Search

Developing and validating a perspective scale of a student’s acceptance or rejection of the evolution and abiogenesis theories regarding the origin of life and biodiversity is potentially significant, particularly considering the importance of these theories in the biology curriculum. Existing instruments, by their nature, may not allow us to fully understand student perspectives on complex and comprehensive biological theories. Therefore, we believe it is necessary to identify belief-based perspectives that significantly influence the acceptance or rejection of these theories, in addition to students’ perspectives on the theories of abiogenesis and evolution. In this context, we believe that a developed instrument can provide additional evidence to researchers who seek to integrate the information obtained from students’ perspectives into educational practices. This article explains the development and validation of the Perspective Scale on the Origin of Life and Biodiversity (PSOLB), a 25-item Likert scale instrument designed to assess students’ belief-based perspectives on the origin of life and biodiversity. Moreover, the potential contributions and significance of the research findings for pedagogical research and practices are emphasised, along with recommendations for the future use of the scale. [ABSTRACT FROM AUTHOR]

An experimental pathway to the spontaneous generation of compositionally diverse synthetic protocells is presented. The pathway is initiated by flat giant unilamellar vesicles (FGUVs) that originate from compositionally different multilamellar lipid reservoirs and undergo spontaneous spreading across solid surfaces. On contact, the spreading FGUVs merge to produce a concentration gradient in membrane lipids across the fusion interface. Subsequent reconstruction through a series of shape transformations produces a network of nanotube‐connected lipid vesicles that inherit different ratios of the membrane constituents derived from the bilayers of the parent FGUVs. The fusion process leads to the engulfment of small FGUVs by larger FGUVs, mimicking predator‐prey behavior in which the observable characteristics of the prey are lost but the constituents are carried by the predator FGUV to the next generation of lipid vesicles. We speculate that our results could provide a feasible pathway to autonomous protocell diversification in origin of life theories and highlight the possible role of solid surfaces in the development of diversity and rudimentary speciation of natural protocells on the early Earth. [ABSTRACT FROM AUTHOR]

The history of life's formation and the origin of its stereochemistry are nearly as multifaceted as the life itself. In this review, we focus on analyzing the step‐by‐step path leading to what we can define as “life” in parallel to what we know about the emergence of enantiomeric imbalance and subsequent transition to full homochirality. We start at the level of assembly of the building blocks of life from inorganic molecules and build up to the polymerization and formation of nucleic acids and peptides. We report and analyze different theories at various stages of this development and try to elucidate the most plausible theory. [ABSTRACT FROM AUTHOR]

Low-molecular-mass organic chemicals are widely discussed as potential indicators of life in extraterrestrial habitats. However, demarcation lines between biotic chemicals and abiotic chemicals have been difficult to define. Here, we have analyzed the potential utility of the quantum chemical property, HOMO-LUMO gap (HLG), as a novel proxy variable of life, since a significant trend towards incrementally smaller HLGs has been described in the genetically encoded amino acids. The HLG is a zeroth-order predictor of chemical reactivity. Comparing a set of 134 abiotic organic molecules recovered from meteorites, with 570 microbial and plant secondary metabolites thought to be exclusively biotic, we found that the average HLG of biotic molecules was significantly narrower (−10.4 ± 0.9 eV versus −12.4 ± 1.6 eV), with an effect size of g = 1.87. Limitation to hydrophilic molecules (XlogP < 2) improved the separation of biotic from abiotic compounds (g = 2.52). The "hydrophilic reactivity" quadrant defined by |HLG| < 11.25 eV and XlogP < 2 was populated exclusively by 183 biotic compounds and 6 abiotic compounds, 5 of which were nucleobases. We conclude that hydrophilic molecules with small HLGs represent valuable indicators of biotic activity, and we discuss the evolutionary plausibility of this inference. [ABSTRACT FROM AUTHOR]

Evolution requires selection. Molecular/chemical/preDarwinian evolution is no exception. One molecule must be selected over another for molecular evolution to occur and advance. Evolution, however, has no goal. The laws of physics have no utilitarian desire, intent or proficiency. Laws and constraints are blind to "usefulness." How then were potential multi-step processes anticipated, valued and pursued by inanimate nature? Can orchestration of formal systems be physico-chemically spontaneous? The purely physico-dynamic self-ordering of Chaos Theory and irreversible non-equilibrium thermodynamic "engines of disequilibria conversion" achieve neither orchestration nor formal organization. Natural selection is a passive and after-the-fact-of-life selection. Darwinian selection reduces to the differential survival and reproduction of the fittest already-living organisms. In the case of abiogenesis, selection had to be 1) Active, 2) Pre-Function, and 3) Efficacious. Selection had to take place at the molecular level prior to the existence of non-trivial functional processes. It could not have been passive or secondary. What naturalistic mechanisms might have been at play? [ABSTRACT FROM AUTHOR]

Many of the fundamental molecules of life share extraordinary pigment-like optical properties in the long-wavelength UV-C spectral region. These include strong photon absorption and rapid (sub-pico-second) dissipation of the induced electronic excitation energy into heat through peaked conical intersections. These properties have been attributed to a "natural selection" of molecules resistant to the dangerous UV-C light incident on Earth's surface during the Archean. In contrast, the "thermodynamic dissipation theory for the origin of life" argues that, far from being detrimental, UV-C light was, in fact, the thermodynamic potential driving the dissipative structuring of life at its origin. The optical properties were thus the thermodynamic "design goals" of microscopic dissipative structuring of organic UV-C pigments, today known as the "fundamental molecules of life", from common precursors under this light. This "UV-C Pigment World" evolved towards greater solar photon dissipation through more complex dissipative structuring pathways, eventually producing visible pigments to dissipate less energetic, but higher intensity, visible photons up to wavelengths of the "red edge". The propagation and dispersal of organic pigments, catalyzed by animals, and their coupling with abiotic dissipative processes, such as the water cycle, culminated in the apex photon dissipative structure, today's biosphere. [ABSTRACT FROM AUTHOR]

