Abiogenic synthesis of prebiotic matter for the Earth’s biosphere as a stage of self-organization on an astrophysical and paleontological time scale

Existing data suggest that an early circumstellar preplanetary disk was the most likely location for primary abiogenic synthesis of prebiotic organic matter from simple molecules along with the “RNA world” and the origin of life. This paper discusses the stages of self-organization that have resulted in the Earth’s modern biosphere, and the relationships between astrophysical and paleontological events in evolution.     

Energy Sources,Self-organization,and the Origin of Life

The emergence and early developments of life are considered from the point of view that contingent events that inevitably marked evolution were accompanied by deterministic driving forces governing the selection between different alternatives. Accordingly, potential energy sources are considered for their propensity to induce self-organization within the scope of the chemical approach to the origin of life. Requirements in terms of quality of energy locate thermal or photochemical activation in the atmosphere as highly likely processes for the formation of activated low-molecular weight organic compounds prone to induce biomolecular self-organization through their ability to deliver quanta of energy matching the needs of early biochemical pathways or the reproduction of self-replicating entities. These lines of reasoning suggest the existence of a direct connection between the free energy content of intermediates of early pathways and the quanta of energy delivered by available sources of energy.     

On the origin of life event

On the assumption of a uniform sample space probability hypothesis it is estimated a maximum number of polypeptides (or other kind of polymers) that could be synthesized in the prebiotic Earth. Besides, on the basis of five premises that are postulated as indispensable requirements for the origin of a living system, under the constraints of a protein-nucleic acid chemistry, it is concluded categorically that the origin of life event could not be the result of unbiased polymerization phenomena. On the contrary, biased and specific patterns of polymerization had to be an essential component in this fundamental event.Finally, several theories on the origin of life and complementary concepts like hypercyclic organization and self-organization phenomena in dissipative structures are discussed in the light of the conclusions arrived at in this work.     

The origin of optical asymmetry on earth.

The nature of optical isomerism, and the problem of the origin of optical asymmetry in relation to the origin of life are defined. Developments in particle physics, such as the discovery of parity non-conservation in weak interactions and more recently, of neutral currents, are described. Their significance is that there are a number of possible mechanisms whereby the fundamental asymmetry of matter could be reflected in a preference for one enantiomer over the other, and that, contrary to long-established views, optical isomers do not have identical energy contents: the difference, however, is estimated to be very small. Theories regarding the origin of optical asymmetry are classified in a two-dimensional matrix (origin by chance or due to already existing order; susceptible or not susceptible to experimental test). Recent experimental results and theoretical speculations are reviewed, and proposals are made for further experimental work.     

Modulated Self-Organization in Complex Amphiphilic Systems

Abstract

We discuss novel simulation methods for 3D pattern formation in complex amphiphilic systems. The focus is on the supra-molecular or mesoscopic level. The building blocks consist of sequences of dissimilar monomers, connected in copolymer chain molecules. Internal factors such as composition and architecture of the polymers, but also external factors such as applied shear, embedded reactions and level of confinement control the self-organization phenomena. Specific examples include dynamical pattern formation in polymer surfactant solution, reactive polymer blends and surface directed structure formation in block copolymer liquids. The approach lives in a twilight zone between scientific disciplines. The ambitious goal is the invention of methods for the rational design of truly complex bio-mimicking materials, in which we combine principles from chemical engineering, physics, chemistry and biology. The keyword is self-organization, of course. But do not be mistaken: autonomous self-organization leads to trouble, modulated self-organization leads to beauty.     

Between history and physics

Biology has traditionally occupied a middle ground between the determinism of classical physics and the uncertainties of history. These issues are analyzed with respect to statistical laws which are applied to the prebiotic domain and strategy laws which characterize evolutionary biology. The differences in approach between biology and physics are discussed in detail. The origin of life is discussed in the context of physical chemical laws. A scenario for biogenesis is presented in terms of known molecular hardware. Evolutionary biology is then examined with respect to the kinds of laws that are possible in a domain where thermal fluctuations (mutations) have macroscopic effects. Game theory is employed to demonstrate the kinds of theory appropriate to this historical domain. The transition point between physics and history is the origin and development of the code. This is discussed and it is concluded that we are not yet able to assign the code to either the deterministic domain or to the arena of history.     

