Scarcity of scale-free topology is universal across biochemical networks

Abstract Biochemical reactions underlie the functioning of all life. Like many examples of biology or technology, the complex set of interactions among molecules within cells and ecosystems poses a challenge for quantification within simple mathematical objects. A large body of research has indicate...

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Autores principales:	Harrison B. Smith, Hyunju Kim, Sara I. Walker
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d6323a16b13d408ab61b4a94b40e4976
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spelling	oai:doaj.org-article:d6323a16b13d408ab61b4a94b40e49762021-12-02T17:04:06ZScarcity of scale-free topology is universal across biochemical networks10.1038/s41598-021-85903-12045-2322https://doaj.org/article/d6323a16b13d408ab61b4a94b40e49762021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-85903-1https://doaj.org/toc/2045-2322Abstract Biochemical reactions underlie the functioning of all life. Like many examples of biology or technology, the complex set of interactions among molecules within cells and ecosystems poses a challenge for quantification within simple mathematical objects. A large body of research has indicated many real-world biological and technological systems, including biochemistry, can be described by power-law relationships between the numbers of nodes and edges, often described as “scale-free”. Recently, new statistical analyses have revealed true scale-free networks are rare. We provide a first application of these methods to data sampled from across two distinct levels of biological organization: individuals and ecosystems. We analyze a large ensemble of biochemical networks including networks generated from data of 785 metagenomes and 1082 genomes (sampled from the three domains of life). The results confirm no more than a few biochemical networks are any more than super-weakly scale-free. Additionally, we test the distinguishability of individual and ecosystem-level biochemical networks and show there is no sharp transition in the structure of biochemical networks across these levels of organization moving from individuals to ecosystems. This result holds across different network projections. Our results indicate that while biochemical networks are not scale-free, they nonetheless exhibit common structure across different levels of organization, independent of the projection chosen, suggestive of shared organizing principles across all biochemical networks.Harrison B. SmithHyunju KimSara I. WalkerNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Harrison B. Smith Hyunju Kim Sara I. Walker Scarcity of scale-free topology is universal across biochemical networks
description	Abstract Biochemical reactions underlie the functioning of all life. Like many examples of biology or technology, the complex set of interactions among molecules within cells and ecosystems poses a challenge for quantification within simple mathematical objects. A large body of research has indicated many real-world biological and technological systems, including biochemistry, can be described by power-law relationships between the numbers of nodes and edges, often described as “scale-free”. Recently, new statistical analyses have revealed true scale-free networks are rare. We provide a first application of these methods to data sampled from across two distinct levels of biological organization: individuals and ecosystems. We analyze a large ensemble of biochemical networks including networks generated from data of 785 metagenomes and 1082 genomes (sampled from the three domains of life). The results confirm no more than a few biochemical networks are any more than super-weakly scale-free. Additionally, we test the distinguishability of individual and ecosystem-level biochemical networks and show there is no sharp transition in the structure of biochemical networks across these levels of organization moving from individuals to ecosystems. This result holds across different network projections. Our results indicate that while biochemical networks are not scale-free, they nonetheless exhibit common structure across different levels of organization, independent of the projection chosen, suggestive of shared organizing principles across all biochemical networks.
format	article
author	Harrison B. Smith Hyunju Kim Sara I. Walker
author_facet	Harrison B. Smith Hyunju Kim Sara I. Walker
author_sort	Harrison B. Smith
title	Scarcity of scale-free topology is universal across biochemical networks
title_short	Scarcity of scale-free topology is universal across biochemical networks
title_full	Scarcity of scale-free topology is universal across biochemical networks
title_fullStr	Scarcity of scale-free topology is universal across biochemical networks
title_full_unstemmed	Scarcity of scale-free topology is universal across biochemical networks
title_sort	scarcity of scale-free topology is universal across biochemical networks
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/d6323a16b13d408ab61b4a94b40e4976
work_keys_str_mv	AT harrisonbsmith scarcityofscalefreetopologyisuniversalacrossbiochemicalnetworks AT hyunjukim scarcityofscalefreetopologyisuniversalacrossbiochemicalnetworks AT saraiwalker scarcityofscalefreetopologyisuniversalacrossbiochemicalnetworks
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Scarcity of scale-free topology is universal across biochemical networks

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