This study proposes a landscape-based scenario for the origin of viruses and cells, focusing on the adaptability of preexisting replicons from the RNP (ribonucleoprotein) world. The scenario postulates that life emerged in a subterranean "warm little pond" where organic matter accumulated, resulting in a prebiotic soup rich in nucleotides, amino acids, and lipids, which served as nutrients for the first self-replicating entities. Over time, the RNA world, followed by the RNP world, came into existence. Replicators/replicons, along with the nutritious soup from the pond, were washed out into the river and diluted. Lipid bubbles, enclosing organic matter, provided the last suitable environment for replicons to replicate. Two survival strategies emerged under these conditions: cell-like structures that obtained nutrients by merging with new bubbles, and virus-like entities that developed various techniques to transmit themselves to fresh bubbles. The presented hypothesis provides the possibility for the common origin of cells and viruses on rocky worlds hosting liquid water, like Earth. [ABSTRACT FROM AUTHOR]

Low-molecular-mass organic chemicals are widely discussed as potential indicators of life in extraterrestrial habitats. However, demarcation lines between biotic chemicals and abiotic chemicals have been difficult to define. Here, we have analyzed the potential utility of the quantum chemical property, HOMO-LUMO gap (HLG), as a novel proxy variable of life, since a significant trend towards incrementally smaller HLGs has been described in the genetically encoded amino acids. The HLG is a zeroth-order predictor of chemical reactivity. Comparing a set of 134 abiotic organic molecules recovered from meteorites, with 570 microbial and plant secondary metabolites thought to be exclusively biotic, we found that the average HLG of biotic molecules was significantly narrower (−10.4 ± 0.9 eV versus −12.4 ± 1.6 eV), with an effect size of g = 1.87. Limitation to hydrophilic molecules (XlogP < 2) improved the separation of biotic from abiotic compounds (g = 2.52). The “hydrophilic reactivity” quadrant defined by |HLG| < 11.25 eV and XlogP < 2 was populated exclusively by 183 biotic compounds and 6 abiotic compounds, 5 of which were nucleobases. We conclude that hydrophilic molecules with small HLGs represent valuable indicators of biotic activity, and we discuss the evolutionary plausibility of this inference.

Within the first billion years of Earth's history, the planet transformed from a hot, barren, and inhospitable landscape to an environment conducive to the emergence and persistence of life. This chapter will review the state of knowledge concerning early Earth's (Hadean/Eoarchean) geochemical environment, including the origin and composition of the planet's moon, crust, oceans, atmosphere, and organic content. It will also discuss abiotic geochemical cycling of the CHONPS elements and how these species could have been converted to biologically relevant building blocks, polymers, and chemical networks. Proposed environments for abiogenesis events are also described and evaluated. An understanding of the geochemical processes under which life may have emerged can better inform our assessment of the habitability of other worlds, the potential complexity that abiotic chemistry can achieve (which has implications for putative biosignatures), and the possibility for biochemistries that are vastly different from those on Earth. [ABSTRACT FROM AUTHOR]

According to the hypothesis of abiogenesis, the simplest cellular, uncials, originated from chemical compounds that already existed in nature. Unfortunately, in spite of ongoing intensive research efforts, abiogenesis owns more difficulties and hopes than advances. That is why new hypotheses try to exempt its difficulties. Particularly, successful modeling of cognizing lets us assume that uncials were designed by some cognizers of the Universe, originated in nature as elementary recurrent classifiers, then evolved to attain the power of cognizing, at least, comparable with the highest human one, allowing them to design uncials analogous to the human design of robots nowadays. In parallel, molecular studying assumes that even elementary units of matter are able to communicate through the IDs of classifiers. And since the constituents of uncials are functionally analogous to those of cognizers, while communication is vital for cognizing, it is worth trying to promote the origin of constituents of cognizers by reaching in abiogenesis and communications. Thus, to promote origination of cognizers, we decompose the nuclei of cognizers to constituents, followed by examining the potential impact of constituents of uncials and molecular recurrent classifiers to the origin of functionally analogous ones of cognizers. Then recall algorithms of formation of 1-/2-place classifiers for possible clues to their origination. Finally, address to the origin of dynamicity of the nuclei of cognizers–doers, to trace dynamicity of doers to the dynamics of a variety of cases in sciences as a footstep to more general models. [ABSTRACT FROM AUTHOR]

