A probabilistic framework for identifying biosignatures using Pathway Complexity

Molecular complexity as a driving force for the advancement of organic synthesis

The generation of molecular complexity is a primary goal in the field of synthetic chemistry. In the context of retrosynthetic analysis, the concept of molecular complexity is central to identifying productive disconnections and the development of efficient total syntheses. However, this field-defining concept is frequently invoked on an intuitive basis without precise definition or appreciation of its subtleties. Methods for quantifying molecular complexity could prove useful for characterizing the state of synthesis in a more rigorous, reliable and reproducible fashion. As a first step to evaluating the importance of these methods to the state of the field, here we present our perspective on the development of molecular complexity quantification and its implications for chemical synthesis. The extension and application of these methods beyond computer-aided synthesis planning and medicinal chemistry to the traditional practice of 'complex molecule' synthesis could have the potential to unearth new opportunities and more efficient approaches for synthesis.

Autocatalytic Sets and Assembly Theory: A Toy Model Perspective

Assembly Theory provides a promising framework to explain the complexity of systems such as molecular structures and the origins of life, with broad applicability across various disciplines. In this study, we explore and consolidate different aspects of Assembly Theory by introducing a simplified Toy Model to simulate the autocatalytic formation of complex structures. This model abstracts the molecular formation process, focusing on the probabilistic control of catalysis rather than the intricate interactions found in organic chemistry. We establish a connection between probabilistic catalysis events and key principles of Assembly Theory, particularly the probability of a possible construction path in the formation of a complex object, and examine how the assembly of complex objects is impacted by the presence of autocatalysis. Our findings suggest that this presence of autocatalysis tends to favor longer consecutive construction sequences in environments with a low probability of catalysis, while this bias diminishes in environments with higher catalysis probabilities, highlighting the significant influence of environmental factors on the assembly of complex structures.

On the salient limitations of the methods of assembly theory and their classification of molecular biosignatures

We demonstrate that the assembly pathway method underlying assembly theory (AT) is an encoding scheme widely used by popular statistical compression algorithms. We show that in all cases (synthetic or natural) AT performs similarly to other simple coding schemes and underperforms compared to system-related indexes based upon algorithmic probability that take into account statistical repetitions but also the likelihood of other computable patterns. Our results imply that the assembly index does not offer substantial improvements over existing methods, including traditional statistical ones, and imply that the separation between living and non-living compounds following these methods has been reported before.

Open-ended versus bounded evolution: Mineral evolution as a case study

To what extent are naturally evolving systems limited in their potential diversity (i.e. "bounded") versus unrestricted ("open-ended")? Minerals provide a quantitative model evolving system, with well-documented increases in mineral diversity through multiple stages of planetary evolution over billions of years. A recent framework that unifies behaviors of both biotic and abiotic evolving systems posits that all such systems are characterized by combinatorial richness subject to selection. In the case of minerals, combinatorial richness derives from the possible combinations of chemical elements coupled with permutations of their formulas' coefficients. Observed mineral species, which are selected for persistence through deep time, represent a miniscule fraction of all possible element configurations. Furthermore, this model predicts that as planetary systems evolve, stable minerals become an ever-smaller fraction of the "possibility space." A postulate is that "functional information," defined as the negative log2 of that fraction, must increase as a system evolves. We have tested this hypothesis for minerals by estimating the fraction of all possible chemical formulas observed from one stage of mineral evolution to the next, based on numbers of different essential elements and the maximum chemical formula complexity at each of nine chronological stages of mineral evolution. We find a monotonic increase in mineral functional information through these nine stages-a result consistent with the hypothesis. Furthermore, analysis of the chemical formulas of minerals demonstrates that the modern Earth may be approaching the maximum limit of functional information for natural mineral systems-a result demonstrating that mineral evolution is not open-ended.

Investigating and Quantifying Molecular Complexity Using Assembly Theory and Spectroscopy

Current approaches to evaluate molecular complexity use algorithmic complexity, rooted in computer science, and thus are not experimentally measurable. Directly evaluating molecular complexity could be used to study directed vs undirected processes in the creation of molecules, with potential applications in drug discovery, the origin of life, and artificial life. Assembly theory has been developed to quantify the complexity of a molecule by finding the shortest path to construct the molecule from building blocks, revealing its molecular assembly index (MA). In this study, we present an approach to rapidly infer the MA of molecules from spectroscopic measurements. We demonstrate that the MA can be experimentally measured by using three independent techniques: nuclear magnetic resonance (NMR), tandem mass spectrometry (MS/MS), and infrared spectroscopy (IR). By identifying and analyzing the number of absorbances in IR spectra, carbon resonances in NMR, or molecular fragments in tandem MS, the MA of an unknown molecule can be reliably estimated. This represents the first experimentally quantifiable approach to determining molecular assembly. This paves the way to use experimental techniques to explore the evolution of complex molecules as well as a unique marker of where an evolutionary process has been operating.

Minimizing Entropy and Complexity in Creative Production from Emergent Pragmatics to Action Semantics

New insights into intractable industrial challenges can be revealed by framing them in terms of natural science. One intractable industrial challenge is that creative production can be much more financially expensive and time consuming than standardized production. Creative products include a wide range of goods that have one or more original characteristics. The scaling up of creative production is hindered by high financial production costs and long production durations. In this paper, creative production is framed in terms of interactions between entropy and complexity during progressions from emergent pragmatics to action semantics. An analysis of interactions between entropy and complexity is provided that relates established practice in creative production to organizational survival in changing environments. The analysis in this paper is related to assembly theory, which is a recent theoretical development in natural science that addresses how open-ended generation of complex physical objects can emerge from selection in biology. Parallels between assembly practice in industrial production and assembly theory in natural science are explained through constructs that are common to both, such as assembly index. Overall, analyses reported in the paper reveal that interactions between entropy and complexity underlie intractable challenges in creative production, from the production of individual products to the survival of companies.

