022; 23:ijms23063157. [PMID: 35328576 PMCID: PMC8949133 DOI: 10.3390/ijms23063157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 02/04/2023] Open
Abstract
We discuss emerging views on the complexity of signals controlling the onset of biological shapes and functions, from the nanoarchitectonics arising from supramolecular interactions, to the cellular/multicellular tissue level, and up to the unfolding of complex anatomy. We highlight the fundamental role of physical forces in cellular decisions, stressing the intriguing similarities in early morphogenesis, tissue regeneration, and oncogenic drift. Compelling evidence is presented, showing that biological patterns are strongly embedded in the vibrational nature of the physical energies that permeate the entire universe. We describe biological dynamics as informational processes at which physics and chemistry converge, with nanomechanical motions, and electromagnetic waves, including light, forming an ensemble of vibrations, acting as a sort of control software for molecular patterning. Biomolecular recognition is approached within the establishment of coherent synchronizations among signaling players, whose physical nature can be equated to oscillators tending to the coherent synchronization of their vibrational modes. Cytoskeletal elements are now emerging as senders and receivers of physical signals, "shaping" biological identity from the cellular to the tissue/organ levels. We finally discuss the perspective of exploiting the diffusive features of physical energies to afford in situ stem/somatic cell reprogramming, and tissue regeneration, without stem cell transplantation.
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Affiliation(s)
- Riccardo Tassinari
- ELDOR LAB, National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems, CNR, Via Gobetti 101, 40129 Bologna, Italy; (R.T.); (C.C.); (E.O.); (V.T.); (C.Z.)
| | - Claudia Cavallini
- ELDOR LAB, National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems, CNR, Via Gobetti 101, 40129 Bologna, Italy; (R.T.); (C.C.); (E.O.); (V.T.); (C.Z.)
| | - Elena Olivi
- ELDOR LAB, National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems, CNR, Via Gobetti 101, 40129 Bologna, Italy; (R.T.); (C.C.); (E.O.); (V.T.); (C.Z.)
| | - Federica Facchin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy;
| | - Valentina Taglioli
- ELDOR LAB, National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems, CNR, Via Gobetti 101, 40129 Bologna, Italy; (R.T.); (C.C.); (E.O.); (V.T.); (C.Z.)
| | - Chiara Zannini
- ELDOR LAB, National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems, CNR, Via Gobetti 101, 40129 Bologna, Italy; (R.T.); (C.C.); (E.O.); (V.T.); (C.Z.)
| | - Martina Marcuzzi
- INBB, Biostructures and Biosystems National Institute, Viale Medaglie d’Oro 305, 00136 Rome, Italy;
| | - Carlo Ventura
- ELDOR LAB, National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems, CNR, Via Gobetti 101, 40129 Bologna, Italy; (R.T.); (C.C.); (E.O.); (V.T.); (C.Z.)
- Correspondence: ; Tel.: +39-347-920-6992
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10
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Tassinari R, Cavallini C, Olivi E, Taglioli V, Zannini C, Ventura C. Unveiling the morphogenetic code: A new path at the intersection of physical energies and chemical signaling. World J Stem Cells 2021; 13:1382-1393. [PMID: 34786150 PMCID: PMC8567452 DOI: 10.4252/wjsc.v13.i10.1382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/16/2021] [Accepted: 09/10/2021] [Indexed: 02/06/2023] Open
Abstract
In this editorial, we discuss the remarkable role of physical energies in the control of cell signaling networks and in the specification of the architectural plan of both somatic and stem cells. In particular, we focus on the biological relevance of bioelectricity in the pattern control that orchestrates both developmental and regenerative pathways. To this end, the narrative starts from the dawn of the first studies on animal electricity, reconsidering the pioneer work of Harold Saxton Burr in the light of the current achievements. We finally discuss the most recent evidence showing that bioelectric signaling is an essential component of the informational processes that control pattern specification during embryogenesis, regeneration, or even malignant transformation. We conclude that there is now mounting evidence for the existence of a Morphogenetic Code, and that deciphering this code may lead to unprecedented opportunities for the development of novel paradigms of cure in regenerative and precision medicine.