Lethal mutants and truncated selection together solve a paradox of the origin of life

Background

Many attempts have been made to describe the origin of life, one of which is Eigen''s cycle of autocatalytic reactions [Eigen M (1971) Naturwissenschaften 58, 465–523], in which primordial life molecules are replicated with limited accuracy through autocatalytic reactions. For successful evolution, the information carrier (either RNA or DNA or their precursor) must be transmitted to the next generation with a minimal number of misprints. In Eigen''s theory, the maximum chain length that could be maintained is restricted to nucleotides, while for the most primitive genome the length is around . This is the famous error catastrophe paradox. How to solve this puzzle is an interesting and important problem in the theory of the origin of life.

Methodology/Principal Findings

We use methods of statistical physics to solve this paradox by carefully analyzing the implications of neutral and lethal mutants, and truncated selection (i.e., when fitness is zero after a certain Hamming distance from the master sequence) for the critical chain length. While neutral mutants play an important role in evolution, they do not provide a solution to the paradox. We have found that lethal mutants and truncated selection together can solve the error catastrophe paradox. There is a principal difference between prebiotic molecule self-replication and proto-cell self-replication stages in the origin of life.

Conclusions/Significance

We have applied methods of statistical physics to make an important breakthrough in the molecular theory of the origin of life. Our results will inspire further studies on the molecular theory of the origin of life and biological evolution.     

The origin of life — A task in molecular engineering

In attempting to understand how life originated, we search for a detailed sequence of experimentally testable physico-chemical steps in an appropriately structured system. This goal is approached in two stages. First we search for the organizational structure of processes leading to systems with the basic features of living organisms. This is an engineering problem: finding a certain construct by taking care of logical requirements and restrictions from physics. Then we face this construct with the chemical and geophysical reality, and this leads to the view that systems with the essential features of early living organisms evolve following a distinct pathway. Energy supply and the presence of a particular structure in space and time are necessary to induce and drive the processes triggered by stochastic events; but if these particular conditions are given, the broad line of the evolutionary processes is determined by logical requirements and by chemical and geophysical constrains and invariants. The genetic machinery considered to evolve in this manner agrees, in its organizational structure and in many details, with the actual genetic machinery of biosystems. A surprising simplicity and transparency is observed in the logic of the basic processes involved in the origin of life.In the present view, the processes leading to the origin of life begin in a very particular, highly structured, small region where the relevant chemistry can be quite different from overall prebiotic chemistry. Energy-rich compounds are present in ample amounts and a succession of physico-chemical processes, which are per se thermodynamically allowed, takes place. This is in contrast to popular views that the origin of life is connected with fundamental thermodynamic questions related to the problem of getting order out of chaos.     

Molecular chirality and the origin of life

In the living systems L-amino acids and D-sugars are found with almost no exceptions. Although all the molecular chirality must have been established prior to the emergence of life, the origin of the asymmetry of molecules is still an unsolved problem. The time of appearance of the asymmetry of molecules, therefore, was quite problematic during chemical evolution.Since Pasteur's discovery in 1848, a large number of works for solving this problem have been carried out on the basis of mathematics, physics or chemistry. All the proposals which put forth for breaking the symmetry are still considered to be too weak to explain the cause of obtaining the chiral purity as a result of the symmetry breaking of molecules. In order to expand our scope, new sources of the symmetry breaking of molecules should be considered.In this article, some approaches to the achiral-chiral transition are reviewed, which will give an idea for the origin of asymmetry of molecules.     

The Lipid World

The continuity of abiotically formed bilayer membraneswith similar structures in contemporary cellular life,and the requirement for microenvironments in whichlarge and small molecules could be compartmentalized, support the idea that amphiphilic boundary structurescontributed to the emergence of life. As an extensionof this notion, we propose here a `Lipid World'scenario as an early evolutionary step in theemergence of cellular life on Earth. This conceptcombines the potential chemical activities of lipidsand other amphiphiles, with their capacity to undergospontaneous self-organization into supramolecularstructures such as micelles and bilayers. Inparticular, the documented chemical rate enhancementswithin lipid assemblies suggest that energy-dependentsynthetic reactions could lead to the growth andincreased abundance of certain amphiphilic assemblies.We further propose that selective processes might acton such assemblies, as suggested by our computersimulations of mutual catalysis among amphiphiles. Asdemonstrated also by other researchers, such mutualcatalysis within random molecular assemblies couldhave led to a primordial homeostatic system displayingrudimentary life-like properties. Taken together,these concepts provide a theoretical framework, andsuggest experimental tests for a Lipid World model forthe origin of life.     

