Defining life

Stem Life: A Framework for Understanding the Prebiotic-Biotic Transition

Abiogenesis is frequently envisioned as a linear, ladder-like progression of increasingly complex chemical systems, eventually leading to the ancestors of extant cellular life. This "pre-cladistics" view is in stark contrast to the well-accepted principles of organismal evolutionary biology, as informed by paleontology and phylogenetics. Applying this perspective to origins, I explore the paradigm of "Stem Life," which embeds abiogenesis within a broader continuity of diversification and extinction of both hereditary lineages and chemical systems. In this new paradigm, extant life's ancestral lineage emerged alongside and was dependent upon many other complex prebiotic chemical systems, as part of a diverse and fecund prebiosphere. Drawing from several natural history analogies, I show how this shift in perspective enriches our understanding of Origins and directly informs debates on defining Life, the emergence of the Last Universal Common Ancestor (LUCA), and the implications of prebiotic chemical experiments.

Rethinking life and predicting its origin

The definition, origin and recreation of life remain elusive. As others have suggested, only once we put life into reductionist physical terms will we be able to solve those questions. To that end, this work proposes the phenomenon of life to be the product of two dissipative mechanisms. From them, one characterises extant biological life and deduces a testable scenario for its origin. The proposed theory of life allows its replication, reinterprets ecological evolution and creates new constraints on the search for life.

The Ethics of Life as It Could Be: Do We Have Moral Obligations to Artificial Life?

The field of Artificial Life studies the nature of the living state by modeling and synthesizing living systems. Such systems, under certain conditions, may come to deserve moral consideration similar to that given to nonhuman vertebrates or even human beings. The fact that these systems are nonhuman and evolve in a potentially radically different substrate should not be seen as an insurmountable obstacle to their potentially having rights, if they are sufficiently sophisticated in other respects. Nor should the fact that they owe their existence to us be seen as reducing their status as targets of moral concern. On the contrary, creators of Artificial Life may have special obligations to their creations, resembling those of an owner to their pet or a parent to their child. For a field that aims to create artificial life-forms with increasing levels of sophistication, it is crucial to consider the possible ethical implications of our activities, with an eye toward assessing potential moral obligations for which we should be prepared. If Artificial Life is larger than life, then the ethics of artificial beings should be larger than human ethics.

Is Life Binary or Gradual?

The binary nature of life is deeply ingrained in daily experiences, evident in the stark distinctions between life and death and the living and the inert. While this binary perspective aligns with disciplines like medicine and much of biology, uncertainties emerge in fields such as microbiology, virology, synthetic biology, and systems chemistry, where intermediate entities challenge straightforward classification as living or non-living. This contribution explores the motivations behind both binary and non-binary conceptualizations of life. Despite the perceived necessity to unequivocally define life, especially in the context of origin of life research and astrobiology, mounting evidence indicates a gray area between what is intuitively clearly alive and what is distinctly not alive. This prompts consideration of a gradualist perspective, depicting life as a spectrum with varying degrees of "lifeness". Given the current state of science, the existence or not of a definite threshold remains open. Nevertheless, shifts in epistemic granularity and epistemic perspective influence the framing of the question, and scientific advancements narrow down possible answers: if a threshold exists, it can only be at a finer level than what is intuitively taken as living or non-living. This underscores the need for a more refined distinction between the inanimate and the living.

Building Synthetic Cells─From the Technology Infrastructure to Cellular Entities

The de novo construction of a living organism is a compelling vision. Despite the astonishing technologies developed to modify living cells, building a functioning cell "from scratch" has yet to be accomplished. The pursuit of this goal alone has─and will─yield scientific insights affecting fields as diverse as cell biology, biotechnology, medicine, and astrobiology. Multiple approaches have aimed to create biochemical systems manifesting common characteristics of life, such as compartmentalization, metabolism, and replication and the derived features, evolution, responsiveness to stimuli, and directed movement. Significant achievements in synthesizing each of these criteria have been made, individually and in limited combinations. Here, we review these efforts, distinguish different approaches, and highlight bottlenecks in the current research. We look ahead at what work remains to be accomplished and propose a "roadmap" with key milestones to achieve the vision of building cells from molecular parts.

Life Is Uncertain: Inherent Variability Exhibited by Organisms, and at Higher Levels of Biological Organization

Organisms act stochastically. A not uncommon view in the ecological literature is that this is mainly due to the observer having insufficient information or a stochastic environment-and not partly because organisms themselves respond with inherent unpredictability. In this study, I compile the evidence that contradicts that view. Organisms generate uncertainty internally, which results in irreducible stochastic responses. I consider why: for instance, stochastic responses are associated with greater adaptability to changing environments and resource availability. Over longer timescales, biologically generated uncertainty influences behavior, evolution, and macroecological processes. Indeed, it could be stated that organisms are systems defined by the internal generation, magnification, and record-keeping of uncertainty as inputs to responses. Important practical implications arise if organisms can indeed be defined by an association with specific classes of inherent uncertainty: not least that isolating those signatures then provides a potential means for detecting life, for considering the forms that life could theoretically take, and for exploring the wider limits to how life might become distributed. These are all fundamental goals in astrobiology.

