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On the early evolutionary origin of biological periodicity
... Perhaps the most well-developed, comprehensive Protometabolism-First model published by any one author is Tibor Ganti's " chemoton theory " [86, 87, 146,234235236237. Tibor Ganti's chemoton model is a hypercycle take-off. ...
... Ganti envisioned interconnected autocatalytic, or at least mutually catalytic [223], Eigen-Schuster type hypercycles213214215216217218219 in well-organized elementary units of life called " chemotons. " [87, 234, 236, 237] Ganti's basic idea is that stoichiometric cycles act as catalysts. No proteins exist yet, and therefore no linear digital prescription is needed. ...
... But they are all purely theoretical with no observational or prediction fulfilling support. The circular intertwined diagrams of Tibor Ganti certainly look plausible at first glance [146, 236, 237] . Upon more careful, critical analysis however, they are merely self-constraining feedbacks, not formally self-controlling feedbacks. ...
... Introduction Based on our current knowledge about life it is safe to say that every recent living creature consists of one or more cells, each cell featuring three functional units/"subsystems" [1,2]: one storing the genetic know-how of self-maintenance and reproduction and passing it down the generations (genetic machinery), another one supporting the other two subsystems with material and energy (metabolism) [1], and a boundary subsystem (e.g. membrane) connecting the previous two to the external world while providing them with individual existence. ...
... Introduction Based on our current knowledge about life it is safe to say that every recent living creature consists of one or more cells, each cell featuring three functional units/"subsystems" [1,2]: one storing the genetic know-how of self-maintenance and reproduction and passing it down the generations (genetic machinery), another one supporting the other two subsystems with material and energy (metabolism) [1], and a boundary subsystem (e.g. membrane) connecting the previous two to the external world while providing them with individual existence. ...
The Metabolically Coupled Replicator System (MCRS) model of early chemical evolution offers a plausible and efficient mechanism for the self-assembly and the maintenance of prebiotic RNA replicator communities, the likely predecessors of all life forms on Earth. The MCRS can keep different replicator species together due to their mandatory metabolic cooperation and limited mobility on mineral surfaces, catalysing reaction steps of a coherent reaction network that produces their own monomers from externally supplied compounds. The complexity of the MCRS chemical engine can be increased by assuming that each replicator species may catalyse more than a single reaction of metabolism, with different catalytic activities of the same RNA sequence being in a trade-off relation: one catalytic activity of a promiscuous ribozyme can increase only at the expense of the others on the same RNA strand. Using extensive spatially explicit computer simulations we have studied the possibility and the conditions of evolving ribozyme promiscuity in an initial community of single-activity replicators attached to a 2D surface, assuming an additional trade-off between replicability and catalytic activity. We conclude that our promiscuous replicators evolve under weak catalytic trade-off, relatively strong activity/replicability trade-off and low surface mobility of the replicators and the metabolites they produce, whereas catalytic specialists benefit from very strong catalytic trade-off, weak activity/replicability trade-off and high mobility. We argue that the combination of conditions for evolving promiscuity are more probable to occur for surface-bound RNA replicators, suggesting that catalytic promiscuity may have been a significant factor in the diversification of prebiotic metabolic reaction networks.
... ISEGORÍA, N.º 55, julio-diciembre, 2016, 551-575, ISSN: 1130-2097 doi: 10.3989/isegoria.2016.055.08La biología sintética como desafío para comprender la autonomía de lo vivo miento estequiométrico de ciclos (1.E), a laGanti (2002). Autocatálisis reflexivas o 'RAF's a laKauffman (1986), de mayor o menor complejidad (1.G y 1.H) -ver:(Hordijk & Steel, 2004). ...
... Se observan muchos casos de ciclos reactivos acoplados (entre otros, la reacción Belousov-Zhabotinskii, donde dos ciclos autocatalíticos se acoplan entre sí, y también a un ciclo de retroalimentación negativa[Ganti 2002], o más recientes implementaciones de sistemas oscilatorios similares haciendo uso de componentes orgánicos prebióticos[Semenov et al. 2016]) los cuales están muy por debajo del umbral mínimo para considerar un sistema propiamente metabólico. Según lo definíamos en la sección 2.2, el metabolismo implica una gestión autónoma del flujo de materia y energía a través de un sistema, lo cual es inviable sin una dinámica auto-productiva más fuerte, que incluya la frontera del sistema, además de una diversidad composicional y funcional más amplia[Moreno & Ruiz-Mirazo 1999]. ...