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Affiliation(s)
- Riccardo Tassinari
- National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems – ELDOR LAB, Bologna 40129, Italy
| | - Claudia Cavallini
- National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems – ELDOR LAB, Bologna 40129, Italy
| | - Elena Olivi
- National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems – ELDOR LAB, Bologna 40129, Italy
| | - Valentina Taglioli
- National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems – ELDOR LAB, Bologna 40129, Italy
| | - Chiara Zannini
- National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems – ELDOR LAB, Bologna 40129, Italy
| | - Carlo Ventura
- National Laboratory of Molecular Biology and Stem Cell Engineering, National Institute of Biostructures and Biosystems – ELDOR LAB, Bologna 40129, Italy
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11
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DiFrisco J, Jaeger J. Genetic Causation in Complex Regulatory Systems: An Integrative Dynamic Perspective. Bioessays 2021; 42:e1900226. [PMID: 32449193 DOI: 10.1002/bies.201900226] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/01/2020] [Indexed: 12/27/2022]
Abstract
The logic of genetic discovery has changed little over time, but the focus of biology is shifting from simple genotype-phenotype relationships to complex metabolic, physiological, developmental, and behavioral traits. In light of this, the traditional reductionist view of individual genes as privileged difference-making causes of phenotypes is re-examined. The scope and nature of genetic effects in complex regulatory systems, in which dynamics are driven by regulatory feedback and hierarchical interactions across levels of organization are considered. This review argues that it is appropriate to treat genes as specific actual difference-makers for the molecular regulation of gene expression. However, they are often neither stable, proportional, nor specific as causes of the overall dynamic behavior of regulatory networks. Dynamical models, properly formulated and validated, provide the tools to probe cause-and-effect relationships in complex biological systems, allowing to go beyond the limitations of genetic reductionism to gain an integrative understanding of the causal processes underlying complex phenotypes.
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Affiliation(s)
| | - Johannes Jaeger
- Complexity Science Hub (CSH) Vienna, Josefstädter Straße 39, Vienna, 1080, Austria.,Department of Molecular Evolution & Development, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
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12
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Abstract
It is well known that electrical signals are deeply associated with living entities. Much of our understanding of excitable tissues is derived from studies of specialized cells of neurons or myocytes. However, electric potential is present in all cell types and results from the differential partitioning of ions across membranes. This electrical potential correlates with cell behavior and tissue organization. In recent years, there has been exciting, and broadly unexpected, evidence linking the regulation of development to bioelectric signals. However, experimental modulation of electrical potential can have multifaceted and pleiotropic effects, which makes dissecting the role of electrical signals in development difficult. Here, I review evidence that bioelectric cues play defined instructional roles in orchestrating development and regeneration, and further outline key areas in which to refine our understanding of this signaling mechanism.
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Affiliation(s)
- Matthew P. Harris
- Department of Genetics, Harvard Medical School, Department of Orthopaedics, Boston Children's Hospital, 300 Longwood Avenue Enders 260, Boston MA 02115, USA
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13
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Burgstaller W. Overflow Metabolism in Penicillium ochrochloron and Causation in Organisms. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:682062. [PMID: 37744154 PMCID: PMC10512369 DOI: 10.3389/ffunb.2021.682062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 04/13/2021] [Indexed: 09/26/2023]
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14
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Marshall P. Biology transcends the limits of computation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 165:88-101. [PMID: 33961842 DOI: 10.1016/j.pbiomolbio.2021.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 11/29/2022]
Abstract
Cognition-sensing and responding to the environment-is the unifying principle behind the genetic code, origin of life, evolution, consciousness, artificial intelligence, and cancer. However, the conventional model of biology seems to mistake cause and effect. According to the reductionist view, the causal chain in biology is chemicals → code → cognition. Despite this prevailing view, there are no examples in the literature to show that the laws of physics and chemistry can produce codes, or that codes produce cognition. Chemicals are just the physical layer of any information system. In contrast, although examples of cognition generating codes and codes controlling chemicals are ubiquitous in biology and technology, cognition remains a mystery. Thus, the central question in biology is: What is the nature and origin of cognition? In order to elucidate this pivotal question, we must cultivate a deeper understanding of information flows. Through this lens, we see that biological cognition is volitional (i.e., deliberate, intentional, or knowing), and while technology is constrained by deductive logic, living things make choices and generate novel information using inductive logic. Information has been called "the hard problem of life' and cannot be fully explained by known physical principles (Walker et al., 2017). The present paper uses information theory (the mathematical foundation of our digital age) and Turing machines (computers) to highlight inaccuracies in prevailing reductionist models of biology, and proposes that the correct causation sequence is cognition → code → chemicals.