Active volcanoes often discharge hot (T ≫ 100 °C) magmatic gases whose original composition has been modified through partial interaction with an externally fed hydrothermal system. The study of methane (CH 4) in these volcanic discharges may provide useful information on the interplay between deep magmatic gases and shallow circulation of hydrothermal fluids. However, the origin of CH 4 in high-temperature volcanic gases and the factors exerting control on its abundance and stable isotope composition are still largely unknown. Here, we present the abundances and stable isotopic composition of CH 4 in hot (99–387 °C) volcanic gases from the La Fossa volcanic crater of Vulcano Island (Southern Italy). Our investigation revealed low (<1.5 μmol/mol) CH 4 concentrations and an extraordinarily large variability in CH 4 stable isotopic composition, with δ13C and δ2H values being positively correlated and varying from −35 to −9.2 ‰ and −670 to −102 ‰, respectively. Notably, CH 4 isotopes measured at Vulcano almost encompasses the global-scale variability observed in natural fluids, with δ2H values ≤ −500 ‰ being the first ever reported in nature. Gases showing extremely negative δ13C-CH 4 and δ2H-CH 4 values systematically display higher CH 4 abundances. We propose two possible scenarios in order to explain the observed huge variation in δ13C and δ2H: (1) mixing of 13C- and 2H-depleted CH 4 with 13C- and 2H-enriched CH 4 of thermogenic origin formed under hydrothermal conditions; (2) post-genetic removal and isotopic alteration of 13C- and 2H-depleted CH 4 occurring during the ascent of volcanic gases. Comparing our dataset with available isotopic data from naturally occurring and artificially produced CH 4 , a thermogenic origin for the isotopically light CH 4 seems unlikely. We postulate that the 13C- and 2H-depleted CH 4 may have formed via kinetically-controlled abiotic synthesis through CO (or CO 2) hydrogenation reactions in the hot ascending gas phase, possibly at temperatures intermediate between those typical of magmatic and hydrothermal conditions. Further investigations of methane in high-temperature volcanic gases are necessary to test this hypothesis. [ABSTRACT FROM AUTHOR]

Would another origin of life resemble Earth's biochemical use of amino acids? Here, we review current knowledge at three levels: (1) Could other classes of chemical structure serve as building blocks for biopolymer structure and catalysis? Amino acids now seem both readily available to, and a plausible chemical attractor for, life as we do not know it. Amino acids thus remain important and tractable targets for astrobiological research. (2) If amino acids are used, would we expect the same L-alpha-structural subclass used by life? Despite numerous ideas, it is not clear why life favors L-enantiomers. It seems clearer, however, why life on Earth uses the shortest possible (alpha-) amino acid backbone, and why each carries only one side chain. However, assertions that other backbones are physicochemically impossible have relaxed into arguments that they are disadvantageous. (3) Would we expect a similar set of side chains to those within the genetic code? Many plausible alternatives exist. Furthermore, evidence exists for both evolutionary advantage and physicochemical constraint as explanatory factors for those encoded by life. Overall, as focus shifts from amino acids as a chemical class to specific side chains used by post-LUCA biology, the probable role of physicochemical constraint diminishes relative to that of biological evolution. Exciting opportunities now present themselves for laboratory work and computing to explore how changing the amino acid alphabet alters the universe of protein folds. Near-term milestones include: (a) expanding evidence about amino acids as attractors within chemical evolution; (b) extending characterization of other backbones relative to biological proteins; and (c) merging computing and laboratory explorations of structures and functions unlocked by xeno peptides. [ABSTRACT FROM AUTHOR]

The fundamental properties of a known form of life are briefly considered, including the fundamental ideas about the chemical evolution of matter and the properties of living matter, which are based on biogeochemistry and molecular biology. The concepts underlying the modern understanding of the origin of life based on chemical and biological evolution are discussed. The basics of astrobiology and the intriguing problem of the existence of extraterrestrial intelligence and the search for life in the Universe are briefly touched upon. [ABSTRACT FROM AUTHOR]

