IMR Press / FBL / Volume 27 / Issue 4 / DOI: 10.31083/j.fbl2704128
Open Access Review
Recruitment: A Problem of Entangled Temporal Parts
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1 Department of Crop Sciences and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
2 Callout Biotech, Albuquerque, NM 87112, USA
3 Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
*Correspondence: gca@illinois.edu (Gustavo Caetano-Anollés)
Academic Editor: Graham Pawelec
Front. Biosci. (Landmark Ed) 2022, 27(4), 128; https://doi.org/10.31083/j.fbl2704128
Submitted: 16 January 2022 | Revised: 4 April 2022 | Accepted: 7 April 2022 | Published: 18 April 2022
Copyright: © 2022 The Author(s). Published by IMR Press.
This is an open access article under the CC BY 4.0 license.
Abstract

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.

Keywords
Evolution
gene ontology
hierarchical modularity
horizontal exchange
endurantism
persistence
metabolic networks
molecular evolution
molecular functions
origin
perdurantism
proteome
ribosome
Figures
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