Assembly Theory: What It Does and What It Does Not Do

A recent publication in Nature has generated much heated discussion about evolution, its tendency towards increasing diversity and complexity, and its potential status above and beyond the known laws of fundamental physics. The argument at the heart of this controversy concerns assembly theory, a method to detect and quantify the influence of higher-level emergent causal constraints in computational worlds made of basic objects and their combinations. In this short essay, I briefly review the theory, its basic principles and potential applications. I then go on to critically examine its authors' assertions, concluding that assembly theory has merit but is not nearly as novel or revolutionary as claimed. It certainly does not provide any new explanation of biological evolution or natural selection, or a new grounding of biology in physics. In this regard, the presentation of the paper is starkly distorted by hype, which may explain some of the outrage it created.

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.

Molecular assembly indices of mineral heteropolyanions: some abiotic molecules are as complex as large biomolecules

Molecular assembly indices, which measure the number of unique sequential steps theoretically required to construct a three-dimensional molecule from its constituent atomic bonds, have been proposed as potential biosignatures. A central hypothesis of assembly theory is that any molecule with an assembly index ≥15 found in significant local concentrations represents an unambiguous sign of life. We show that abiotic molecule-like heteropolyanions, which assemble in aqueous solution as precursors to some mineral crystals, range in molecular assembly indices from 2 for H2CO3 or Si(OH)4 groups to as large as 21 for the most complex known molecule-like subunits in the rare minerals ewingite and ilmajokite. Therefore, values of molecular assembly indices ≥15 do not represent unambiguous biosignatures.

False Positives and the Challenge of Testing the Alien Hypothesis

The origin of life and the detection of alien life have historically been treated as separate scientific research problems. However, they are not strictly independent. Here, we discuss the need for a better integration of the sciences of life detection and origins of life. Framing these dual problems within the formalism of Bayesian hypothesis testing, we demonstrate via simple examples how high confidence in life detection claims require either (1) a strong prior hypothesis about the existence of life in a particular alien environment, or conversely, (2) signatures of life that are not susceptible to false positives. As a case study, we discuss the role of priors and hypothesis testing in recent results reporting potential detection of life in the venusian atmosphere and in the icy plumes of Enceladus. While many current leading biosignature candidates are subject to false positives because they are not definitive of life, our analyses demonstrate why it is necessary to shift focus to candidate signatures that are definitive. This indicates a necessity to develop methods that lack substantial false positives, by using observables for life that rely on prior hypotheses with strong theoretical and empirical support in identifying defining features of life. Abstract theories developed in pursuit of understanding universal features of life are more likely to be definitive and to apply to life-as-we-don't-know-it. We discuss Molecular Assembly theory as an example of such an observable which is applicable to life detection within the solar system. In the absence of alien examples these are best validated in origin of life experiments, substantiating the need for better integration between origins of life and biosignature science research communities. This leads to a conclusion that extraordinary claims in astrobiology (e.g., definitive detection of alien life) require extraordinary explanations, whereas the evidence itself could be quite ordinary.

Is There Such a Thing as a Biosignature?

The concept of a biosignature is widely used in astrobiology to suggest a link between some observation and a biological cause, given some context. The term itself has been defined and used in several ways in different parts of the scientific community involved in the search for past or present life on Earth and beyond. With the ongoing acceleration in the search for life in distant time and/or deep space, there is a need for clarity and accuracy in the formulation and reporting of claims. Here, we critically review the biosignature concept(s) and the associated nomenclature in light of several problems and ambiguities emphasized by recent works. One worry is that these terms and concepts may imply greater certainty than is usually justified by a rational interpretation of the data. A related worry is that terms such as "biosignature" may be inherently misleading, for example, because the divide between life and non-life-and their observable effects-is fuzzy. Another worry is that different parts of the multidisciplinary community may use non-equivalent or conflicting definitions and conceptions, leading to avoidable confusion. This review leads us to identify a number of pitfalls and to suggest how they can be circumvented. In general, we conclude that astrobiologists should exercise particular caution in deciding whether and how to use the concept of biosignature when thinking and communicating about habitability or life. Concepts and terms should be selected carefully and defined explicitly where appropriate. This would improve clarity and accuracy in the formulation of claims and subsequent technical and public communication about some of the most profound and important questions in science and society. With this objective in mind, we provide a checklist of questions that scientists and other interested parties should ask when assessing any reported detection of a "biosignature" to better understand exactly what is being claimed.

A robust, agnostic molecular biosignature based on machine learning

The search for definitive biosignatures-unambiguous markers of past or present life-is a central goal of paleobiology and astrobiology. We used pyrolysis-gas chromatography coupled to mass spectrometry to analyze chemically disparate samples, including living cells, geologically processed fossil organic material, carbon-rich meteorites, and laboratory-synthesized organic compounds and mixtures. Data from each sample were employed as training and test subsets for machine-learning methods, which resulted in a model that can identify the biogenicity of both contemporary and ancient geologically processed samples with ~90% accuracy. These machine-learning methods do not rely on precise compound identification: Rather, the relational aspects of chromatographic and mass peaks provide the needed information, which underscores this method's utility for detecting alien biology.

