Extremophiles may be irrelevant to the origin of life

Chapter 9: Life as We Don't Know It

While Earth contains the only known example of life in the universe, it is possible that life elsewhere is fundamentally different from what we are familiar with. There is an increased recognition in the astrobiology community that the search for life should steer away from terran-specific biosignatures to those that are more inclusive to all life-forms. To start exploring the space of possibilities that life could occupy, we can try to dissociate life from the chemistry that composes it on Earth by envisioning how different life elsewhere could be in composition, lifestyle, medium, and form, and by exploring how the general principles that govern living systems on Earth might be found in different forms and environments across the Solar System. Exotic life-forms could exist on Mars or Venus, or icy moons like Europa and Enceladus, or even as a shadow biosphere on Earth. New perspectives on agnostic biosignature detection have also begun to emerge, allowing for a broader and more inclusive approach to seeking exotic life with unknown chemistry that is distinct from life as we know it on Earth.

An open source computational workflow for the discovery of autocatalytic networks in abiotic reactions

A central question in origins of life research is how non-entailed chemical processes, which simply dissipate chemical energy because they can do so due to immediate reaction kinetics and thermodynamics, enabled the origin of highly-entailed ones, in which concatenated kinetically and thermodynamically favorable processes enhanced some processes over others. Some degree of molecular complexity likely had to be supplied by environmental processes to produce entailed self-replicating processes. The origin of entailment, therefore, must connect to fundamental chemistry that builds molecular complexity. We present here an open-source chemoinformatic workflow to model abiological chemistry to discover such entailment. This pipeline automates generation of chemical reaction networks and their analysis to discover novel compounds and autocatalytic processes. We demonstrate this pipeline's capabilities against a well-studied model system by vetting it against experimental data. This workflow can enable rapid identification of products of complex chemistries and their underlying synthetic relationships to help identify autocatalysis, and potentially self-organization, in such systems. The algorithms used in this study are open-source and reconfigurable by other user-developed workflows.

Prebiotic oligomerization and self-assembly of structurally diverse xenobiological monomers

Prebiotic chemists often study how modern biopolymers, e.g., peptides and nucleic acids, could have originated in the primitive environment, though most contemporary biomonomers don't spontaneously oligomerize under mild conditions without activation or catalysis. However, life may not have originated using the same monomeric components that it does presently. There may be numerous non-biological (or "xenobiological") monomer types that were prebiotically abundant and capable of facile oligomerization and self-assembly. Many modern biopolymers degrade abiotically preferentially via processes which produce thermodynamically stable ring structures, e.g. diketopiperazines in the case of proteins and 2', 3'-cyclic nucleotide monophosphates in the case of RNA. This weakness is overcome in modern biological systems by kinetic control, but this need not have been the case for primitive systems. We explored here the oligomerization of a structurally diverse set of prebiotically plausible xenobiological monomers, which can hydrolytically interconvert between cyclic and acyclic forms, alone or in the presence of glycine under moderate temperature drying conditions. These monomers included various lactones, lactams and a thiolactone, which varied markedly in their stability, propensity to oligomerize and apparent modes of initiation, and the oligomeric products of some of these formed self-organized microscopic structures which may be relevant to protocell formation.

Chemistry of Abiotic Nucleotide Synthesis

The chemistry of abiotic nucleotide synthesis of RNA and DNA in the context of their prebiotic origins on early earth is a continuing challenge. How did (or how can) the nucleotides form and assemble from the small molecule inventories and under conditions that prevailed on early earth 3.5-4 billion years ago? This review provides a background and up-to-date progress that will allow the reader to judge where the field stands currently and what remains to be achieved. We start with a brief primer on the biological synthesis of nucleotides, followed by an extensive focus on the prebiotic formation of the components of nucleotides-either via the synthesis of ribose and the canonical nucleobases and then joining them together or by building both the conjoined sugar and nucleobase, part-by-part-toward the ultimate goal of forming RNA and DNA by polymerization. The review will emphasize that there are-and will continue to be-many more questions than answers from the synthetic, mechanistic, and analytical perspectives. We wrap up the review with a cautionary note in this context about coming to conclusions as to whether the problem of chemistry of prebiotic nucleotide synthesis has been solved.

