Understanding life through its origins reveals the groundwork underlying the differentiations of its autonomous generative matrixes. Following the primogenital matrix of generation, the three generative matrixes of the specifically human sense of life establish humanness within the creative human condition as the existential sphere of sharing-in-life.

I defend origins of life research against an argument, given by Roger White in 2007, that it rests on a mistake. I show how the Bayesian machinery can illuminate the rational search for alternative explanations of currently inexplicable, improbable data, and in particular how it can illuminate the rational search for a secular explanation of the origins of life and of the fine-tuning of the universe.

Plato placed great importance on the natural number one. Plato stated that the three properties of Plato’s one are indivisible, invariable, and equal and that an ideal one has no physical properties. If we regard differences among lives as differences among genes and gene products and life as the container of genes, then life has properties similar to Plato’s one. Furthermore, life has properties of multiplying when it survives and disappearing when it dies. These properties of (...) class='Hi'>life are prerequisites for natural selection. Natural selection makes DNA become digital information, enabling accurate copies of DNA. Furthermore, DNA bases, essential for survival, become close to Plato’s one by natural selection. In addition, the information content of life must be sufficiently large for death to be irreversible, and the irreversibility of death is a prerequisite for natural selection. (shrink)

Origin of life on earth transpired once and from then on, it emerges as an endless eternal process. Matter and energy are constants of the cosmos and the hypothesis is that the origin of life is a moment when these constants intertwined or interacted. Energy from the cosmos interacted with inorganic matter to support matter with retention of this riveted energy, as energy to be circulated within the primitive channelized structures to conserve energy by the materialization of the (...) proton homeostasis mechanisms developed from the obtainable inorganic matter. The driver for these processes as we now confirm, exists in the quantum world and through quantum phenomenal processes could have combined these constants to create the magic of life. Primitive earth was a chemical reactive system that triggered a macromolecular evolution by means of open thermodynamic systems, driven by cyclic gradients of temperature, electromagnetic radiation and chemical potentials which sustained life and proto-consciousness in the first life forms driven by the quantum processes. The origin of life is always an intriguing topic but the purpose for finding the cause should never be inclined towards obliterating it; for if that is the case, the further we seek, the farther it will go. (shrink)

The problem of how a mixture of chemicals can spontaneously transform themselves into even a simple living organism remains one of the great outstanding challenges to science. Various primordial soup theories have been proposed in which chemical self- organization brings about the required level of complexity. Major conceptual obstacles remain, however, such as the emergence of the genetic code, and the “chicken-and-egg” problem concerning which came first: nucleic acids or proteins. Currently fashionable is the so-called RNA world theory, which casts (...) RNA in the role of both chicken and egg. Other theories assume that protein chemistry and even clay crystal life came before nucleic acids. To be fully successful, a theory of biogenesis has to explain not merely the emergence of molecular replication and chemical complexity, but the crucial information content and information processing capabilities of the living cell. (shrink)

This volume is the latest in a series of books and articles stretching back more than three decades on a theme quite startling in its claims and implications: that terrestrial life did not originate on Earth but arrived in the form of cells or bacteria from outer space. The idea of “panspermia,” that the seeds of life are spread from planet to planet, dates to the 19th century with the ideas of Lord Kelvin. It was championed by the (...) Swedish physicist, chemist, and Nobelist Svante Arrhenius at the beginning of the 20th century. Once scientists recognized the difficulties of life surviving in the conditions of interplanetary and interstellar space, by the 1960s a neo-panspermia became popular: not life itself, but prebiotic chemicals were the new seeds of life, made more likely by the discovery of numerous complex organic molecules in meteorites, comets, and interstellar molecular clouds. But the difficulties of synthesizing anything more complicated than amino acids in the wake of the famous Miller-Urey experiment in 1953 kept alive the idea that life itself may be spread throughout the universe. At the center of this work is Chandra Wickramasinghe, a research student of the maverick astronomer Fred Hoyle. In 1962 Hoyle became interested in the origin and nature of interstellar dust, in particular as found in dense molecular clouds, and he and Wickramasinghe set to work on the problem. They became convinced that dust could not form inside molecular clouds, but must have originated in the atmospheres of cool stars, protoplanetary discs, or supernova ejecta, a theory now widely accepted. It was the next steps that became increasingly controversial: that the spectroscopic signature of dust was best explained by complex biomolecules such as cellulose; that biomolecules were assembled into still more complex forms inside comets; and that the living cells and bacteria generated there were responsible for the origin of life on Earth. And not only that: Hoyle and Wickramasinghe argued that the delivery of bacteria from space continues, affecting both the origin and the ongoing evolution of life, and may even be responsible for certain diseases on Earth. These theories were not only reported in reputable scientific journals such as Nature, but also in popular books including Lifecloud (1978), Diseases from Space (1979), and Evolution from Space (1981). Biologists were not impressed; Lynn Margulis, not known for the timidity of her own theories such as endosymbiosis, called the first book “wanton, amusing, promiscuous fiction.”. (shrink)