Solid-State Single-Molecule Sensing with the Electronic Life-Detection Instrument for Enceladus/Europa (ELIE)

Growing evidence of the potential habitability of Ocean Worlds across our solar system is motivating the advancement of technologies capable of detecting life as we know it-sharing a common ancestry or physicochemical origin with life on Earth-or don't know it, representing a distinct emergence of life different than our one known example. Here, we propose the Electronic Life-detection Instrument for Enceladus/Europa (ELIE), a solid-state single-molecule instrument payload that aims to search for life based on the detection of amino acids and informational polymers (IPs) at the parts per billion to trillion level. As a first proof-of-principle in a laboratory environment, we demonstrate the single-molecule detection of the amino acid L-proline at a 10 μM concentration in a compact system. Based on ELIE's solid-state quantum electronic tunneling sensing mechanism, we further propose the quantum property of the HOMO-LUMO gap (energy difference between a molecule's highest energy-occupied molecular orbital and lowest energy-unoccupied molecular orbital) as a novel metric to assess amino acid complexity. Finally, we assess the potential of ELIE to discriminate between abiotically and biotically derived α-amino acid abundance distributions to reduce the false positive risk for life detection. Nanogap technology can also be applied to the detection of nucleobases and short sequences of IPs such as, but not limited to, RNA and DNA. Future missions may utilize ELIE to target preserved biosignatures on the surface of Mars, extant life in its deep subsurface, or life or its biosignatures in a plume, surface, or subsurface of ice moons such as Enceladus or Europa. One-Sentence Summary: A solid-state nanogap can determine the abundance distribution of amino acids, detect nucleic acids, and shows potential for detecting life as we know it and life as we don't know it.

Organic Catalytic Activity as a Method for Agnostic Life Detection

An ideal life detection instrument would have high sensitivity but be insensitive to abiotic processes and would be capable of detecting life with alternate molecular structures. In this study, we propose that catalytic activity can be the basis of a nearly ideal life detection instrument. There are several advantages to catalysis as an agnostic life detection method. Demonstrating catalysis does not necessarily require culturing/growing the alien life and in fact may persist even in dead biomass for some time, and the amplification by catalysis is large even by minute amounts of catalysts and, hence, can be readily detected against abiotic background rates. In specific, we propose a hydrolytic catalysis detection instrument that could detect activity in samples of extraterrestrial organic material from unknown life. The instrument uses chromogenic assay-based detection of various hydrolytic catalytic activities, which are matched to corresponding artificial substrates having the same, chromogenic (preferably fluorescent) upon release, group; D- and L-enantiomers of these substrates can be used to also answer the question whether unknown life is chiral. Since catalysis is a time-proportional product-concentration amplification process, hydrolytic catalytic activity can be measured on a sample of even a minute size, and with instruments based on, for example, optofluidic chip technology.

An Overview of Lipid Biomarkers in Terrestrial Extreme Environments with Relevance for Mars Exploration

Lipid molecules are organic compounds, insoluble in water, and based on carbon-carbon chains that form an integral part of biological cell membranes. As such, lipids are ubiquitous in life on Earth, which is why they are considered useful biomarkers for life detection in terrestrial environments. These molecules display effective membrane-forming properties even under geochemically hostile conditions that challenge most of microbial life, which grants lipids a universal biomarker character suitable for life detection beyond Earth, where a putative biological membrane would also be required. What discriminates lipids from nucleic acids or proteins is their capacity to retain diagnostic information about their biological source in their recalcitrant hydrocarbon skeletons for thousands of millions of years, which is indispensable in the field of astrobiology given the time span that the geological ages of planetary bodies encompass. This work gathers studies that have employed lipid biomarker approaches for paleoenvironmental surveys and life detection purposes in terrestrial environments with extreme conditions: hydrothermal, hyperarid, hypersaline, and highly acidic, among others; all of which are analogous to current or past conditions on Mars. Although some of the compounds discussed in this review may be abiotically synthesized, we focus on those with a biological origin, namely lipid biomarkers. Therefore, along with appropriate complementary techniques such as bulk and compound-specific stable carbon isotope analysis, this work recapitulates and reevaluates the potential of lipid biomarkers as an additional, powerful tool to interrogate whether there is life on Mars, or if there ever was.

The hierarchical organization of autocatalytic reaction networks and its relevance to the origin of life

Prior work on abiogenesis, the emergence of life from non-life, suggests that it requires chemical reaction networks that contain self-amplifying motifs, namely, autocatalytic cores. However, little is known about how the presence of multiple autocatalytic cores might allow for the gradual accretion of complexity on the path to life. To explore this problem, we develop the concept of a seed-dependent autocatalytic system (SDAS), which is a subnetwork that can autocatalytically self-maintain given a flux of food, but cannot be initiated by food alone. Rather, initiation of SDASs requires the transient introduction of chemical "seeds." We show that, depending on the topological relationship of SDASs in a chemical reaction network, a food-driven system can accrete complexity in a historically contingent manner, governed by rare seeding events. We develop new algorithms for detecting and analyzing SDASs in chemical reaction databases and describe parallels between multi-SDAS networks and biological ecosystems. Applying our algorithms to both an abiotic reaction network and a biochemical one, each driven by a set of simple food chemicals, we detect SDASs that are organized as trophic tiers, of which the higher tier can be seeded by relatively simple chemicals if the lower tier is already activated. This indicates that sequential activation of trophically organized SDASs by seed chemicals that are not much more complex than what already exist could be a mechanism of gradual complexification from relatively simple abiotic reactions to more complex life-like systems. Interestingly, in both reaction networks, higher-tier SDASs include chemicals that might alter emergent features of chemical systems and could serve as early targets of selection. Our analysis provides computational tools for analyzing very large chemical/biochemical reaction networks and suggests new approaches to studying abiogenesis in the lab.

