The Origin of Cellular Life and Biosemiotics

Evolutionary Biology: Exobiology and Evolutionary Mechanisms, 2013

The idea that autocatalytic sets played an important role in the origin of life is not new. Neither is the idea that autocatalytic sets can tell us something about the evolution and functional organization of living systems. However, most of these ideas have, until recently, remained at a conceptual level, and very few concrete, mathematically sound, and practically applicable results had been achieved. In this chapter, we review and discuss recent results on a mathematical framework of autocatalytic sets that could take the idea out of the conceptual realm, and provide a formal and powerful way to investigate autocatalytic sets in the context of the origin of life, evolution, and functional organization.

Chemistry – A European Journal, 2009

Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life, 2015

It is proposed that processes characteristic of biology today, autocatalysis, selection of molecules for linkage by their electrical shape, and evolution by survival selection were also the processes that initiated biology. A reconnaissance is made of both paradoxes and potential questions. It is argued that the minimal requirement for initiating Darwinian evolution is not a molecule copying process, but a linkage copying process. Survival selection evolution does not require a heterocatalytic polymer and a separate replicase process until there is uncertainty where molecular additions will occur. It is argued that a linkage directing process will be found for a lipid membrane (though this needs to be verified) and may in the right environment result in initial evolution, including initiation of α-helices, the development of a single chirality and NTPs. The system has at this point become sufficiently complex that higher precision copying is needed. However it seems likely that this...

2018.03.20-ESSENCE AND EMERGENCE OF BIOLOGICAL LIFE (2002)

Added probably the last missing element in the foundation of the biological sciences. This element consists in describing the nucleation of living molecules from inanimate ones. The origin of life coincides with the appearance of vibrations of molecular flagella under the action of quanta of energy flowing from a molecule to water. The evolution of living molecules to cellular organisms has been speculatively traced. An attempt has been made, while not rigorous, to inscribe this element in the existing system of biological knowledge. The role of living molecules in modern organisms has been established. Several new hypotheses have been formulated with the participation of a new element: on aging, on diabetes; about the causes of cancer and some others. For further advancement, it is necessary to concentrate theoretical efforts in the detected directions.

Proceedings of the National Academy of Sciences, 2007

Euresis Journal, 2013

In the last few decades, mainly due to technological advances, the molecular objects and mechanisms being continuously at work in living beings, and supporting their unique performance, have become accessible to an unprecedented detail. In particular, the number of complete genome sequences being determined and annotated has been growing exponentially; exhaustive inventories of cellular RNAs (transcriptomes) are being established, revealing a multitude of non-protein-coding RNAs (ncRNAs) of unknown function; whole sets of different protein species populating cells and sub-cellular organelles (proteomes) are being massively identified, quantified and chemically characterized; genome-wide cartographies are being drawn for site-specific DNA methylation and chromatin protein signatures, revealing their interconnected influences on DNA accessibility and gene expression (epigenomes); protein-protein interactions, multiprotein complexes and gene-gene interactions occurring within living cells are being systematically put in light and integrated into networks of astonishing complexity (interactomes). Besides posing a serious challenge to our actual ability to manage and interpret such a high amount of analytical information, these “post-genomic” studies are opening new, surprising perspectives on the nature of genes, on the complexity of cellular regulatory networks, on the biogenesis, roles and interplay of biological macromolecules participating in these networks. We now realize, more clearly than ever before, that what we call life depends on a molecular scenario whose intricacy is destined to increase proportionally with the power of our analytical tools. Such a dependence of the living status on indefinitely ramified and dynamic chemical interaction networks appears to be in contrast with the unitary sense of being we experience, as living individuals, from the “inner side” of life, and the reasonable suspect may arise that even the ultimate analytical description of our material arrangement would not allow us to infer from it the living status we directly experience. Mainly based on Hans Jonas’ philosophical reflection on the living organism, I will discuss the thesis that life, even in its non-human forms, cannot be satisfactorily described in terms of the particular arrangements of chemical entities it depends on, and that a rational approach to the question of life should not exclude an inward, subjective dimension that is at the same time inaccessible to scientific investigation, yet essential to fully understand the objects revealed by it. Viewed in this light, modern biology offers a unique opportunity to appreciate the immeasurable character of reality, of which life itself is not simply a part, but the one and only point of access and manifestation.