The osmotic activity produced by internal, non‐permeable, anionic nucleic acids and metabolites causes a persistent and life‐threatening cell swelling, or cellular edema, produced by the Gibbs‐Donnan effect. This evolutionary‐critical osmotic challenge must have been resolved by LUCA or its ancestors, but we lack a cell‐physiology look into the biophysical constraints to the solutions. Like mycoplasma, early cells conceivably preserved their volume with Cl−, Na+, and K+‐channels, Na+/H+‐exchangers, and a light‐dependent bacteriorhodopsin‐like H+‐pump. Here, I simulated protocells having these ionic‐permeabilities and (...) inhabiting an oceanic pond before the Great‐Oxygenation‐Event. Protocells showed better volume control and stable resting potentials at lower external pH and higher temperatures, favoring a certain type of extremophile life. Prevention of Na+‐influx at night, with low bacteriorhodopsin activity, required deep shutdown of highly voltage‐sensitive Na+‐channels and extremely selective K+‐channels, two conserved features essential for modern neuronal encoding. The Gibbs‐Donnan effect universality implies that extraterrestrial cells, if they exist, may reveal similar volume‐controlling mechanisms. (shrink)

The ‘managed-metabolism’ hypothesis suggests that a ‘cooperation barrier’ must be overcome if self-producing chemical organizations are to undergo the transition from non-life to life. This dynamical barrier prevents un-managed autocatalytic networks of molecular species from individuating into complex, cooperative organizations. The barrier arises because molecular species that could otherwise make significant cooperative contributions to the success of an organization will often not be supported within the organization, and because side reactions and other ‘free-riding’ processes will undermine cooperation. As (...) a result, the barrier seriously impedes the emergence of individuality, complex functionality and the transition to life. This barrier is analogous to the cooperation barrier that also impedes the emergence of complex cooperation at all levels of living organization. As has been shown at other levels of organization, the barrier can be overcome comprehensively by appropriate ‘management’. Management implements a system of evolvable constraints that can overcome the cooperation barrier by ensuring that beneficial co-operators are supported within the organization and by suppressing free-riders. In this way, management can control and manipulate the chemical processes of a collectively autocatalytic organization, producing novel processes that serve the interests of the organization as a whole and that could not arise and persist in an un-managed chemical organization. Management self-organizes because it is able to capture some of the benefits that are produced when its interventions promote cooperation, thereby enhancing productivity. Selection will therefore favour the emergence of managers that take over and manage chemical organizations so as to overcome the cooperation barrier. The managed-metabolism hypothesis demonstrates that if management is to overcome the cooperation barrier comprehensively, its interventions must be digitally coded. In this way, the hypothesis accounts for the two-tiered structure of all living cells in which a digitally-coded genetic apparatus manages an analogically-informed metabolism.GraphicalOpen image in new window. (shrink)