Circular at the very beginning: on the initial genomes in the RNA world

It is likely that an RNA world existed in early life, when RNA played both the roles of the genome and functional molecules, thereby undergoing Darwinian evolution. However, even with only one type of polymer, it seems quite necessary to introduce a labour division concerning these two roles because folding is required for functional molecules (ribozymes) but unfavourable for the genome (as a template in replication). Notably, while ribozymes tend to have adopted a linear form for folding without constraints, a circular form, which might have been topologically hindered in folding, seems more suitable for an RNA template. Another advantage of involving a circular genome could have been to resist RNA's end-degradation. Here, we explore the scenario of a circular RNA genome plus linear ribozyme(s) at the precellular stage of the RNA world through computer modelling. The results suggest that a one-gene scene could have been 'maintained', albeit with rather a low efficiency for the circular genome to produce the ribozyme, which required precise chain-break or chain-synthesis. This strict requirement may have been relieved by introducing a 'noncoding' sequence into the genome, which had the potential to derive a second gene through mutation. A two-gene scene may have 'run well' with the two corresponding ribozymes promoting the replication of the circular genome from different respects. Circular genomes with more genes might have arisen later in RNA-based protocells. Therefore, circular genomes, which are common in the modern living world, may have had their 'root' at the very beginning of life.

Concepts of a synthetic minimal cell: Information molecules, metabolic pathways, and vesicle reproduction

How do the living systems emerge from non-living molecular assemblies? What physical and chemical principles supported the process? To address these questions, a promising strategy is to artificially reconstruct living cells in a bottom-up way. Recently, the authors developed the "synthetic minimal cell" system showing recursive growth and division cycles, where the concepts of information molecules, metabolic pathways, and cell reproduction were artificially and concisely redesigned with the vesicle-based system. We intentionally avoided using the sophisticated molecular machinery of the biological cells and tried to redesign the cells in the simplest forms. This review focuses on the similarities and differences between the biological cells and our synthetic minimal cell concerning each concept of cells. Such comparisons between natural and artificial cells will provide insights on how the molecules should be assembled to create living systems to the wide readers in the field of synthetic biology, artificial cells, and protocells research. This review article is an extended version of the Japanese article "Growth and division of vesicles coupled with information molecules," published in SEIBUTSU-BUTSURI vol. 61, p. 378-381 (2021).

Life detection in a universe of false positives: Can the Fatal Flaws of Exoplanet Biosignatures be Overcome Absent a Theory of Life?

Astrobiology aims to determine the distribution and diversity of life in the universe. But as the word "biosignature" suggests, what will be detected is not life itself, but an observation implicating living systems. Our limited access to other worlds suggests this observation is more likely to reflect out-of-equilibrium gasses than a writhing octopus. Yet, anything short of a writhing octopus will raise skepticism about what has been detected. Resolving that skepticism requires a theory to delineate processes due to life and those due to abiotic mechanisms. This poses an existential question for life detection: How do astrobiologists plan to detect life on exoplanets via features shared between non-living and living systems? We argue that you cannot without an underlying theory of life. We illustrate this by analyzing the hypothetical detection of an "Earth 2.0" exoplanet. Without a theory of life, we argue the community should focus on identifying unambiguous features of life via four areas: examining life on Earth, building life in the lab, probing the solar system, and searching for technosignatures. Ultimately, we ask, what exactly do astrobiologists hope to learn by searching for life?

Is Darwinian selection a retrograde driving force of evolution?

Modern science has still not provided a satisfactory empirical explanation for the increasing complexity of living organisms through evolutionary history. As no agreed-upon definitions of the complexity exist, the working definition of biological complexity has been formulated. There is no theoretical reason to expect evolutionary lineages to increase in complexity over time, and there is no empirical evidence that they do so. In our discussion we have assumed the hypothesis that at the origins of life, evolution had to first involve autocatalytic systems that only subsequently acquired the capacity of genetic heredity. We discuss the role of Darwinian selection in evolution and pose the hypothesis that Darwinian selection acts predominantly as a retrograde driving force of evolution. In this context we understand the term retrograde evolution as a degeneration of living systems from higher complexity towards living systems with lower complexity. With the proposed hypothesis we have closed the gap between Darwinism and Lamarckism early in the evolutionary process. By Lamarckism, the action of a special principle called complexification force is understood here rather than inheritance of acquired characteristics.

The Call for a New Definition of Biosignature

The term biosignature has become increasingly prevalent in astrobiology literature as our ability to search for life advances. Although this term has been useful to the community, its definition is not settled. Existing definitions conflict sharply over the balance of evidence needed to establish a biosignature, which leads to misunderstanding and confusion about what is being claimed when biosignatures are purportedly detected. To resolve this, we offer a new definition of a biosignature as any phenomenon for which biological processes are a known possible explanation and whose potential abiotic causes have been reasonably explored and ruled out. This definition is strong enough to do the work required of it in multiple contexts-from the search for life on Mars to exoplanet spectroscopy-where the quality and indeed quantity of obtainable evidence is markedly different. Moreover, it addresses the pernicious problem of unconceived abiotic mimics that is central to biosignature research. We show that the new definition yields intuitively satisfying judgments when applied to historical biosignature claims. We also reaffirm the importance of multidisciplinary work on abiotic mimics to narrow the gap between the detection of a biosignature and a confirmed discovery of life.

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.

