Computer-modeling origin of a simple genetic apparatus

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.

A computer-glimpse of the origin of life

Evolution is assumed to begin in a very particular compartmentalized location with periodic conditions. A highly diversified world is the driving force for the continuous increase in complexity by colonizing increasingly less favourable regions. Modeling the "origin-of-life" a Darwinian cyclic process is simulated (multiplication with sporadic errors followed by a construction and selection).Starting from a RNA-world (R-strands of R(1) and R(2) monomers building Hairpin-Assembler devices) and introducing another kind of monomers (A(1) and A(2) which interlink to the Hairpin-Assembler devices such that they become bound and form an A-oligomer) it is shown that a simple translation apparatus evolves producing enzymes (specific sequences of A(1) and A(2) monomers given by the sequences of R(1) and R(2) monomers on the assembler-strands). Later on D-strands are introduced, which are not capable of participating in the synthesis of A-oligomers. These D-strands become carriers of the genetic information and induce the formation of increasingly complex entities of functionally interplaying components.

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.

Survival chances of mutants starting with one individual

A simple theoretical model of a Darwinian system (a periodic system with a multiplication phase and a selection phase) of entities (initial form of polymer strand, primary mutant and satellite mutants) is given.

FIRST CASE

one mutant is considered. One individual of the mutant appears in the multiplication phase of the first generation. The probabilities to find N individuals of the mutant W(n)(S)(N) after the multiplication phase M of the n-th generation (with probability delta of an error in the replication, where all possible errors are fatal errors) and W(n)(S)(N) after the following selection phase S (with probability beta that one individual survives) are given iteratively. The evolutionary tree is evaluated. Averages from the distributions and the probability of extinction W(infinity)(S)(0) are obtained. Second case: two mutants are considered (primary mutant and new form). One individual of the primary mutant appears in the multiplication phase of the first generation. The probabilities to find N(p) individuals of the primary mutant and N(m) individuals of the new form W(n)(M)(N(p), N(m)) after the multiplication phase M of the n-th generation (probability varepsilon of an error in the replication of the primary mutant giving the new form) and W(n)(S)(N(p), N(m) after the following selection phase S (probabilities beta(p) and beta(m) that one individual each of the primary mutant and of the new form survives) are given iteratively. Again the evolutionary tree is evaluated. Averages from the distributions are obtained.

Survival chances of mutants starting with one individual

A simple theoretical model of a Darwinian system (a periodic system with a multiplication phase and a selection phase) of entities (initial form of polymer strand, primary mutant and satellite mutants) is given.

FIRST CASE

one mutant is considered. One individual of the mutant appears in the multiplication phase of the first generation. The probabilities to find N mutants W(n) (M)(N) after the multiplication phase M of the n-th generation (with probability δ of an error in the replication, where all possible errors are fatal errors) and W(n) (S)(N) after the following selection phase S (with probability β that one individual survives) are given iteratively. The evolutionary tree is evaluated. Averages from the distributions and the probability of extinction W(∞) (S)(0) are obtained.Second case: two mutants are considered (primary mutant and new form). One individual of the primary mutant appears in the multiplication phase of the first generation. The probabilities to find N(p) primary mutants and N(m) of the new form W(n) (M)(N(p), N(m)) after the multiplication phase M of the n-th generation (probability ε of an error in the replication of the primary mutant giving the new form) and W(n) (S)(N(p), N(m)) after the following selection phase S (probabilities β(p) and β(m) that one individual each of the primary mutant and of the new form survives) are given iteratively. Again the evolutionary tree is evaluated. Averages from the distributions are obtained.

Genetic material in the early evolution of bacteria

DNA and RNA are nucleic acids that cells and viruses use to produce copies of themselves. However, there is an immense paucity of knowledge on how these nucleic acids originated and changed as early bacteria became capable of growth and cell division. One possibility is that parallel evolution of the genetic code and protein synthesis was required for assembly of the first cells capable of growth and division. It is also possible that DNA-RNA duplices were intermediate genetic material in the early assembly of the first cells. These ideas will be discussed as well as other aspects of the assembly of the first cells on the Earth.