Towards an evolutionary theory of the origin of life based on kinetics and thermodynamics

A sudden transition in a system from an inanimate state to the living state—defined on the basis of present day living organisms—would constitute a highly unlikely event hardly predictable from physical laws. From this uncontroversial idea, a self-consistent representation of the origin of life process is built up, which is based on the possibility of a series of intermediate stages. This approach requires a particular kind of stability for these stages—dynamic kinetic stability (DKS)—which is not usually observed in regular chemistry, and which is reflected in the persistence of entities capable of self-reproduction. The necessary connection of this kinetic behaviour with far-from-equilibrium thermodynamic conditions is emphasized and this leads to an evolutionary view for the origin of life in which multiplying entities must be associated with the dissipation of free energy. Any kind of entity involved in this process has to pay the energetic cost of irreversibility, but, by doing so, the contingent emergence of new functions is made feasible. The consequences of these views on the studies of processes by which life can emerge are inferred.     

Confounding asymmetries in evolutionary diversification and character change

Studies of character evolution often assume that a phylogeny's shape is determined independently of the characters, which then evolve as mere passengers along the tree's branches. However, if the characters help shape the tree, but this is not considered, biased inferences can result. Simulations of asymmetrical speciation (i.e., one character state conferring a higher rate of speciation than another) result in data that are interpreted to show a higher rate of change toward the diversification-enhancing state, even though the rates to and from this state were in fact equal. Conversely, simulations of asymmetrical character change yield data that could be misinterpreted as showing asymmetrical rates of speciation. Studies of biased diversification and biased character change need to be unified by joint models and estimation methods, although how successfully the two processes can be teased apart remains to be seen.     

On phylogenetic tests of irreversible evolution

"Dollo's law" states that, following loss, a complex trait cannot reevolve in an identical manner. Although the law has previously fallen into disrepute, it has only recently been challenged with statistical phylogenetic methods. We employ simulation studies of an irreversible binary character to show that rejections of Dollo's law based on likelihood-ratio tests of transition rate constraints or on reconstructions of ancestral states are frequently incorrect. We identify two major causes of errors: incorrect assignment of root state frequencies, and neglect of the effect of the character state on rates of speciation and extinction. Our findings do not necessarily overturn the conclusions of phylogenetic studies claiming reversals, but we demonstrate devastating flaws in the methods that are the foundation of all such studies. Furthermore, we show that false rejections of Dollo's law can be reduced by the use of appropriate existing models and model selection procedures. More powerful tests of irreversibility require data beyond phylogenies and character states of extant taxa, and we highlight empirical work that incorporates additional information.     

Research Progress on Negative Electrodes for Practical Li‐Ion Batteries: Beyond Carbonaceous Anodes

Research activities related to the development of negative electrodes for construction of high‐performance Li‐ion batteries (LIBs) with conventional cathodes such as LiCoO₂, LiFePO₄, and LiMn₂O₄ are described. The anode materials are classified in to three main categories, insertion, conversion, and alloying type, based on their reactivity with Li. Although numerous materials have been proposed (i.e., for half‐cell assembly), few of them have reached commercial applications, apart from graphite, Li₄Ti₅O₁₂, Si, and Sn‐Co‐C. This clearly demonstrates that full‐cell studies are desperately needed rather than just characterizing materials in half‐cell assemblies. Additionally, the performance of such anodes in practical Li‐ion configurations (full‐cell) is much more important than merely proposing materials for LIBs. Irreversible capacity loss, huge volume variation, unstable solid electrolyte interface layer formation, and poor cycleability are the main issues for conversion and alloy type anodes. This review addresses how best to circumvent the mentioned issues during the construction of Li‐ion cells and the future prospects of such anodes are described in detail.     

ON THE REVERSIBILITY OF MANDIBULAR SYMPHYSEAL FUSION

Experimental and comparative studies suggest that a major determinant of increased ossification of the mandibular symphysis is elevated masticatory stress related to a mechanically challenging diet. However, the morphology of this joint tracks variation in dietary properties in only some mammalian clades. Extant anthropoid primates are a notable exception: synostosis is ubiquitous in this speciose group, despite its great age and diverse array of feeding adaptations. One possible explanation for this pattern is that, once synostosis evolves, reversion to a lesser degree of fusion is unlikely or even constrained. If correct, this has important implications for functional and phylogenetic analyses of the mammalian feeding apparatus. To test this hypothesis, we generated a molecular tree for 76 vespertilionoid and noctilionoid chiropterans using Bayesian phylogenetic analysis and examined character evolution using parsimony and likelihood ancestral-state reconstructions along with the binary state speciation and extinction (BiSSE) model. Results indicate that reversals have occurred within Vespertilionoidea. In contrast, noctilionoids exhibit an anthropoid-like pattern, which suggests that more detailed comparisons of the functional and developmental bases for fusion in these bat clades may provide insight into why fusion is maintained in some lineages but not in others. Potential functional and developmental explanations for the lack of reversal are discussed.     

