Recruitment: A Problem of Entangled Temporal Parts

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 4dimensional '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.

Agency in evolution of biomolecular communication

“…(i) Accretion: Accretion is a process of evolutionary growth in which newly evolved parts (novelties) are integrated piecemeal into an evolving biological system. 19 This construction process creates molecular and cellular makeup. Each new stable integration of a part into its whole establishes an evolutionary step of accretion and a new mapping relationship between lower-level parts and a higher-level whole.…”

“…29 Epistemologically, accretion aligns with constructivism (e.g., multilevel semiotic networks 30 ) but also with perdurantism and the belief that things are four-dimensional (i.e., they have both spatial parts in different places and temporal parts at different times. 19 ) (ii) Modularity: Modularity is a special kind of inter-level redundancy that arises from the emergence of modules. Modules are structured entities, sets of integrated parts that are functionally coordinated with each other and are cooperating to perform tasks.…”

“…33 prototypes acted as true modular units-engaging in a combinatorial process of recruitment that enhanced functional novelties associated with protein structure. 19 Figure 2B describes how loop prototypes were accreted to form the helix-turn-helix containing the winged helix domain that is central to the process of transcription. Accretion often produces modules in evolution, which can either stand-alone or combine with other modules to increase a system's capacity.…”

“…It remains up to this day despite the discovery of transgenerational epigenetic inheritance (countering the unshakeable Weismannian axiom 14 ) and the increasingly strong contradicting evidence from genomics and systems biology. 15,16 Here, I dissect the emergence of agency in biomolecular communication with knowledge grounded in over two decades of evolutionary genomic and bioinformatic exploration of molecular structure (recently reviewed [17][18][19] ). I posit that the birth of molecular modules and the establishment of hierarchical patterns of biological…”

Twenty-five Years at the Frontiers of Knowledge: A Quarter-century of “Frontiers in Bioscience”

“…Of the 22 papers, half are original research on highly diverse topics including a detailed analysis of signaling pathways in insect heart development [1], stress management in breast cancer patients [2], regulation of myelopoiesis in zebrafish [3], an analysis of heat shock protein expression in human glioblastomas [4], a new method for screening for human topoisomerase inhibitors using genetically-modified yeast [5], genetic influences on systemic iron levels in humans [6], transcriptomics studies on frog development [7], clinical studies on malnourished children with diarrhoea [8], a theoretical investigation of approaches to characterizing logic operations in model neurons, synapses, and neural circuits [9], the effects of methionine-restricted diets on the growth of pigs [10], and the effects of iron on kidney disease in rats [11]. The other half of the papers are reviews on an equally diverse range of topics, including drugs for Alzheimer's Disease [12], spheroid cell cultures [13], bioactive polyphenols [14], ribosome evolution [15], purinergic signaling in bone cancer [16], spontaneous regressions in cancer [17], genetic analyses of pituitary cancers [18], pharmacological chaperones [19], drug targeting for SARS-CoV-2 infection [20], calcium signaling in mesenchymal stem cells [21], and relationships between the control of circadian rhythm and neurodegeneration [22]. We sincerely thank all authors and readers for their interest in the Journal and look forward to the next 25 years of exciting advances in the biological sciences and an expanded role for the Journal in the OA publishing landscape.…”