Universality of Thermodynamic Constants Governing Biological Growth Rates

Background: Mathematical models exist that quantify the effect of temperature on poikilotherm growth rate. One family of such models assumes a single rate-limiting ‘master reaction ’ using terms describing the temperature-dependent denaturation of the reaction’s enzyme. We consider whether such a model can describe growth in each domain of life. Methodology/Principal Findings: A new model based on this assumption and using a hierarchical Bayesian approach fits simultaneously 95 data sets for temperature-related growth rates of diverse microorganisms from all three domains of life, Bacteria, Archaea and Eukarya. Remarkably, the model produces credible estimates of fundamental thermodynamic parameters describing protein thermal stability predicted over 20 years ago. Conclusions/Significance: The analysis lends support to the concept of universal thermodynamic limits to microbial growth rate dictated by protein thermal stability that in turn govern biological rates. This suggests that the thermal stability of proteins is a unifying property in the evolution and adaptation of life on earth. The fundamental nature of this conclusion has importance for many fields of study including microbiology, protein chemistry, thermal biology, and ecological theory including, for example, the influence of the vast microbial biomass and activity in the biosphere that is poorly described in current climate models

Structure and mechanics of active colloids

11 pages Acknowledgments MCM thanks Xingbo Yang and Lisa Manning for their contribution to some aspects of the work reviewed here and for fruitful discussions. MCM was supported by NSF-DMR-305184. MCM and AP acknowledge support by the NSF IGERT program through award NSF-DGE-1068780. MCM, AP and DY were additionally supported by the Soft Matter Program at Syracuse University. AP acknowledges use of the Syracuse University HTC Campus Grid which is supported by NSF award ACI-1341006. YF was supported by NSF grant DMR-1149266 and the Brandeis Center for Bioinspired Soft Materials, an NSF MRSEC, DMR-1420382.Peer reviewedPreprin

Hegel and the Logical Form

The concept of logical form, as influentially specified by Frege and Bolzano, is accompanied by a paradox: to capture some universal property of discourse, we must specify that property, thereby rendering it particular and thus unsuitable for the universal purpose. Thus, instead of a single form, we have rather a sequence of them, corresponding to the logics of Aristotle, Frege, Brouwer, and others. In this paper, I argue that Hegel’s conception of logical form focuses on this historical aspect of the problem. Thus, he does not create a new logical form, e.g., that of dialectical logic, as Marx, as well as Priest and others, believe, but makes the attitude towards “fixed determinations” of logic part of these determinations themselves. This corresponds to Hegel’s differentiation between three layers of logic: formal, dialectical, and speculative

The compositional and evolutionary logic of metabolism

Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which layers of that system emerged. Metabolism also serves as the foundation in other hierarchies, at least up to cellular integration including bioenergetics and molecular replication, and trophic ecology. The recapitulation of patterns first seen in metabolism, in these higher levels, suggests metabolism as a source of causation or constraint on many forms of organization in the biosphere. We identify as modules widely reused subsets of chemicals, reactions, or functions, each with a conserved internal structure. At the small molecule substrate level, module boundaries are generally associated with the most complex reaction mechanisms and the most conserved enzymes. Cofactors form a structurally and functionally distinctive control layer over the small-molecule substrate. Complex cofactors are often used at module boundaries of the substrate level, while simpler ones participate in widely used reactions. Cofactor functions thus act as "keys" that incorporate classes of organic reactions within biochemistry. The same modules that organize the compositional diversity of metabolism are argued to have governed long-term evolution. Early evolution of core metabolism, especially carbon-fixation, appears to have required few innovations among a small number of conserved modules, to produce adaptations to simple biogeochemical changes of environment. We demonstrate these features of metabolism at several levels of hierarchy, beginning with the small-molecule substrate and network architecture, continuing with cofactors and key conserved reactions, and culminating in the aggregation of multiple diverse physical and biochemical processes in cells.Comment: 56 pages, 28 figure