Osamu Ueno

An effective hierarchical model for the biomolecular covalent bond: An approach integrating artificial chemistry and an actual terrestrial life system

Under the AChem paradigm and the programmed self-decomposition (PSD) model, we propose a hierarchical model for the biomolecular covalent bond (HBCB model). This model assumes that terrestrial organisms arrange their biomolecules in a hierarchical structure according to the energy strength of their covalent bonds. It also assumes that they have evolutionarily selected the PSD mechanism of turning biological polymers (BPs) into biological monomers (BMs) as an efficient biomolecular recycling strategy. We have examined the validity and effectiveness of the HBCB model by coordinating two complementary approaches: biological experiments using existent terrestrial life, and simulation experiments using an AChem system. Biological experiments have shown that terrestrial life possesses a PSD mechanism as an endergonic, genetically regulated process and that hydrolysis, which decomposes a BP into BMs, is one of the main processes of such a mechanism. In simulation experiments, we compared different virtual self-decomposition processes. The virtual species in which the self-decomposition process mainly involved covalent bond cleavage from a BP to BMs showed evolutionary superiority over other species in which the self-decomposition process involved cleavage from BP to classes lower than BM. These converging findings strongly support the existence of PSD and the validity and effectiveness of the HBCB model.

Artificial life based on the programmed self-decomposition model, SIVA

To examine the effect and significance of the phenomenon of death, we have developed an artificial life simulator, SIVA-III (simulator for individuals of virtual automata III), based on a “programmed self-decomposition model”. The architecture of this simulator consists of a “finite heterogeneous habitation environment” and “artificial life with programmed individual death and concurrent self-decomposition”. We conducted experiments under various settings to comparare and contrast mortal life and immortal life. The results clearly demonstrated the validity of a self-decomposing, programmed individual death, and the limitations inherent in immortal life, suggesting a striking superiority of mortal life over immortal life.

Evolutionary acquisition of a mortal genetic program: The origin of an altruistic gene

As part of our research on programmed self-decomposition, we formed the hypothesis that originally immortal terrestrial organisms evolve into ones that are programmed for autonomous death. We then conducted evolutionary simulation experiments in which we examined this hypothesis using an artificial ecosystem that we designed to resemble a terrestrial ecosystem endowed with artificial chemistry. Notable results corroborating our hypothesis were obtained, which showed that mortal organisms emerged from indigenous immortal organisms through mutation; such mortal organisms survived and left behind offspring, albeit very rarely, and, having survived, surpassed immortal organisms without exception. In this article, we report the details of the above findings and also discuss a background framework we previously constructed for approaching altruism.

Induction of prolonged natural lifespans in mice exposed to acoustic environmental enrichment

We investigated the effect of acoustic environmental enrichment (EE) on the lifespans and behaviours of mice to the end of their natural lifespan in different acoustic environments. Acoustic EE induced a significantly prolonged natural lifespan (nearly 17% longer) and was associated with increased voluntary movements. However, no correlation between lifespan and voluntary movements was detected, suggesting that increased voluntary movements are not a primary cause of lifespan prolongation. Analyses of individual differences in lifespan demonstrated that lifespan extension induced by acoustic EE could be related to changes in social relationships (e.g., reduction of social conflict) among individuals kept within a cage. Therefore, an acoustic component may be an important factor inducing the positive effects of EE.

Heterogeneity and complexity of a simulated terrestrial environment account for the superiority of the atruistic gene.

Recent research on the notion of altruism in terrestrial life has focused on certain altruistic behaviors, which are regarded as beneficial to animal life, especially with respect to individual animal species. Such findings throw light on individualoriented mechanisms and their evolution in helping to clarify so-called intentional interactions between individuals based on discrimination of other individuals and remembered information as advanced by developments in biological information processing, ranging from molecular recognition to activation of the neural system. In 2006, Nowak classified these mechanisms into five types. In the current study, we have zeroed in on the process of autolysis universally observed in all terrestrial lives, as characterized by genetically programmed death accompanied by altruistic self-decomposition, whose model we call the “programmed self-decomposition model (PSD Model)”. In our view, altruistic phenomena target no specific individuals yet prove beneficial to the ecosystem, in part and as a whole. Using our PSD Model we ran evolutionary simulations of altruistic phenomena in the SIVA Series, which is an artificial life system designed to resemble a terrestrial ecosystem, and one that excludes both discrimination of individuals and interactions between individuals. In our simulations no individual-oriented evolutionary mechanism was observable while the ecosystem-oriented mechanism positively contributed to the evolution of the altruistic gene. Our research has thus sought to determine factors that promote superior evolutionary characteristics of altruistic phenomena in a terrestrial ecosystem model. The current study argues that the high heterogeneity and complexity of a terrestrial environment and the eternality of evolutionary time play an important role in the selective process of programmed death in the terrestrial ecosystem, which is accompanied by altruistic selfdecomposition. Based on the above findings, we investigated the inseparable relationship existing between a terrestrial ecosystem and the altruistic gene.

Sumiwake structure in a finite and heterogeneous ecosystem

As previously reported [1], we developed a general platform for simulation and visualization called SIVA. With SIVA, one can simulate life activities and their evolution in conditions that approximate an actual terrestrial ecosystem and living organisms. These simulations are based on the development and examination of SIVA-I, II, and III as prototypes of the simulator. SIVA is characterized by simulated environmental conditions that are finite and heterogeneous, and by simulated individuals that are able to self-decompose as well as selfreproduce. The Java language source program of SIVA version 1.1 is distributed by ATR. In the present study, we conducted simulations with SIVA to examine evolutionary adaptation, and tried to clarify through examination of the simulation results whether the development of a broad distribution of individuals was the result of divergent proliferation of the most prolific individuals or the result of a complication of habitat segregation. It was found through a comparative analysis of visualized habitable area and of the degree of correspondence of genetic information that the complications of habitat segregation led to a broad distribution of individuals. This finding will introduce a way method to investigate the constructive mechanism of habitat segregation in an actual terrestrial ecosystem, and also points to a survival strategy for human beings.