Deciphering Biosignatures in Planetary Contexts

Microbial life permeates Earth's critical zone and has likely inhabited nearly all our planet's surface and near subsurface since before the beginning of the sedimentary rock record. Given the vast time that Earth has been teeming with life, do astrobiologists truly understand what geological features untouched by biological processes would look like? In the search for extraterrestrial life in the Universe, it is critical to determine what constitutes a biosignature across multiple scales, and how this compares with "abiosignatures" formed by nonliving processes. Developing standards for abiotic and biotic characteristics would provide quantitative metrics for comparison across different data types and observational time frames. The evidence for life detection falls into three categories of biosignatures: (1) substances, such as elemental abundances, isotopes, molecules, allotropes, enantiomers, minerals, and their associated properties; (2) objects that are physical features such as mats, fossils including trace-fossils and microbialites (stromatolites), and concretions; and (3) patterns, such as physical three-dimensional or conceptual n-dimensional relationships of physical or chemical phenomena, including patterns of intermolecular abundances of organic homologues, and patterns of stable isotopic abundances between and within compounds. Five key challenges that warrant future exploration by the astrobiology community include the following: (1) examining phenomena at the "right" spatial scales because biosignatures may elude us if not examined with the appropriate instrumentation or modeling approach at that specific scale; (2) identifying the precise context across multiple spatial and temporal scales to understand how tangible biosignatures may or may not be preserved; (3) increasing capability to mine big data sets to reveal relationships, for example, how Earth's mineral diversity may have evolved in conjunction with life; (4) leveraging cyberinfrastructure for data management of biosignature types, characteristics, and classifications; and (5) using three-dimensional to n-D representations of biotic and abiotic models overlain on multiple overlapping spatial and temporal relationships to provide new insights.

Astrovirology, Astrobiology, Artificial Intelligence: Extra-Solar System Investigations

This chapter attempts to encompass and tackle a large problem in Astrovirology and Astrobiology. There is a huge anthropomorphic prejudice that although life is unlikely, the just-right Goldilocks terrestrial conditions mean that the just-right balance of minerals and basic small molecules inevitably result in life as we know it throughout our solar system, galaxy, and the rest of the universe. Moreover, when such conditions on planets such as ours may not be quite right for the origin of life, it is popularly opined that asteroids and comets magically produce life or at the very least, the important, if not crucial components of terrestrial life so that life then blooms, when their fragments cruise the solar system, stars, and galaxies, and plummet onto appropriately bedecked planets and moons.

It is no longer extraordinary to detect extraterrestrial solar systems. Moreover, since extra-solar system space exploration has commenced, this provides the problem of detecting life with enhanced achievability. Small organisms, which replicate outside of a living cell or host, would not be catalogued as viruses. How about viruses that cohabit with life? On the Earth, viruses are a major, if underestimated, condition of life – will that be the case elsewhere? Detection of extra-solar system viruses, if they exist, requires finding life, since viruses necessitate life to replicate. (It should be noted, though, that viruses could be detected through various types of portable ultra-microscopes, including Electron Microscopes (EM) (scanning and transmission) as well as Atomic Force Microscopes (AFM).) However, extra-solar system detection of life does not oblige that viruses exist ubiquitously. Viruses are important potential components of biospheres because of their multiple interactions and influence on evolution, although viruses are small and obligatory parasitic. In addition, nanotechnology – living or replicating nano-synthetic machine organisms might also be present out there, and require consideration as well. An imposing caveat is that, if found, could some extraterrestrial viruses and synthetic nanotechnological microorganisms infect humans?

Possibly, intelligence and cognition may at times be contemporaneous with life. Concomitantly, life and viruses that may be detected, could well be impacted upon by intelligences existing on such exoplanets (and vice versa). Coming to an understanding of the plurality of extraterrestrial intelligence is an optimal objective, in order to avoid causing harm on exoplanets, as well as avoiding conflict and possible human devastation. This is especially the case if we encounter greatly advanced galactic-level civilizations, compared to terrestrial civilizations. Their machine and bionic technologies on the Dyson engineering civilization scale may be prominently superior to ours; their biological expertise may be similarly critically radical. For example, they may use viruses for purposes for which we are barely aware, and which could be utterly deadly for humans.