En este artículo se ofrece una visión de la biología sintética alternativa a los planteamientos ingenieriles que marcan gran parte de la agenda de investigación del campo. Nuestro análisis se centra en enfoques, teóricos y experimentales, cuyo objetivo fundamental es la comprensión del fenómeno de la vida per se. Una revisión detallada de varios casos de implementación artificial, in vitro, de sistemas químicos ‘auto-productivos’ nos ayudará a reflexionar sobre el enorme reto que supone transformar una disciplina científica eminentemente descriptiva, como la biología, en un proyecto que incluya y potencie líneas de investigación basadas en la idea de síntesis o fabricación. El reto es mayúsculo debido al carácter intrínsecamente metabólico de los sistemas biológicos, lo cual hace que nuestro empeño en controlarlos o en construirlos de novo sea mucho más dificultoso, forzándonos a desarrollar plataformas de intervención/implementación a nivel molecular que no pongan en compromiso esa inherente dimensión autónoma de lo vivo.
... The dots in the template subsystem indicate the iterative development of the template replication from pV2n · pV1 to pV2n · pV2n−1. must reach a state where both the surface and the inner components have doubled their initial amount [5] . At this precise moment, it is assumed that, due to the concentration decay , an osmotic vacuum develops and the membrane sphere is elongated, with a neck forming in the middle leading to the subsequent division (none of these physical events are really introduced in the model explicitly). ...
... As discussed in the introduction, the chemoton model [5] is an important step toward an integrated model of a protocell capable of performing the essential functions of a living sys- tem [7, 9]. The importance of this model relies on the fact that it is the simplest existent model which includes the three essential processing units: the metabolism, the membrane compartment and the " genetic information " . ...
Gánti's chemoton model (Cell.Biol.Int. 26, 729, 2002) is considered as an iconic example of a minimal proto-cell including three key ingredients: membrane, metabolism and information. The three subsystems are coupled and it is suggested they guarantee a stable, homeostatic replication cycle. However, a detailed exploration of the model indicates that it displays a wide range of complex dynamics, from regularity to chaos. Here we report the presence of a very rich set of dynamical patterns potentially displayed by a protocell as described by the chemoton model. The implications for early cellular evolution and synthesis of artificial cells are discussed.
... In fact, although we regard the chemoton model as a very interesting scheme to study an intermediate stage in the process of the origin of life (e.g. a kind of 'polynucleotide world' embedded in a cellular protometabolism), the purpose of this work was to analyse previous transitions, which involved a lower level of molecular complexity (so modular 'templates', for instance, could not yet be there) and a higher level of noise and fluctuations (originally not present in the neat chemical design of Ganti). Therefore, the final decision was to go for a less complicated reaction scheme, also inspired by Ganti's work (Ganti 1987(Ganti , 2002: a sort of simplified version of the chemoton, which does not include the 'template subsystem'. Therefore, this proto-chemoton consists of only two coupled autocatalytic subsystems: the membrane and the protometabolic network. ...
... (d) R-scheme 3: proto-chemoton cells The final scenario explored with our simulation program is the case of a cell that is able to produce lipids, thanks to the internal protometabolic cycle (see scheme 3 in figure 1). Introducing Ganti's (2002) simplified scheme in our way to model cell dynamics involves the following boundary conditions. ...
This paper is a theoretical attempt to gain insight into the problem of how self-assembling vesicles (closed bilayer structures) could progressively turn into minimal self-producing and self-reproducing cells, i.e. into interesting candidates for (proto)biological systems. With this aim, we make use of a recently developed object-oriented platform to carry out stochastic simulations of chemical reaction networks that take place in dynamic cellular compartments. We apply this new tool to study the behaviour of different minimal cell models, making realistic assumptions about the physico-chemical processes and conditions involved (e.g. thermodynamic equilibrium/non-equilibrium, variable volume-to-surface relationship, osmotic pressure, solute diffusion across the membrane due to concentration gradients, buffering effect). The new programming platform has been designed to analyse not only how a single protometabolic cell could maintain itself, grow or divide, but also how a collection of these cells could 'evolve' as a result of their mutual interactions in a common environment.
... In the absence of such empirical falsification, a plausible model of mechanism at the very least for both Strong and Type IV emergence (formal self-organization) is needed. Manfred Eigen [25][26][27][28][29][30][31][32][33][34][35][36] and Tibor Ganti [37][38][39][40][41] have been leaders in the search for mechanisms of biologic emergence from abiotic environments. Shuster joined with Eigen to hypothesize hypercycles [42][43][44][45][46][47][48][49]. ...