A Law of Redundancy Compounds the Problem of Cancer and Precision Medicine

Genetics and molecular biology research have progressed for over a century; however, no laws of biology resembling those of physics have been identified, despite the expectations of some physicists. It may be that it is not the properties of matter alone but evolved properties of matter in combination with atomic physics and chemistry that gave rise to the origin and complexity of life. It is proposed that any law of biology must also be a product of evolution that co-evolved with the origin and progression of life. It was suggested that molecular complexity and redundancy exponentially increase over time and have the following relationship: DNA sequence complexity (Cd) < molecular complexity (Cm) < phenotypic complexity (Cp). This study presents a law of redundancy, which together with the law of complexity, is proposed as an evolutionary law of biology. Molecular complexity and redundancy are inseparable aspects of biochemical pathways, and molecular redundancy provides the first line of defense against environmental challenges, including those of deleterious mutations. Redundancy can create problems for precision medicine because in addition to the issues arising from the involvement of multiple genes, redundancy arising from alternate pathways between genotypes and phenotypes can complicate gene detection for complex diseases and mental disorders. This study uses cancer as an example to show how cellular complexity, molecular redundancy, and hidden variation affect the ability of cancer cells to evolve and evade detection and elimination. Characterization of alternate biochemical pathways or "escape routes" can provide a step in the fight against cancer.

Biological Catalysis and Information Storage Have Relied on N-Glycosyl Derivatives of β-D-Ribofuranose since the Origins of Life

Most naturally occurring nucleotides and nucleosides are N-glycosyl derivatives of β-d-ribose. These N-ribosides are involved in most metabolic processes that occur in cells. They are essential components of nucleic acids, forming the basis for genetic information storage and flow. Moreover, these compounds are involved in numerous catalytic processes, including chemical energy production and storage, in which they serve as cofactors or coribozymes. From a chemical point of view, the overall structure of nucleotides and nucleosides is very similar and simple. However, their unique chemical and structural features render these compounds versatile building blocks that are crucial for life processes in all known organisms. Notably, the universal function of these compounds in encoding genetic information and cellular catalysis strongly suggests their essential role in the origins of life. In this review, we summarize major issues related to the role of N-ribosides in biological systems, especially in the context of the origin of life and its further evolution, through the RNA-based World(s), toward the life we observe today. We also discuss possible reasons why life has arisen from derivatives of β-d-ribofuranose instead of compounds based on other sugar moieties.

Prominent Roles and Conflicted Attitudes of Eumelanin in the Living World

Eumelanin, a macromolecule widespread in all the living world and long appreciated for its protective action against harmful UV radiation, is considered the beneficial component of the melanin family (ευ means good in ancient Greek). This initially limited picture has been rather recently extended and now includes a variety of key functions performed by eumelanin in order to support life also under extreme conditions. A lot of still unexplained aspects characterize this molecule that, in an evolutionary context, survived natural selection. This paper aims to emphasize the unique characteristics and the consequent unusual behaviors of a molecule that still holds the main chemical/physical features detected in fossils dating to the late Carboniferous. In this context, attention is drawn to the duality of roles played by eumelanin, which occasionally reverses its functional processes, switching from an anti-oxidant to a pro-oxidant behavior and implementing therefore harmful effects.

Origins of life: first came evolutionary dynamics

When life arose from prebiotic molecules 3.5 billion years ago, what came first? Informational molecules (RNA, DNA), functional ones (proteins), or something else? We argue here for a different logic: rather than seeking a molecule type, we seek a dynamical process. Biology required an ability to evolve before it could choose and optimise materials. We hypothesise that the evolution process was rooted in the peptide folding process. Modelling shows how short random peptides can collapse in water and catalyse the elongation of others, powering both increased folding stability and emergent autocatalysis through a disorder-to-order process.

Prebiotic Foam Environments to Oligomerize and Accumulate RNA

When water interacts with porous rocks, its wetting and surface tension properties create air bubbles in large number. To probe their relevance as a setting for the emergence of life, we microfluidically created foams that were stabilized with lipids. A persistent non-equilibrium setting was provided by a thermal gradient. The foam's large surface area triggers capillary flows and wet-dry reactions that accumulate, aggregate and oligomerize RNA, offering a compelling habitat for RNA-based early life as it offers both wet and dry conditions in direct neighborhood. Lipids were screened to stabilize the foams. The prebiotically more probable myristic acid stabilized foams over many hours. The capillary flow created by the evaporation at the water-air interface provided an attractive force for molecule localization and selection for molecule size. For example, self-binding oligonucleotide sequences accumulated and formed micrometer-sized aggregates which were shuttled between gas bubbles. The wet-dry cycles at the foam bubble interfaces triggered a non-enzymatic RNA oligomerization from 2',3'-cyclic CMP and GMP which despite the small dry reaction volume was superior to the corresponding dry reaction. The found characteristics make heated foams an interesting, localized setting for early molecular evolution.

Configurations of Proto-Cell Aggregates with Anisotropy: Gravity Promotes Complexity in Theoretical Biology

This contribution considers proto-cell structures associated with asymmetries, mainly gravity, in the framework of reaction-diffusion. There are equivalent solutions for defined morphogen parameters in the equations that allow for defining proto-tissue complexity and configurational entropy. Using RNA data, improvements to the complexity and entropy due to the Earth's gravity are presented. The theoretical proto-tissues complexity estimation, as a function of arbitrary surface gravity, is likewise proposed. In this sense, hypothetical aggregates of proto-cells on Mars would have a lower complexity than on Earth, which is equally valid for the Moon. Massive planets, or exoplanets like BD+20594b, could have major proto-tissue complexity and, eventually, rich biodiversity.