Life Began When Evolution Began: A Lipidic Vesicle-Based Scenario

The research on the origin of life, as such, seems to have reached an impasse as a clear and universal scientific definition of life is probably impossible. On the contrary, the research on the origin of evolution may provide a clue. But it is necessary to identify the minimum requirements that allowed evolution to emerge on early Earth. The classical approach, the ‘RNA world hypothesis’ is one way, but an alternative based on nonlinear dynamics dealing with far-from-equilibrium self-organization and dissipative structures can also be proposed. The conditions on early Earth, near deep-sea hydrothermal sites, were favorable to the emergence of dissipative structures such as vesicles with bilayer membranes composed of a mixture of amphiphilic and hydrophobic molecules. Experimentally these vesicles are able to self-reproduce but not to evolve. A plausible scenario for the emergence of a positive feedback process giving them the capability of evolving on early Earth is suggested. The possibilities offered by such a process are described in regard to specific characteristics of extant biological organisms and leads for future research in the field are suggested.     

Order without design

Experimental reality in molecular and cell biology, as revealed by advanced research technologies and methods, is manifestly inconsistent with the design perspective on the cell, thus creating an apparent paradox: where do order and reproducibility in living systems come from if not from design?I suggest that the very idea of biological design (whether evolutionary or intelligent) is a misconception rooted in the time-honored and thus understandably precious error of interpreting living systems/organizations in terms of classical mechanics and equilibrium thermodynamics. This error, introduced by the founders and perpetuated due to institutionalization of science, is responsible for the majority of inconsistencies, contradictions, and absurdities plaguing modern sciences, including one of the most startling paradoxes - although almost everyone agrees that any living organization is an open nonequilibrium system of continuous energy/matter flow, almost everyone interprets and models living systems/organizations in terms of classical mechanics, equilibrium thermodynamics, and engineering, i.e., in terms and concepts that are fundamentally incompatible with the physics of life.The reinterpretation of biomolecules, cells, organisms, ecosystems, and societies in terms of open nonequilibrium organizations of energy/matter flow suggests that, in the domain of life, order and reproducibility do not come from design. Instead, they are natural and inevitable outcomes of self-organizing activities of evolutionary successful, and thus persistent, organizations co-evolving on multiple spatiotemporal scales as biomolecules, cells, organisms, ecosystems, and societies. The process of self-organization on all scales is driven by economic competition, obeys empirical laws of nonequilibrium thermodynamics, and is facilitated and, thus, accelerated by memories of living experience persisting in the form of evolutionary successful living organizations and their constituents.     

The emergence of emergence: a critique of "design, observation, surprise!".

Artificial life research begins from the premise that Alife subsumes real life. A criterion for emergence in Alife has been formulated that, however, excludes real life and postulates the need for a real life Designer and an Observer. This in effect nullifies the premise of Alife and takes us back to the argument for God from design of Bishop Paley in 1802. An alternative is to realize that Alife could include two properties: simulated organisms that both design themselves and are the observers. Self-design can come about via evolution in a population of mating organisms, especially via mutations that are gene or higher order duplications. Duplications permit novelty while retaining previously attained functions. The ability to observe can itself evolve, if its construction process evolves. This may now be possible to simulate, if new paradigms for embryogenesis, such as positional information or differentiation waves, prove accurate, or at least sufficiently robust to construct a wide diversity of observational abilities. The evolution of perception, however, may be limited by the physics available to the Alife organisms, which can come in three forms: simulated physics, real physics accessible to robots, or "Cyberspace physics".     

The protein folds as platonic forms: new support for the pre-Darwinian conception of evolution by natural law

Before the Darwinian revolution many biologists considered organic forms to be determined by natural law like atoms or crystals and therefore necessary, intrinsic and immutable features of the world order, which will occur throughout the cosmos wherever there is life. The search for the natural determinants of organic form-the celebrated "Laws of Form"-was seen as one of the major tasks of biology. After Darwin, this Platonic conception of form was abandoned and natural selection, not natural law, was increasingly seen to be the main, if not the exclusive, determinant of organic form. However, in the case of one class of very important organic forms-the basic protein folds-advances in protein chemistry since the early 1970s have revealed that they represent a finite set of natural forms, determined by a number of generative constructional rules, like those which govern the formation of atoms or crystals, in which functional adaptations are clearly secondary modifications of primary "givens of physics." The folds are evidently determined by natural law, not natural selection, and are "lawful forms" in the Platonic and pre-Darwinian sense of the word, which are bound to occur everywhere in the universe where the same 20 amino acids are used for their construction. We argue that this is a major discovery which has many important implications regarding the origin of proteins, the origin of life and the fundamental nature of organic form. We speculate that it is unlikely that the folds will prove to be the only case in nature where a set of complex organic forms is determined by natural law, and suggest that natural law may have played a far greater role in the origin and evolution of life than is currently assumed.     

