Some notes on the problem of uncertainty in biological measurements

Problems of measurement and instrumentation in biolog

A window in time for the first evolutionary radiation

The window in time between the last globally sterilizing event and the evidence for a complex procaryotic ecosystem is quite narrow, perhaps as small as 200 million years. We will present a heuristic model outlining the first evolutionary radiation that could have led from primordial vesicles to the universal ancestor. The concept of the universal ancestor will be developed in terms of contemporary molecular biology

The thermodynamic dual structure of linear-dissipative driven systems

The spontaneous emergence of dynamical order, such as persistent currents, is sometimes argued to require principles beyond the entropy maximization of the second law of thermodynamics. I show that, for linear dissipation in the Onsager regime, current formation can be driven by exactly the Jaynesian principle of entropy maximization, suitably formulated for extended systems and nonequilibrium boundary conditions. The Legendre dual structure of equilibrium thermodynamics is also preserved, though it requires the admission of current-valued state variables, and their correct incorporation in the entropy

Proceedings of the 2014 A.S.P.E.N. Research Workshop

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141886/1/jpen0167.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/141886/2/jpen0167-sup-0001.pd

Analytical study of non Gaussian fluctuations in a stochastic scheme of autocatalytic reactions

A stochastic model of autocatalytic chemical reactions is studied both numerically and analytically. The van Kampen perturbative scheme is implemented, beyond the second order approximation, so to capture the non Gaussianity traits as displayed by the simulations. The method is targeted to the characterization of the third moments of the distribution of fluctuations, originating from a system of four populations in mutual interaction. The theory predictions agree well with the simulations, pointing to the validity of the van Kampen expansion beyond the conventional Gaussian solution.Comment: 15 pages, 8 figures, submitted to Phys. Rev.

Unified analysis of terminal-time control in classical and quantum systems

Many phenomena in physics, chemistry, and biology involve seeking an optimal control to maximize an objective for a classical or quantum system which is open and interacting with its environment. The complexity of finding an optimal control for maximizing an objective is strongly affected by the possible existence of sub-optimal maxima. Within a unified framework under specified conditions, control objectives for maximizing at a terminal time physical observables of open classical and quantum systems are shown to be inherently free of sub-optimal maxima. This attractive feature is of central importance for enabling the discovery of controls in a seamless fashion in a wide range of phenomena transcending the quantum and classical regimes.Comment: 10 page

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

The origin of large molecules in primordial autocatalytic reaction networks

Large molecules such as proteins and nucleic acids are crucial for life, yet their primordial origin remains a major puzzle. The production of large molecules, as we know it today, requires good catalysts, and the only good catalysts we know that can accomplish this task consist of large molecules. Thus the origin of large molecules is a chicken and egg problem in chemistry. Here we present a mechanism, based on autocatalytic sets (ACSs), that is a possible solution to this problem. We discuss a mathematical model describing the population dynamics of molecules in a stylized but prebiotically plausible chemistry. Large molecules can be produced in this chemistry by the coalescing of smaller ones, with the smallest molecules, the `food set', being buffered. Some of the reactions can be catalyzed by molecules within the chemistry with varying catalytic strengths. Normally the concentrations of large molecules in such a scenario are very small, diminishing exponentially with their size. ACSs, if present in the catalytic network, can focus the resources of the system into a sparse set of molecules. ACSs can produce a bistability in the population dynamics and, in particular, steady states wherein the ACS molecules dominate the population. However to reach these steady states from initial conditions that contain only the food set typically requires very large catalytic strengths, growing exponentially with the size of the catalyst molecule. We present a solution to this problem by studying `nested ACSs', a structure in which a small ACS is connected to a larger one and reinforces it. We show that when the network contains a cascade of nested ACSs with the catalytic strengths of molecules increasing gradually with their size (e.g., as a power law), a sparse subset of molecules including some very large molecules can come to dominate the system.Comment: 49 pages, 17 figures including supporting informatio