Ladderpath Approach: How Tinkering and Reuse Increase Complexity and Information

The notion of information and complexity are important concepts in many scientific fields such as molecular biology, evolutionary theory and exobiology. Many measures of these quantities are either difficult to compute, rely on the statistical notion of information, or can only be applied to strings. Based on assembly theory, we propose the notion of a ladderpath, which describes how an object can be decomposed into hierarchical structures using repetitive elements. From the ladderpath, two measures naturally emerge: the ladderpath-index and the order-index, which represent two axes of complexity. We show how the ladderpath approach can be applied to both strings and spatial patterns and argue that all systems that undergo evolution can be described as ladderpaths. Further, we discuss possible applications to human language and the origin of life. The ladderpath approach provides an alternative characterization of the information that is contained in a single object (or a system) and could aid in our understanding of evolving systems and the origin of life in particular.

Science Autonomy for Ocean Worlds Astrobiology: A Perspective

Astrobiology missions to ocean worlds in our solar system must overcome both scientific and technological challenges due to extreme temperature and radiation conditions, long communication times, and limited bandwidth. While such tools could not replace ground-based analysis by science and engineering teams, machine learning algorithms could enhance the science return of these missions through development of autonomous science capabilities. Examples of science autonomy include onboard data analysis and subsequent instrument optimization, data prioritization (for transmission), and real-time decision-making based on data analysis. Similar advances could be made to develop streamlined data processing software for rapid ground-based analyses. Here we discuss several ways machine learning and autonomy could be used for astrobiology missions, including landing site selection, prioritization and targeting of samples, classification of "features" (e.g., proposed biosignatures) and novelties (uncharacterized, "new" features, which may be of most interest to agnostic astrobiological investigations), and data transmission.

Lipid Profiles From Fresh Biofilms Along a Temperature Gradient on a Hydrothermal Stream at El Tatio (Chilean Andes), as a Proxy for the Interpretation of Past and Present Biomarkers Beyond Earth

Hydrothermal systems and their deposits are primary targets in the search for fossil evidence of life beyond Earth. However, to learn how to decode fossil biomarker records in ancient hydrothermal deposits, we must first be able to interpret unambiguously modern biosignatures, their distribution patterns, and their association with physicochemical factors. Here, we investigated the molecular and isotopic profile of microbial biomarkers along a thermal gradient (from 29 to 72°C) in a hot spring (labeled Cacao) from El Tatio, a geyser field in the Chilean Andes with abundant opaline silica deposits resembling the nodular and digitate structures discovered on Mars. As a molecular forensic approach, we focused on the analysis of lipid compounds bearing recognized resistance to degradation and the potential to reconstruct the paleobiology of an environment on a broader temporal scale than other, more labile, biomolecules. By exploiting the lipid biomarkers' potential to diagnose biological sources and carbon fixation pathways, we reconstructed the microbial community structure and its ecology along the Cacao hydrothermal transect. The taxonomic adscription of the lipid biomarkers was qualitatively corroborated with DNA sequencing analysis. The forensic capacity of the lipid biomarkers to identify biosources in fresh biofilms was validated down to the genus level for Roseiflexus, Chloroflexus, and Fischerella. We identified lipid biomarkers and DNA of several new cyanobacterial species in El Tatio and reported the first detection of Fischerella biomarkers at a temperature as high as 72°C. This, together with ecological peculiarities and the proportion of clades being characterized as unclassified, illustrates the ecological singularity of El Tatio and strengthens its astrobiological relevance. The Cacao hydrothermal ecosystem was defined by a succession of microbial communities and metabolic traits associated with a high- (72°C) to low-(29°C) temperature gradient that resembled the inferred metabolic sequence events from the 16S rRNA gene universal phylogenetic tree from thermophilic to anoxygenic photosynthetic species and oxygenic phototrophs. The locally calibrated DNA-validated lipidic profile in the Cacao biofilms provided a modern (molecular and isotopic) end member to facilitate the recognition of past biosources and metabolisms from altered biomarkers records in ancient silica deposits at El Tatio analogous to Martian opaline silica structures.

Formalising the Pathways to Life Using Assembly Spaces

Assembly theory (referred to in prior works as pathway assembly) has been developed to explore the extrinsic information required to distinguish a given object from a random ensemble. In prior work, we explored the key concepts relating to deconstructing an object into its irreducible parts and then evaluating the minimum number of steps required to rebuild it, allowing for the reuse of constructed sub-objects. We have also explored the application of this approach to molecules, as molecular assembly, and how molecular assembly can be inferred experimentally and used for life detection. In this article, we formalise the core assembly concepts mathematically in terms of assembly spaces and related concepts and determine bounds on the assembly index. We explore examples of constructing assembly spaces for mathematical and physical objects and propose that objects with a high assembly index can be uniquely identified as those that must have been produced using directed biological or technological processes rather than purely random processes, thereby defining a new scale of aliveness. We think this approach is needed to help identify the new physical and chemical laws needed to understand what life is, by quantifying what life does.