Many scientists and researchers agree that biological life on earth most likely arose naturally, but they cannot account for the exact method by which life arose. Numerous experiments and observations have provided evidence that the basic building blocks of life (amino acids) can form spontaneously under the conditions thought to be those present on ancient earth. The recent discovery of Extremophiles (organisms that thrive in extreme conditions such as high temperature and pressure) gave further impetus to the belief that it is possible for unguided, random mechanisms to produce life. However, contrary to scientists who present contemporary scientific evidence as proof of life having a natural origin, there is a growing number of authoritative scholars who claim that the a priori conditions for life to exist at all, as well as its complexity, are indicative of carefully planned, guided mechanisms. Contrary to a materialistic/atheistic view, these researchers advocate a willingness to follow contemporary data to its most likely, logical conclusion. This conclusion involves the continuous involvement of a Creator right from the moment of creation, to the present. The group of theories that centre around a belief that life was created by a supernatural force or deity is known as Creationism. It is based on religious beliefs that determine the way in which natural scientific data is interpreted. Creationists argue that the complexity of living organisms, as well as the existence of consciousness, cannot be explained by random, unguided processes and must have been designed by a higher power. One of the arguments for a supernatural origin of life, is the Anthropocentric principle (or the so-called “fi ne-tuning” argument), which claims that the universe has precise values for certain physical constants and laws that make it possible for life to exist. Proponents of this view argue that the universe’s design could only have been orchestrated by a conscious, purposeful designer. Further evidence cited for supernatural involvement includes the Cambrian explosion and other discontinuities in the paleontological record, as well as the belief that the information in the DNA (deoxyribonucleic acid) molecule must have had an intelligent author. Criticism of Creationism is that there is no scientific evidence that the universe was finetuned solely for the purpose of facilitating life, or that a conscious designer was responsible for it. Furthermore, the “Multiverse” hypothesis, which postulates that there can be many universes with different physical constants, offers a possible naturalistic explanation for why our universe possesses the properties that are observed. As for the paleontological discontinuities and the information in DNA, these are indeed interesting phenomena that have been and still are the subject of much scientific investigation. However, it is important to note that there is ongoing scientific debate about possible unguided mechanisms that could have caused the Cambrian explosion, and the information in DNA can, according to materialists, also be explained by natural processes such as evolution through natural selection. One of the Naturalistic theories about the origin of life on earth is Abiogenesis, which claims that life arose spontaneously from non-living matter through an optimal coincidence of chemical reactions under favourable conditions. This theory is based on the idea that the conditions on the early earth were perfect for the formation of simple organic molecules, which eventually gave rise to more complex structures capable of self-replication. The Miller)Urey experiment, for example, showed that simple organic molecules formed under conditions that, according to the knowledge at the time, were identical to those on early earth. However, this experiment was discredited over time because the researchers assumed that the primordial atmosphere consisted mainly of methane, ammonia, and water vapour, but later research showed that the early atmosphere more likely consisted of nitrogen, carbon dioxide and water vapour. In addition, some scientists have pointed out that the conditions simulated in the experiment were too reducing in nature (that is, too poor in oxygen), to accurately reflect the conditions on the early earth which had a more oxidizing atmosphere. Therefore, while the Miller-Urey experiment remains an important milestone in the history of origin of life research, it is widely recognised that its results should be viewed with caution and that its implications for the natural formation of life on earth should not be overstated. Another naturalistic theory is that life was brought to earth by comets or meteorites. This theory, known as Panspermia, suggests that life may have originated elsewhere in the universe and was transported to earth by comets or meteorites. Panspermia is supported by the discovery of organic molecules and microorganisms in some meteorites, as well as the presence of microbial life in extreme environments on earth that may be similar to conditions on other planets. Each of these theories has its own strengths and weaknesses and there is no consensus among scientists as to which theory is the most accurate. Abiogenesis, for example, is supported by the evidence of the formation of simple organic molecules under conditions, presumably like those on the early earth, but it is difficult to explain how these molecules gave rise to complex structures capable of self-replication. Panspermia is in turn supported by the discovery of organic molecules and microorganisms in some meteorites, but this does not explain the original origin of life itself. Creationism, on the other hand is not directly supported by scientific evidence but is based on the interpretation of empirical data from a religious paradigm. The origin of life on earth therefore remains a subject of scientific inquiry and naturalistic explanations, based on empirical evidence and well-established scientific theories are still considered in mainstream science to be the only valid basis of human understanding of this complex and interesting subject. However, this normative materialist interpretation is increasingly being questioned by a growing number of eminent scholars. This article focuses on the origin and complexity of information as found in life on earth. All forms of information known to man, whether hieroglyphs, radio signals, printed media or TV broadcasts have an intelligent author, and the question is why mainstream science insists on considering the most complex information observed by humankind to date (namely the code in the DNA molecule), as strictly materialistic in origin. [ABSTRACT FROM AUTHOR]

Life on Earth builds genetically encoded proteins by using a standard alphabet of just 20 L-α-amino acids, although many others were available to life's origins and early evolution. To better understand the causes of this foundational evolutionary outcome, we extend previous analyses which have identified a highly unusual distribution of biophysical properties within the set used by life. Specifically, we use a heuristic search algorithm to identify other sets of amino acids, from a library of plausible alternatives, that emulate life's signature. We find that a subset of amino acids seems predisposed to forming such sets. We present other examples of such alphabets under various assumptions, along with analysis and reasoning about why each might be simplistic. We do so to introduce the central, open question that remains: while fundamental biophysics related to protein folding can potentially reduce a library of 1054 possible amino acid alphabets by 7 orders of magnitude, the framework of assumptions that does so leaves a further 1045 possibilities. It is therefore tempting to ask what additional assumptions can further reduce these 45 orders of magnitude? We thus conclude with a focus on library and alphabet construction as a useful target for subsequent research that may help future science speak with more confidence about what an alien amino acid alphabet would look like and why. [ABSTRACT FROM AUTHOR]

At the origin of life, extremely diverse mixtures of oligomers and polymers could be obtained from relatively simple molecular bricks. Here, we present an example of the polymerization of two amidonitriles derived from cysteine, Cys-Ala-CN and Cys-Met-CN. The thiol function in a molecule adds onto the nitrile group of another one, allowing efficient condensation reactions and making available an extensive range of polymers containing amide bonds and/or five-membered heterocycles, namely thiazolines. Macrocycles were also identified, the biggest one containing sixteen residues (cyclo(Cys-Met)8). MALDI-TOF mass spectrometry was used to identify all the present species. What these examples show is that complex mixtures are likely to have formed on the primitive Earth and that, ultimately, the selection that must have followed may have been an even more crucial step towards life than the synthesis of the pre-biological species themselves. [ABSTRACT FROM AUTHOR]

The more than thirty spacetime theorems developed over the past five decades establish that the universe and its spacetime dimensions have emerged from a cause/causal agent beyond the cosmos. Thus, to infer that this cause/causal agent may have intervened in the origin and history of Earth and Earth's life resides well within the bounds of reason. Meanwhile, proponents of each of the three prevailing naturalistic models (abiogenesis, panspermia, and directed panspermia) for the origin and history of Earth's life have marshaled arguments and evidence that effectively undermine and refute the other two models. A biblical perspective and approach to Earth's life can help resolve this impasse. While a superficial and pervasive appeal to divine intervention thwarts scientific advance, so does a rigid adherence to naturalism. A productive way forward is to identify which models (or parts of models), whether naturalistic, theistic, or a combination, most effectively narrow, rather than widen, knowledge gaps, minimize anomalies, offer the most comprehensive and detailed explanation of the data, and prove most successful in predicting scientific discoveries. [ABSTRACT FROM AUTHOR]

