A computer-glimpse of the origin of life

Immune response to a variable pathogen: a stochastic model with two interlocked Darwinian entities

This paper presents the modeling of a host immune system, more precisely the immune effector cell and immune memory cell population, and its interaction with an invading pathogen population. It will tackle two issues of interest; on the one hand, in defining a stochastic model accounting for the inherent nature of organisms in population dynamics, namely multiplication with mutation and selection; on the other hand, in providing a description of pathogens that may vary their antigens through mutations during infection of the host. Unlike most of the literature, which models the dynamics with first-order differential equations, this paper proposes a Galton-Watson type branching process to describe stochastically by whole distributions the population dynamics of pathogens and immune cells. In the first model case, the pathogen of a given type is either eradicated or shows oscillatory chronic response. In the second model case, the pathogen shows variational behavior changing its antigen resulting in a prolonged immune reaction.

An information-carrying and knowledge-producing molecular machine. A Monte-Carlo simulation

The concept called Knowledge is a measure of the quality of genetically transferred information. Its usefulness is demonstrated quantitatively in a Monte-Carlo simulation on critical steps in a origin of life model. The model describes the origin of a bio-like genetic apparatus by a long sequence of physical-chemical steps: it starts with the presence of a self-replicating oligomer and a specifically structured environment in time and space that allow for the formation of aggregates such as assembler-hairpins-devices and, at a later stage, an assembler-hairpins-enzyme device-a first translation machine.

Adding to Hans Kuhn's thesis on the emergence of the genetic apparatus: of the Darwinian advantage to be neither too soluble, nor too insoluble, neither too solid, nor completely liquid

A scenario of the origin of the genetic apparatus is described where the surface and physico-chemical properties of lipid bilayers and multilayers of vesicles play a crucial role. Peptides, nucleic acids and lipids are 'collaborating' to bring about a first successful genetic apparatus. Lipidic vesicles acquire new properties through hosting nucleic acids that are transiently but covalently linked to lipophilic peptides. These peptides anchor the associated nucleic acids into the surface of lipidic vesicles. In the interior of such vesicles, within the lipidic bilayer, peptidyl transfers occur that are reminiscent of modern-day ribosomal peptidyl transfer reactions. One can expect that the growing peptides eventually acquire, stepwise and essentially arbitrarily, new functions different from anchoring nucleic acids, such as specific aminoacylation of nucleic acids, template-assisted nucleic acid synthesis, nucleotide deoxygenation and fatty acid synthesis.