To what degree could chaos and complexity have organized a Peptide or RNA World of crude yet necessarily integrated protometabolism? How far could such protolife evolve in the absence of a heritable linear digital symbol system that could mutate, instruct, regulate, optimize and maintain metabolic homeostasis? To address these questions, chaos, complexity, self-ordered states, and organization must all be carefully defined and distinguished. In addition their cause-and-effect relationships and mechanisms of action must be delineated. Are there any formal (non physical, abstract, conceptual, algorithmic) components to chaos, complexity, self-ordering and organization, or are they entirely physicodynamic (physical, mass/energy interaction alone)? Chaos and complexity can produce some fascinating self-ordered phenomena. But can spontaneous chaos and complexity steer events and processes toward pragmatic benefit, select function over non function, optimize algorithms, integrate circuits, produce computational halting, organize processes into formal systems, control and regulate existing systems toward greater efficiency? The question is pursued of whether there might be some yet-to-be discovered new law of biology that will elucidate the derivation of prescriptive information and control. "System" will be rigorously defined. Can a lowinformational rapid succession of Prigogine's dissipative structures self-order into bona fide organization?.
... Let us review the advantage of using GVs for constructing a modular association evolution system. Considering the chemoton, the most basic unit of evolution advocated by Gánti [47], the production of compartment molecules is explicitly assumed. The production of components requires the supply of the substrates from the outer environment. ...
Experimental evolution in chemical models of cells could reveal the fundamental mechanisms of cells today. Various chemical cell models, water-in-oil emulsions, oil-on-water droplets, and vesicles have been constructed in order to conduct research on experimental evolution. In this review, firstly, recent studies with these candidate models are introduced and discussed with regards to the two hierarchical directions of experimental evolution (chemical evolution and evolution of a molecular self-assembly). Secondly, we suggest giant vesicles (GVs), which have diameters larger than 1 µm, as promising chemical cell models for studying experimental evolution. Thirdly, since technical difficulties still exist in conventional GV experiments, recent developments of microfluidic devices to deal with GVs are reviewed with regards to the realization of open-ended evolution in GVs. Finally, as a future perspective, we link the concept of messy chemistry to the promising, unexplored direction of experimental evolution in GVs.
... Network models such as autopoiesis [33,34], which provide only qualitative definitions without explicit kinetics are inadequate for homeostasis-related scrutiny. The Chemoton model [35] consists of three stoichiometrically coupled autocatalytic cycles: metabolism, template replication and membrane, with simulateable internal feedback that couples membrane and content growth [36]. Yet, Chemoton analyses have not so far quantitatively address network homeostasis. ...
Life is that which replicates and evolves, but there is no consensus on how life emerged. We advocate a systems protobiology view, whereby the first replicators were assemblies of spontaneously accreting, heterogeneous and mostly non-canonical amphiphiles. This view is substantiated by rigorous chemical kinetics simulations of the graded autocatalysis replication domain (GARD) model, based on the notion that the replication or reproduction of compositional information predated that of sequence information. GARD reveals the emergence of privileged non-equilibrium assemblies (composomes), which portray catalysis-based homeostatic (concentration-preserving) growth. Such a process, along with occasional assembly fission, embodies cell-like reproduction. GARD pre-RNA evolution is evidenced in the selection of different composomes within a sparse fitness landscape, in response to environmental chemical changes. These observations refute claims that GARD assemblies (or other mutually catalytic networks in the metabolism first scenario) cannot evolve. Composomes represent both a genotype and a selectable phenotype, anteceding present-day biology in which the two are mostly separated. Detailed GARD analyses show attractor-like transitions from random assemblies to self-organized composomes, with negative entropy change, thus establishing composomes as dissipative systems-hallmarks of life. We show a preliminary new version of our model, metabolic GARD (M-GARD), in which lipid covalent modifications are orchestrated by non-enzymatic lipid catalysts, themselves compositionally reproduced. M-GARD fills the gap of the lack of true metabolism in basic GARD, and is rewardingly supported by a published experimental instance of a lipid-based mutually catalytic network. Anticipating near-future far-reaching progress of molecular dynamics, M-GARD is slated to quantitatively depict elaborate protocells, with orchestrated reproduction of both lipid bilayer and lumenal content. Finally, a GARD analysis in a whole-planet context offers the potential for estimating the probability of life's emergence. The invigorated GARD scrutiny presented in this review enhances the validity of autocatalytic sets as a bona fide early evolution scenario and provides essential infrastructure for a paradigm shift towards a systems protobiology view of life's origin.