Science Objectives for Flagship-Class Mission Concepts for the Search for Evidence of Life at Enceladus

Cassini revealed that Saturn's Moon Enceladus hosts a subsurface ocean that meets the accepted criteria for habitability with bio-essential elements and compounds, liquid water, and energy sources available in the environment. Whether these conditions are sufficiently abundant and collocated to support life remains unknown and cannot be determined from Cassini data. However, thanks to the plume of oceanic material emanating from Enceladus' south pole, a new mission to Enceladus could search for evidence of life without having to descend through kilometers of ice. In this article, we outline the science motivations for such a successor to Cassini, choosing the primary science goal to be determining whether Enceladus is inhabited and assuming a resource level equivalent to NASA's Flagship-class missions. We selected a set of potential biosignature measurements that are complementary and orthogonal to build a robust case for any life detection result. This result would be further informed by quantifications of the habitability of the environment through geochemical and geophysical investigations into the ocean and ice shell crust. This study demonstrates that Enceladus' plume offers an unparalleled opportunity for in situ exploration of an Ocean World and that the planetary science and astrobiology community is well equipped to take full advantage of it in the coming decades.

Determining the "Biosignature Threshold" for Life Detection on Biotic, Abiotic, or Prebiotic Worlds

The field of prebiotic chemistry has demonstrated that complex organic chemical systems that exhibit various life-like properties can be produced abiotically in the laboratory. Understanding these chemical systems is important for astrobiology and life detection since we do not know the extent to which prebiotic chemistry might exist or have existed on other worlds. Nor do we know what signatures are diagnostic of an extant or "failed" prebiotic system. On Earth, biology has suppressed most abiotic organic chemistry and overprints geologic records of prebiotic chemistry; therefore, it is difficult to validate whether chemical signatures from future planetary missions are remnant or extant prebiotic systems. The "biosignature threshold" between whether a chemical signature is more likely to be produced by abiotic versus biotic chemistry on a given world could vary significantly, depending on the particular environment, and could change over time, especially if life were to emerge and diversify on that world. To interpret organic signatures detected during a planetary mission, we advocate for (1) gaining a more complete understanding of prebiotic/abiotic chemical possibilities in diverse planetary environments and (2) involving experimental prebiotic samples as analogues when generating comparison libraries for "life-detection" mission instruments.

Exploring and mapping chemical space with molecular assembly trees

The rule-based search of chemical space can generate an almost infinite number of molecules, but exploration of known molecules as a function of the minimum number of steps needed to build up the target graphs promises to uncover new motifs and transformations. Assembly theory is an approach to compare the intrinsic complexity and properties of molecules by the minimum number of steps needed to build up the target graphs. Here, we apply this approach to prebiotic chemistry, gene sequences, plasticizers, and opiates. This allows us to explore molecules connected to the assembly tree, rather than the entire space of molecules possible. Last, by developing a reassembly method, based on assembly trees, we found that in the case of the opiates, a new set of drug candidates could be generated that would not be accessible via conventional fragment-based drug design, thereby demonstrating how this approach might find application in drug discovery.

A Proposed Geobiology-Driven Nomenclature for Astrobiological In Situ Observations and Sample Analyses

As the exploration of Mars and other worlds for signs of life has increased, the need for a common nomenclature and consensus has become significantly important for proper identification of nonterrestrial/non-Earth biology, biogenic structures, and chemical processes generated from biological processes. The fact that Earth is our single data point for all life, diversity, and evolution means that there is an inherent bias toward life as we know it through our own planet's history. The search for life "as we don't know it" then brings this bias forward to decision-making regarding mission instruments and payloads. Understandably, this leads to several top-level scientific, theoretical, and philosophical questions regarding the definition of life and what it means for future life detection missions. How can we decide on how and where to detect known and unknown signs of life with a single biased data point? What features could act as universal biosignatures that support Darwinian evolution in the geological context of nonterrestrial time lines? The purpose of this article is to generate an improved nomenclature for terrestrial features that have mineral/microbial interactions within structures and to confirm which features can only exist from life (biotic), features that are modified by biological processes (biogenic), features that life does not affect (abiotic), and properties that can exist or not regardless of the presence of biology (abiogenic). These four categories are critical in understanding and deciphering future returned samples from Mars, signs of potential extinct/ancient and extant life on Mars, and in situ analyses from ocean worlds to distinguish and separate what physical structures and chemical patterns are due to life and which are not. Moreover, we discuss hypothetical detection and preservation environments for extant and extinct life, respectively. These proposed environments will take into account independent active and ancient in situ detection prospects by using previous planetary exploration studies and discuss the geobiological implications within an astrobiological context.

The Multiple Paths to Multiple Life

We argue for multiple forms of life realized through multiple different historical pathways. From this perspective, there have been multiple origins of life on Earth—life is not a universal homology. By broadening the class of originations, we significantly expand the data set for searching for life. Through a computational analogy, the origin of life describes both the origin of hardware (physical substrate) and software (evolved function). Like all information-processing systems, adaptive systems possess a nested hierarchy of levels, a level of function optimization (e.g., fitness maximization), a level of constraints (e.g., energy requirements), and a level of materials (e.g., DNA or RNA genome and cells). The functions essential to life are realized by different substrates with different efficiencies. The functional level allows us to identify multiple origins of life by searching for key principles of optimization in different material form, including the prebiotic origin of proto-cells, the emergence of culture, economic, and legal institutions, and the reproduction of software agents.

The Grayness of the Origin of Life

In the search for life beyond Earth, distinguishing the living from the non-living is paramount. However, this distinction is often elusive, as the origin of life is likely a stepwise evolutionary process, not a singular event. Regardless of the favored origin of life model, an inherent "grayness" blurs the theorized threshold defining life. Here, we explore the ambiguities between the biotic and the abiotic at the origin of life. The role of grayness extends into later transitions as well. By recognizing the limitations posed by grayness, life detection researchers will be better able to develop methods sensitive to prebiotic chemical systems and life with alternative biochemistries.