Resumen: Varios filósofos han hecho notar que el naturalismo metafísico ha sido un supuesto compartido por los miembros de la comunidad científica involucrada en la investigación acerca del origen de la vida. Es una consecuencia de esta presuposición que la emergencia de la vida debe haber sido muy probable bajo las condiciones físicas y químicas de la Tierra primitiva. El estado de la investigación sobre el origen de la vida, sin embargo, está muy lejos de poseer una hipótesis naturalista convincente (...) en los términos buscados. La actitud de los investigadores y de algunos filósofos ha sido suponer que estos fracasos no son una razón para pensar que alguna otra hipótesis naturalista no fuese a funcionar. Aquí se ofrece una reconstrucción epistemológica de esta actitud en términos bayesianos. Se argumenta, luego, que el aislamiento del naturalismo metafísico respecto de la desconfirmación no es racional, y podría convertirse en un obstáculo para el avance del conocimiento. Abstract: Several philosophers have noted that metaphysical naturalism has been an assumption shared by the members of the scientific community involved in the research concerning the origin of life. It is a consequence of this presupposition that the emergence of life should have been very probable under the physical and chemical conditions in the primitive Earth. The state of the research on the origin of life, though, is very far from having a convincing naturalist hypothesis in the terms sought after. The attitude of the researchers and some philosophers has been to suppose that these failures are not reason to think that some other naturalist hypothesis won’t work. Here, an epistemological reconstruction of this attitude in Bayesian terms is offered. It is argued that the insulation of metaphysical naturalism from disconfirmation is not rational, and would become an obstacle to the advancement of knowledge. (shrink)

The building blocks and origins of life have fascinated scientists since the earliest of times. What is required for life to work in terms of building blocks? An outline of the building blocks that have to be present in living systems to allow the processes that are required for life is given. These building blocks have to be organised in a specific way to allow living processes to be functional, which are summarised in what is referred (...) to as the seven pillars of life. In essence, these are the fundamental characteristics of all living systems. Evidences of when and how living systems developed on the Earth shortly after the Earth established itself as a planet are discussed. This comes from the growing body of geological evidence of the age of rocks and rock formations in different places on the Earth. This review is concluded with the latest evidence of where on Earth living systems may have started. A large amount of uncertainty exists about these processes, but more and more consilient evidence is giving us important pointers as to the origins of life on the planet Earth.Contribution: As part of this special collection, the building blocks or origins of life give insights into the chemical principles and constituents of living organisms and how their interactions allow life to function on earth. (shrink)

The role of evolutionary theory at the origin of life is an extensively debated topic. The origin and early development of life is usually separated into a prebiotic phase and a protocellular phase, ultimately leading to the Last Universal Common Ancestor. Most likely, the Last Universal Common Ancestor was subject to Darwinian evolution, but the question remains to what extent Darwinian evolution applies to the prebiotic and protocellular phases. In this review, we reflect on the current status of (...) evolutionary theory in origins of life research by bringing together philosophy of science, evolutionary biology, and empirical research in the origins field. We explore the various ways in which evolutionary theory has been extended beyond biology; we look at how these extensions apply to the prebiotic development of (proto)metabolism; and we investigate how the terminology from evolutionary theory is currently being employed in state-of-the-art origins of life research. In doing so, we identify some of the current obstacles to an evolutionary account of the origins of life, as well as open up new avenues of research. (shrink)

Recent successes of systems biology clarified that biological functionality is multilevel. We point out that this fact makes it necessary to revise popular views about macromolecular functions and distinguish between local, physico-chemical and global, biological functions. Our analysis shows that physico-chemical functions are merely tools of biological functionality. This result sheds new light on the origin of cellular life, indicating that in evolutionary history, assignment of biological functions to cellular ingredients plays a crucial role. In this wider picture, even (...) if aggregation of chance mutations of replicator molecules and spontaneously self-assembled proteins led to the formation of a system identical with a living cell in all physical respects but devoid of biological functions, it would remain an inanimate physical system, a pseudo-cell or a zombie-cell but not a viable cell. In the origin of life scenarios, a fundamental circularity arises, since if cells are the minimal units of life, it is apparent that assignments of cellular functions require the presence of cells and vice versa. Resolution of this dilemma requires distinguishing between physico-chemical and biological symbols as well as between physico-chemical and biological information. Our analysis of the concepts of symbol, rule and code suggests that they all rely implicitly on biological laws or principles. We show that the problem is how to establish physico-chemically arbitrary rules assigning biological functions without the presence of living organisms. We propose a solution to that problem with the help of a generalized action principle and biological harnessing of quantum uncertainties. By our proposal, biology is an autonomous science having its own fundamental principle. The biological principle ought not to be regarded as an emergent phenomenon. It can guide chemical evolution towards the biological one, progressively assigning greater complexity and functionality to macromolecules and systems of macromolecules at all levels of organization. This solution explains some perplexing facts and posits a new context for thinking about the problems of the origin of life and mind. (shrink)