A series of steps is being taken in space exploration. Scientists hypothesize and claim that types of life may be near the Earth, in the solar system, and outside the solar system, similar to ours in the sense that only such conditions, Goldilocks conditions, are key sine qua non requirements, based on our terrestrial chemistry and biochemistry. If detected within the solar system, will life or its remnants resemble terrestrial life? Outside the solar system a similar chauvinism exists, although the likelihood for life, in any event, remains probably low, according to more cautious approaches to the problem. The study of our solar system includes planets, asteroids, comets, and other planetesimals that have been in overall contiguity during several billion years; anthropomorphisms claims life consequently has been developing along terrestrial-type mechanisms. However, a non-anthropomorphic view would surmise, probably not, especially for extra-solar system locales. The prime warning and admonition in all these deliberations is the contamination and damage, which current and past practice and procedures has caused and continues, due to insufficient biocontainment concepts and technology to date.

Advances in the development of robotics, artificial intelligence (AI), and high capacity ultrafast quantum computers (QC) greatly enhance the sophisticated control and logical development of extra-solar system studies. Consequently, future long-range manned space exploration seems unwarranted. Clearly, reduced dangers to human health and safety, will result from the use of intelligent machine-based investigations and besides, with increased cost-effectiveness. Space exploration comes at great cost to humanity as a whole and utilizes global resources. Consequently, appropriate organizational measures and planning/cooperation need to be in place. Moreover, the bottom line is that despite all the slogans and claims, there have been next to no financial benefits to our planet as a whole. Such financial and heedless difficulties need to be addressed, the sooner the better. In addition, prior to exposure to exoplanetary life, deep understanding of the problems of infectious diseases and immune dysfunction risks are needed. In addition, global efforts should avoid serendipity and stochasticity as this work should be directed with long-term organization, commitment, scientific, and technological methodology. This chapter briefly reviews such questions assuming a new paradigm for oversight of extrasolar system viral investigations including intelligence and life. Finances are included as an essential adjunct.

Subsumed complexity: abiogenesis as a by-product of complex energy transduction

The origins of life bring into stark relief the inadequacy of our current synthesis of thermodynamic, chemical, physical and information theory to predict the conditions under which complex, living states of organic matter can arise. Origins research has traditionally proceeded under an array of implicit or explicit guiding principles in lieu of a universal formalism for abiogenesis. Within the framework of a new guiding principle for prebiotic chemistry called subsumed complexity, organic compounds are viewed as by-products of energy transduction phenomena at different scales (subatomic, atomic, molecular and polymeric) that retain energy in the form of bonds that inhibit energy from reaching the ground state. There is evidence for an emergent level of complexity that is overlooked in most conceptualizations of abiogenesis that arises from populations of compounds formed from atomic energy input. We posit that different forms of energy input can exhibit different degrees of dissipation complexity within an identical chemical medium. By extension, the maximum capacity for organic chemical complexification across molecular and macromolecular scales subsumes, rather than emerges from, the underlying complexity of energy transduction processes that drive their production and modification.This article is part of the themed issue 'Reconceptualizing the origins of life'.

The Abiotic Chemistry of Thiolated Acetate Derivatives and the Origin of Life

Thioesters and thioacetic acid (TAA) have been invoked as key reagents for the origin of life as activated forms of acetate analogous to acetyl-CoA. These species could have served as high-energy group-transfer reagents and allowed carbon insertions to form higher molecular weight compounds such as pyruvate. The apparent antiquity of the Wood-Ljungdahl CO2 fixation pathway and its presence in organisms which inhabit hydrothermal (HT) environments has also led to suggestions that there may be a connection between the abiotic chemistry of compounds similar to TAA and the origins of metabolism. These compounds' apparent chemical simplicity has made their prebiotic availability assumed, however, although the kinetic behavior and thermochemical properties of TAA and analogous esters have been preliminarily explored in other contexts, the geochemical relevance of these compounds merits further evaluation. Therefore, the chemical behavior of the simplest thiolated acetic acid derivatives, TAA and methylthioacetate (MTA) were explored here. Using laboratory measurements, literature data, and thermochemical models, we examine the plausibility of the accumulation of these compounds in various geological settings. Due to the high free energy change of their hydrolysis and corresponding low equilibrium constants, it is unlikely that these species could have accumulated abiotically to any significant extant.

