Breath-giving cooperation: critical review of origin of mitochondria hypotheses Major unanswered questions point to the importance of early ecology

The origin of mitochondria is a unique and hard evolutionary problem, embedded within the origin of eukaryotes. The puzzle is challenging due to the egalitarian nature of the transition where lower-level units took over energy metabolism. Contending theories widely disagree on ancestral partners, initial conditions and unfolding of events. There are many open questions but there is no comparative examination of hypotheses. We have specified twelve questions about the observable facts and hidden processes leading to the establishment of the endosymbiont that a valid hypothesis must address. We have objectively compared contending hypotheses under these questions to find the most plausible course of events and to draw insight on missing pieces of the puzzle. Since endosymbiosis borders evolution and ecology, and since a realistic theory has to comply with both domains' constraints, the conclusion is that the most important aspect to clarify is the initial ecological relationship of partners. Metabolic benefits are largely irrelevant at this initial phase, where ecological costs could be more disruptive. There is no single theory capable of answering all questions indicating a severe lack of ecological considerations. A new theory, compliant with recent phylogenomic results, should adhere to these criteria

Two Different Template Replicators Coexisting in the Same Protocell: Stochastic Simulation of an Extended Chemoton Model

The simulation of complex biochemical systems, consisting of intertwined subsystems, is a challenging task in computational biology. The complex biochemical organization of the cell is effectively modeled by the minimal cell model called chemoton, proposed by Gánti. Since the chemoton is a system consisting of a large but fixed number of interacting molecular species, it can effectively be implemented in a process algebra-based language such as the BlenX programming language. The stochastic model behaves comparably to previous continuous deterministic models of the chemoton. Additionally to the well-known chemoton, we also implemented an extended version with two competing template cycles. The new insight from our study is that the coupling of reactions in the chemoton ensures that these templates coexist providing an alternative solution to Eigen's paradox. Our technical innovation involves the introduction of a two-state switch to control cell growth and division, thus providing an example for hybrid methods in BlenX. Further developments to the BlenX language are suggested in the Appendix

The Social and Mental Dynamics of Cooperation = SOCIAL AND MENTAL DYNAMICS OF COOPERATION

Az ESF Eurocores The Evolution of Cooperation and Trading (TECT) programjához kapcsolódó nemzetközi kutatási program keretén belül négy kutatási altémával foglalkoztunk: (1) A nyelv biológiai alapjai és eredete, (2) Akooperáció evolúciójának általános problémái, (3) A replikátor elmélet, és végül (4) A neuronális replikátor hipotézis. A kiemelkedő eredmények rendre a következők: (1) Biological Foundations and Origins of Syntax c. könyv szerkesztése az MIT Press gondozásában; egy, a hierarchikus kifejezés-szerkezet feldolgozására alkalmas, veremmemóriát működtető neuronális modell; Az emberi nyelvkészség és a kooperáció közös eredete, (2) Az erős altruizmus kezdeti elterjedésének lehetőségét megalapozó modell a hasonló egyedek pozitív asszociációja nélkül; A korai evolúcióban az ásványi felszíneken kibontakozó, növekvő komplexitást eredményező szelekciós dinamika vizsgálata (3) A replikátorok újszerű,hierarchikus osztályozása, (4) Annak megmutatása, hogy elvben miként lehetséges a neuronok közötti lokális kapcsolati háló másolása ismert neurális komponens-folyamatok segítségével; dacára annak, hogy az idegsejtek nem szaporodnak. | Within the ESF Eurocores The Evolution of Cooperation and Trading (TECT) we have been doing research on four topics: (1) The biological foundations and origins of language, (2) General problems of the evolution of cooperation, (3) Replicator theory, and (4) The neuronal replicator hypothesis. The most important results obtained in order are: (1) Editing of the book Biologocal Foundations and Origins of Syntax by MIT Press; a neuronal model able to handle inputs conforming to phrase structure grammar; The common origins of human language and cooperation, (2) Inital spread of strong altruism without positive assortment in groups; Dynamics of competing and cooperating molecular replicators on mineral surfaces, (3) A novel, hierarchical classification of replicators, (4) The feasiblilty of neuronal replicators in the brain: connectivity copying of local neuronal groups by known component mechanisms, without the reproduction of neurons

One problem, too many solutions: How costly is honest signalling of need?