For centuries the question of the origin of life had focused on the question of the spontaneous generation of life, at least primitive forms of life, from inanimate matter, an idea that had been promoted most prominently by Aristotle. The widespread belief in spontaneous generation, which had been adopted by the Church, too, was finally abandoned at the beginning of the twentieth century, when the question of the origin of life became related to that of the (...) artificial generation of life in the laboratory. This paper examines the role of social authorities, researchers’ basic beliefs, crucial experiments, and scientific advance in the controversies about spontaneous generation from the seventeenth to the nineteenth centuries and analyzes the subsequent debates about the synthesis of artificial life in the changing scientific contexts of the nineteenth and early-twentieth centuries. It shows that despite the importance of social authorities, basic beliefs, and crucial experiments scientific advances, especially those in microbiology, were the single most important factor in the stepwise abandoning of the doctrine of spontaneous generation. Research on the origin of life and the artificial synthesis of life became scientifically addressed only when it got rid of the idea of constant smooth transitions between inanimate matter and life and explored possible chemical and physical mechanisms of the specificity of basic molecules and processes of life. (shrink)

After deconstructing the thermodynamic concepts of work and waste, I take up Howard Odum’s idea of energy quality, which tallies the overall amount of energy needed to be dissipated in order to accomplish some work of interest. This was developed from economic considerations that give obvious meaning to the work accomplished. But the energy quality idea can be used to import meaning more generally into Nature. It could be viewed as projecting meaning back from any marked work into preceding energy (...) gradient dissipations that immediately paved the way for it. But any work done by an abiotic dissipative structure, since it would be without positive economic significance, would also be difficult to mark as a starting point for the energy quality calculation. Furthermore, any destructive work as by hurricanes or floods, with negative economic significance, would not seem to merit the quality calculation either. But there has been abiotic work of keen interest to us—that which mediated the origin of life. Some kind of abiotic dissipative structures had to have been the framework that fostered this process, regardless of how it might come to be understood in detail. Since all dissipative structures have the same thermodynamic and informational organization in common, any of them might provide the material context for the origin of something. So we can pick any starting point we wish, and calculate backward what sequence of energy usages would have been necessary to set it up. Given such an open ended project, we could not find an obvious place in any sequence to stop and start the forward the calculation, and so we would need to take it right back to an ultimate beginning, like the insolation of some area, or the outpouring of Earth’s thermal energy. Any energy dissipation might be the beginning of something of importance, and so Nature is as replete with potential meanings as it is with energy gradients. (shrink)

This disagreement extends to the fundamental details of physical and biochemical theories. On the other hand, (2) There is almostuniversal agreementthatlife did notfirstcome aboutmerely by chance. This is not to say that all scientists think that life’s existence was inevitable. The common view is that given a fuller understanding of the physical and biological conditions and processes involved, the emergence of life should be seen to be quite likely, or at least not very surprising. The view which is (...) almost universally rejected by researchers in the field is that the numerous and prima facie improbable physical and biological requirements for life all fell together just by a fluke, like so many dice tumbling out of a bag and landing all sixes. Most importantly, for the purposes of the following discussion, (3) The conviction that life did not arise largely by chance is treated as epistem- ically prior to the development of alternative theories. C 2007, Copyright the Authors Journal compilation C 2007, Blackwell Publishing, Inc. (shrink)

Teachers’ conceptions about the origin of life in three Latin American countries with contrasting levels of secularism were analyzed: Argentina, Brazil, and Uruguay. A European survey questionnaire was used and the interpretation of the results drew on Barbour's four categories concerning the relationships of science and religion. A large majority of Argentinian and Uruguayan teachers were clearly evolutionist, even when believing in God, with no difference between Argentina and Uruguay. The majority of Brazilian teachers assumed a religious position about (...) the origin of life, being creationist or evolutionary creationist. Differences of Brazilian teachers’ conceptions may result from the higher percentage of evangelicals and lower proportion of agnostics/atheists. Brazilian Catholic teachers were more creationist than their Catholic colleagues in Argentina and Uruguay. Distinct patterns were found, but further research is needed to understand possible classroom impacts. (shrink)