Relevance and Significance of Extraterrestrial Abiological Hydrocarbon Chemistry

Astrophysical observations show similarity of observed abiological "organics"-i.e., hydrocarbons, their derivatives, and ions (carbocations and carbanions)-with studied terrestrial chemistry. Their formation pathways, their related extraterrestrial hydrocarbon chemistry originating from carbon and other elements after the Big Bang, their parent hydrocarbon and derivative (methane and methanol, respectively), and transportation of derived building blocks of life by meteorites or comets to planet Earth are discussed in this Perspective. Their subsequent evolution on Earth under favorable "Goldilocks" conditions led to more complex molecules and biological systems, and eventually to humans. The relevance and significance of extraterrestrial hydrocarbon chemistry to the limits of science in relation to the physical aspects of evolution on our planet Earth are also discussed.

Prebiotic chemistry: geochemical context and reaction screening

The origin of life on Earth is widely believed to have required the reactions of organic compounds and their self- and/or environmental organization. What those compounds were remains open to debate, as do the environment in and process or processes by which they became organized. Prebiotic chemistry is the systematic organized study of these phenomena. It is difficult to study poorly defined phenomena, and research has focused on producing compounds and structures familiar to contemporary biochemistry, which may or may not have been crucial for the origin of life. Given our ignorance, it may be instructive to explore the extreme regions of known and future investigations of prebiotic chemistry, where reactions fail, that will relate them to or exclude them from plausible environments where they could occur. Come critical parameters which most deserve investigation are discussed.

Is boron a prebiotic element? A mini-review of the essentiality of boron for the appearance of life on earth

Boron is probably a prebiotic element with special importance in the so-called "sugars world". Boron is not present on Earth in its elemental form. It is found only in compounds, e.g., borax, boric acid, kernite, ulexite, colemanite and other borates. Volcanic spring waters sometimes contain boron-based acids (e.g., boric, metaboric, tetraboric and pyroboric acid). Borates influence the formation of ribofuranose from formaldehyde that feeds the "prebiotic metabolic cycle". The importance of boron in the living world is strongly related to its implications in the prebiotic origins of genetic material; consequently, we believe that throughout the evolution of life, the primary role of boron has been to provide thermal and chemical stability in hostile environments. The complexation of boric acid and borates with organic cis-diols remains the most probable chemical mechanism for the role of this element in the evolution of the living world. Because borates can stabilize ribose and form borate ester nucleotides, boron may have provided an essential contribution to the "pre-RNA world".

The Very Early Stages of Biological Evolution and the Nature of the Last Common Ancestor of the Three Major Cell Domains

Quantitative estimates of the gene complement of the last common ancestor of all extant organisms, that is, the cenancestor, may be hindered by ancient horizontal gene transfer events and polyphyletic gene losses, as well as by biases in genome databases and methodological artifacts. Nevertheless, most reports agree that the last common ancestor resembled extant prokaryotes. A significant number of the highly conserved genes are sequences involved in the synthesis, degradation, and binding of RNA, including transcription and translation. Although the gene complement of the cenancestor includes sequences that may have originated in different epochs, the extraordinary conservation of RNA-related sequences supports the hypothesis that the last common ancestor was an evolutionary outcome of the so-called RNA/protein world. The available evidence suggests that the cenancestor was not a hyperthermophile, but it is currently not possible to assess its ecological niche or its mode of energy acquisition and carbon sources.

The astrobiology primer: an outline of general knowledge--version 1, 2006

The Astrobiology Primer has been created as a reference tool for those who are interested in the interdisciplinary field of astrobiology. The field incorporates many diverse research endeavors, but it is our hope that this slim volume will present the reader with all he or she needs to know to become involved and to understand, at least at a fundamental level, the state of the art. Each section includes a brief overview of a topic and a short list of readable and important literature for those interested in deeper knowledge. Because of the great diversity of material, each section was written by a different author with a different expertise. Contributors, authors, and editors are listed at the beginning, along with a list of those chapters and sections for which they were responsible. We are deeply indebted to the NASA Astrobiology Institute (NAI), in particular to Estelle Dodson, David Morrison, Ed Goolish, Krisstina Wilmoth, and Rose Grymes for their continued enthusiasm and support. The Primer came about in large part because of NAI support for graduate student research, collaboration, and inclusion as well as direct funding. We have entitled the Primer version 1 in hope that it will be only the first in a series, whose future volumes will be produced every 3-5 years. This way we can insure that the Primer keeps up with the current state of research. We hope that it will be a great resource for anyone trying to stay abreast of an ever-changing field.

