TY - JOUR
T1 - The Compressed Vocabulary of Microbial Life
AU - Caetano-Anollés, Gustavo
N1 - Research was supported by grants from the National Institute of Food and Agriculture (ILLU-802-909 and ILLU-483-625), the Illinois Campus Cluster Program (ICCP), and Blue Waters supercomputing allocations from the National Center for Supercomputing Applications (NCSA).
PY - 2021/7/7
Y1 - 2021/7/7
N2 - Communication is an undisputed central activity of life that requires an evolving molecular language. It conveys meaning through messages and vocabularies. Here, I explore the existence of a growing vocabulary in the molecules and molecular functions of the microbial world. There are clear correspondences between the lexicon, syntax, semantics, and pragmatics of language organization and the module, structure, function, and fitness paradigms of molecular biology. These correspondences are constrained by universal laws and engineering principles. Macromolecular structure, for example, follows quantitative linguistic patterns arising from statistical laws that are likely universal, including the Zipf’s law, a special case of the scale-free distribution, the Heaps’ law describing sublinear growth typical of economies of scales, and the Menzerath–Altmann’s law, which imposes size-dependent patterns of decreasing returns. Trade-off solutions between principles of economy, flexibility, and robustness define a “triangle of persistence” describing the impact of the environment on a biological system. The pragmatic landscape of the triangle interfaces with the syntax and semantics of molecular languages, which together with comparative and evolutionary genomic data can explain global patterns of diversification of cellular life. The vocabularies of proteins (proteomes) and functions (functionomes) revealed a significant universal lexical core supporting a universal common ancestor, an ancestral evolutionary link between Bacteria and Eukarya, and distinct reductive evolutionary strategies of language compression in Archaea and Bacteria. A “causal” word cloud strategy inspired by the dependency grammar paradigm used in catenae unfolded the evolution of lexical units associated with Gene Ontology terms at different levels of ontological abstraction. While Archaea holds the smallest, oldest, and most homogeneous vocabulary of all superkingdoms, Bacteria heterogeneously apportions a more complex vocabulary, and Eukarya pushes functional innovation through mechanisms of flexibility and robustness.
AB - Communication is an undisputed central activity of life that requires an evolving molecular language. It conveys meaning through messages and vocabularies. Here, I explore the existence of a growing vocabulary in the molecules and molecular functions of the microbial world. There are clear correspondences between the lexicon, syntax, semantics, and pragmatics of language organization and the module, structure, function, and fitness paradigms of molecular biology. These correspondences are constrained by universal laws and engineering principles. Macromolecular structure, for example, follows quantitative linguistic patterns arising from statistical laws that are likely universal, including the Zipf’s law, a special case of the scale-free distribution, the Heaps’ law describing sublinear growth typical of economies of scales, and the Menzerath–Altmann’s law, which imposes size-dependent patterns of decreasing returns. Trade-off solutions between principles of economy, flexibility, and robustness define a “triangle of persistence” describing the impact of the environment on a biological system. The pragmatic landscape of the triangle interfaces with the syntax and semantics of molecular languages, which together with comparative and evolutionary genomic data can explain global patterns of diversification of cellular life. The vocabularies of proteins (proteomes) and functions (functionomes) revealed a significant universal lexical core supporting a universal common ancestor, an ancestral evolutionary link between Bacteria and Eukarya, and distinct reductive evolutionary strategies of language compression in Archaea and Bacteria. A “causal” word cloud strategy inspired by the dependency grammar paradigm used in catenae unfolded the evolution of lexical units associated with Gene Ontology terms at different levels of ontological abstraction. While Archaea holds the smallest, oldest, and most homogeneous vocabulary of all superkingdoms, Bacteria heterogeneously apportions a more complex vocabulary, and Eukarya pushes functional innovation through mechanisms of flexibility and robustness.
KW - Heaps’ law
KW - Menzerath-Altmann’s law
KW - Zipf’s law
KW - evolution
KW - molecular functions
KW - persistence triangle
KW - semantics
KW - word clouds
UR - http://www.scopus.com/inward/record.url?scp=85107897920&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85107897920&partnerID=8YFLogxK
U2 - 10.3389/fmicb.2021.655990
DO - 10.3389/fmicb.2021.655990
M3 - Article
C2 - 34305827
AN - SCOPUS:85107897920
SN - 1664-302X
VL - 12
JO - Frontiers in Microbiology
JF - Frontiers in Microbiology
M1 - 655990
ER -