Henry Charlton Bastian's support for spontaneous generation is shown to have developed from his commitment to the new evolutionary science of Darwin, Spencer, Huxley and Tyndall. Tracing Bastian's early career development shows that he was one of the most talented rising young stars among the Darwinians in the 1860s. His argument for a logically necessary link between evolution and spontaneous generation was widely believed among those sympathetic to Darwin's ideas. Spontaneous generation implied materialism to many, however, and it had associations (...) in Britain with radical politics and amateur science. Huxley and the X Club were trying to create a public posture of Darwinism that kept it at arm's length from those negative associations. Thus, the conflict that developed when Huxley and the X Club opposed Bastian was at least as much about factional in-fighting among the Darwinians as it was about the experiments under dispute. Huxley's strategy to defeat Bastian and define his position as "non-Darwinian" contributed significantly to the shaping of Huxley's famous address "Biogenesis and Abiogenesis." Rhetorically separating Darwinism from Bastian was thus responsible for Huxley's first clear public statement that a naturalistic origin of life was compatible with Darwin's ideas, but only in the earth's distant past. The final separation of the discourse on the meaning of Brownian movement and "active molecules" from any possible link with spontaneous generation also grew out of Huxley's strategy to defeat Bastian. Clashes between Bastian and the X Club are described at the BAAS, the Royal Society, and in the pages of "Nature" and other journals. (shrink)

As to the primary morphogenesis which occurred after the origin of life, two conditions are considered. It must be a non-specific pattern. It must be one of the simplest patterns.The above conditions are satisfied by the morphogenetic polarity. Actually, the simplest polar pattern is divided into two classes. The first of these is represented by a regional protrusion of the surface of a sphere , and the second by a regional inversion . That means that the first morphogenesis might (...) take place towards two directions: regional protrusion and regional inversion of the globular organism. Both of them might be conditioned by the appearance of protoplasmic polarity. (shrink)

During the course of its short history the discipline concerned with the origin of life has given birth to several scientific programmes in the Lakatosian sense, two of the most prominent and widespread being those initiated by Oparin (life began from protein entities) and Muller-Haldane (life began from genetic entities). The present paper sets down the bases for the rational reconstruction of both views by identifying their hard core and some of their successive developments. An assessment is (...) made of the various stages in the evolution of these programmes with respect to the crucial Lakatosian notions of progressivity and regressivity and of how their arguments stand up against one another. This epistemological analysis also establishes the internal reasons why the RNA version of the genotype programme (developed in particular by L. Orgel and S. Spiegelman) has today taken on a progressive character and enjoys recognition by the international scientific community. (shrink)

A closer look at Wilhelm Ostwald's articles that originally proposed the concept of autocatalysis reveals that he accepted reactants, not just products, as potential autocatalysts. Therefore, that a process is catalyzed by some of its products, which is the common definition of autocatalysis, is only a proper subset of what Ostwald meant by “Autokatalyse.” As a result, it is necessary to reconsider the definition of autocatalysis, which is especially important for origins‐of‐life research because autocatalysis provides an abiotic mechanism (...) that yields reproduction‐like dynamics. Here, we translate and briefly review the two key publications on autocatalysis by Ostwald to revive his understanding of autocatalysis, and we introduce the concepts of recessive and expansive autocatalysis. Then we discuss the twofold significance of such a revival: first, facilitating the search for candidate processes underlying the origins of life, and second, updating our view of autocatalysis in complex reaction networks and metabolism. (shrink)

Despite thermodynamic, bioenergetic and phylogenetic failings, the 81‐year‐old concept of primordial soup remains central to mainstream thinking on the origin of life. But soup is homogeneous in pH and redox potential, and so has no capacity for energy coupling by chemiosmosis. Thermodynamic constraints make chemiosmosis strictly necessary for carbon and energy metabolism in all free‐living chemotrophs, and presumably the first free‐living cells too. Proton gradients form naturally at alkaline hydrothermal vents and are viewed as central to the origin of (...) life. Here we consider how the earliest cells might have harnessed a geochemically created proton‐motive force and then learned to make their own, a transition that was necessary for their escape from the vents. Synthesis of ATP by chemiosmosis today involves generation of an ion gradient by means of vectorial electron transfer from a donor to an acceptor. We argue that the first donor was hydrogen and the first acceptor CO2. (shrink)