Molecular imprints of organisms serving as both the agents and the products of the underlying sign activities are quantum mechanical in their origins. In particular, molecules in any reaction networks constituting a biological organism are semiotic or context-dependent in the sense that their activities reside within the proper coordination of the entire networks. The origin of life could have been related to a specific aspect of molecular semiotics, especially in the transition from molecules as the physical symbols of material units to molecules as the semiotic signs having the capacity of pointing to something else other than the molecules themselves. Quantum mechanical underpinning of the molecular imprints leading to the emergence of life is in the appraisal of the material capacities of both coherent assimilation and decoherent dissociation already latent in the imprints. One empirical evidence suggesting the likelihood of both coherent assimilation and decoherent dissociation in prebiotic settings could have been found in synthetic chemical reactions running in hydrothermal circulation of seawater through hot vents in the Haedean ocean on the primitive Earth.

Frontiers in Physiology

Origins of Life: Self-Organization and/or Biological Evolution?, 2009

The spontaneous assembly of amphiphiles into micelles and bilayer membranes, as well as the dynamical self-assembly properties of nucleic acids, suggest that selforganization phenomena played a role in the origin of life. However, current biology indicates that life could have not evolved in the absence of a genetic replicating mechanism insuring the stability and diversification of its basic components. This does not imply that explanations on the appearance of life should reduce themselves to the issue of the emergence of RNA or its predecessors.

Communications Chemistry

The chemical space of prebiotic chemistry is extremely large, while extant biochemistry uses only a few thousand interconnected molecules. Here we discuss how the connection between these two regimes can be investigated, and explore major outstanding questions in the origin of life. As we search for habitable and inhabited planets beyond Earth, defining life and understanding how it originates is critical to designing life detection missions 1. Though scientists from many fields have tried to understand the origins of life, and many hypotheses exist, a precise definition of life remains elusive 2 , and we do not presently know how life began. From interstellar observations and carbonaceous meteorites, it is known that complex organic chemistry occurs widely in primitive solar system environments (e.g., ref. 3). Conversely, we have the single data point of the chemistry produced by our biosphere. The space between these data points is sparsely filled by experiment, model, and hypothesis. Experimentally addressing the chemical origins of life is complicated by the size of organic chemical space 4 , and the tandem sparsity and complexity of reactions which could give rise to autocatalytic, replicative and ultimately living chemistry. A large amount of chemistry remains to be explored, and it is likely the field will benefit from a combination of experimental, observational and computational studies. For example, computational chemists can algorithmically explore chemical space using graph "grammars" 5 much more rapidly than "wet" chemists can experimentally, though such computations are still hampered by accuracy and computational capacity 6. Origins of life models, regardless of biases along heterotrophic/autotrophic axes 7 , all depend on the origin of chemical reaction networks. But life is more than a collection of reactions and compounds, it is a systemic phenomenon characterized by feedbacks that modulate kinetics. Within reaction networks, slight differences in reactivity can cause large systemic effects. Network closure, in which the edges (in this case reactions) and nodes (here, chemical compounds) of a network form a single connected component 8 , is a unifying concept defining hierarchically functional and selectable biological units (e.g., metabolic pathways, genes, organelles, cells,

2004

Generally unicellular prokaryotes are considered the most fundamental form of living system. Many researchers include viruses since they commandeer cellular machinery in their replication; while others insist viruses are merely complex infective proteins. New biological principles are introduced suggesting that even the prion, the infectious protein responsible for transmissible spongiform encephalopathies, qualifies as the most fundamental form of life; and remains in general concordance with the six-point definition of living systems put forth by Humberto Maturana and his colleagues in their original characterization of living organisms as a class of complex self-organized autopoietic systems in 1974.

