Abstract
The intricate molecular and cellular structure of organisms converts energy to work, which builds and maintains structure. Evolving structure implements modules, in which parts are tightly linked. Each module performs characteristic functions. In this work we propose that a module can emerge through two phases of diversification of parts. Early in the first phase of this biphasic pattern, the parts have weak linkage—they interact weakly and associate variously. The parts diversify and compete. Under selection for performance, interactions among the parts increasingly constrain their structure and associations. As many variants are eliminated, parts self-organize into modules with tight linkage. Linkage may increase in response to exogenous stresses as well as endogenous processes. In the second phase of diversification, variants of the module and its functions evolve and become new parts for a new cycle of generation of higher-level modules. This linkage hypothesis can interpret biphasic patterns in the diversification of protein domain structure, RNA and protein shapes, and networks in metabolism, codes, and embryos, and can explain hierarchical levels of structural organization that are widespread in biology.
Highlights
In evolution, a pattern of change may recur in diverse contexts
We focus on biphasic patterns of diversification, in which diversity decreases to a minimum and increases again
In this paper we propose a general linkage hypothesis to explain evolutionary biphasic patterns that exist at many levels of biological organization
Summary
A pattern of change may recur in diverse contexts. Classic examples include punctuated equilibrium, with alternation of stasis and rapid change; prolonged trends of increase in size; adaptive radiation; convergence; and mass extinction. As a consequence, increasing linkage decreased the rate of survival of new FSFs. During competitive optimization parts link to form modules, which may diversify in various ways (Caetano-Anollés et al, 2009a). Competitive optimization among a diversifying set of interacting proteins produced a module, the network of protein-mediated processes in ancestral cells In these cells new possibilities for diversification arose and were used. COMPETITIVE OPTIMIZATION IN THE EVOLUTION OF DEVELOPMENT AND EPIGENETICS In the development of an embryo, linkage is manifest in the connectivity of signaling networks, gene regulatory networks, and networks of interacting proteins These change the state of differentiation and aggregation of macromolecules and cells to build the structure of the embryo. This process may have contributed to the evolution of diverse sncRNAs—tRNAs, snoRNAs, microRNAs, siRNAs, and piRNAs
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