Viruses in astrobiology

Viruses are the most abundant biological entities on Earth, and yet, they have not received enough consideration in astrobiology. Viruses are also extraordinarily diverse, which is evident in the types of relationships they establish with their host, their strategies to store and replicate their genetic information and the enormous diversity of genes they contain. A viral population, especially if it corresponds to a virus with an RNA genome, can contain an array of sequence variants that greatly exceeds what is present in most cell populations. The fact that viruses always need cellular resources to multiply means that they establish very close interactions with cells. Although in the short term these relationships may appear to be negative for life, it is evident that they can be beneficial in the long term. Viruses are one of the most powerful selective pressures that exist, accelerating the evolution of defense mechanisms in the cellular world. They can also exchange genetic material with the host during the infection process, providing organisms with capacities that favor the colonization of new ecological niches or confer an advantage over competitors, just to cite a few examples. In addition, viruses have a relevant participation in the biogeochemical cycles of our planet, contributing to the recycling of the matter necessary for the maintenance of life. Therefore, although viruses have traditionally been excluded from the tree of life, the structure of this tree is largely the result of the interactions that have been established throughout the intertwined history of the cellular and the viral worlds. We do not know how other possible biospheres outside our planet could be, but it is clear that viruses play an essential role in the terrestrial one. Therefore, they must be taken into account both to improve our understanding of life that we know, and to understand other possible lives that might exist in the cosmos.

Vitalism and cognition in a conscious universe

According to the current scientific paradigm, what we call ‘life’, ‘mind’, and ‘consciousness’ are considered epiphenomenal occurrences, or emergent properties or functions of matter and energy. Science does not associate these with an inherent and distinct existence beyond a materialistic/energetic conception. ‘Life’ is a word pointing at cellular and multicellular processes forming organisms capable of specific functions and skills. ‘Mind’ is a cognitive ability emerging from a matrix of complex interactions of neuronal processes, while ‘consciousness’ is an even more elusive concept, deemed a subjective epiphenomenon of brain activity. Historically, however, this has not always been the case, even in the scientific and academic context. Several prominent figures took vitalism seriously, while some schools of Western philosophical idealism and Eastern traditions promoted conceptions in which reality is reducible to mind or consciousness rather than matter. We will argue that current biological sciences did not falsify these alternative paradigms and that some forms of vitalism could be linked to some forms of idealism if we posit life and cognition as two distinct aspects of consciousness preeminent over matter. However, we will not argue in favor of vitalistic and idealistic conceptions. Rather, contrary to a physicalist doctrine, these were and remain coherent worldviews and cannot be ruled out by modern science.

Focused ultrasound extraction versus microwave-assisted extraction for extraterrestrial objects analysis

Search for organic bioindicators in the solar system is a fundamental challenge for the space research community. If tremendous improvements have been achieved in detection, little or no research has been dedicated to extraction of the targets from the studied mineral matrices. Apart from thermodesorption, no extraction step was ever performed in situ within the context of biomarker detection experiments. This work presents an extraction protocol compatible with in situ space constraints. Two extraction methods, i.e., microwave-assisted extraction (MAE) and focused ultrasonic extraction (FUSE), were optimized with the aim of extracting molecules having an astrobiological interest (amino acids, nucleobases, polyaromatic carboxylic acids) and that are included in mineral matrices representative of the Martian soil. Higher efficiency was obtained with the FUSE method (20 kHz, amplitude 80%, pulse and relaxation 1 s each, for 10 min) with yields ranging from 30 to 95%. It was then applied on an Atacama Desert soil sample and Aguas Zarcas meteorite fragment. Both water-soluble and organic-soluble compounds present at trace levels were extracted using this short extraction time, and small amounts of sample and solvent compliant with in situ requirements (50 mg, 500 μL). This unique FUSE/derivatization-GC-MS approach gave similar yields to usual 24 h hot water extraction and increased the recovery of the target molecules compared to the derivatization-GC-MS method already used for in situ space experiments by a factor from 2 to 8. The data highlighted the suitability of a focused ultrasonic method for the extraction of trace organic compounds from extraterrestrial samples.

Toward a theory of evolution as multilevel learning

We apply the theory of learning to physically renormalizable systems in an attempt to outline a theory of biological evolution, including the origin of life, as multilevel learning. We formulate seven fundamental principles of evolution that appear to be necessary and sufficient to render a universe observable and show that they entail the major features of biological evolution, including replication and natural selection. It is shown that these cornerstone phenomena of biology emerge from the fundamental features of learning dynamics such as the existence of a loss function, which is minimized during learning. We then sketch the theory of evolution using the mathematical framework of neural networks, which provides for detailed analysis of evolutionary phenomena. To demonstrate the potential of the proposed theoretical framework, we derive a generalized version of the Central Dogma of molecular biology by analyzing the flow of information during learning (back propagation) and predicting (forward propagation) the environment by evolving organisms. The more complex evolutionary phenomena, such as major transitions in evolution (in particular, the origin of life), have to be analyzed in the thermodynamic limit, which is described in detail in the paper by Vanchurin et al. [V. Vanchurin, Y. I. Wolf, E. V. Koonin, M. I. Katsnelson, Proc. Natl. Acad. Sci. U.S.A. 119, 10.1073/pnas.2120042119 (2022)].