Identifying molecules as biosignatures with assembly theory and mass spectrometry

The search for alien life is hard because we do not know what signatures are unique to life. We show why complex molecules found in high abundance are universal biosignatures and demonstrate the first intrinsic experimentally tractable measure of molecular complexity, called the molecular assembly index (MA). To do this we calculate the complexity of several million molecules and validate that their complexity can be experimentally determined by mass spectrometry. This approach allows us to identify molecular biosignatures from a set of diverse samples from around the world, outer space, and the laboratory, demonstrating it is possible to build a life detection experiment based on MA that could be deployed to extraterrestrial locations, and used as a complexity scale to quantify constraints needed to direct prebiotically plausible processes in the laboratory. Such an approach is vital for finding life elsewhere in the universe or creating de-novo life in the lab.

Classification of the Biogenicity of Complex Organic Mixtures for the Detection of Extraterrestrial Life

Searching for life in the Universe depends on unambiguously distinguishing biological features from background signals, which could take the form of chemical, morphological, or spectral signatures. The discovery and direct measurement of organic compounds unambiguously indicative of extraterrestrial (ET) life is a major goal of Solar System exploration. Biology processes matter and energy differently from abiological systems, and materials produced by biological systems may become enriched in planetary environments where biology is operative. However, ET biology might be composed of different components than terrestrial life. As ET sample return is difficult, in situ methods for identifying biology will be useful. Mass spectrometry (MS) is a potentially versatile life detection technique, which will be used to analyze numerous Solar System environments in the near future. We show here that simple algorithmic analysis of MS data from abiotic synthesis (natural and synthetic), microbial cells, and thermally processed biological materials (lab-grown organisms and petroleum) easily identifies relational organic compound distributions that distinguish pristine and aged biological and abiological materials, which likely can be attributed to the types of compounds these processes produce, as well as how they are formed and decompose. To our knowledge this is the first comprehensive demonstration of the utility of this analytical technique for the detection of biology. This method is independent of the detection of particular masses or molecular species samples may contain. This suggests a general method to agnostically detect evidence of biology using MS given a sufficiently strong signal in which the majority of the material in a sample has either a biological or abiological origin. Such metrics are also likely to be useful for studies of possible emergent living phenomena, and paleobiological samples.

Multiscale structural complexity of natural patterns

Complexity of patterns is key information for human brain to differ objects of about the same size and shape. Like other innate human senses, the complexity perception cannot be easily quantified. We propose a transparent and universal machine method for estimating structural (effective) complexity of two-dimensional and three-dimensional patterns that can be straightforwardly generalized onto other classes of objects. It is based on multistep renormalization of the pattern of interest and computing the overlap between neighboring renormalized layers. This way, we can define a single number characterizing the structural complexity of an object. We apply this definition to quantify complexity of various magnetic patterns and demonstrate that not only does it reflect the intuitive feeling of what is "complex" and what is "simple" but also, can be used to accurately detect different phase transitions and gain information about dynamics of nonequilibrium systems. When employed for that, the proposed scheme is much simpler and numerically cheaper than the standard methods based on computing correlation functions or using machine learning techniques.

Evolutionary History of Bioessential Elements Can Guide the Search for Life in the Universe

Our understanding of life in the universe comes from one sample, life on Earth. Current and next-generation space missions will target exoplanets as well as planets and moons in our own solar system with the primary goal of detecting, interpreting and characterizing indications of possible biological activity. Thus, understanding life's fundamental characteristics is increasingly critical for detecting and interpreting potential biological signatures elsewhere in the universe. Astrobiologists have outlined the essential roles of carbon and water for life, but we have yet to decipher the rules governing the evolution of how living organisms use bioessential elements. Does the suite of life's essential chemical elements on Earth constitute only one possible evolutionary outcome? Are some elements so essential for biological functions that evolution will select for them despite low availability? How would this play out on other worlds that have different relative element abundances? When we look for life in the universe, or the conditions that could give rise to life, we must learn how to recognize it in extremely different chemical and environmental conditions from those on Earth. We argue that by exposing self-organizing biotic chemistries to different combinations of abiotic materials, and by mapping the evolutionary history of metalloenzyme biochemistry onto geological availabilities of metals, alternative element choices that are very different from life's present-day molecular structure might result. A greater understanding of the paleomolecular evolutionary history of life on Earth will create a predictive capacity for detecting and assessing life's existence on worlds where alternate evolutionary paths might have been taken.

Evaluating Biosignatures for Life Detection

Conceptual frameworks are developed for evaluating the ability of different biosignatures to provide evidence for the presence of life in planned missions or observational studies. The focus is on intrinsic characteristics of biosignatures in space environments rather than on their detection, which depends on technology. Evaluation procedures are drawn from extensive studies in decision theory on related problems in business, engineering, medical fields, and the social arena. Three approaches are particularly useful. Two of them, Signal Detection Theory and Bayesian hypothesis testing, are based on probabilities. The third approach is based on utility theory. In all the frameworks, knowledge about a subject matter has to be translated into probabilities and/or utilities in a multistep process called elicitation. We present the first attempt to cover all steps, from acquiring knowledge about biosignatures to assigning probabilities or utilities to global quantities, such as false positives and false negatives. Since elicitation involves human judgment that is always prone to perceptual and cognitive biases, the relevant biases are discussed and illustrated in examples. We further discuss at which stage of elicitation human judgment should be involved to ensure the most reliable outcomes. An example, how evaluating biosignatures might be implemented, is given in the Supplementary Information.