... 7: 170050 individuals: (i) direct reaction couplings (i.e. transformation processes that share one or more chemical species); (ii) negative and positive feedback loops (autocatalytic cycles); (iii) stoichiometric couplings between several autocatalytic cycles, a la Ganti [94,95]; (iv) physical restrictions on molecular movement (by means of diverse kinds of boundaries); (v) osmotic couplings, if the chemical system is encapsulated within a volume-changing compartment (like a lipid vesicle) [96]; (vi) self-assembly processes (sustaining supramolecular structures); (vii) oligomerization reactions; (viii) endergonicexergonic couplings (like (i), but with an energy currency involved); (ix) catalyst-mediated couplings (like in reflexive autocatalytic sets, a la Kauffman) [53,55]; and (x) regulatory couplings (second-order control mechanisms, in response to internal/external perturbations) [97]. ...
In recent years, an extension of the Darwinian framework is being considered for the study of prebiotic chemical evolution, shifting the attention from homogeneous populations of naked molecular species to populations of heterogeneous, compartmentalized and functionally integrated assemblies of molecules. Several implications of this shift of perspective are analysed in this critical review, both in terms of the individual units, which require an adequate characterization as self-maintaining systems with an internal organization, and also in relation to their collective and long-term evolutionary dynamics, based on competition, collaboration and selection processes among those complex individuals. On these lines, a concrete proposal for the set of molecular control mechanisms that must be coupled to bring about autonomous functional systems, at the interface between chemistry and biology, is provided.
... It is not sufficient to keep stating "That is too complex to have been there from the beginning". Simpler Ganti like scenarios [49][50][51] are too accidental and momentary to be sustained without linear digital memory and heritability programmatically organizing and maintaining that protometabolism. The wheel would have to be reinvented with each new generation. ...
Self-ordering phenomena should not be confused with self-organization. Self-ordering events occur spontaneously according to natural “law” propensities and are purely physicodynamic. Crystallization and the spontaneously forming dissipative structures of Prigogine are examples of self-ordering. Self-ordering phenomena involve no decision nodes, no dynamically-inert configurable switches, no logic gates, no steering toward algorithmic success or “computational halting”. Hypercycles, genetic and evolutionary algorithms, neural nets, and cellular automata have not been shown to self-organize spontaneously into nontrivial functions. Laws and fractals are both compression algorithms containing minimal complexity and information. Organization typically contains large quantities of prescriptive information. Prescriptive information either instructs or directly produces nontrivial optimized algorithmic function at its destination. Prescription requires choice contingency rather than chance contingency or necessity. Organization requires prescription, and is abstract, conceptual, formal, and algorithmic. Organization utilizes a sign/symbol/token system to represent many configurable switch settings. Physical switch settings allow instantiation of nonphysical selections for function into physicality. Switch settings represent choices at successive decision nodes that integrate circuits and instantiate cooperative management into conceptual physical systems. Switch positions must be freely selectable to function as logic gates. Switches must be set according to rules, not laws. Inanimacy cannot “organize” itself. Inanimacy can only self-order. “Self-organization” is without empirical and prediction-fulfilling support. No falsifiable theory of self-organization exists. “Self-organization” provides no mechanism and offers no detailed verifiable explanatory power. Care should be taken not to use the term “self-organization” erroneously to refer to low-informational, natural-process, self-ordering events, especially when discussing genetic information.
... In the absence of such empirical falsification , a plausible model of mechanism at the very least for both Strong and Type IV emergence (formal self-organization) is needed. Manfred Eigen424344457677787980818283 and Tibor Ganti8485868788 have been leaders in the search for mechanisms of biologic emergence from abiotic environments. Shuster joined with Eigen to hypothesize hypercycles [48, 49,899091929394. ...
Could a composome, chemoton, or RNA vesicular protocell come to life in the absence of formal instructions, controls and regulation? Redundant, low-informational self-ordering is not organization. Organization must be programmed. Intertwined circular constraints (e.g. complex hypercylces), even with negative and positive feedback, do not steer physicochemical reactions toward formal function or metabolic success. Complex hypercycles quickly and selfishly exhaust sequence and other phase spaces of potential metabolic resources. Unwanted cross-reactions are invariably ignored in these celebrated models. Formal rules pertain to uncoerced (physiodynamically indeterminate) voluntary behavior. Laws describe and predict invariant physicodynamic interactions. Constraints and laws cannot program or steer physicality towards conceptual organization, computational success, pragmatic benefit, the goal of integrated holistic metabolism, or life. The formal controls and regulation observed in molecular biology are unique. Only constraints, not controls, are found in the inanimate physical world. Cybernetics should be the corner stone of any definition of life. All known life utilizes a mutable linear digital material symbol system (MSS) to represent and record programming decisions made in advance of any selectable phenotypic fitness. This fact is not undone by additional epigenetic formal controls and multi-layered Prescriptive Information (PI) instantiated into diverse molecular devices and machines.
