24 research outputs found
On biological homochirality
Generalizing Landau's spontaneous symmetry breaking arguments using the standard groupoid approach to stereochemistry allows reconsideration of the origin of biological homochirality. On Earth, limited metabolic free energy density may have served as a low temperature analog to 'freeze' the system into the set of simplest homochiral transitive groupoids representing reproductive chemistries. These engaged in Darwinian competition until a single configuration survived. Subsequent path dependent evolutionary process licked in this initial condition. Astrobiological outcomes, in the presence of higher initial metabolic free energy densities, could well be considerably richer, perhaps of mixed chirality. One result would be a complicated distribution of biological chirality across a statistically large sample of extraterrestrial stereochemistry, in contrast with a recent prediction of a racemic average
Astrobiological Perspectives on Consciousness
The Stanley Miller experiment suggests that amino acid-based life is ubiquitous in our universe, although its varieties are not likely to have followed the particular, highly contingent and path-dependent, trajectory found on Earth. Are many of these life forms likely to be conscious in ways that we would recognize? Almost certainly. Will many conscious entities develop high order technology? Less likely. If so, will we be able to communicate with them? Only on a basic level, and only with profound difficulty. The argument is straightforward
On the social induction of Alzheimer's disease: An index theorem aging model for amyloid formation
The central 'risk factor' for Alzheimer's disease (AD) is age. From first principles, we construct a mathematical model of protein folding and its in vivo regulation that gives this result in a natural manner. We extend the basic approach using topological information theory methods, and examine a case history of socially-induced premature aging in the United States
The Evolution of Homochirality
It is possible to reconsider the origin of biological homochirality in a novel way by formally invoking the standard groupoid approach to stereochemistry in a thermodynamic context that generalizes Landau's spontaneous symmetry breaking arguments. On Earth, limited metabolic free energy may have served as a low temperature analog to 'freeze' the system in the lowest energy state, i.e., the set of simplest homochiral transitive groupoids representing reproductive chemistries. These engaged in a Darwinian competition until a single configuration survived. Subsequent path dependent evolutionary process locked in this initial condition, in spite of increases in available metabolic free energy. Astrobiological outcomes, given higher initial metabolic free energy densities, could well be considerably richer, for example, of mixed chirality. One result would be a complicated distribution of biological chirality across a statistically large sample of extraterrestrial stereochemisty, in marked contrast with published predictions of a racemic average
Types for BioAmbients
The BioAmbients calculus is a process algebra suitable for representing
compartmentalization, molecular localization and movements between
compartments. In this paper we enrich this calculus with a static type system
classifying each ambient with group types specifying the kind of compartments
in which the ambient can stay. The type system ensures that, in a well-typed
process, ambients cannot be nested in a way that violates the type hierarchy.
Exploiting the information given by the group types, we also extend the
operational semantics of BioAmbients with rules signalling errors that may
derive from undesired ambients' moves (i.e. merging incompatible tissues).
Thus, the signal of errors can help the modeller to detect and locate unwanted
situations that may arise in a biological system, and give practical hints on
how to avoid the undesired behaviour
Unnatural Selection: A new formal approach to punctuated equilibrium in economic systems
Generalized Darwinian evolutionary theory has emerged as central to the description of economic process (e.g., Aldrich et. al., 2008). Here we demonstrate that, just as Darwinian principles provide necessary, but not sufficient, conditions for understanding the dynamics of social entities, in a similar manner the asymptotic limit theorems of information theory provide another set of necessary conditions that constrain the evolution of socioeconomic process. These latter constraints can, however, easily be formulated as a statistics-like analytic toolbox for the study of empirical data that is consistent with a generalized Darwinism, and this is no small thing
A Process Calculus for Molecular Interaction Maps
We present the MIM calculus, a modeling formalism with a strong biological
basis, which provides biologically-meaningful operators for representing the
interaction capabilities of molecular species. The operators of the calculus
are inspired by the reaction symbols used in Molecular Interaction Maps (MIMs),
a diagrammatic notation used by biologists. Models of the calculus can be
easily derived from MIM diagrams, for which an unambiguous and executable
interpretation is thus obtained. We give a formal definition of the syntax and
semantics of the MIM calculus, and we study properties of the formalism. A case
study is also presented to show the use of the calculus for modeling
biomolecular networks.Comment: 15 pages; 8 figures; To be published on EPTCS, proceedings of MeCBIC
200
Stochastic Calculus of Wrapped Compartments
The Calculus of Wrapped Compartments (CWC) is a variant of the Calculus of
Looping Sequences (CLS). While keeping the same expressiveness, CWC strongly
simplifies the development of automatic tools for the analysis of biological
systems. The main simplification consists in the removal of the sequencing
operator, thus lightening the formal treatment of the patterns to be matched in
a term (whose complexity in CLS is strongly affected by the variables matching
in the sequences).
We define a stochastic semantics for this new calculus. As an application we
model the interaction between macrophages and apoptotic neutrophils and a
mechanism of gene regulation in E.Coli
Modelling the Dynamics of an Aedes albopictus Population
We present a methodology for modelling population dynamics with formal means
of computer science. This allows unambiguous description of systems and
application of analysis tools such as simulators and model checkers. In
particular, the dynamics of a population of Aedes albopictus (a species of
mosquito) and its modelling with the Stochastic Calculus of Looping Sequences
(Stochastic CLS) are considered. The use of Stochastic CLS to model population
dynamics requires an extension which allows environmental events (such as
changes in the temperature and rainfalls) to be taken into account. A simulator
for the constructed model is developed via translation into the specification
language Maude, and used to compare the dynamics obtained from the model with
real data.Comment: In Proceedings AMCA-POP 2010, arXiv:1008.314