The Origin of Genetic Code and Translation in the Framework of Current Concepts on the Origin of Life

The origin of genetic code and translation system is probably the central and most difficult problem in the investigations on the origin of life and one of the most complex problems in the evolutionary biology in general. There are multiple hypotheses on the emergence and development of existing genetic systems that propose the mechanisms for the origin and early evolution of genetic code, as well as for the emergence of replication and translation. Here, we discuss the most well-known of these hypotheses, although none of them provides a description of the early evolution of genetic systems without gaps and assumptions. The RNA world hypothesis is a currently prevailing scientific idea on the early evolution of biological and pre-biological structures, the main advantage of which is the assumption that RNAs as the first living systems were self-sufficient, i.e., capable of functioning as both catalysts and templates. However, this hypothesis has also significant limitations. In particular, no ribozymes with processive polymerase activity have been yet discovered or synthesized. Taking into account the mutual need of proteins and nucleic acids in each other in the current world, many authors propose the early evolution scenarios based on the co-evolution of these two classes of organic molecules. They postulate that the emergence of translation was necessary for the replication of nucleic acids, in contrast to the RNA world hypothesis, according to which the emergence of translation was preceded by the era of self-replicating RNAs. Although such scenarios are less parsimonious from the evolutionary point of view, since they require simultaneous emergence and evolution of two classes of organic molecules, as well as the emergence of synchronized replication and translation, their major advantage is that they explain the development of processive and much more accurate protein-dependent replication.

The Seed and the Metabolism Regulation

Simple Summary

Seeds are the reproductive units of higher plants. They have a significant place in agriculture and plant diversity maintenance. Because they are dehydrated, they can remain viable in the environment for centuries. This review explores the dry seed as a metabolically inactive organism, but well organized to protect its components and enter intensive repair to restore metabolic activities upon imbibition for the completion of germination. Metabolism regulation is also critical for the most important seed traits, dormancy, and ageing recovery capacity.

Abstract

The seed represents a critical stage in the life cycle of flowering plants. It corresponds to a dry structure carrying the plant embryo in dormant or quiescent state. Orthodox seeds possess a very low water content, preventing biochemical reactions, especially respiration. If the desiccation of living organisms leads to a loss of homeostasis, structure, and metabolism, the seeds go through it successfully thanks to their structure, cellular organization, and growth regulation. Seeds set up a certain number of sophisticated molecules to protect valuable macromolecules or organelles from dehydration/rehydration cycles. Moreover, dormancy takes place in a coordinated process with environmental cues in order to ensure embryo development at the most appropriate conditions for the establishment of the new plant. Moreover, repair processes are programmed to be ready to operate to maximize germination success and seed longevity. This review focuses on the physiology of the seed as related to hydration forces, respiration, and biochemical reactions in the transition from thermodynamically undefined dry state to self-sustained living system. Such processes are of importance for basic knowledge of the regulation of metabolism of living organisms, but also for the control of germination in the context of climate change due to global warming.

Development of quantitative assay for simultaneous measurement of purine metabolites and creatinine in biobanked urine by liquid chromatography-tandem mass spectrometry

Purine metabolism is essential for all known living creatures, including humans in whom elevated serum concentration of purine break-down product uric acid (UA) is probably an independent risk factor for mortality, type 2 diabetes and cardiovascular events. An automated multiplex assay that measures several purine metabolites could therefore prove useful in many areas of medical, veterinary and biological research. The aim of the present work was to develop a sensitive LC-MS/MS method for simultaneous quantitation of xanthine, hypoxanthine, UA, allantoin, and creatinine in biobanked urine samples. This article describes details and performance of the new method studied in 55 samples of human urine. Archival sample preparation and effect of storage conditions on stability of the analytes are addressed. The intra-day and inter-day coefficients of variation were small for all the analytes, not exceeding 1% and 10%, respectively. Measurements of UA and creatinine in biobanked urine showed good agreement with values obtained using routine enzymatic assays on fresh urine. Spearman's correlation coefficients were 0.869 (p < .001) for creatinine and 0.964 (p < .001) for UA. Conclusion: the newly developed LC-MS/MS method allows reliable quantitative assessment of xanthine, hypoxanthine, allantoin, UA and creatinine. The proposed pre-analytical processing makes the method suitable for both fresh and biobanked urine stored frozen at -80 °C for at least 5.5 years.

Prebiotic Aggregates (Tissues) Emerging from Reaction-Diffusion: Formation Time, Configuration Entropy and Optimal Spatial Dimension

For the formation of a proto-tissue, rather than a protocell, the use of reactant dynamics in a finite spatial region is considered. The framework is established on the basic concepts of replication, diversity, and heredity. Heredity, in the sense of the continuity of information and alike traits, is characterized by the number of equivalent patterns conferring viability against selection processes. In the case of structural parameters and the diffusion coefficient of ribonucleic acid, the formation time ranges between a few years to some decades, depending on the spatial dimension (fractional or not). As long as equivalent patterns exist, the configuration entropy of proto-tissues can be defined and used as a practical tool. Consequently, the maximal diversity and weak fluctuations, for which proto-tissues can develop, occur at the spatial dimension 2.5.

Interstellar space biology via Project Starlight

Our ability to explore the cosmos by direct contact has been limited to a small number of lunar and interplanetary missions. However, the NASA Starlight program points a path forward to send small, relativistic spacecraft far outside our solar system via standoff directed-energy propulsion. These miniaturized spacecraft are capable of robotic exploration but can also transport seeds and organisms, marking a profound change in our ability to both characterize and expand the reach of known life. Here we explore the biological and technological challenges of interstellar space biology, focusing on radiation-tolerant microorganisms capable of cryptobiosis. Additionally, we discuss planetary protection concerns and other ethical considerations of sending life to the stars.