Small molecule interactions were central to the origin of life

Many scientists believe life began with the spontaneous formation of a replicator. This idea has been supported by "prebiotic" syntheses carried out by chemists using modern apparatus and purified reagents. The probability that such reactions would take place spontaneously on the early Earth is minute. These points are illustrated here by considering the often cited oligomerization of activated RNA components by clay minerals. A more likely alternative for the origin of life is one in which a collection of small organic molecules multiply their numbers through catalyzed reaction cycles, driven by a flow of available free energy. Although a number of possible systems of this type have been discussed, no experimental demonstration has been made. The inclusion of a "driver" reaction, directly coupled to the energy source, may lead to a solution.

Experimentally tracing the key steps in the origin of life: The aromatic world

Life is generally believed to emerge on Earth, to be at least functionally similar to life as we know it today, and to be much simpler than modern life. Although minimal life is notoriously difficult to define, a molecular system can be considered alive if it turns resources into building blocks, replicates, and evolves. Primitive life may have consisted of a compartmentalized genetic system coupled with an energy-harvesting mechanism. How prebiotic building blocks self-assemble and transform themselves into a minimal living system can be broken into two questions: (1) How can prebiotic building blocks form containers, metabolic networks, and informational polymers? (2) How can these three components cooperatively organize to form a protocell that satisfies the minimal requirements for a living system? The functional integration of these components is a difficult puzzle that requires cooperation among all the aspects of protocell assembly: starting material, reaction mechanisms, thermodynamics, and the integration of the inheritance, metabolism, and container functionalities. Protocells may have been self-assembled from components different from those used in modern biochemistry. We propose that assemblies based on aromatic hydrocarbons may have been the most abundant flexible and stable organic materials on the primitive Earth and discuss their possible integration into a minimal life form. In this paper we attempt to combine current knowledge of the composition of prebiotic organic material of extraterrestrial and terrestrial origin, and put these in the context of possible prebiotic scenarios. We also describe laboratory experiments that might help clarify the transition from nonliving to living matter using aromatic material. This paper presents an interdisciplinary approach to interface state of the art knowledge in astrochemistry, prebiotic chemistry, and artificial life research.

Extreme life on Earth—past, present and possibly beyond

Life may have been present on Earth since about 3.8 billion years ago or earlier. Multidisciplinary research, especially on the paleobiology and evolution of early microorganisms on Earth and the microbiology of extremophiles in the Earth's environments and under space conditions, enables the defining of strategies for the detection of potential extraterrestrial life by determining biosignatures and the environmental envelope of life.

A minimal estimate for the gene content of the last universal common ancestor--exobiology from a terrestrial perspective

Using an algorithm for ancestral state inference of gene content, given a large number of extant genome sequences and a phylogenetic tree, we aim to reconstruct the gene content of the last universal common ancestor (LUCA), a hypothetical life form that presumably was the progenitor of the three domains of life. The method allows for gene loss, previously found to be a major factor in shaping gene content, and thus the estimate of LUCA's gene content appears to be substantially higher than that proposed previously, with a typical number of over 1000 gene families, of which more than 90% are also functionally characterized. More precisely, when only prokaryotes are considered, the number varies between 1006 and 1189 gene families while when eukaryotes are also included, this number increases to between 1344 and 1529 families depending on the underlying phylogenetic tree. Therefore, the common belief that the hypothetical genome of LUCA should resemble those of the smallest extant genomes of obligate parasites is not supported by recent advances in computational genomics. Instead, a fairly complex genome similar to those of free-living prokaryotes, with a variety of functional capabilities including metabolic transformation, information processing, membrane/transport proteins and complex regulation, shared between the three domains of life, emerges as the most likely progenitor of life on Earth, with profound repercussions for planetary exploration and exobiology.

Raman spectroscopy in astrobiology

Raman spectroscopy is proposed as a valuable analytical technique for planetary exploration because it is sensitive to organic and inorganic compounds and able to unambiguously identify key spectral markers in a mixture of biological and geological components; furthermore, sample manipulation is not required and any size of sample can be studied without chemical or mechanical pretreatment. NASA and ESA are considering the adoption of miniaturised Raman spectrometers for inclusion in suites of analytical instrumentation to be placed on robotic landers on Mars in the near future to search for extinct or extant life signals. In this paper we review the advantages and limitations of Raman spectroscopy for the analysis of complex specimens with relevance to the detection of bio- and geomarkers in extremophilic organisms which are considered to be terrestrial analogues of possible extraterrestial life that could have developed on planetary surfaces.