This article concludes a three-part series on abiogenesis that suggests meaningful configurations of organic components can arise spontaneously, leading to organisms that successfully survive and reproduce. While the complexity of the disorganized abiotic world makes it appear to some that such a feat of organization would require the nonnatural intervention of an intelligent mind (including but not limited to supernatural intervention), we suggest that careful considerations of thermodynamics and information lead to the plausibility of a natural occurrence. No specific, complete pathway for abiogenesis has yet been identified, but the fundamental processes that enable such a path can be articulated more clearly now than ever before as a result of new and continuing research in multiple disciplines. This concluding article centers on the way in which complex states of molecular organic information can be generated to produce the most meaningful configurations. [ABSTRACT FROM AUTHOR]

Theories on life's origin generally acknowledge the advantage of a semi-permeable vesicle (protocell) for enhancing the chemical reaction–diffusion processes involved in abiogenesis. However, more and more evidence indicates that the origin of life is concerned with the photo-chemical dissipative structuring of the fundamental molecules under soft UV-C light (245–275 nm). In this paper, we analyze the Mie UV scattering properties of such a vesicle created with long-chain fatty acids. We find that the vesicle could have provided early life with a shield from the faint but destructive hard UV-C ionizing light (180–210 nm) that probably bathed Earth's surface from before the origin of life and at least until 1200 million years after, until the formation of a protective ozone layer as a result of the evolution of oxygenic photosynthesis. [ABSTRACT FROM AUTHOR]

Would another origin of life resemble Earth’s biochemical use of amino acids? Here, we review current knowledge at three levels: (1) Could other classes of chemical structure serve as building blocks for biopolymer structure and catalysis? Amino acids now seem both readily available to, and a plausible chemical attractor for, life as we do not know it. Amino acids thus remain important and tractable targets for astrobiological research. (2) If amino acids are used, would we expect the same L-alpha-structural subclass used by life? Despite numerous ideas, it is not clear why life favors L-enantiomers. It seems clearer, however, why life on Earth uses the shortest possible (alpha-) amino acid backbone, and why each carries only one side chain. However, assertions that other backbones are physicochemically impossible have relaxed into arguments that they are disadvantageous. (3) Would we expect a similar set of side chains to those within the genetic code? Many plausible alternatives exist. Furthermore, evidence exists for both evolutionary advantage and physicochemical constraint as explanatory factors for those encoded by life. Overall, as focus shifts from amino acids as a chemical class to specific side chains used by post-LUCA biology, the probable role of physicochemical constraint diminishes relative to that of biological evolution. Exciting opportunities now present themselves for laboratory work and computing to explore how changing the amino acid alphabet alters the universe of protein folds. Near-term milestones include: (a) expanding evidence about amino acids as attractors within chemical evolution; (b) extending characterization of other backbones relative to biological proteins; and (c) merging computing and laboratory explorations of structures and functions unlocked by xeno peptides.

Biogenesis and abiogenesis stages of natural evolution are the well-known terms to characterize a quite different phases of life development on the Earth. It is accustomed to think that an abiogenesis as the early stage of evolution is predominantly the chemistry phase dealing with interaction between less or more complex polymer chains when possible appearances of life if any assumes significant involvement of collective effects. A biogenesis as the later stage of evolution is the time for predominance of Darwin's laws manifesting, in part, in competition among individual species in the form of variability-heredity game. In this report, we discuss possible nature of abiogenesis-biogenesis transition as a natural result of energy development in an evolutionary cybernetic system simulated by mathematical model of open thermodynamic system with unlimited number of energy links with its surroundings. [ABSTRACT FROM AUTHOR]

This paper considers the measurements of fossils and markers of geologic time as they appear throughout Moby-Dick, complicating histories of bodies and their remainders. Looking for instances where Ishmael’s measurements fall short or fail to include the “odd inches,” I argue that such ellipses around quantifiable materiality and ontological ideality urge us to reimagine new subject positions from which to perceive narrative, social and deep time. Reading across Ishmael’s survey of antediluvian remains, I’ll begin with a historicist consideration of debates around biogenesis in Melville’s mid-19th century, moving toward discussion on the coeval times of extinction and exhaustion in Moby-Dick’s antediluvian chronologies, concluding in suggestion that fossil measurement in Melville might best be read as one mode of what Spinoza called an adequate idea, distinguishing the contingent from an extra-historical whole, and, in Melville’s deep vision, a general time which is as prehistorical as it is post-epochal.

We have proposed that the abiogenesis of life around the beginning of the Archean may have been an example of "spontaneous" microscopic dissipative structuring of UV-C pigments under the prevailing surface ultraviolet solar spectrum. The thermodynamic function of these Archean pigments (the "fundamental molecules of life"), as for the visible pigments of today, was to dissipate the incident solar light into heat. We have previously described the non-equilibrium thermodynamics and the photochemical mechanisms which may have been involved in the dissipative structuring of the purines adenine and hypoxanthine from the common precursor molecules of hydrogen cyanide and water under this UV light. In this article, we extend our analysis to include the production of the other two important purines, guanine and xanthine. The photochemical reactions are presumed to occur within a fatty acid vesicle floating on a hot (∼80 °C) neutral pH ocean surface exposed to the prevailing UV-C light. Reaction–diffusion equations are resolved under different environmental conditions. Significant amounts of adenine (∼ 10 − 5 M) and guanine (∼ 10 − 6 M) are obtained within 60 Archean days, starting from realistic concentrations of the precursors hydrogen cyanide and cyanogen (∼ 10 − 5 M). [ABSTRACT FROM AUTHOR]