Mars Extant Life: What's Next? Conference Report

On November 5-8, 2019, the "Mars Extant Life: What's Next?" conference was convened in Carlsbad, New Mexico. The conference gathered a community of actively publishing experts in disciplines related to habitability and astrobiology. Primary conclusions are as follows: A significant subset of conference attendees concluded that there is a realistic possibility that Mars hosts indigenous microbial life. A powerful theme that permeated the conference is that the key to the search for martian extant life lies in identifying and exploring refugia ("oases"), where conditions are either permanently or episodically significantly more hospitable than average. Based on our existing knowledge of Mars, conference participants highlighted four potential martian refugium (not listed in priority order): Caves, Deep Subsurface, Ices, and Salts. The conference group did not attempt to reach a consensus prioritization of these candidate environments, but instead felt that a defensible prioritization would require a future competitive process. Within the context of these candidate environments, we identified a variety of geological search strategies that could narrow the search space. Additionally, we summarized a number of measurement techniques that could be used to detect evidence of extant life (if present). Again, it was not within the scope of the conference to prioritize these measurement techniques-that is best left for the competitive process. We specifically note that the number and sensitivity of detection methods that could be implemented if samples were returned to Earth greatly exceed the methodologies that could be used at Mars. Finally, important lessons to guide extant life search processes can be derived both from experiments carried out in terrestrial laboratories and analog field sites and from theoretical modeling.

Enceladus: First Observed Primordial Soup Could Arbitrate Origin-of-Life Debate

A recent breakthrough publication has reported complex organic molecules in the plumes emanating from the subglacial water ocean of Saturn's moon Enceladus (Postberg et al., 2018, Nature 558:564-568). Based on detailed chemical scrutiny, the authors invoke primordial or endogenously synthesized carbon-rich monomers (<200 u) and polymers (up to 8000 u). This appears to represent the first reported extraterrestrial organics-rich water body, a conceivable milieu for early steps in life's origin ("prebiotic soup"). One may ask which origin-of-life scenario appears more consistent with the reported molecular configurations on Enceladus. The observed monomeric organics are carbon-rich unsaturated molecules, vastly different from present-day metabolites, amino acids, and nucleotide bases, but quite chemically akin to simple lipids. The organic polymers are proposed to resemble terrestrial insoluble kerogens and humic substances, as well as refractory organic macromolecules found in carbonaceous chondritic meteorites. The authors posit that such polymers, upon long-term hydrous interactions, might break down to micelle-forming amphiphiles. In support of this, published detailed analyses of the Murchison chondrite are dominated by an immense diversity of likely amphiphilic monomers. Our specific quantitative model for compositionally reproducing lipid micelles is amphiphile-based and benefits from a pronounced organic diversity. It thus contrasts with other origin models, which require the presence of very specific building blocks and are expected to be hindered by excess of irrelevant compounds. Thus, the Enceladus finds support the possibility of a pre-RNA Lipid World scenario for life's origin.

The Ladder of Life Detection

We describe the history and features of the Ladder of Life Detection, a tool intended to guide the design of investigations to detect microbial life within the practical constraints of robotic space missions. To build the Ladder, we have drawn from lessons learned from previous attempts at detecting life and derived criteria for a measurement (or suite of measurements) to constitute convincing evidence for indigenous life. We summarize features of life as we know it, how specific they are to life, and how they can be measured, and sort these features in a general sense based on their likelihood of indicating life. Because indigenous life is the hypothesis of last resort in interpreting life-detection measurements, we propose a small but expandable set of decision rules determining whether the abiotic hypothesis is disproved. In light of these rules, we evaluate past and upcoming attempts at life detection. The Ladder of Life Detection is not intended to endorse specific biosignatures or instruments for life-detection measurements, and is by no means a definitive, final product. It is intended as a starting point to stimulate discussion, debate, and further research on the characteristics of life, what constitutes a biosignature, and the means to measure them.

Physical foundations of biological complexity

Biological systems reach hierarchical complexity that has no counterpart outside the realm of biology. Undoubtedly, biological entities obey the fundamental physical laws. Can today's physics provide an explanatory framework for understanding the evolution of biological complexity? We argue that the physical foundation for understanding the origin and evolution of complexity can be gleaned at the interface between the theory of frustrated states resulting in pattern formation in glass-like media and the theory of self-organized criticality (SOC). On the one hand, SOC has been shown to emerge in spin-glass systems of high dimensionality. On the other hand, SOC is often viewed as the most appropriate physical description of evolutionary transitions in biology. We unify these two faces of SOC by showing that emergence of complex features in biological evolution typically, if not always, is triggered by frustration that is caused by competing interactions at different organizational levels. Such competing interactions lead to SOC, which represents the optimal conditions for the emergence of complexity. Competing interactions and frustrated states permeate biology at all organizational levels and are tightly linked to the ubiquitous competition for limiting resources. This perspective extends from the comparatively simple phenomena occurring in glasses to large-scale events of biological evolution, such as major evolutionary transitions. Frustration caused by competing interactions in multidimensional systems could be the general driving force behind the emergence of complexity, within and beyond the domain of biology.

Exoplanet Biosignatures: Future Directions

We introduce a Bayesian method for guiding future directions for detection of life on exoplanets. We describe empirical and theoretical work necessary to place constraints on the relevant likelihoods, including those emerging from better understanding stellar environment, planetary climate and geophysics, geochemical cycling, the universalities of physics and chemistry, the contingencies of evolutionary history, the properties of life as an emergent complex system, and the mechanisms driving the emergence of life. We provide examples for how the Bayesian formalism could guide future search strategies, including determining observations to prioritize or deciding between targeted searches or larger lower resolution surveys to generate ensemble statistics and address how a Bayesian methodology could constrain the prior probability of life with or without a positive detection. Key Words: Exoplanets-Biosignatures-Life detection-Bayesian analysis. Astrobiology 18, 779-824.

