The Nucleation of Semantic Information in Prebiotic Matter

Küppers, Bernd‐Olaf

doi:10.1007/82_2015_454

Cited by 10 publications

(12 citation statements)

References 15 publications

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“…As an interpretation of the results, we proposed broadly diversifying selection as an attribute of viral quasispecies dynamics, manifested when viruses replicate in environments that do not experience external perturbations (24). A likely driver of broadly diversifying selection is the modification of mutant spectrum composition due to mutational input (11,24,46). The diversity indices quantified in previous studies did not inform of the relationships among the sequences present in mutant spectra.…”

Section: Mutation Types and Amino Acid Substitution Tolerance In Haplotypes From Low And High Fitness Peaksmentioning

confidence: 82%

A two-level, dynamic fitness landscape of hepatitis C virus revealed by self-organized haplotype maps

Delgado

Perales

García-Crespo

et al. 2021

Preprint

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Fitness landscapes reflect the adaptive potential of viruses. There is no information on how fitness peaks evolve when a virus replicates extensively in a controlled cell culture environment. Here we report the construction of Self-Organized Maps (SOMs), based on deep sequencing reads of three amplicons of the NS5A-NS5B-coding region of hepatitis C virus (HCV). A two-dimensional neural network was constructed and organized according to sequence relatedness. The third dimension of the fitness profile was given by the haplotype frequencies at each neuron. Fitness maps were derived for 44 HCV populations that share a common ancestor that was passaged up to 210 times in human hepatoma Huh-7.5 cells. As the virus increased its adaptation to the cells, the number of fitness peaks expanded, and their distribution shifted in sequence space. The landscape consisted of an extended basal platform, and a lower number of protruding higher fitness peaks. The function that relates fitness level and peak abundance corresponds a power law, a relationship observed with other complex natural phenomena. The dense basal platform may serve as spring-board to attain high fitness peaks. The study documents a highly dynamic, double-layer fitness landscape of HCV when evolving in a monotonous cell culture environment. This information may help interpreting HCV fitness landscapes in complex in vivo environments.IMPORTANCEThe study provides for the first time the fitness landscape of a virus in the course of its adaptation to a cell culture environment, in absence of external selective constraints. The deep sequencing-based self-organized maps document a two-layer fitness distribution with an ample basal platform, and a lower number of protruding, high fitness peaks. This landscape structure offers potential benefits for virus resilience to mutational inputs.

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Section: Mutation Types and Amino Acid Substitution Tolerance In Haplotypes From Low And High Fitness Peaksmentioning

confidence: 82%

A two-level, dynamic fitness landscape of hepatitis C virus revealed by self-organized haplotype maps

Delgado

Perales

García-Crespo

et al. 2021

Preprint

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“…(2.3.2), it is easy to see the connection with the recent work of Schmeikal on geometric Clifford algebra of space-time, establishing novel relations between logic and geometry [79]. Note that context-dependence of genetic information pushing semantic information in prebiotic matter has recently been reviewed by Küppers [80].…”