At the origin of life, extremely diverse mixtures of oligomers and polymers could be obtained from relatively simple molecular bricks. Here, we present an example of the polymerization of two amidonitriles derived from cysteine, Cys-Ala-CN and Cys-Met-CN. The thiol function in a molecule adds onto the nitrile group of another one, allowing efficient condensation reactions and making available an extensive range of polymers containing amide bonds and/or five-membered heterocycles, namely thiazolines. Macrocycles were also identified, the biggest one containing sixteen residues (cyclo(Cys-Met)8). MALDI-TOF mass spectrometry was used to identify all the present species. What these examples show is that complex mixtures are likely to have formed on the primitive Earth and that, ultimately, the selection that must have followed may have been an even more crucial step towards life than the synthesis of the pre-biological species themselves.

The more than thirty spacetime theorems developed over the past five decades establish that the universe and its spacetime dimensions have emerged from a cause/causal agent beyond the cosmos. Thus, to infer that this cause/causal agent may have intervened in the origin and history of Earth and Earth’s life resides well within the bounds of reason. Meanwhile, proponents of each of the three prevailing naturalistic models (abiogenesis, panspermia, and directed panspermia) for the origin and history of Earth’s life have marshaled arguments and evidence that effectively undermine and refute the other two models. A biblical perspective and approach to Earth’s life can help resolve this impasse. While a superficial and pervasive appeal to divine intervention thwarts scientific advance, so does a rigid adherence to naturalism. A productive way forward is to identify which models (or parts of models), whether naturalistic, theistic, or a combination, most effectively narrow, rather than widen, knowledge gaps, minimize anomalies, offer the most comprehensive and detailed explanation of the data, and prove most successful in predicting scientific discoveries.

Unlike its shorter analog, cysteine, and its methylated derivative, methionine, homocysteine is not today a proteinogenic amino acid. However, this thiol containing amino acid is capable of forming an activated species intramolecularly. Its thiolactone could have made it an interesting molecular building block at the origin of life on Earth. Here we study the cyclization of homocysteine in water and show theoretically and experimentally that in an acidic medium the proportion of thiolactone is significant. This thiolactone easily reacts with amino acids to form dipeptides. We envision that these reactions may help interpret why a methionine residue is introduced at the start of all protein synthesis. [ABSTRACT FROM AUTHOR]

The history of modern biochemistry started with the cellular theory of life. By putting aside the holistic protoplasmic theory, scientists of the XX century were able to advance the functional classification of cellular components significantly. The cell became the unit of the living. Current theories on the abiogenesis of life must account for a moment in evolution (chemical or biological) when this was not the case. Investigating the role of compartments and membranes along chemical and biotic evolution can lead a more generalised idea of living organisms that is fundamental to advance our efforts in astrobiology, origin of life and artificial life studies. Furthermore, it may provide insights in unexplained evolutionary features such as the lipid divide between Archaea and Eubacteria. By surveying our current understanding of the involvement of compartments in abiogenesis and evolution, the idea of cells as atomistic units of a general theory of biology will be discussed. The aim is not to undermine the validity of the cellular theory of life, but rather to elucidate possible biases with regards to cellularity and the origin of life. An open discussion in these regards could show the inherent limitations of non-cellular compartmentalization that may lead to the necessity of cellular structures to support complex life.

Close and contextual analysis of Thoreau's early expansion of Walden's famous sandbank passage provides considerable insight into his shift toward greater literary and scientific naturalism. Together with its subsequent revisions, this passage, drafted in the spring 1848 Journal six or seven months after he left the Pond, already comprises the core of the narrative's universally celebrated climactic epiphany. Although scholars have long known of its existence, when its revisions are dated and examined in the contexts of the Walden manuscript's development, Thoreau's practice of using the Journal to compose Walden material, the contemporary evolution debate, and his engagement in what historians call public science, this remarkable event can be seen both to illuminate and to complicate Thoreau's career-defining "turn to science" in the early 1850s. [ABSTRACT FROM AUTHOR]

Evolution in modern life requires high replication fidelity to allow for natural selection. A simulation model utilizing simulated phenotype data on cellular probability of survival was developed to determine how self-replication fidelity could evolve in early life. The results indicate that initial survivability and replication fidelity both contribute to overall fitness as measured by growth rates of the cell population. Survival probability was the more dominant feature, and evolution was possible even with zero replication fidelity. A derived formula for the relationship of survival probability and replication fidelity with growth rate was consistent with the simulated empirical data. Quantitative assessment of continuity and other evidence was obtained for a saltation (non-continuous) evolutionary process starting from low to moderate levels of survival probability and self-replication fidelity to reach the high levels seen in modern life forms. [ABSTRACT FROM AUTHOR]

Two sulfur-containing amino acids are included in the list of the 20 classical protein amino acids. A methionine residue is introduced at the start of the synthesis of all current proteins. Cysteine, thanks to its thiol function, plays an essential role in a very large number of catalytic sites. Here we present what is known about the prebiotic synthesis of these two amino acids and homocysteine, and we discuss their introduction into primitive peptides and more elaborate proteins. 1 Introduction 2 Sulfur Sources 3 Prebiotic Synthesis of Cysteine 4 Prebiotic Synthesis of Methionine 5 Homocysteine and Its Thiolactone 6 Methionine and Cystine in Proteins 7 Prebiotic Scenarios Using Sulfur Amino Acids 8 Introduction of Cys and Met in the Genetic Code 9 Conclusion [ABSTRACT FROM AUTHOR]