The evolution of self-compatible and self-incompatible populations in a hermaphroditic perennial, <Emphasis Type="Italic">Trillium camschatcense</Emphasis> (Melanthiaceae)

The evolution of selfing from outcrossing ancestors is known to have occurred repeatedly in angiosperms. Theoretical studies have argued that the transition from outcrossing to selfing is accomplished more easily than the reverse case, and phylogenetic analyses involving self-compatible (SC) and self-incompatible (SI) species has basically supported this assumption. The evolutionary direction of self-compatibility and self-incompatibility was examined in Trillium camschatcense, which contains geographically widespread SC populations, and restricted SI populations. Ecological surveys have revealed that the SC populations were suitable for outcrossing, and selfing in these populations did not confer any fitness advantage. Since reproductive fitness indicates the possibility of an evolutionary shift from self-compatibility to self-incompatibility, the phylogenetic relationships of SI and SC populations of T. camschatcense were investigated based on cpDNA variations and nuclear DNA microsatellite polymorphisms. Although phylogenetic analyses did not provide credible evidence to determine evolutionary direction, the SI populations turned out to be monophyletic with extremely low genetic differentiation. Based on these results, we proposed two possible scenarios for the evolutionary backgrounds of SI and SC populations in T. camschatcense. The plausibility of each scenario was evaluated based on the reproductive and geographical features of the mating systems. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Unfolding of triosephosphate isomerase from Trypanosoma brucei: identification of intermediates and insight into the denaturation pathway using tryptophan mutants

The unfolding of triosephosphate isomerase (TIM) from Trypanosoma brucei (TbTIM) induced by guanidine hydrochloride (GdnHCl) was characterized. In contrast to other TIMs, where unfolding is a two or three state process, TbTIM showed two intermediates. The solvent exposure of different regions of the protein in the unfolding process was characterized spectroscopically with mutant proteins in which tryptophans (W) were changed to phenlylalanines (F). The midpoints of the transitions measured by circular dichroism, intrinsic fluorescence, and catalytic activity, as well as the increase in 1-aniline 8-naphthalene sulfonate fluorescence, show that the native state was destabilized in the W12F and W12F/W193F mutants, relative to the wild-type enzyme. Using the hydrodynamic profile for the unfolding of a monomeric TbTIM mutant (RMM0-1TIM) measured by size-exclusion chromatography as a standard, we determined the association state of these intermediates: D*, a partially expanded dimer, and M*, a partially expanded monomeric intermediate. High-molecular-weight aggregates were also detected. At concentrations over 2.0 M GdnHCl, the hydrodynamic properties of TbTIM and RMM0-1TIM are the same, suggesting that the dimeric intermediate dissociates and the unfolding proceeds through the denaturation of an expanded monomeric intermediate. The analysis of the denaturation process of the TbTIM mutants suggests a sequence for the gradual exposure of W residues: initially the expansion of the native dimer to form D* affects the environments of W12 and W159. The dissociation of D* to M* and further unfolding of M* to U induces the exposure of W170. The role of protein concentration in the formation of intermediates and aggregates is discussed considering the irreversibility of this unfolding process.     

The Levinthal paradox of the interactome

The central biological question of the 21st century is: how does a viable cell emerge from the bewildering combinatorial complexity of its molecular components? Here, we estimate the combinatorics of self-assembling the protein constituents of a yeast cell, a number so vast that the functional interactome could only have emerged by iterative hierarchic assembly of its component sub-assemblies. A protein can undergo both reversible denaturation and hierarchic self-assembly spontaneously, but a functioning interactome must expend energy to achieve viability. Consequently, it is implausible that a completely “denatured” cell could be reversibly renatured spontaneously, like a protein. Instead, new cells are generated by the division of pre-existing cells, an unbroken chain of renewal tracking back through contingent conditions and evolving responses to the origin of life on the prebiotic earth. We surmise that this non-deterministic temporal continuum could not be reconstructed de novo under present conditions.     

REVERSIBILITY IN EVOLUTION: A MAXIMUM LIKELIHOOD APPROACH TO CHARACTER GAIN/LOSS BIAS IN PHYLOGENIES

Statistical methods are used to test the hypothesis that rate of gain is equal to rate of loss for a single character on a cladogram. Ancestral character states are used as input for maximum likelihood (ML) rate estimation. Two markovian models of character evolution are considered: one has equality of rate across branches; the other permits variation in rate according to predetermined weights for branches. ML estimates are derived for both models, and their properties in large and small trees are investigated. Bias and error are significant in small trees. Error is greatest for characters in which rate of gain is low, and is greater for the loss estimate than for the gain estimate. Likelihood ratio (LR) tests of the null hypothesis of equality of gain/loss rate are derived, and their properties investigated. The distribution of -2 log LR is close to χ² with 1 df with as few as 32 taxa. However, the power of the test is low unless the character is evolving rapidly. Methods for increasing power are examined, including selection of rapidly evolving subsets of characters, and pooling across characters. A goodness of fit test is presented to determine if pooling is justified. An example using published restriction site data on the Asteraceae demonstrates significant deviation from the null model in the direction predicted on the basis of the molecular biology of restriction enzyme site recognition, but only for one large subset of the data in which pooling is warranted.