22 research outputs found
Calculation of the relative metastabilities of proteins in subcellular compartments of Saccharomyces cerevisiae
[abridged] Background: The distribution of chemical species in an open system
at metastable equilibrium can be expressed as a function of environmental
variables which can include temperature, oxidation-reduction potential and
others. Calculations of metastable equilibrium for various model systems were
used to characterize chemical transformations among proteins and groups of
proteins found in different compartments of yeast cells.
Results: With increasing oxygen fugacity, the relative metastability fields
of model proteins for major subcellular compartments go as mitochondrion,
endoplasmic reticulum, cytoplasm, nucleus. In a metastable equilibrium setting
at relatively high oxygen fugacity, proteins making up actin are predominant,
but those constituting the microtubule occur with a low chemical activity. A
reaction sequence involving the microtubule and spindle pole proteins was
predicted by combining the known intercompartmental interactions with a
hypothetical program of oxygen fugacity changes in the local environment. In
further calculations, the most-abundant proteins within compartments generally
occur in relative abundances that only weakly correspond to a metastable
equilibrium distribution. However, physiological populations of proteins that
form complexes often show an overall positive or negative correlation with the
relative abundances of proteins in metastable assemblages.
Conclusions: This study explored the outlines of a thermodynamic description
of chemical transformations among interacting proteins in yeast cells. The
results suggest that these methods can be used to measure the degree of
departure of a natural biochemical process or population from a local minimum
in Gibbs energy.Comment: 32 pages, 7 figures; supporting information is available at
http://www.chnosz.net/yeas
The emerging structure of the Extended Evolutionary Synthesis: where does Evo-Devo fit in?
The Extended Evolutionary Synthesis (EES) debate is gaining ground in contemporary evolutionary biology. In parallel, a number of philosophical standpoints have emerged in an attempt to clarify what exactly is represented by the EES. For Massimo Pigliucci, we are in the wake of the newest instantiation of a persisting Kuhnian paradigm; in contrast, Telmo Pievani has contended that the transition to an EES could be best represented as a progressive reformation of a prior Lakatosian scientific research program, with the extension of its Neo-Darwinian core and the addition of a brand-new protective belt of assumptions and auxiliary hypotheses. Here, we argue that those philosophical vantage points are not the only ways to interpret what current proposals to âextendâ the Modern Synthesis-derived âstandard evolutionary theoryâ (SET) entail in terms of theoretical change in evolutionary biology. We specifically propose the image of the emergent EES as a vast network of models and interweaved representations that, instantiated in diverse practices, are connected and related in multiple ways. Under that assumption, the EES could be articulated around a paraconsistent network of evolutionary theories (including some elements of the SET), as well as models, practices and representation systems of contemporary evolutionary biology, with edges and nodes that change their position and centrality as a consequence of the co-construction and stabilization of facts and historical discussions revolving around the epistemic goals of this area of the life sciences. We then critically examine the purported structure of the EESâpublished by Laland and collaborators in 2015âin light of our own network-based proposal. Finally, we consider which epistemic units of Evo-Devo are present or still missing from the EES, in preparation for further analyses of the topic of explanatory integration in this conceptual framework
Two approaches to the study of the origin of life.
This paper compares two approaches that attempt to explain the origin of life, or biogenesis. The more established approach is one based on chemical principles, whereas a new, yet not widely known approach begins from a physical perspective. According to the first approach, life would have begun with - often organic - compounds. After having developed to a certain level of complexity and mutual dependence within a non-compartmentalised organic soup, they would have assembled into a functioning cell. In contrast, the second, physical type of approach has life developing within tiny compartments from the beginning. It emphasises the importance of redox reactions between inorganic elements and compounds found on two sides of a compartmental boundary. Without this boundary, ÂżlifeÂż would not have begun, nor have been maintained; this boundary - and the complex cell membrane that evolved from it - forms the essence of life
Selection without replicators: the origin of genes, and the replicator/interactor distinction in etiobiology
Genes are thought to have evolved from long-lived and multiply-interactive molecules in the early stages of the origins of life. However, at that stage there were no replicators, and the distinction between interactors and replicators did not yet apply. Nevertheless, the process of evolution that proceeded from initial autocatalytic hypercycles to full organisms was a Darwinian process of selection of favourable variants. We distinguish therefore between Neo-Darwinian evolution and the related Weismannian and Central Dogma divisions, on the one hand, and the more generic category of Darwinian evolution on the other. We argue that Hull's and Dawkins' replicator/interactor distinction of entities is a sufficient, but not necessary, condition for Darwinian evolution to take place. We conceive the origin of genes as a separation between different types of molecules in a thermodynamic state space, and employ a notion of reproducers.John S. Wilkins, Clem Stanyon, Ian Musgrav