Building a community to engineer synthetic cells and organelles from the bottom-up

Employing concepts from physics, chemistry and bioengineering, 'learning-by-building' approaches are becoming increasingly popular in the life sciences, especially with researchers who are attempting to engineer cellular life from scratch. The SynCell2020/21 conference brought together researchers from different disciplines to highlight progress in this field, including areas where synthetic cells are having socioeconomic and technological impact. Conference participants also identified the challenges involved in designing, manipulating and creating synthetic cells with hierarchical organization and function. A key conclusion is the need to build an international and interdisciplinary research community through enhanced communication, resource-sharing, and educational initiatives.

Call for a framework for reporting evidence for life beyond Earth

Our generation could realistically be the one to discover evidence of life beyond Earth. With this privileged potential comes responsibility. The magnitude of the question of whether we are alone in the Universe, and the public interest therein, opens the possibility that results may be taken to imply more than the observations support, or than the observers intend. As life-detection objectives become increasingly prominent in space sciences, it is essential to open a community dialogue about how to convey information in a subject matter that is diverse, complicated and has a high potential to be sensationalized. Establishing best practices for communicating about life detection can serve to set reasonable expectations on the early stages of a hugely challenging endeavour, attach value to incremental steps along the path, and build public trust by making clear that false starts and dead ends are an expected and potentially productive part of the scientific process. Here we endeavour to motivate and seed the discussion with basic considerations and offer an example of how such considerations might be incorporated and applied in a proof-of-concept-level framework. Everything mentioned herein, including the name of the confidence scale, is intended not as a prescription, but simply as the beginning of an important dialogue.

Chance and Necessity in the Evolution of Matter to Life: A Comprehensive Hypothesis

Specialists in several branches of life sciences are trying to solve, piece by piece, the immensely complex puzzle of the origin of life. Some parts of the puzzle seem to appear with a rather high degree of clarity, while others remain totally obscure. We cannot be sure that life emerged only on our Earth, but we believe that the presence of large amounts of water in its liquid state is absolutely essential for the emergence and evolution of living matter. We can also assume that the latter exploits everywhere the same light elements, mainly C, H, O, N, S, and P, and somehow manipulates the same simple monomeric and polymeric organic compounds, such as alpha-amino acids, carbohydrates, nucleic bases, and surface-active carboxylic acids. The author contributes to the field by stating that all fundamental particles of our matter are “homochiral” and predominantly produce in an absolute asymmetric synthesis amino acids of L-configuration and carbohydrates of D-series. Another important point is that free atmospheric oxygen mainly stems from the photolysis of water molecules by cosmic irradiation and is not necessarily bound to living organisms on the planet.

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.

What is life?

Background

Many traditional biological concepts continue to be debated by biologists, scientists and philosophers of science. The specific objective of this brief reflection is to offer an alternative vision to the definition of life taking as a starting point the traits common to all living beings.

Results and Conclusions

Thus, I define life as a process that takes place in highly organized organic structures and is characterized by being preprogrammed, interactive, adaptative and evolutionary. If life is the process, living beings are the system in which this process takes place. I also wonder whether viruses can be considered living things or not. Taking as a starting point my definition of life and, of course, on what others have thought about it, I am in favor of considering viruses as living beings. I base this conclusion on the fact that viruses satisfy all the vital characteristics common to all living things and on the role they have played in the evolution of species. Finally, I argue that if there were life elsewhere in the universe, it would be very similar to what we know on this planet because the laws of physics and the composition of matter are universal and because of the principle of the inexorability of life.

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.

Analytical Chemistry in Astrobiology

This Feature introduces and discusses the findings of key analytical techniques used to study planetary bodies in our solar system in the search for life beyond Earth, future missions planned for high-priority astrobiology targets in our solar system, and the challenges we face in performing these investigations.

Self-Reproduction and Darwinian Evolution in Autocatalytic Chemical Reaction Systems

Understanding the emergence of life from (primitive) abiotic components has arguably been one of the deepest and yet one of the most elusive scientific questions. Notwithstanding the lack of a clear definition for a living system, it is widely argued that heredity (involving self-reproduction) along with compartmentalization and metabolism are key features that contrast living systems from their non-living counterparts. A minimal living system may be viewed as "a self-sustaining chemical system capable of Darwinian evolution". It has been proposed that autocatalytic sets of chemical reactions (ACSs) could serve as a mechanism to establish chemical compositional identity, heritable self-reproduction, and evolution in a minimal chemical system. Following years of theoretical work, autocatalytic chemical systems have been constructed experimentally using a wide variety of substrates, and most studies, thus far, have focused on the demonstration of chemical self-reproduction under specific conditions. While several recent experimental studies have raised the possibility of carrying out some aspects of experimental evolution using autocatalytic reaction networks, there remain many open challenges. In this review, we start by evaluating theoretical studies of ACSs specifically with a view to establish the conditions required for such chemical systems to exhibit self-reproduction and Darwinian evolution. Then, we follow with an extensive overview of experimental ACS systems and use the theoretically established conditions to critically evaluate these empirical systems for their potential to exhibit Darwinian evolution. We identify various technical and conceptual challenges limiting experimental progress and, finally, conclude with some remarks about open questions.