Exoplanet Biosignatures: At the Dawn of a New Era of Planetary Observations

The rapid rate of discoveries of exoplanets has expanded the scope of the science possible for the remote detection of life beyond Earth. The Exoplanet Biosignatures Workshop Without Walls (EBWWW) held in 2016 engaged the international scientific community across diverse scientific disciplines, to assess the state of the science and technology in the search for life on exoplanets, and to identify paths for progress. The workshop activities resulted in five major review papers, which provide (1) an encyclopedic review of known and proposed biosignatures and models used to ascertain them (Schwieterman et al., 2018 in this issue); (2) an in-depth review of O2 as a biosignature, rigorously examining the nuances of false positives and false negatives for evidence of life (Meadows et al., 2018 in this issue); (3) a Bayesian framework to comprehensively organize current understanding to quantify confidence in biosignature assessments (Catling et al., 2018 in this issue); (4) an extension of that Bayesian framework in anticipation of increasing planetary data and novel concepts of biosignatures (Walker et al., 2018 in this issue); and (5) a review of the upcoming telescope capabilities to characterize exoplanets and their environment (Fujii et al., 2018 in this issue). Because of the immense content of these review papers, this summary provides a guide to their complementary scope and highlights salient features. Strong themes that emerged from the workshop were that biosignatures must be interpreted in the context of their environment, and that frameworks must be developed to link diverse forms of scientific understanding of that context to quantify the likelihood that a biosignature has been observed. Models are needed to explore the parameter space where measurements will be widespread but sparse in detail. Given the technological prospects for large ground-based telescopes and space-based observatories, the detection of atmospheric signatures of a few potentially habitable planets may come before 2030. Key Words: Exoplanets-Biosignatures-Remote observation-Spectral imaging-Bayesian analysis. Astrobiology 18, 619-626.

Exploring Strategies To Bias Sequence in Natural and Synthetic Oligomers and Polymers

Millions of years of biological evolution have driven the development of highly sophisticated molecular machinery found within living systems. These systems produce polymers such as proteins and nucleic acids with incredible fidelity and function. In nature, the precise molecular sequence is the factor that determines the function of these macromolecules. Given that the ability to precisely define sequence emerges naturally, the fact that biology achieves unprecedented control over the unit sequence of the monomers through evolved enzymatic catalysis is incredible. Indeed, the ability to engineer systems that allow polymer synthesis with precise sequence control is a feat that technology is yet to replicate in artificial synthetic systems. This is the case because, without access to evolutionary control for finely tuned biological catalysts, the inability to correct errors or harness multiple competing processes means that the prospects for digital control of polymerization have been firmly bootstrapped to biological systems or limited to stepwise synthetic protocols. In this Account, we give an overview of strategies that have been used over the last 5 years in efforts to program polymer synthesis with sequence control in the laboratory. We also briefly explore how the use of robotics, algorithms, and stochastic chemical processes might lead to new understanding, mechanisms, and strategies to achieve full digital control. The aim is to see whether it is possible to go beyond bootstrapping to biological polymers or stepwise chemical synthesis. We start by describing nonenzymatic techniques used to obtain sequence-controlled natural polymers, a field that lends itself to direct application of insights gleaned from biology. We discuss major advances, such as the use of rotaxane-based molecular machines and templated approaches, including the utilization of biological polymers as templates for purely synthetic chains. We then discuss synthetic polymer chemistry, whose array of techniques allows the production of polymers with enormous structural and functional diversity, but so far with only limited control over the unit sequence itself. Synthetic polymers can be subdivided into multiple classes depending on the nature of processes used to synthesize them, such as by addition or condensation. Consequently, varied approaches for sequence control have been demonstrated in the area, including but not limited to click reactions, iterative solid-phase chemistry, and exploiting the chemical affinity of the monomers themselves. In addition to those, we highlight the importance of environmental bias in possible control of polymerization at the single-unit level, such as using catalyst switching or external stimuli. Even the most successful experimental sequence control approach needs appropriate tools to verify its scope and validity; therefore, we devote part of the present Account to possible analytical approaches to sequence readout, starting with well-established tandem mass spectrometry techniques and touching on those more applicable to specific classes of processes, such as diffusion-ordered NMR spectroscopy. Finally, we discuss progress in modeling and automation of sequence-controlled polymers. We postulate that developments in analytical chemistry, bioinformatics, and computer modeling will lead to new ways of exploring the development of new strategies for the realization of sequence control by means of sequence bias. This is the case because treating the assembly of polymers as a network of chemical reactions will enable the development of control strategies that can bias the outcome of the polymer assembly. The grand aim would be the synthesis of complex polymers in one step with a precisely defined digital sequence.

Re-conceptualizing the origins of life

Over the last several hundred years of scientific progress, we have arrived at a deep understanding of the non-living world. We have not yet achieved an analogous, deep understanding of the living world. The origins of life is our best chance at discovering scientific laws governing life, because it marks the point of departure from the predictable physical and chemical world to the novel, history-dependent living world. This theme issue aims to explore ways to build a deeper understanding of the nature of biology, by modelling the origins of life on a sufficiently abstract level, starting from prebiotic conditions on Earth and possibly on other planets and bridging quantitative frameworks approaching universal aspects of life. The aim of the editors is to stimulate new directions for solving the origins of life. The present introduction represents the point of view of the editors on some of the most promising future directions.This article is part of the themed issue 'Reconceptualizing the origins of life'.