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Affiliation(s)
- Perry Marshall
- Evolution 2.0, 805 Lake Street #295 Oak Park, IL, 60301, USA.
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15
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Zakirov B, Charalambous G, Thuret R, Aspalter IM, Van-Vuuren K, Mead T, Harrington K, Regan ER, Herbert SP, Bentley K. Active perception during angiogenesis: filopodia speed up Notch selection of tip cells in silico and in vivo. Philos Trans R Soc Lond B Biol Sci 2021; 376:20190753. [PMID: 33550953 PMCID: PMC7934951 DOI: 10.1098/rstb.2019.0753] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2020] [Indexed: 12/19/2022] Open
Abstract
How do cells make efficient collective decisions during tissue morphogenesis? Humans and other organisms use feedback between movement and sensing known as 'sensorimotor coordination' or 'active perception' to inform behaviour, but active perception has not before been investigated at a cellular level within organs. Here we provide the first proof of concept in silico/in vivo study demonstrating that filopodia (actin-rich, dynamic, finger-like cell membrane protrusions) play an unexpected role in speeding up collective endothelial decisions during the time-constrained process of 'tip cell' selection during blood vessel formation (angiogenesis). We first validate simulation predictions in vivo with live imaging of zebrafish intersegmental vessel growth. Further simulation studies then indicate the effect is due to the coupled positive feedback between movement and sensing on filopodia conferring a bistable switch-like property to Notch lateral inhibition, ensuring tip selection is a rapid and robust process. We then employ measures from computational neuroscience to assess whether filopodia function as a primitive (basal) form of active perception and find evidence in support. By viewing cell behaviour through the 'basal cognitive lens' we acquire a fresh perspective on the tip cell selection process, revealing a hidden, yet vital time-keeping role for filopodia. Finally, we discuss a myriad of new and exciting research directions stemming from our conceptual approach to interpreting cell behaviour. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.
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Affiliation(s)
- Bahti Zakirov
- Cellular Adaptive Behaviour Lab, Francis Crick Institute, London, NW1 1AT, UK
- Department of Informatics, King's College London, London, UK
| | - Georgios Charalambous
- Division of Developmental Biology and Medicine, University of Manchester, Manchester, UK
| | - Raphael Thuret
- Division of Developmental Biology and Medicine, University of Manchester, Manchester, UK
| | - Irene M. Aspalter
- Cellular Adaptive Behaviour Lab, Francis Crick Institute, London, NW1 1AT, UK
| | - Kelvin Van-Vuuren
- Cellular Adaptive Behaviour Lab, Francis Crick Institute, London, NW1 1AT, UK
| | - Thomas Mead
- Cellular Adaptive Behaviour Lab, Francis Crick Institute, London, NW1 1AT, UK
- Department of Informatics, King's College London, London, UK
| | - Kyle Harrington
- Virtual Technology and Design, University of Idaho, Moscow, ID, USA
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Erzsébet Ravasz Regan
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Department of Pathology, Harvard Medical School, Boston, MA, USA
- Department of Biology, The College of Wooster, Wooster, OH, USA
| | - Shane Paul Herbert
- Division of Developmental Biology and Medicine, University of Manchester, Manchester, UK
| | - Katie Bentley
- Cellular Adaptive Behaviour Lab, Francis Crick Institute, London, NW1 1AT, UK
- Department of Informatics, King's College London, London, UK
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Department of Pathology, Harvard Medical School, Boston, MA, USA
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16
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Bongard J, Levin M. Living Things Are Not (20th Century) Machines: Updating Mechanism Metaphors in Light of the Modern Science of Machine Behavior. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.650726] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
One of the most useful metaphors for driving scientific and engineering progress has been that of the “machine.” Much controversy exists about the applicability of this concept in the life sciences. Advances in molecular biology have revealed numerous design principles that can be harnessed to understand cells from an engineering perspective, and build novel devices to rationally exploit the laws of chemistry, physics, and computation. At the same time, organicists point to the many unique features of life, especially at larger scales of organization, which have resisted decomposition analysis and artificial implementation. Here, we argue that much of this debate has focused on inessential aspects of machines – classical properties which have been surpassed by advances in modern Machine Behavior and no longer apply. This emerging multidisciplinary field, at the interface of artificial life, machine learning, and synthetic bioengineering, is highlighting the inadequacy of existing definitions. Key terms such as machine, robot, program, software, evolved, designed, etc., need to be revised in light of technological and theoretical advances that have moved past the dated philosophical conceptions that have limited our understanding of both evolved and designed systems. Moving beyond contingent aspects of historical and current machines will enable conceptual tools that embrace inevitable advances in synthetic and hybrid bioengineering and computer science, toward a framework that identifies essential distinctions between fundamental concepts of devices and living agents. Progress in both theory and practical applications requires the establishment of a novel conception of “machines as they could be,” based on the profound lessons of biology at all scales. We sketch a perspective that acknowledges the remarkable, unique aspects of life to help re-define key terms, and identify deep, essential features of concepts for a future in which sharp boundaries between evolved and designed systems will not exist.
