The Role of Energy in the Emergence of Biology from Chemistry

Any scenario of the transition from chemistry to biology should include an ??energy module?? because life can exist only when supported by energy flow(s). We addressed the problem of primordial energetics by combining physico-chemical considerations with phylogenomic analysis. We propose that the first replicators could use abiotically formed, exceptionally photostable activated cyclic nucleotides both as building blocks and as the main energy source. Nucleoside triphosphates could replace cyclic nucleotides as the principal energy-rich compounds at the stage of the first cells, presumably because the metal chelates of nucleoside triphosphates penetrated membranes much better than the respective metal complexes of nucleoside monophosphates. The ability to exploit natural energy flows for biogenic production of energy-rich molecules could evolve only gradually, after the emergence of sophisticated enzymes and ion-tight membranes. We argue that, in the course of evolution, sodium-dependent membrane energetics preceded the proton-based energetics which evolved independently in bacteria and archaea.     

On the Evolution of Feathers from an Aerodynamic and Constructional View Point

The evolution of birds and feathers are examined in terms ofthe aerodynamic constraints imposed by the arboreal and cursorialmodels of flight evolution. The cursorial origin of flight isassociated with the putative coelurosaurian ancestry of birds.As presently known, coelurosaurs have a center of mass locatedin the pelvic region and an elongated pubis that is ventrallyor anteriorly directed. Both of these characteristics make itdifficult to postulate an origin of flight that would involvea gliding phase because the abdomen cannot be flattened intoan aerodynamic shape. Moreover, the cursorial model must counteractgravity using the hindlimb and, thus, selection for the powerrequirement for lift-off would not focus on the forelimb. Therefore,if the hypothesis proposing a coelurosaurian ancestry of birdsis to remain viable, it must be via an as yet undiscovered taxonthat is compatible with the morphological and aerodynamic constraintsimposed by flight evolution. The arboreal model, currently centers around non-dinosauriantaxa and is more parsimonious in that early archosaurs haveshort pubes that do not preclude an aerodynamic body profile.Moreover, the arboreal proavis uses gravity to create the airflowover the body surfaces and is, thus, energy efficient. Considerationof the initial aerodynamic roles of feathers and feather designare consistent with a precursory gliding phase. Whether avianancestry lies among coelurosaur theropods or earlier archosaurs,we must remain mindful of the complex aerodynamic dictates ofgliding and powered flight and avoid formalistic approachesthat co-opt sister taxa, with their known body form, as functionalancestors.     

Functional Translational Readthrough: A Systems Biology Perspective

Translational readthrough (TR) has come into renewed focus because systems biology approaches have identified the first human genes undergoing functional translational readthrough (FTR). FTR creates functional extensions to proteins by continuing translation of the mRNA downstream of the stop codon. Here we review recent developments in TR research with a focus on the identification of FTR in humans and the systems biology methods that have spurred these discoveries.     

Immortality from a Scientific Point of View

At such moments in history as the present, when almost every day brings us news of the death of hundreds, even thousands, of people on the battlefields, questions concerning "eternal" life and the immortality of the human personality arise with particular persistence. Of course, they also arise under the ordinary, mundane conditions of life, in which, at every step, we are confronted with the loss, from natural or violent causes, of friends, relatives, and acquaintances.     

Optimization and Control of Agent-Based Models in Biology: A Perspective

Agent-based models (ABMs) have become an increasingly important mode of inquiry for the life sciences. They are particularly valuable for systems that are not understood well enough to build an equation-based model. These advantages, however, are counterbalanced by the difficulty of analyzing and using ABMs, due to the lack of the type of mathematical tools available for more traditional models, which leaves simulation as the primary approach. As models become large, simulation becomes challenging. This paper proposes a novel approach to two mathematical aspects of ABMs, optimization and control, and it presents a few first steps outlining how one might carry out this approach. Rather than viewing the ABM as a model, it is to be viewed as a surrogate for the actual system. For a given optimization or control problem (which may change over time), the surrogate system is modeled instead, using data from the ABM and a modeling framework for which ready-made mathematical tools exist, such as differential equations, or for which control strategies can explored more easily. Once the optimization problem is solved for the model of the surrogate, it is then lifted to the surrogate and tested. The final step is to lift the optimization solution from the surrogate system to the actual system. This program is illustrated with published work, using two relatively simple ABMs as a demonstration, Sugarscape and a consumer-resource ABM. Specific techniques discussed include dimension reduction and approximation of an ABM by difference equations as well systems of PDEs, related to certain specific control objectives. This demonstration illustrates the very challenging mathematical problems that need to be solved before this approach can be realistically applied to complex and large ABMs, current and future. The paper outlines a research program to address them.     

Exploring the Chemistry and Biology of Vanadium-dependent Haloperoxidases

Nature has developed an exquisite array of methods to introduce halogen atoms into organic compounds. Most of these enzymes are oxidative and require either hydrogen peroxide or molecular oxygen as a cosubstrate to generate a reactive halogen atom for catalysis. Vanadium-dependent haloperoxidases contain a vanadate prosthetic group and utilize hydrogen peroxide to oxidize a halide ion into a reactive electrophilic intermediate. These metalloenzymes have a large distribution in nature, where they are present in macroalgae, fungi, and bacteria, but have been exclusively characterized in eukaryotes. In this minireview, we highlight the chemistry and biology of vanadium-dependent haloperoxidases from fungi and marine algae and the emergence of new bacterial members that extend the biological function of these poorly understood halogenating enzymes.     

Evolution and RNA Relics. A Systems Biology View

The genetic code has evolved from its initial non-degenerate wobble version until reaching its present state of degeneracy. By using the stereochemical hypothesis, we revisit the problem of codon assignations to the synonymy classes of amino-acids. We obtain these classes with a simple classifier based on physico-chemical properties of nucleic bases, like hydrophobicity and molecular weight. Then we propose simple RNA (or more generally XNA, with X for D, P or R) ring structures that present, overlap included, one and only one codon by synonymy class as solutions of a combinatory variational problem. We compare these solutions to sequences of present RNAs considered as relics, with a high interspecific invariance, like invariant parts of (t)RNAs and micro-RNAs. We conclude by emphasizing some optimal properties of the genetic code.