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Networks of Networks: An Essay on Multi-Level Biological Organization

The multi-level organization of nature is self-evident: proteins do interact among them to give rise to an organized metabolism, while in the same time each protein (a single node of such interaction network) is itself a network of interacting amino-acid residues allowing coordinated motion of the m...

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Autores principales: Uversky, Vladimir N., Giuliani, Alessandro
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8255927/
https://www.ncbi.nlm.nih.gov/pubmed/34234818
http://dx.doi.org/10.3389/fgene.2021.706260
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author Uversky, Vladimir N.
Giuliani, Alessandro
author_facet Uversky, Vladimir N.
Giuliani, Alessandro
author_sort Uversky, Vladimir N.
collection PubMed
description The multi-level organization of nature is self-evident: proteins do interact among them to give rise to an organized metabolism, while in the same time each protein (a single node of such interaction network) is itself a network of interacting amino-acid residues allowing coordinated motion of the macromolecule and systemic effect as allosteric behavior. Similar pictures can be drawn for structure and function of cells, organs, tissues, and ecological systems. The majority of biologists are used to think that causally relevant events originate from the lower level (the molecular one) in the form of perturbations, that “climb up” the hierarchy reaching the ultimate layer of macroscopic behavior (e.g., causing a specific disease). Such causative model, stemming from the usual genotype-phenotype distinction, is not the only one. As a matter of fact, one can observe top-down, bottom-up, as well as middle-out perturbation/control trajectories. The recent complex network studies allow to go further the pure qualitative observation of the existence of both non-linear and non-bottom-up processes and to uncover the deep nature of multi-level organization. Here, taking as paradigm protein structural and interaction networks, we review some of the most relevant results dealing with between networks communication shedding light on the basic principles of complex system control and dynamics and offering a more realistic frame of causation in biology.
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spelling pubmed-82559272021-07-06 Networks of Networks: An Essay on Multi-Level Biological Organization Uversky, Vladimir N. Giuliani, Alessandro Front Genet Genetics The multi-level organization of nature is self-evident: proteins do interact among them to give rise to an organized metabolism, while in the same time each protein (a single node of such interaction network) is itself a network of interacting amino-acid residues allowing coordinated motion of the macromolecule and systemic effect as allosteric behavior. Similar pictures can be drawn for structure and function of cells, organs, tissues, and ecological systems. The majority of biologists are used to think that causally relevant events originate from the lower level (the molecular one) in the form of perturbations, that “climb up” the hierarchy reaching the ultimate layer of macroscopic behavior (e.g., causing a specific disease). Such causative model, stemming from the usual genotype-phenotype distinction, is not the only one. As a matter of fact, one can observe top-down, bottom-up, as well as middle-out perturbation/control trajectories. The recent complex network studies allow to go further the pure qualitative observation of the existence of both non-linear and non-bottom-up processes and to uncover the deep nature of multi-level organization. Here, taking as paradigm protein structural and interaction networks, we review some of the most relevant results dealing with between networks communication shedding light on the basic principles of complex system control and dynamics and offering a more realistic frame of causation in biology. Frontiers Media S.A. 2021-06-21 /pmc/articles/PMC8255927/ /pubmed/34234818 http://dx.doi.org/10.3389/fgene.2021.706260 Text en Copyright © 2021 Uversky and Giuliani. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Uversky, Vladimir N.
Giuliani, Alessandro
Networks of Networks: An Essay on Multi-Level Biological Organization
title Networks of Networks: An Essay on Multi-Level Biological Organization
title_full Networks of Networks: An Essay on Multi-Level Biological Organization
title_fullStr Networks of Networks: An Essay on Multi-Level Biological Organization
title_full_unstemmed Networks of Networks: An Essay on Multi-Level Biological Organization
title_short Networks of Networks: An Essay on Multi-Level Biological Organization
title_sort networks of networks: an essay on multi-level biological organization
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8255927/
https://www.ncbi.nlm.nih.gov/pubmed/34234818
http://dx.doi.org/10.3389/fgene.2021.706260
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