Increase in Complexity and Information through Molecular Evolution

Abstract

Biological evolution progresses by essentially three different mechanisms: (I) optimization of properties through natural selection in a population of competitors; (II) development of new capabilities through cooperation of competitors caused by catalyzed reproduction; and (III) variation of genetic information through mutation or recombination. Simplified evolutionary processes combine two out of the three mechanisms: Darwinian evolution combines competition (I) and variation (III) and is represented by the quasispecies model, major transitions involve cooperation (II) of competitors (I), and the third combination, cooperation (II) and variation (III) provides new insights in the role of mutations in evolution. A minimal kinetic model based on simple molecular mechanisms for reproduction, catalyzed reproduction and mutation is introduced, cast into ordinary differential equations (ODEs), and analyzed mathematically in form of its implementation in a flow reactor. Stochastic aspects are investigated through computer simulation of trajectories of the corresponding chemical master equations. The competition-cooperation model, mechanisms (I) and (II), gives rise to selection at low levels of resources and leads to symbiontic cooperation in case the material required is abundant. Accordingly, it provides a kind of minimal system that can undergo a (major) transition. Stochastic effects leading to extinction of the population through self-enhancing oscillations destabilize symbioses of four or more partners. Mutations (III) are not only the basis of change in phenotypic properties but can also prevent extinction provided the mutation rates are sufficiently large. Threshold phenomena are observed for all three combinations: The quasispecies model leads to an error threshold, the competition-cooperation model allows for an identification of a resource-triggered bifurcation with the transition, and for the cooperation-mutation model a kind of stochastic threshold for survival through sufficiently high mutation rates is observed. The evolutionary processes in the model are accompanied by gains in information on the environment of the evolving populations. In order to provide a useful basis for comparison, two forms of information, syntactic or Shannon information and semantic information are introduced here. Both forms of information are defined for simple evolving systems at the molecular level. Selection leads primarily to an increase in semantic information in the sense that higher fitness allows for more efficient exploitation of the environment and provides the basis for more progeny whereas understanding transitions involves characteristic contributions from both Shannon information and semantic information.

Science-Driven Societal Transformation, Part I: Worldview

“…A person is an independent agent at the meter scale. A cell is an independent agent at the micrometer scale, and so on down to the molecular and atomic levels [58,[172][173][174][175][176]. Moving in the opposite direction, the random and intrinsic fluctuations at scales below a given Markov blanket are progressively suppressed [32].…”

Molecular evolution between chemistry and biology

“…In the simple form in which the model was introduced here, it has been tested experimentally by in vitro evolution experiments [For an overview of early works on this subject see (Spiegelman 1971 ; Biebricher 1983 ); as a recent review we mention (Joyce 2007 )]. The kinetic equations describing replication and mutation were introduced 1971 by Manfred Eigen in his scholarly written paper on self-organization of biological macromolecules (Eigen 1971 ).…”

“…1984 , 1985 ) and an appropriate replication assay serves for in vitro evolution studies (Mills et al. 1967 ; Biebricher 1983 ). The mutation-selection scenario was found to provide an appropriate molecular basis for understanding also virus evolution [For a recent survey see the contributed volume (Domingo and Schuster 2016 )].…”

Science-Driven Societal Transformation, Part I: Worldview

“…They act (reflexively) to reduce stress, and have memory. Some molecular species can even be said to self-replicate and evolve over time, and to engage in metabolism and cooperation [174][175][176][177][178]. Moving in the opposite direction, the random and intrinsic fluctuations at scales below a given Markov blanket are progressively suppressed [33].…”