The capacity to sense gradients efficiently and acquire information about the ambient environment confers many advantages such as facilitating movement toward nutrient sources or away from toxic chemicals. The amplified dispersal evinced by organisms endowed with motility is possibly beneficial in related contexts. Hence, the connections between information acquisition, motility, and microbial size are explored from an explicitly astrobiological standpoint. By using prior theoretical models, the constraints on organism size imposed by gradient detection and motility are elucidated in the form of simple heuristic scaling relations. It is argued that environments such as alkaline hydrothermal vents, which are distinguished by the presence of steep gradients, might be conducive to the existence of "small" microbes (with radii of ≳0.1 μm) in principle, when only the above two factors are considered; other biological functions (e.g., metabolism and genetic exchange) could, however, regulate the lower bound on microbial size and elevate it. The derived expressions are potentially applicable to a diverse array of settings, including those entailing solvents other than water; for example, the lakes and seas of Titan. The article concludes with a brief exposition of how this formalism may be of practical and theoretical value to astrobiology. [ABSTRACT FROM AUTHOR]

In a series of recent publications in Organic Geochemistry and elsewhere, investigators from State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry and their collaborators have reported position-specific δ13C of propane obtained from natural reservoirs and pyrolysis experiments. Based solely on the very negative Δ C-T values (δ13C center – δ13C terminal), ranging from −7 to −10 ‰, they advocated for abiogenic origins of the propanes from sedimentary settings (shale and coal deposits). However, they never demonstrated accuracy of the data and it is likely that correct Δ C-T values for these propanes are close to zero ‰. Therefore, their discussion and interpretation in terms of geochemical processes, including a putative abiogenic origin, are not substantiated. [ABSTRACT FROM AUTHOR]

Understanding how membrane forming amphiphiles are synthesized and aggregate in prebiotic settings is required for understanding the origins of life on Earth 4 billion years ago. Amino acids decyl esters were prepared by dehydration of decanol and amino acid as a model for a plausible prebiotic reaction at two temperatures. Fifteen amino acids were tested with a range of side chain chemistries to understand the role of amino acid identity on synthesis and membrane formation. Products were analyzed using LC-MS as well as microscopy. All amino acids tested produced decyl esters, and some of the products formed membranes when rehydrated in ultrapure water. One of the most abundant prebiotic amino acids, alanine, was remarkably easy to get to generate abundant, uniform membranes, indicating that this could be a selection mechanism for both amino acids and their amphiphilic derivatives.

We have proposed that the abiogenesis of life around the beginning of the Archean may have been an example of “spontaneous” microscopic dissipative structuring of UV-C pigments under the prevailing surface ultraviolet solar spectrum. The thermodynamic function of these Archean pigments (the “fundamental molecules of life”), as for the visible pigments of today, was to dissipate the incident solar light into heat. We have previously described the non-equilibrium thermodynamics and the photochemical mechanisms which may have been involved in the dissipative structuring of the purines adenine and hypoxanthine from the common precursor molecules of hydrogen cyanide and water under this UV light. In this article, we extend our analysis to include the production of the other two important purines, guanine and xanthine. The photochemical reactions are presumed to occur within a fatty acid vesicle floating on a hot (∼80 °C) neutral pH ocean surface exposed to the prevailing UV-C light. Reaction–diffusion equations are resolved under different environmental conditions. Significant amounts of adenine (∼10−5 M) and guanine (∼10−6 M) are obtained within 60 Archean days, starting from realistic concentrations of the precursors hydrogen cyanide and cyanogen (∼10−5 M).

Unlike its shorter analog, cysteine, and its methylated derivative, methionine, homocysteine is not today a proteinogenic amino acid. However, this thiol containing amino acid is capable of forming an activated species intramolecularly. Its thiolactone could have made it an interesting molecular building block at the origin of life on Earth. Here we study the cyclization of homocysteine in water and show theoretically and experimentally that in an acidic medium the proportion of thiolactone is significant. This thiolactone easily reacts with amino acids to form dipeptides. We envision that these reactions may help interpret why a methionine residue is introduced at the start of all protein synthesis.

Rock fragments from the deepest parts of a buried hydrothermal system belonging to the Mesozoic Tethys Ocean entered as xenoliths in a Miocenic diatreme, hence brought to the surface, in the Hyblean Plateau (Sicily). Some xenoliths consist of strongly serpentinized ultramafic rocks bearing blebs of abiotic organic matter, where clusters of amorphous carbon nanoparticles, including nanodiamonds, are immersed. Such an occurrence conjures up established hypotheses that diamond surfaces are suitable catalytic platforms stimulating the assemblage of complex bio-organic molecules relevant to the emergence of life on Earth. The appearance of bio-organic molecules under primitive Earth conditions is one of the major unsolved questions on the origin of life. Here we report new micro-Raman spectra on blebs of abiotic organic matter from a selected xenolith. Diamond bands were related to hydrogenated nanocrystalline diamonds, with size of nearly 1–1.6 ​nm, formed from organics at low pressures and temperatures. In particular, diamond surfaces can give rise to crystalline interfacial water layers that may have played a fundamental role in the early biosphere evolution as a good medium for rapidly transporting positive charges in the form of hydrated protons. Nowadays, proton gradients in alkaline hydrothermal vents along oceanic ridges are generally viewed as key pre-biotic factors. In general, serpentinites span the entire geological record, including prebiotic times. These hydrous ultramafic rocks often display evidence of abiotic carbon species, both organic and inorganic, including nanodiamonds, being also capable to give rise to chemiosmotic processes and proton gradients necessary to the organisms, such as the "Last Universal Common Ancestor" (LUCA), in the prebiotic Earth. Image 1 • Nanodiamonds and abiotic organics coexist in a serpentinite xenolith from Sicily. • Carbon clusters record a hydrothermal history in sub-seafloor setting. • Diamond surface is an effective catalyst of fundamental proto-biochemical reactions. • Complex prebiotic compounds can be formed on diamond-bearing carbon clusters. [ABSTRACT FROM AUTHOR]