... Gánti shows [5] that the only division that leads to osmotic stability is the one that splits the membrane into two identicalFigure 1. Schematic representation of a chemoton (adapted from [6]). A chemoton consists of three stoichiometrically coupled autocatalytic cycles: a metabolism, a template replication system, and a membrane. ...
Gánti's chemoton model is an illustrious example of a minimal cell model. It is composed of three stoichiometrically coupled autocatalytic subsystems: a metabolism, a template replication process, and a membrane enclosing the other two. Earlier studies on chemoton dynamics yield inconsistent results. Furthermore, they all appealed to deterministic simulations, which do not take into account the stochastic effects induced by small population sizes. We present, for the first time, results of a chemoton simulation in which these stochastic effects have been taken into account. We investigate the dynamics of the system and analyze in depth the mechanisms responsible for the observed behavior. Our results suggest that, in contrast to the most recent study by Munteanu and Solé, the stochastic chemoton reaches a unique stable division time after a short transient phase. We confirm the existence of an optimal template length and show that this is a consequence of the monomer concentration, which depends on the template length and the initiation threshold. Since longer templates imply shorter division times, these results motivate the selective pressure toward longer templates observed in nature.
... Organic acids formed from hydrocarbons form an autocatalytic network of CO 2 fixation, which is able to reproduce itself. The hydrocarbon-aqueous environment provides an opportunity of compartmentation by the formation of lipid micelles and liposomal membranes (Furuuchi et al., 2005;Macia and Solh e, 2007;Segrh e et al., 2001;Tomas and Rana, 2007), while the conjugation of autocatalytic cycles inside membrane vesicles and their self-development and propagation can result in the development of life-like systems (stable to external fluctuations) with supramolecular functional properties (Ganti, 1997(Ganti, , 2002Fernando and Rowe, 2007;Goldstein, 2006;Kauffman et al., 2008;Smith and Morowitz, 2004). ...
The parageneses physico-chemical analysis based on a method of thermodynamic potentials has been used to study the system of C-H-O organic compounds, which are, in particular, components of biomimetically built primordial cycles of carbon dioxide chemoautotrophic fixation. Thermodynamic data for aqueous organic compounds allowed one to construct the chemical potential diagrams and establish the areas of thermodynamic stability (facies) of components of CO2 fixation pathways in hydrothermal systems, in particular, a reductive citric cycle (RCC), 3-hydroxypropionate cycle (3-HPC) and acetyl-CoA pathway. An alternative deep source of carbon (hydrocarbons) proved by the data on endogenous emission of hydrocarbons in hydrothermal fields of oceanic ridges was suggested. The system was determined, which combines hydrocarbons, CO2 and components of RCC, 3-HPC and acetyl-CoA pathway with characteristic parageneses of methane and ethylene with acetate in two-component CH4-CO2 and C2H4-O2 subsystems, respectively. The thermodynamic analysis of a redox mode at various pressures and temperatures allowed one to uniquely determine hydrocarbon-organic system able to independently generate acetate and succinate at oxidation of deep hydrothermal hydrocarbon fluids emerging on sea surface. The limits for thermodynamic stability of CO2 archaic fixation (CAF) components responsible for generation and self-organization in hydrothermal environment was identified. The tentative integrated system of CAF was developed as a combined acetyl-CoA pathway, 3-HPC and RCC containing a succinate-fumarate core, capable of switching electron flow in forward or reverse direction depending on redox potential of geochemical environment that is governed by the (CH)2(COOH)2+H2=(CH2)2(COOH)2 reaction. This core is a "redox switch", which is sensitive to certain conditions of hydrothermal environment and defines electron flow direction. The redox geochemical mode caused by temperature, pressure, composition of a hydrothermal fluid and a mineralogical setting defines stability of CAF cycle components in paragenesis with hydrocarbons and possibility of cycle self-organization.
... In one of Gánti's papers (Gánti, 2002), the circuit diagram of his Figure 1 is essentially the chemical equivalent of the Volterra and Lotka population dynamics of an oscillating system. ...