Molecules, Information and the Origin of Life: What Is Next?

How life did originate and what is life, in its deepest foundation? The texture of life is known to be held by molecules and their chemical-physical laws, yet a thorough elucidation of the aforementioned questions still stands as a puzzling challenge for science. Focusing solely on molecules and their laws has indirectly consolidated, in the scientific knowledge, a mechanistic (reductionist) perspective of biology and medicine. This occurred throughout the long historical path of experimental science, affecting subsequently the onset of the many theses and speculations about the origin of life and its maintenance. Actually, defining what is life, asks for a novel epistemology, a ground on which living systems’ organization, whose origin is still questioned via chemistry, physics and even philosophy, may provide a new key to focus onto the complex nature of the human being. In this scenario, many issues, such as the role of information and water structure, have been long time neglected from the theoretical basis on the origin of life and marginalized as a kind of scenic backstage. On the contrary, applied science and technology went ahead on considering molecules as the sole leading components in the scenery. Water physics and information dynamics may have a role in living systems much more fundamental than ever expected. Can an organism be simply explained by a mechanistic view of its nature or we need “something else”? Probably, we can earn sound foundations about life by simply changing our prejudicial view about living systems simply as complex, highly ordered machines. In this manuscript we would like to reappraise many fundamental aspects of molecular and chemical biology and reading them through a new paradigm, which includes Prigogine’s dissipative structures and informational dissipation (Shannon dissipation). This would provide readers with insightful clues about how biology and chemistry may be thoroughly revised, referring to new models, such as informational dissipation. We trust they are enabled to address a straightforward contribution in elucidating what life is for science. This overview is not simply a philosophical speculation, but it would like to affect deeply our way to conceive and describe the foundations of organisms’ life, providing intriguing suggestions for readers in the field.

Informational architecture across non-living and living collectives

Collective behavior is widely regarded as a hallmark property of living and intelligent systems. Yet, many examples are known of simple physical systems that are not alive, which nonetheless display collective behavior too, prompting simple physical models to often be adopted to explain living collective behaviors. To understand collective behavior as it occurs in living examples, it is important to determine whether or not there exist fundamental differences in how non-living and living systems act collectively, as well as the limits of the intuition that can be built from simpler, physical examples in explaining biological phenomenon. Here, we propose a framework for comparing non-living and living collectives as a continuum based on their information architecture: that is, how information is stored and processed across different degrees of freedom. We review diverse examples of collective phenomena, characterized from an information-theoretic perspective, and offer views on future directions for quantifying living collective behaviors based on their informational structure.

A Place for Viruses on the Tree of Life

Viruses are ubiquitous. They infect almost every species and are probably the most abundant biological entities on the planet, yet they are excluded from the Tree of Life (ToL). However, there can be no doubt that viruses play a significant role in evolution, the force that facilitates all life on Earth. Conceptually, viruses are regarded by many as non-living entities that hijack living cells in order to propagate. A strict separation between living and non-living entities places viruses far from the ToL, but this may be theoretically unsound. Advances in sequencing technology and comparative genomics have expanded our understanding of the evolutionary relationships between viruses and cellular organisms. Genomic and metagenomic data have revealed that co-evolution between viral and cellular genomes involves frequent horizontal gene transfer and the occasional co-option of novel functions over evolutionary time. From the giant, ameba-infecting marine viruses to the tiny Porcine circovirus harboring only two genes, viruses and their cellular hosts are ecologically and evolutionarily intertwined. When deciding how, if, and where viruses should be placed on the ToL, we should remember that the Tree functions best as a model of biological evolution on Earth, and it is important that models themselves evolve with our increasing understanding of biological systems.

An organisational systems-biology view of viruses explains why they are not alive

Whether or not viruses are alive remains unsettled. Discoveries of giant viruses with translational genes and large genomes have kept the debate active. Here, a fresh approach is introduced, based on the organisational definition of life from within systems biology. It views living as a circular process of self-organisation and self-construction which is 'closed to efficient causation'. How information combines with force to fabricate and organise environmentally obtained materials, given an energy source, is here explained as a physical embodiment of informational constraint. Comparing a general virus replication cycle with Rosen's (M,R)-system shows it to be linear, rather than closed. Some viruses contribute considerable organisational information, but so far none is known to supply all required, nor the material nor energy necessary to complete their replication cycle. As a result, no known virus replication cycle is closed to efficient causation: unlike cellular obligate parasites, viruses do not match the causal structure of an (M,R)-system. Analysis based in identifying a Markov blanket in causal structure proved inconclusive, but using Integrated Information Theory on a Boolean representation, it was possible to show that the causal structure of a virocell is not different from that of the host cell.

On the definition of a self-sustaining chemical reaction system and its role in heredity

Background

The ability to self-sustain is one of the essential properties of life. However, a consistent and satisfying definition of self-sustainability is still missing. Currently, self-sustainability refers to either “no-intervention by a higher entity” or “regeneration of all the system’s components”. How to connect self-sustainability with heredity, another essential of life, is another problem, as they are often considered to be independent of each other. Last but not least, current definitions of self-sustainability failed to provide a practical method to empirically discern whether a chemical system is self-sustaining or not.