Abiogenesis is the proposed process through which inanimate matter eventually led to life on earth. As a research area, the issue is certainly loaded with fodder for debate and philosophical and ideological disagreement about what life is and how it came to be. Dealing with the origin of life (OoL) obviously has the potential to tread into spiritual and religious grounds for both scientists interested in this area but also for the public at large when any debate about "where did we come from?" arises. However, it is not just the general public that struggles with balancing religious and spiritual explanations for how people came into being with scientific evidence. As we will show, there is a lively debate among OoL researchers about a similar set of scientific facts pointing to the intervention of a transcendent designer or such an idea being incompatible with science generally. Furthermore, we note that much of this debate is centered around the concepts of ontological and methodological materialism. While we make no claims about resolving or contributing meaningfully to the debate it is worth pointing out, especially to outside observers, that such a debate is in fact alive and well among OoL researchers. Thus, it is certainly possible for OoL researchers to view abiogenesis as an atheistic endeavor and many do. However, atheism is not a requirement to believe that abiogenesis played a role in the OoL as many scientists view such discoveries as a "mark of the Creator" as opposed to merely an idea that life must have come from inanimate matter. [ABSTRACT FROM AUTHOR]

Intracellular potassium concentrations, [K+], are high in all types of living cells, but the origins of this K+ are unknown. The simplest hypothesis is that life emerged in an environment that was high in K+. One such environment is the spaces between the sheets of the clay mineral mica. The best mica for life’s origins is the black mica, biotite, because it has a high content of Mg++ and because it has iron in various oxidation states. Life also has many of the characteristics of the environment between mica sheets, giving further support for the possibility that mica was the substrate on and within which life emerged. Here, a scenario for life’s origins is presented, in which the necessary processes and components for life arise in niches between mica sheets; vesicle membranes encapsulate these processes and components; the resulting vesicles fuse, forming protocells; and eventually, all of the necessary components and processes are encapsulated within individual cells, some of which survive to seed the early Earth with life. This paper presents three new foci for the hypothesis of life’s origins between mica sheets: (1) that potassium is essential for life’s origins on Earth; (2) that biotite mica has advantages over muscovite mica; and (3) that micaceous clay is a better environment than isolated mica for life’s origins.

Ernst Haeckel (1834–1919) is most recalled in the history of biology for his Recapitulation Theory and the allegedly fudged illustrations of embryos that he presented in support of that case. Less well known is his contribution to abiogenesis theory, which he incorporated into evolutionary theory. In so doing, Haeckel, a vitriolic atheist, was instrumental in inserting atheism into the evolutionary mindset. While anti-evolution propaganda commonly makes Darwin out to be the villain of the piece, the association of evolution in the broad sense of the word with atheism arises more from the Haeckelian legacy than from Darwin's initially conciliatory deism or Huxley's non-committal agnosticism. [ABSTRACT FROM AUTHOR]

Life is the urge for perpetuation and cancer as the agent of disorder is the force that drives this urge in the direction of unrestrained proliferation. The oncovirus strains like HPV and HCV are as old as life itself from its initial incipient stages and the evolution of such viruses has determined the course of evolution of species from within in a bottom-up manner purely through this urge for unrestrained proliferation. The cosmic ordering principle(COP) acts in the direction of arresting the increase of disorder (cancer) by evolving various cancer suppression or evasion mechanisms and thus both contribute to the evolution of all life. [ABSTRACT FROM AUTHOR]

Theoretical and experimental work has been conducted about possible prebiotic syntheses of cysteine. Activated derivatives of this amino acid can oligomerize and polymerize to afford various poly‐thiazolines and cysteine‐rich chains. [ABSTRACT FROM AUTHOR]

Evolution requires self-replication. But, what was the very first self-replicator directly ancestral to all life? The currently favoured RNA World theory assigns this role to RNA alone but suffers from a number of seemingly intractable problems. Instead, we suggest that the self-replicator consisted of both peptides and nucleic acid strands. Such a nucleopeptide replicator is more feasible both in the light of the replication machinery currently found in cells and the complexity of the evolutionary path required to reach them. Recent theoretical and mathematical work supports this idea and provide a blueprint for future investigations. The first ancestor to all life was a self-replicating entity capable of evolving but must have been much simpler than a cell; that is, a molecular replicator. Recent work on RNA polymerase ribozymes supports the view that the molecular replicator was made of RNA, and no other molecule was required (the RNA World). The RNA World is challenged by the fact that a self-replicating RNA polymerase ribozyme has yet to be demonstrated and that little evidence for its existence is seen in life today as well as problems in how the transition from RNA-only to RNA–protein world could have occurred. A molecular replicator with two components –RNA and peptide – overcomes these problems and may be a better fit. [ABSTRACT FROM AUTHOR]