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17
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Heng J, Heng HH. Genome chaos: Creating new genomic information essential for cancer macroevolution. Semin Cancer Biol 2020; 81:160-175. [PMID: 33189848 DOI: 10.1016/j.semcancer.2020.11.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/26/2020] [Accepted: 11/04/2020] [Indexed: 12/15/2022]
Abstract
Cancer research has traditionally focused on the characterization of individual molecular mechanisms that can contribute to cancer. Due to the multiple levels of genomic and non-genomic heterogeneity, however, overwhelming molecular mechanisms have been identified, most with low clinical predictability. It is thus necessary to search for new concepts to unify these diverse mechanisms and develop better strategies to understand and treat cancer. In recent years, two-phased cancer evolution (comprised of the genome reorganization-mediated punctuated phase and gene mutation-mediated stepwise phase), initially described by tracing karyotype evolution, was confirmed by the Cancer Genome Project. In particular, genome chaos, the process of rapid and massive genome reorganization, has been commonly detected in various cancers-especially during key phase transitions, including cellular transformation, metastasis, and drug resistance-suggesting the importance of genome-level changes in cancer evolution. In this Perspective, genome chaos is used as a discussion point to illustrate new genome-mediated somatic evolutionary frameworks. By rephrasing cancer as a new system emergent from normal tissue, we present the multiple levels (or scales) of genomic and non-genomic information. Of these levels, evolutionary studies at the chromosomal level are determined to be of ultimate importance, since altered genomes change the karyotype coding and karyotype change is the key event for punctuated cellular macroevolution. Using this lens, we differentiate and analyze developmental processes and cancer evolution, as well as compare the informational relationship between genome chaos and its various subtypes in the context of macroevolution under crisis. Furthermore, the process of deterministic genome chaos is discussed to interpret apparently random events (including stressors, chromosomal variation subtypes, surviving cells with new karyotypes, and emergent stable cellular populations) as nonrandom patterns, which supports the new cancer evolutionary model that unifies genome and gene contributions during different phases of cancer evolution. Finally, the new perspective of using cancer as a model for organismal evolution is briefly addressed, emphasizing the Genome Theory as a new and necessary conceptual framework for future research and its practical implications, not only in cancer but evolutionary biology as a whole.
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Affiliation(s)
- Julie Heng
- Harvard College, 86 Brattle Street Cambridge, MA, 02138, USA
| | - Henry H Heng
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI, 48201, USA; Department of Pathology, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
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18
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Zablotskii V, Polyakova T, Dejneka A. Modulation of the Cell Membrane Potential and Intracellular Protein Transport by High Magnetic Fields. Bioelectromagnetics 2020; 42:27-36. [PMID: 33179821 DOI: 10.1002/bem.22309] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 10/16/2020] [Accepted: 10/22/2020] [Indexed: 01/26/2023]
Abstract
To explore cellular responses to high magnetic fields (HMF), we present a model of the interactions of cells with a homogeneous HMF that accounts for the magnetic force exerted on paramagnetic/diamagnetic species. There are various chemical species inside a living cell, many of which may have large concentration gradients. Thus, when an HMF is applied to a cell, the concentration-gradient magnetic forces act on paramagnetic or diamagnetic species and can either assist or oppose large particle movement through the cytoplasm. We demonstrate possibilities for changing the machinery in living cells with HMFs and predict two new mechanisms for modulating cellular functions with HMFs via (i) changes in the membrane potential and (ii) magnetically assisted intracellular diffusiophoresis of large proteins. By deriving a generalized form for the Nernst equation, we find that an HMF can change the membrane potential of the cell and thus have a significant impact on the properties and biological functionality of cells. The elaborated model provides a universal framework encompassing current studies on controlling cell functions by high static magnetic fields. Bioelectromagnetics. 2021;42:27-36. © 2020 Bioelectromagnetics Society.