The present study is just an overview of the opening of the geochemical stage for the appearance of life. But that opening would not have been sufficient for the intellectual discovery of the origin of life! The excellent works and many commendable efforts that advance this explanation have not shown the fundamental elements that participate in the theoretical frame of biological evolution. The latter imply the existence of evolutionary transitions and the production of new levels of organization. In this brief analysis we do not intend to introduce the audience to the philosophy of biology. But we do expect to provide a modest overview, in which the geochemical chemolithoautotrophic opening of the stage should be seen, at most, as the initial metabolism that enabled organic compounds to follow the road where a chemical fluid machinery was thus able to undertake the more "sublime" course of organic biological evolution. We think that Tibor Gánti's chemoton is the most significant contribution to theoretical biology, and the only course now available to comprehend the unit of evolution problem without the structuralist and functionalist conflict prevalent in theoretical biology. In our opinion Gánti's chemoton theory travels to the "locus" where evolutionary theory dares to extend itself to entities at many levels of structural organization, beyond the gene or the group above. Therefore, in this and subsequent papers on the prebiotic conditions for the eventual appearance of the genetic code, we explore the formation and the presence of metal sulfide minerals, from the assembly of metal sulfide clusters through the precipitation of nanocrystals and the further reactions resulting in bulk metal sulfide phases. We endeavor to characterize pristine reactions and the modern surfaces, utilizing traditional surface science techniques and computational methods. Moreover, mechanistic details of the overall oxidation of metal sulfide minerals are set forth. We hope that this paper will lead our audience to accept that in a chemically oscillating system the chemoton is a model fluid state automaton capable of growth and self-reproduction. This is not simply a matter of transmitting a pattern, as in inorganic crystals; such self-reproduction must be more complex than crystal growth. Indeed that is what Gánti's theoretical and abstract model offers to us all: we finally have a philosophy of evolutionary units in theoretical biology.
... Our approach is a step forward with regard to previous models of proto-metabolic cells (e.g.: [Varela et al. 1974; McMullin & Varela 1997; Dyson 1982; Csendes 1984; Segré and Lancet 2000; Fernando & Di Paolo 2004; Munteanu & Solé 2006; Ono & Ikegami 1999; Madina et al. 2003; Macía & Solé 2006]) precisely because it tries to capture the active role and dynamic properties of the cellular compartment itself (the membrane), as a bilayer made of amphiphilic molecules (with specific properties --e.g.: volume, head area, etc.--) plus other compounds (like peptide chains), enclosing an 'aqueous core' where different reactions take place. As the reader may notice, our model cell shares some features with Ganti's 'chemoton' [Ganti 1975; 2002;, but also keeps important differences. For instance, diffusion and transport processes are here explicitly taken into account, as well as the possibility of the membrane to change its composition and functional properties. ...
In this paper, we apply a recently developed stochastic simulation platform to investigate the dynamic behaviour of minimal 'self-(re-)producing' cellular systems. In particular, we study a set of preliminary conditions for appearance of the simplest forms of autonomy in the context of lipid vesicles (more specifically, lipid-peptide vesicles) that enclose an autocatalytic/proto-metabolic reaction network. The problem is approached from a 'bottom-up' perspective, in the sense that we try to show how relatively simple cell components/processes could engage in a far-from-equilibrium dynamics, staying in those conditions thanks to a rudimentary but effective control of the matter-energy flow through it. In this general scenario, basic autonomy and, together with it, minimal agent systems would appear when (hypothetically pre-biological) cellular systems establish molecular trans-membrane mechanisms that allow them to couple internal chemical reactions with transport processes, in a way that they channel/transform external material-energetic resources into their own means and actively regulate boundary conditions (e.g., osmotic gradients, inflow/outflow of different compounds, ...) that are critical for their constitution and persistence as proto-metabolic cells. The results of our simulations indicate that, before that stage is reached, there are a number of relevant issues that have to be carefully analysed and clarified: especially the immediate effects that the insertion of peptide chains (channel precursors) in the lipid bilayer may have in the structural properties of the membrane (elasticity, permeability, ...) and in the overall dynamic behaviour of the cell.
This thesis broadly concerns the origins of life problem, pursuing a joint approach that combines general philosophical/conceptual reflection on the problem along with more detailed and formal scientific modelling work oriented in the conceptual perspective developed. The central subject matter addressed is the emergence and maintenance of compartmentalised chemistries as precursors of more complex systems with a proper cellular organization. Whereas an evolutionary conception of life dominates prebiotic chemistry research and overflows into the protocells field, this thesis defends that the 'autonomous systems perspective' of living phenomena is a suitable - arguably the most suitable - conceptual framework to serve as a backdrop for protocell research. The autonomy approach allows a careful and thorough reformulation of the origins of cellular life problem as the problem of how integrated autopoietic chemical organisation, present in all full-fledged cells, originated and developed from more simple far-from-equilibrium chemical aggregate systems.