We draw on Short’s work on Peirce’s theory of signs to propose a new general definition of interpretation. Short argues that Peirce’s semiotics rests on his naturalised teleology. Our proposal extends Short’s work by modifying his definition of interpretation so as to make it more generally applicable to putatively interpretative processes in biological systems. We use our definition as the basis of an account of different kinds of misinterpretation and we discuss some questions raised by the definition by reference to (...) parallel problems in the field of teleosemantics. We propose that interpretative responses fulfilling the criteria of our definition may be made by relatively simple molecular entities and we suggest two specific empirical applications of the definition to experimental work in the field of origin of life research. Our wider aim is to suggest that a well formulated naturalistic definition of interpretation will allow a re-evaluation of the role of semiotic phenomena in biological systems, including the generation of empirically testable hypotheses. (shrink)

According to the model presented in this paper, the beginning of life was marked by the coupling of two complementary nucleotide bases: adenine and thymine. The adenine-thymine system received photons from the sun and stored their energy in the form of a chemical high-energy bond between two phosphoric acid molecules, which were before-hand fixed by adenine from the aqueous environment. The energy of the high-energy bond was then delivered in the form of two waves of electronic excitation. These were (...) utilized to synthesize new molecules, starting from the carbonic acid and ammonia molecules, fixed from the aqueous environment by the polar groups of the nucleotide bases. In this way, a nucleotides-histone protosystem was self-synthesized, evolving step by step towards complexity, by means of some internal cybernetic and informational mechanisms. During its evolution, the NHPS synthesized a limiting membrane, produced the organizing elements of the cellular organelles and constructed microtubules and microfilaments. Subsequently, the NHPS evolved to the building of DNA-histone system and formed the cellular nucleus. (shrink)

Deacon develops a minimal model of a nonparasitic virus to explore how nucleotide sequences came to be characterized by a code-like informational at the origin of life. The model serves to problematize the concept of biological normativity because it highlights two common yet typically implicit assumptions: that life could consist as an inert form, were it not for extrinsic sources of physical instability, and that life could have originated as a singular self-contained individual. I propose that the (...) origin of life, the genetic code, and biological normativity more generally, lead us to reject this passive individualism. (shrink)

For decades most scientists assumed that life emerged billions of years ago in a “primordial soup” somewhere on the Earth’s surface. Evidence is mounting, however, that life may have begun deep beneath the surface, perhaps near a volcanic ocean vent or even inside the hot crust itself. Since there are hints that life’s history on Earth extends back through the phase of massive cosmic bombardment, it may be that life started on Mars and came here later, (...) perhaps inside rocks ejected from the Red Planet by large impacts. The traffic of intact rocks between Mars and Earth is now an established fact, and experiments confirm that microbes could survive the rigours of the journey through space if cocooned within such material. Unfortunately, this planetary cross- contamination compromises astrobiologists’ hope of finding a second genesis in the solar system. (shrink)

We offer a general definition of interpretation based on a naturalized teleology. The definition tests and extends the biosemiotic paradigm by seeking to provide a philosophically robust resource for investigating the possible role of semiosis (processes of representation and interpretation) in biological systems. We show that our definition provides a way of understanding various possible kinds of misinterpretation, illustrate the definition using examples at the cellular and subcellular level, and test the definition by applying it to a potential counterexample. We (...) explain how we propose to use the definition as a way of asking new questions about what distinguishes life from non-life and of formulating testable hypotheses within the field of origin-of-life research. If the definition leads to fruitful new empirical approaches to the scientific problem of the origin of life, it will help to establish biosemiotics as a legitimate philosophical approach in theoretical biology and will thereby support a theological appropriation of the biosemiotic perspective as the basis of a new theology of nature. (shrink)

Many solar systems in the universe may be expected to contain rocky planets that have accreted organic compounds. These compounds are likely to be universally found. In addition, the chemistry of sulfur, phosphorus, and iron is likely to dominate energy transductions and monomer activation, leading to the eventual emergence of polymers. Proteins and polynucleotides provide living matter with function, structure, and information. The conceptual puzzle regarding their emergence is discussed. The fitness of various elements to serve various roles is analyzed (...) from the viewpoint of electron orbitals. Elements with d orbitals are of central importance. (shrink)