Section: Afterwordmentioning

confidence: 88%

The Origin and Evolution of Complex Enough Systems in Biology

Brändas

2017

Quantum Systems in Physics, Chemistry, and Biology

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Recent criticisms of Neo-Darwinism are considered and disputed within the setting of recent advances in chemical physics. A related query, viz., the ontological thesis, that everything is physical, confronts a crucial test on the validity of reductionism as a fundamental approach to science. While traditional 'physicalism' interprets evolution as a sequence of physical accidents governed by the second law of thermodynamics, the concepts of biology concern processes that owe their goal-directedness to the influence of an evolved program. This disagreement is met by unifying basic aspects of chemistry and physics, formulating the Correlated Dissipative Ensemble, CDE, as a characterization of a 'complex enough systems', CES, in biology. The latter entreats dissipative dynamics; non-Hermitian quantum mechanics together with modern quantum statistics thereby establish a precise spatio-temporal order of significance for living systems. The CDE grants a unitary transformation structure that comprises communication protocols of embedded Poisson statistics for molecular recognition and cellular differentiation, providing cell-hierarchies in the organism. The present conception of evolution, founded on communication with a built-in self-referential order, offers a valid argument in favour of Neo-Darwinism, providing an altogether solid response and answer to the criticisms voiced above. Introductory Remarks Reductionism in Natural ScienceA frequent understanding of natural sciences contends that biology reduces to chemistry and chemistry to physics. Even if the traditional analytic interpretation of mathematics as a language or tool to convert knowledge about nature, i.e. a formal science not being incorporated amongst the branches of physical or life sciences, some recent propositions impart that also physics can be reduced to mathematics [1]. Within such views, based on strict reductionnism, see more below, one argues that the present laws of physics are not only commensurate to biology, but also contain the necessary natural laws for expressing all the known biological facts.There are numerous differences of opinion regarding the scheme outlined above, e.g. the impossibility to derive the Coulomb Hamiltonian corresponding to a molecule from first principles and the general problem of quantum chemistry to treat nuclei and electrons on a more or less equivalent basis, see Löwdin [2]. Other arguments concern the concepts of biology as the laws of physics, at present, exclude a fundamental understanding of biological processes governed by an evolved program [3,4].Observation and deliberate experiments instigate rational, deductive theory, formulated in the language of mathematics, with the so accumulated knowledge discussed and contained by the methods of philosophy in general and the concepts of biology in particular. Recognizing the acquired demarcation between the philosophy of science, including biology, and the enactment of reductionism as embodied in the laws of physics, the endwise connections between them ...

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“…We suggest that such a cause is a permanent population disequilibrium that pushes HCV to explore new regions of sequence space even when external selective constraints are absent. According to theoretical studies on quasispecies dynamics, in molecular evolution, the assumption of a constant environment is an idealized condition that cannot be realized since the individuals of a population of molecules contribute to the environment of the population [ 65 ]. In the case of HCV replication in cell culture, an internal effect of the mutant spectrum within individual infected cells or replicative organelles may be triggered by the random occurrence of mutations that renders the replicative context unique at each successive time point.…”

Section: A Unifying Disequilibrium Model For Expanded Adaptive Potentialmentioning

confidence: 99%

Population Disequilibrium as Promoter of Adaptive Explorations in Hepatitis C Virus

García-Crespo

Gallego

Soria

et al. 2021

Viruses

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Replication of RNA viruses is characterized by exploration of sequence space which facilitates their adaptation to changing environments. It is generally accepted that such exploration takes place mainly in response to positive selection, and that further diversification is boosted by modifications of virus population size, particularly bottleneck events. Our recent results with hepatitis C virus (HCV) have shown that the expansion in sequence space of a viral clone continues despite prolonged replication in a stable cell culture environment. Diagnosis of the expansion was based on the quantification of diversity indices, the occurrence of intra-population mutational waves (variations in mutant frequencies), and greater individual residue variations in mutant spectra than those anticipated from sequence alignments in data banks. In the present report, we review our previous results, and show additionally that mutational waves in amplicons from the NS5A-NS5B-coding region are equally prominent during HCV passage in the absence or presence of the mutagenic nucleotide analogues favipiravir or ribavirin. In addition, by extending our previous analysis to amplicons of the NS3- and NS5A-coding region, we provide further evidence of the incongruence between amino acid conservation scores in mutant spectra from infected patients and in the Los Alamos National Laboratory HCV data banks. We hypothesize that these observations have as a common origin a permanent state of HCV population disequilibrium even upon extensive viral replication in the absence of external selective constraints or changes in population size. Such a persistent disequilibrium—revealed by the changing composition of the mutant spectrum—may facilitate finding alternative mutational pathways for HCV antiviral resistance. The possible significance of our model for other genetically variable viruses is discussed.

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The Nucleation of Semantic Information in Prebiotic Matter

Cited by 10 publications

References 15 publications

A two-level, dynamic fitness landscape of hepatitis C virus revealed by self-organized haplotype maps

A two-level, dynamic fitness landscape of hepatitis C virus revealed by self-organized haplotype maps

The Origin and Evolution of Complex Enough Systems in Biology

Population Disequilibrium as Promoter of Adaptive Explorations in Hepatitis C Virus

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