The uniqueness of biological self-organization: challenging the Darwinian paradigm

Here we discuss the challenge posed by self-organization to the Darwinian conception of evolution. As we point out, natural selection can only be the major creative agency in evolution if all or most of the adaptive complexity manifest in living organisms is built up over many generations by the cumulative selection of naturally occurring small, random mutations or variants, i.e., additive, incremental steps over an extended period of time. Biological self-organization—witnessed classically in the folding of a protein, or in the formation of the cell membrane—is a fundamentally different means of generating complexity. We agree that self-organizing systems may be fine-tuned by selection and that self-organization may be therefore considered a complementary mechanism to natural selection as a causal agency in the evolution of life. But we argue that if self-organization proves to be a common mechanism for the generation of adaptive order from the molecular to the organismic level, then this will greatly undermine the Darwinian claim that natural selection is the major creative agency in evolution. We also point out that although complex self-organizing systems are easy to create in the electronic realm of cellular automata, to date translating in silico simulations into real material structures that self-organize into complex forms from local interactions between their constituents has not proved easy. This suggests that self-organizing systems analogous to those utilized by biological systems are at least rare and may indeed represent, as pre-Darwinists believed, a unique ascending hierarchy of natural forms. Such a unique adaptive hierarchy would pose another major challenge to the current Darwinian view of evolution, as it would mean the basic forms of life are necessary features of the order of nature and that the major pathways of evolution are determined by physical law, or more specifically by the self-organizing properties of biomatter, rather than natural selection.     

Adolescent Self-Organization and Adult Smoking and Drinking over Fifty Years of Follow-Up: The British 1946 Birth Cohort

Variations in markers of adolescent self-organization predict a range of economic and health-related outcomes in general population studies. Using a population-based birth cohort study we investigated associations between adolescent self-organization and two common factors over adulthood influencing health, smoking and alcohol consumption. The MRC National Survey of Health and Development (the British 1946 birth cohort) was used to test associations between a dimensional measure of adolescent self-organization derived from teacher ratings, and summary longitudinal measures of smoking and alcohol consumption over the ensuing five decades. Multinomial regression models were adjusted for sex, adolescent emotional and conduct problems, occupational social class of origin, childhood cognition, educational attainment and adult occupational social class. With all covariates adjusted, higher adolescent self-organization was associated with fewer smoking pack years, although not with quitting; there was no association with alcohol consumption across adulthood (none or heavy compared with light to moderate). Adolescent self-organization appears to be protective against smoking, but not against heavy alcohol consumption. Interpretation of this differential effect should be embedded in an understanding of the social and sociodemographic context in which these health behaviours occur over time.     

Origin and evolution of heredity-metabolism system

The role of "theoretical physics" in the elucidation of the origin of life has been advanced by Eigen's hypercycle theory on ancient protein synthesis system and by Dyson's random drift theory on the autocatalytic formation of enzymes, although these approaches from the informational side involve many problems to be resolved. On the other hand, our C4N model calls for a stronger role of physico-chemistry in the understanding of the origin of life. Plant virus and movable genes could be the fossil vestiges of the ancient protein synthetic system, where tRNA identical to mRNA identical to gene. It is pointed out that functional differentiation of proteins closely correlates with the structure of the primitive tRNAs. Possible initial forms of the primitive tRNAs used by the earliest organisms are explicitly shown, in which the above correlation is carefully taken into account. The system of the primitive genes and the primitive enzymes in the proto-cellular membrane, say the marigranule, might simulate the earliest organism.     

The Soft Underbelly of Evolution?

Evolution and the origin of life are separate, if connected, topics, but they are frequently conflated??especially by creationists. Regarding the natural origin of life as ??the soft underbelly?? of evolution, creationists argue that it is impossible, improbable, or insusceptible to scientific investigation. Underlying their arguments is the hope that the failure of scientific research on the origin of life is evidence for a supernatural account. It is crucial for teachers to understand the nature of science in order to be able to explain why appeals to the supernatural are out of place in explaining the origin of life and why scientific research on the origin of life is not intrinsically a threat to faith.     

Suitable microscopic entropy for the origin of microbial life: Microbiological methods are challenges

A hypothesis is proposed that the first living microbial cell(s) on Earth assembled about 3.6-4 billion years ago when an environmental microscopic entropy (balance between order and disorder; suitable amount of randomness) was within a range suitable for the origin of microbial cell(s) in a hydrogel environment. An earlier origin of microbial life was not possible as the elements, molecules and entropy conditions necessary for life were not available at the microscopic level. Methodology limitations to study postulated past origin of microbial life events and to mimic these events in the laboratory, are still obstacles to understanding the origin of life.