The “cost of begging” is a prominent prediction of costly signalling theory, suggesting that offspring begging has to be costly in order to be honest. Seminal signalling models predict that there is a unique equilibrium cost function for the offspring that results in honest signalling and this cost function must be proportional to parent’s fitness loss. This prediction is only valid if signal cost and offspring condition is assumed to be independent. Here we generalize these models by allowing signal cost to depend on offspring condition. We demonstrate in the generalized model that any signal cost proportional to the fitness gain of the offspring also results in honest signalling. Moreover, we show that any linear combination of the two cost functions (one proportional to parent’s fitness loss, as in previous models, the other to offspring’s fitness gain) also leads to honest signalling in equilibrium, yielding infinitely many solutions. Furthermore, we demonstrate that there exist linear combinations such that the equilibrium cost of signals is negative and the signal is honest. Our results show that costly signalling theory cannot predict a unique equilibrium cost in signalling games of parent-offspring conflicts if signal cost depends on offspring condition. It follows, contrary to previous claims, that the existence of parent-offspring conflict does not imply costly equilibrium signals. As an important consequence, it is meaningless to measure the “cost of begging” as long as the dependence of signal cost on offspring condition is unknown. Any measured equilibrium cost in case of condition-dependent signal cost has to be compared both to the parent’s fitness loss and to the offspring’s fitness gain in order to provide meaningful interpretation

The dynamics of the RNA world : Insights and challenges

The problem of the origin of life is not only one of structure but also that of dynamics. Ever since the seminal result of Manfred Eigen in 1971 showing that early template replication suffers from an error threshold, research has tackled the issue of how early genomes could have been dynamically stable without highly evolved mechanisms such as accurate replication and chromosomes. We review the theory of the origin, maintenance and enhancement of the RNA world as an evolving population of dynamical systems. Investigation of sequence space has revealed how structures are allocated in sequence space and how this affects the nature of the error threshold that sets the selectively maintainable genome length. New applications of old dynamical theory are still possible: the application of Gause’s principle of competitive exclusion, based on resource utilisation, to RNA replication predicts that at most four pairs (plus and minus strands) can stably be maintained on four nucleotides. Other mechanisms of early template coexistence should be regarded as additional means to raise the number of coexisting species above the number set by the competitive exclusion principle. One such example is the hypercycle in which templates were postulated to help replication of the next member in a cycle superimposed on individual replication cycles. Although the hypercycle is ecologically unstable it is evolutionarily unstable because it cannot efficiently compete against emerging parasites. Population structure can modify this conclusion but not without further qualification. The simplest form of population structure is limited diffusion on a surface. This simple mechanism can ensure the coexistence of competing ribozymes contributing to surface metabolism as well as the spread of efficient replicases despite the parasite problem. Hypercycles can only be saved by active compartmentalization when replicators are enclosed in reproducing protocells. Once there are protocells there is no need for internal hypercyclic organization, however. Finally we review two crucial adaptations that enhanced the RNA world: chromosomes and enzymatic metabolism. Interestingly, it was shown that these two have been presumably coevolutionarily linked because protocells harbouring unlinked, competing ribozymes are better off if the ribozymes remain inefficient but generalists. The appearance of chromosomes alleviates intragenomic conflict and is enabling constraint for the emergence of specific and efficient enzymes

The dynamics of the RNA world : Insights and challenges

The problem of the origin of life is not only one of structure but also that of dynamics. Ever since the seminal result of Manfred Eigen in 1971 showing that early template replication suffers from an error threshold, research has tackled the issue of how early genomes could have been dynamically stable without highly evolved mechanisms such as accurate replication and chromosomes. We review the theory of the origin, maintenance and enhancement of the RNA world as an evolving population of dynamical systems. Investigation of sequence space has revealed how structures are allocated in sequence space and how this affects the nature of the error threshold that sets the selectively maintainable genome length. New applications of old dynamical theory are still possible: the application of Gause’s principle of competitive exclusion, based on resource utilisation, to RNA replication predicts that at most four pairs (plus and minus strands) can stably be maintained on four nucleotides. Other mechanisms of early template coexistence should be regarded as additional means to raise the number of coexisting species above the number set by the competitive exclusion principle. One such example is the hypercycle in which templates were postulated to help replication of the next member in a cycle superimposed on individual replication cycles. Although the hypercycle is ecologically unstable it is evolutionarily unstable because it cannot efficiently compete against emerging parasites. Population structure can modify this conclusion but not without further qualification. The simplest form of population structure is limited diffusion on a surface. This simple mechanism can ensure the coexistence of competing ribozymes contributing to surface metabolism as well as the spread of efficient replicases despite the parasite problem. Hypercycles can only be saved by active compartmentalization when replicators are enclosed in reproducing protocells. Once there are protocells there is no need for internal hypercyclic organization, however. Finally we review two crucial adaptations that enhanced the RNA world: chromosomes and enzymatic metabolism. Interestingly, it was shown that these two have been presumably coevolutionarily linked because protocells harbouring unlinked, competing ribozymes are better off if the ribozymes remain inefficient but generalists. The appearance of chromosomes alleviates intragenomic conflict and is enabling constraint for the emergence of specific and efficient enzymes