Results

Here I propose a definition of self-sustainability. It takes into account the chemical reaction network itself and the external environment which is simplified as a continuous-flow stirred tank reactor. One distinct property of self-sustaining systems is that the system can only proceed if molecular triggers (or called, seeds) are present initially. The molecular triggers are able to establish the whole system, indicating that they carry the preliminary heredity of the system. Consequently, life and a large group of fires (and other dissipative systems) can be distinguished. Besides, the general properties and various real-life examples of self-sustaining systems discussed here together indicate that self-sustaining systems are not uncommon.

Conclusions

The definition I proposed here naturally connects self-sustainability with heredity. As this definition involves the continuous-flow stirred tank reactor, it gives a simple way to empirically test whether a system is self-sustaining or not. Moreover, the general properties and various real-life examples of self-sustaining systems discussed here provide practical guidance on how to construct and detect such systems in real biology and chemistry.

Reviewers

This article was reviewed by Wentao Ma and David Baum.

Stability and robustness of asymptotic autocatalytic systems

Here, we address the consequences of the extension in the space of a simple model of a system that is closed to efficient causation: the (M,R)-system model. To do so, we use a diffusion term to describe the collective motion of the nutrients’ concentration across the compartmentalized space that defines the organism. We show that the non-trivial stable steady state remains despite such generalization, as long as the system is small enough to deal with the transport of the precursors to feed the entire protocell and dispose of a sufficient concentration of it in its surroundings. Such consideration explains the emergence of a bifurcation with two parameters that we characterize. Finally, we show that the robustness of the system under catastrophic losses of catalysts also remains, preserving the original’s model character.

Perfusion Chamber for Observing a Liposome-Based Cell Model Prepared by a Water-in-Oil Emulsion Transfer Method

For the construction of a chemical model of contemporary living cells, the so-called water-in-oil emulsion transfer (WOET) method has drawn much attention as one of the promising preparation protocols for cell-sized liposomes encapsulating macromolecules and even micrometer-sized colloidal particles in high yields. Combining the throughput and accuracy of the observation is the key to developing a synthetic approach based on the liposomes prepared by the WOET method. Recent advances in microfluidic technology can provide a solution. By means of surface modification of a poly(dimethylsiloxane)-type microfluidic device integrating size-sorting and trapping modules, here, we enabled a simultaneous direct observation of the liposomes with a narrow size distribution, which were prepared by the WOET method. As a demonstration, we evaluated the variance of encapsulation of polystyrene colloidal particles and water permeability of the cell-sized liposomes prepared by the WOET method in the device. Since the liposomes prepared by the WOET method are useful for constructing cell models with an easy protocol, the current system will lead to a critical development of not only supramolecular chemistry and soft matter physics but also synthetic biology.

What is (synthetic) life? basic concepts of life in synthetic biology

One of the central aims of synthetic biology (SB) is to better understand the mechanisms of life by trying to develop and synthesize new forms and perhaps modes of life. While the question of what is life has occupied mankind for centuries, there is a lack of empirical research examining the basic concepts of life scientists within SB themselves refer to and build on. In order to gain insights into these fundamental concepts, we conducted a qualitative interview study with scientists working in the field of SB. The aim was to gain a better understanding of the underlying understandings, principles, and characteristics of (synthetic) life on the one hand, and the entangled consequences for the conducted experiments and studies as well as the pursued scientific approaches. We identified four primarily underlying basic concepts of life which serve as a fundamental framework for current and further scientific research within SB and have implications for research questions, approaches and aims as well as for the evaluation of scientific results.

Retinal energy metabolism in health and glaucoma

Energy metabolism refers to the processes by which life transfers energy to do cellular work. The retina's relatively large energy demands make it vulnerable to energy insufficiency. In addition, evolutionary pressures to optimize human vision have been traded against retinal ganglion cell bioenergetic fragility. Details of the metabolic profiles of the different retinal cells remain poorly understood and are challenging to resolve. Detailed immunohistochemical mapping of the energy pathway enzymes and substrate transporters has provided some insights and highlighted interspecies differences. The different spatial metabolic patterns between the vascular and avascular retinas can account for some inconsistent data in the literature. There is a consilience of evidence that at least some individuals with glaucoma have impaired RGC energy metabolism, either due to impaired nutrient supply or intrinsic metabolic perturbations. Bioenergetic-based therapy for glaucoma has a compelling pathophysiological foundation and is supported by recent successes in animal models. Recent demonstrations of visual and electrophysiological neurorecovery in humans with glaucoma is highly encouraging and motivates longer duration trials investigating bioenergetic neuroprotection.

(Re-)Designing Nature? An Overview and Outlook on the Ethical and Societal Challenges in Synthetic Biology

This structured literature analysis aims to map the current, emerging, and predicted future of synthetic biology (SB) by putting the focus on the implied conceptual, societal, and ethical challenges. The central objective of the analysis is to provide an initial systematization of the ethical and socio-scientific debate on SB by structuring and categorizing widely discussed issues within the debate in recent years. Starting with the quest for possible definitions, issues of biosafety and biosecurity are emphasized. Furthermore, the focus is on the more conceptual challenges of SB, including the relationship between natural and synthetic, or concepts of life and living. From the very beginning, one specific characteristic of SB has been a strong entanglement with different forms of public participation. In some respects SB has already taken a leading position in claiming and orchestrating itself as an integrative and participatory discipline. After addressing SB as an emerging biotechnology at the interface between science and society, a venture is initiated to focus on the possible regulatory and governmental challenges which are entangled in SB.