Here we review chemical and biological replicators that were either engineered (artificially) or evolved (either naturally or artificially). They are automata even though they need not be electro-mechanical machines or computer programs. Gánti has described the class of fluid automata (Gánti, 2003a) into which almost (but perhaps not) all biological replicators fall. Replicators are very special because they are the foundation of evolution by natural selection. Evolution by natural selection occurs whenever there are units of evolution. Units of evolution must be capable of replication (i.e. multiplication), variation and heredity (Maynard Smith 1987; Szathmáry and Maynard Smith 1993, 1995). Without selection the relative frequency of variants changes by neutral drift, but if an environment tends to allow some variants to replicate faster than others, then these fitter variants can dominate.
A model is here presented to analyse how vesicles may turn into protocells that synthesize their own lipid components and
the consequences that this may have on the properties of the resulting membrane (in particular, on its permeability), as well
as on the overall stability of the system.
A recently developed and presented stochastic simulation platform (‘ENVIRONMENT’ [12, 25]), which extends Gillespie’s algorithm
for chemically reacting, fixed-volume, homogeneous systems to volume-changing and globally heterogeneous conditions, is applied
to investigate the dynamic behaviour of self-(re-)producing vesicles whose membrane consists of both lipids and small peptides.
We claim that it is through the integration of these two types of relatively simple –and prebiotically plausible– components
that protocells could start their development into functional supramolecular structures, allowing the formation of increasingly
complex reaction networks in their internal aqueous milieu. The model is not spatially explicit, but takes into account quite
realistically volume-surface constraints, osmotic pressure, diffusion/transport processes, structural elasticity ... In this
framework the time evolution of non-equilibrium proto-metabolic cellular systems is studied, paying special attention to the
capacity of the system to get rid of its waste material, which proved critical for balanced cell growth (avoiding the risk
of an osmotic burst). We also investigate the effects of including an explicit feedback mechanism in the system: the case
in which waste transport mediated by peptide chains takes place only under osmotic stress conditions.
Genetic cybernetics preceded human consciousness in its algorithmic programming and control. Nucleic acid instructions reside in linear, resortable, digital, and unidirectionally read sign sequences. Prescriptive information instructs and manages even epigenetic factors through the production of diverse regulatory proteins and small RNA’s. The “meaning” (significance) of prescriptive information is the function that information instructs or produces at its metabolic destination. Constituents of the cytoplasmic environment (e.g., chaperones, regulatory proteins, transport proteins, small RNA’s) contribute to epigenetic influence. But the rigid covalently-bound sequence of these players constrains their minimum-free-energy folding space. Weaker H-bonds, charge interactions, hydrophobicities, and van der Waals forces act on completed primary structures. Nucleotide selections at each locus in the biopolymeric string correspond to algorithmic switch-settings at successive decision nodes. Nucleotide additions are configurable switches. Selection must occur at the genetic level prior to selection at the phenotypic level, in order to achieve programming of computational utility. This is called the GS Principle. Law-like cause-and-effect determinism precludes freedom of selection so critical to algorithmic control. Functional Sequence Complexity (FSC) requires this added programming dimension of freedom of selection at successive decision nodes in the string. A sign represents each genetic decision-node selection. Algorithms are processes or procedures that produce a needed result, whether it is computation or the end products of biochemical pathways. Algorithmic programming alone accounts for biological organization.
The computational platform ENVIRONMENT, developed to simulate stochastically reaction systems in varying compartmentalized conditions [Mavelli and Ruiz-Mirazo: Philos Trans R Soc Lond B Biol Sci 362:1789-1802, 2007; Physical Biology 7(3): 036002, 2010], is here applied to study the dynamic properties and stability of model protocells that start producing their own lipid molecules (e.g., phospholipids), which get inserted in previously self-assembled vesicles, made of precursor amphiphiles (e.g., fatty acids). Attention is mainly focused on the changes that this may provoke in the permeability of the compartment, as well as in its eventual osmotic robustness.