Open biology, 2013

The origin of life (OOL) problem remains one of the more challenging scientific questions of all time. In this essay, we propose that following recent experimental and theoretical advances in systems chemistry, the underlying principle governing the emergence of life on the Earth can in its broadest sense be specified, and may be stated as follows: all stable (persistent) replicating systems will tend to evolve over time towards systems of greater stability. The stability kind referred to, however, is dynamic kinetic stability, and quite distinct from the traditional thermodynamic stability which conventionally dominates physical and chemical thinking. Significantly, that stability kind is generally found to be enhanced by increasing complexification, since added features in the replicating system that improve replication efficiency will be reproduced, thereby offering an explanation for the emergence of life's extraordinary complexity. On the basis of that simple principle, a f...

Physical emergence-crystals, rocks, sandpiles, turbulent eddies, planets, stars-is fundamentally different from biological emergence-amoeba, mice, humans-even though the latter is based in the former. This paper points out that the essential difference is that causation in biological systems has a logical nature at each level of the hierarchy of emergence, from the biomolecular level up. The key link between physics and life enabling this to happen is provided by bio-molecules, such as voltage gated ion channels, which enable logic to emerge from the underlying physics. They can only have come into being via the contextually dependent processes of natural selection, which selects them for their biological function. 1 1 Physics vs Biology How can a universe that is ruled by natural laws give rise to aims and intentions? Whether or not a human observer exists, the natural laws would continue to operate as they are indefinitely. The key difference between physics and biology is function or purpose. There is, in the standard scientific interpretation, no purpose in the existence of the Moon 2 or an electron or in a collision of two gas particles. By contrast, there is purpose and function in all life [22]: " Although living systems obey the laws of physics and chemistry, the notion of function or purpose differentiates biology from other natural sciences. Organisms exist to reproduce, whereas, outside religious belief, rocks and stars have no purpose. Selection for function has produced the living cell, with a unique set of properties that distinguish it from inanimate systems of interacting molecules. Cells exist far from thermal equilibrium by harvesting energy from their environment. They are composed of thousands of different types of molecule. They contain information for their survival and reproduction, in the form of their DNA ". 1 This paper is based in an FQXI essay written by one of us (GE). 2 It is true that the existence of the Moon was probably essential for the origin of life as we know it, so one might claim that the purpose of the Moon was to enable life on Earth to emerge from the sea to dry land through its effects on tides. However the Moon is unaware of this effect: it was, as far as the Moon was concerned, an unintended by product of its orbital motion round the Earth.

Life Science Press, 2017

This review paper aims at a better understanding of the origin and physical foundation of life's dual-metabolic and genetic-nature. First, I give a concise 'top-down' survey of the origin of life, i.e., backwards in time from extant DNA/RNA/protein-based life over the RNA world to the earliest, pre-RNA stages of life's origin, with special emphasis on the metabolism-first versus gene/replicator-first controversy. Secondly, I critically assess the role of minerals in the earliest origins of bothmetabolism and genetics. And thirdly, relying on the work of Erwin Schrödinger, Carl Woese and Stuart Kauffman, I sketch and reframe the origin of metabolism and genetics from a physics, i.e., thermodynamics, perspective. I conclude that life's dual nature runs all the way back to the very dawn and physical constitution of life on Earth. Relying on the current state of research, I argue that life's origin stems from the congregation of two kinds of sources of negentropy-thermodynamic and statistical negentropy. While thermodynamic negentropy (which could have been provided by solar radiation and/or geochemical and thermochemical sources), led to life's combustive and/or metabolic aspect, the abundant presence of mineral surfaces on the prebiotic Earth-with their selectively adsorbing and catalysing (thus 'organizing') micro-crystalline structure or order-arguably provided for statistical negentropy for life to originate, eventually leading to life's crystalline and/or genetic aspect. However, the transition from a prebiotic world of relatively simple chemical compounds including periodically structured mineral surfaces towards the complex aperiodic and/or informational structure, specificity and organization of biopolymers and biochemical reaction sequences remains a 'hard problem' to solve.

This paper clarifies why it is not possible to understand or explain life and mind with only the knowledge of physics and chemistry. Both the process of emergence and hierarchic structural organization are required in addition to physics and chemistry for there to be life and mind.