Recruitment: A Problem of Entangled Temporal Parts
Recruitment is a pervasive activity of life that is at the center of novelty generation and persistence. Without recruitment, novelties cannot spread and biological systems cannot maintain identity through time. Here we explore the problem of identity and change unfolding in space and time. We illus...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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IMR Press
2022-04-01
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| Series: | Frontiers in Bioscience-Landmark |
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| Online Access: | https://www.imrpress.com/journal/FBL/27/4/10.31083/j.fbl2704128 |
| _version_ | 1828403598826930176 |
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| author | Gustavo Caetano-Anollés M. Fayez Aziz Fizza Mughal Ibrahim Koç Kelsey Caetano-Anollés Derek Caetano-Anollés |
| author_facet | Gustavo Caetano-Anollés M. Fayez Aziz Fizza Mughal Ibrahim Koç Kelsey Caetano-Anollés Derek Caetano-Anollés |
| author_sort | Gustavo Caetano-Anollés |
| collection | DOAJ |
| description | Recruitment is a pervasive activity of life that is at the center of novelty generation and persistence. Without recruitment, novelties cannot spread and biological systems cannot maintain identity through time. Here we explore the problem of identity and change unfolding in space and time. We illustrate recruitment operating at different timescales with metabolic networks, protein domain makeup, the functionome, and the rise of viral ‘variants of concern’ during the coronavirus disease 2019 (COVID-19) pandemic. We define persistence within a framework of fluxes of matter-energy and information and signal processing in response to internal and external challenges. A ‘triangle of persistence’ describing reuse, innovation and stasis defines a useful polytope in a phase space of trade-offs between economy, flexibility and robustness. We illustrate how the concept of temporal parts embraced by the perdurantist school provides a processual 4-dimensional ‘worm’ view of biology that is historical and atemporal. This view is made explicit with chronologies and evolving networks inferred with phylogenomic methodologies. Exploring the origin and evolution of the ribosome reveals recruitment of helical segments and/or large fragments of interacting rRNA molecules in a unification process of accretion that is counteracted by diversification. A biphasic (bow-tie) theory of module generation models this frustrated dynamics. Finally, we further elaborate on a theory of entanglement that takes advantage of the dimensionality reduction offered by holographic principles to propose that short and long-distance interactions are responsible for the increasingly granular and tangled structure of biological systems. |
| first_indexed | 2024-12-10T10:21:56Z |
| format | Article |
| id | doaj.art-28d03181ceb64b21844eba526088571d |
| institution | Directory Open Access Journal |
| issn | 2768-6701 |
| language | English |
| last_indexed | 2024-12-10T10:21:56Z |
| publishDate | 2022-04-01 |
| publisher | IMR Press |
| record_format | Article |
| series | Frontiers in Bioscience-Landmark |
| spelling | doaj.art-28d03181ceb64b21844eba526088571d2022-12-22T01:52:50ZengIMR PressFrontiers in Bioscience-Landmark2768-67012022-04-0127412810.31083/j.fbl2704128S2768-6701(22)00469-5Recruitment: A Problem of Entangled Temporal PartsGustavo Caetano-Anollés0M. Fayez Aziz1Fizza Mughal2Ibrahim Koç3Kelsey Caetano-Anollés4Derek Caetano-Anollés5Department of Crop Sciences and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USADepartment of Crop Sciences and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USADepartment of Crop Sciences and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USADepartment of Crop Sciences and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USACallout Biotech, Albuquerque, NM 87112, USAData Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USARecruitment is a pervasive activity of life that is at the center of novelty generation and persistence. Without recruitment, novelties cannot spread and biological systems cannot maintain identity through time. Here we explore the problem of identity and change unfolding in space and time. We illustrate recruitment operating at different timescales with metabolic networks, protein domain makeup, the functionome, and the rise of viral ‘variants of concern’ during the coronavirus disease 2019 (COVID-19) pandemic. We define persistence within a framework of fluxes of matter-energy and information and signal processing in response to internal and external challenges. A ‘triangle of persistence’ describing reuse, innovation and stasis defines a useful polytope in a phase space of trade-offs between economy, flexibility and robustness. We illustrate how the concept of temporal parts embraced by the perdurantist school provides a processual 4-dimensional ‘worm’ view of biology that is historical and atemporal. This view is made explicit with chronologies and evolving networks inferred with phylogenomic methodologies. Exploring the origin and evolution of the ribosome reveals recruitment of helical segments and/or large fragments of interacting rRNA molecules in a unification process of accretion that is counteracted by diversification. A biphasic (bow-tie) theory of module generation models this frustrated dynamics. Finally, we further elaborate on a theory of entanglement that takes advantage of the dimensionality reduction offered by holographic principles to propose that short and long-distance interactions are responsible for the increasingly granular and tangled structure of biological systems.https://www.imrpress.com/journal/FBL/27/4/10.31083/j.fbl2704128evolutiongene ontologyhierarchical modularityhorizontal exchangeendurantismpersistencemetabolic networksmolecular evolutionmolecular functionsoriginperdurantismproteomeribosome |
| spellingShingle | Gustavo Caetano-Anollés M. Fayez Aziz Fizza Mughal Ibrahim Koç Kelsey Caetano-Anollés Derek Caetano-Anollés Recruitment: A Problem of Entangled Temporal Parts Frontiers in Bioscience-Landmark evolution gene ontology hierarchical modularity horizontal exchange endurantism persistence metabolic networks molecular evolution molecular functions origin perdurantism proteome ribosome |
| title | Recruitment: A Problem of Entangled Temporal Parts |
| title_full | Recruitment: A Problem of Entangled Temporal Parts |
| title_fullStr | Recruitment: A Problem of Entangled Temporal Parts |
| title_full_unstemmed | Recruitment: A Problem of Entangled Temporal Parts |
| title_short | Recruitment: A Problem of Entangled Temporal Parts |
| title_sort | recruitment a problem of entangled temporal parts |
| topic | evolution gene ontology hierarchical modularity horizontal exchange endurantism persistence metabolic networks molecular evolution molecular functions origin perdurantism proteome ribosome |
| url | https://www.imrpress.com/journal/FBL/27/4/10.31083/j.fbl2704128 |
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