To what degree could chaos and complexity have organized a Peptide or RNA World of crude yet necessarily integrated protometabolism? How far could such protolife evolve in the absence of a heritable linear digital symbol system that could mutate, instruct, regulate, optimize and maintain metabolic homeostasis? To address these questions, chaos, complexity, self-ordered states, and organization must all be carefully defined and distinguished. In addition their cause-and-effect relationships and mechanisms of action must be delineated. Are there any formal (non physical, abstract, conceptual, algorithmic) components to chaos, complexity, self-ordering and organization, or are they entirely physicodynamic (physical, mass/energy interaction alone)? Chaos and complexity can produce some fascinating self-ordered phenomena. But can spontaneous chaos and complexity steer events and processes toward pragmatic benefit, select function over non function, optimize algorithms, integrate circuits, produce computational halting, organize processes into formal systems, control and regulate existing systems toward greater efficiency? The question is pursued of whether there might be some yet-to-be discovered new law of biology that will elucidate the derivation of prescriptive information and control. "System" will be rigorously defined. Can a low-informational rapid succession of Prigogine's dissipative structures self-order into bona fide organization?
Gánti's chemoton model (Gánti, T., 2002. On the early evolution of biological periodicity. Cell. Biol. Int. 26, 729) is considered as an iconic example of a minimal protocell including three key subsystems: membrane, metabolism and information. The three subsystems are connected through stoichiometrical coupling which ensures the existence of a replication cycle for the chemoton. Our detailed exploration of a version of this model indicates that it displays a wide range of complex dynamics, from regularity to chaos. Here, we report the presence of a very rich set of dynamical patterns potentially displayed by a protocell as described by this implementation of a chemoton-like model. The implications for early cellular evolution and synthesis of artificial cells are discussed.
In this short paper we argue for the relevance and value of theoretical models in the field of origins of life, but also claim that both theoreticians and experimentalists should make an effort to come together and interact more closely to obtain more fruitful and significant results. As an example, we present our own modeling approach to protocell dynamics, including some simulation results, to show that it is possible to develop computational tools that start bridging that traditional gap between theory and experiments.
This contribution is aimed to give support to 'bottom-up' approaches to the minimal or early cell research project. Even if, from this perspective, the most simple living cell still seems very far away, the analysis of less complex, infrabiological cellular systems (some of which could be relatively soon implemented in the lab) probably holds the key, or one of the fundamental keys, to the problem of origins of life. On these lines, we propose a simulation model to study the transition from proto-metabolic 'lipid' cells to 'lipid-peptide' cells, as a critical step in which self-reproducing vesicles could develop into more functionalized supramolecular systems.
In this paper properties and dynamical behaviour of a theoretical biological model, the chemoton are discussed. The chemoton features the general, common properties of the unicellular living beings. Since the reaction-kinetical function of the chemoton is governed by a set of nonlinear differential equations, the study of its dynamical behaviour required computer simulation. This was carried out by using CSMP programs. The results proved that the model is capable of stable functioning, growing and multiplication.
A general type of oscillating chemical network is presented in which two autocatalytic chemical cycles are coupled by an OR branching, and the second cycle is broached. The results are compatible with the Lotka model and the results of Noszticzius et al. A similar model is proposed also for the Belousov-Zhabotinskii reaction.
Synthetic cell-sized organic microstructures effect the long-wavelength UV photosynthesis of organic products from carbonate. Formaldehyde is the most abundant photoproduct and water is the major proton donor for this reduced form of carbon. The apparent quantum yield is ~10-5 carbon atoms per incident UV 254-nm photon. We show here that these results for model phase-bounded systems are consistent with the postulate that metabolism of progenitors to the earliest living cells could have been, at least in part, photosynthetic.
The Principle of life (in Hungarian) Budapest, Gondolat; 2nd revised edition (1978) Organization of chemical reactions into divid-ing and metabolizing units: The Chemotons
- G
G T, 1971. The Principle of life (in Hungarian). Budapest, Gondolat; 2nd revised edition (1978); 6th edition (in English) (1987). Budapest, OMIKK. G T, 1975. Organization of chemical reactions into divid-ing and metabolizing units: The Chemotons. Biosystems 7: 15–21.
Chemoton Theory. Vol. I. Theoretical Foundation of Fluid Machineries (in Hungarian) Biogenesis itself
- G
- Omikk Budapest
- G
-
G T, 1984b. Chemoton Theory. Vol. I. Theoretical Foundation of Fluid Machineries (in Hungarian). Budapest, OMIKK. G T, 1989. Chemoton Theory. Vol. II. Theory of Living Systems (in Hungarian). Budapest, OMIKK. G T, 1997. Biogenesis itself. J theor Biol 187: 583–593.
The conditions for a growing microsphere to divide
- G T
- G
- Cs
G T, G CS, 1978. The conditions for a growing microsphere to divide. Acta Chim Acad Sci Hung 98: 278–283.
Organization of chemical reactions into dividing and metabolizing units: The Chemotons
G´G´G´ T, 1975. Organization of chemical reactions into dividing and metabolizing units: The Chemotons. Biosystems 7:
15–21.