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Affiliation(s)
- Vitalii Zablotskii
- Institute of Physics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tatyana Polyakova
- Institute of Physics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Alexandr Dejneka
- Institute of Physics of the Czech Academy of Sciences, Prague, Czech Republic
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19
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Kuchling F, Friston K, Georgiev G, Levin M. Integrating variational approaches to pattern formation into a deeper physics: Reply to comments on "Morphogenesis as Bayesian inference: A variational approach to pattern formation and manipulation in complex biological systems". Phys Life Rev 2020; 33:125-128. [PMID: 32682906 DOI: 10.1016/j.plrev.2020.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 10/23/2022]
Affiliation(s)
- Franz Kuchling
- Biology Department, Allen Discovery Center at Tufts University, Medford, MA, USA
| | - Karl Friston
- The Wellcome Trust Centre for Neuroimaging, Institute of Neurology, Queen Square, London, UK
| | - Georgi Georgiev
- Assumption College, Department of Physics, 500 Salisbury St., Worcester, MA, USA
| | - Michael Levin
- Biology Department, Allen Discovery Center at Tufts University, Medford, MA, USA.
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20
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Jose AM. A framework for parsing heritable information. J R Soc Interface 2020; 17:20200154. [PMID: 32315573 PMCID: PMC7211480 DOI: 10.1098/rsif.2020.0154] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/01/2020] [Indexed: 12/21/2022] Open
Abstract
Living systems transmit heritable information using the replicating gene sequences and the cycling regulators assembled around gene sequences. Here, I develop a framework for heredity and development that includes the cycling regulators parsed in terms of what an organism can sense about itself and its environment by defining entities, their sensors and the sensed properties. Entities include small molecules (ATP, ions, metabolites, etc.), macromolecules (individual proteins, RNAs, polysaccharides, etc.) and assemblies of molecules. While concentration may be the only relevant property measured by sensors for small molecules, multiple properties that include concentration, sequence, conformation and modification may all be measured for macromolecules and assemblies. Each configuration of these entities and sensors that is recreated in successive generations in a given environment thus specifies a potentially vast amount of information driving complex development in each generation. This entity-sensor-property framework explains how sensors limit the number of distinguishable states, how distinct molecular configurations can be functionally equivalent and how regulation of sensors prevents detection of some perturbations. Overall, this framework is a useful guide for understanding how life evolves and how the storage of information has itself evolved with complexity since before the origin of life.
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Affiliation(s)
- Antony M. Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, Room 2136, Bioscience Research Building (Building #413), College Park, MD 20742, USA
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21
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Sonnenschein C, Soto AM. Over a century of cancer research: Inconvenient truths and promising leads. PLoS Biol 2020; 18:e3000670. [PMID: 32236102 PMCID: PMC7153880 DOI: 10.1371/journal.pbio.3000670] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/13/2020] [Indexed: 12/17/2022] Open
Abstract
Despite over a century of intensive efforts, the great gains promised by the War on Cancer nearly 50 years ago have not materialized. Since 1999, we have analyzed the lack of progress in explaining and "curing" cancer by examining the merits of the premises that determine how cancer is understood and treated. Our ongoing critical analyses have aimed at clarifying the sources of misunderstandings at the root of the cancer puzzle while providing a plausible and comprehensive biomedical perspective as well as a new theory of carcinogenesis that is compatible with evolutionary theory. In this essay, we explain how this new theory, the tissue organization field theory (TOFT), can help chart a path to progress for cancer researchers by explaining features of cancer that remain unexplainable from the perspective of the still hegemonic somatic mutation theory (SMT) and its variants. Of equal significance, the premises underlying the TOFT offer new perspectives on basic biological phenomena.
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Affiliation(s)
- Carlos Sonnenschein
- Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Centre Cavaillès, Ecole Normale Supérieure, Paris, France
| | - Ana M. Soto
- Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Centre Cavaillès, Ecole Normale Supérieure, Paris, France
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