scholarly journals The Prebiotic Kitchen: A Guide to Composing Prebiotic Soup Recipes to Test Origins of Life Hypotheses

Life ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1221
Author(s):  
Lena Vincent ◽  
Stephanie Colón-Santos ◽  
H. James Cleaves ◽  
David A. Baum ◽  
Sarah E. Maurer

“Prebiotic soup” often features in discussions of origins of life research, both as a theoretical concept when discussing abiological pathways to modern biochemical building blocks and, more recently, as a feedstock in prebiotic chemistry experiments focused on discovering emergent, systems-level processes such as polymerization, encapsulation, and evolution. However, until now, little systematic analysis has gone into the design of well-justified prebiotic mixtures, which are needed to facilitate experimental replicability and comparison among researchers. This paper explores principles that should be considered in choosing chemical mixtures for prebiotic chemistry experiments by reviewing the natural environmental conditions that might have created such mixtures and then suggests reasonable guidelines for designing recipes. We discuss both “assembled” mixtures, which are made by mixing reagent grade chemicals, and “synthesized” mixtures, which are generated directly from diversity-generating primary prebiotic syntheses. We discuss different practical concerns including how to navigate the tremendous uncertainty in the chemistry of the early Earth and how to balance the desire for using prebiotically realistic mixtures with experimental tractability and replicability. Examples of two assembled mixtures, one based on materials likely delivered by carbonaceous meteorites and one based on spark discharge synthesis, are presented to illustrate these challenges. We explore alternative procedures for making synthesized mixtures using recursive chemical reaction systems whose outputs attempt to mimic atmospheric and geochemical synthesis. Other experimental conditions such as pH and ionic strength are also considered. We argue that developing a handful of standardized prebiotic recipes may facilitate coordination among researchers and enable the identification of the most promising mechanisms by which complex prebiotic mixtures were “tamed” during the origin of life to give rise to key living processes such as self-propagation, information processing, and adaptive evolution. We end by advocating for the development of a public prebiotic chemistry database containing experimental methods (including soup recipes), results, and analytical pipelines for analyzing complex prebiotic mixtures.

Science ◽  
2020 ◽  
Vol 369 (6511) ◽  
pp. eaaw1955 ◽  
Author(s):  
Agnieszka Wołos ◽  
Rafał Roszak ◽  
Anna Żądło-Dobrowolska ◽  
Wiktor Beker ◽  
Barbara Mikulak-Klucznik ◽  
...  

The challenge of prebiotic chemistry is to trace the syntheses of life’s key building blocks from a handful of primordial substrates. Here we report a forward-synthesis algorithm that generates a full network of prebiotic chemical reactions accessible from these substrates under generally accepted conditions. This network contains both reported and previously unidentified routes to biotic targets, as well as plausible syntheses of abiotic molecules. It also exhibits three forms of nontrivial chemical emergence, as the molecules within the network can act as catalysts of downstream reaction types; form functional chemical systems, including self-regenerating cycles; and produce surfactants relevant to primitive forms of biological compartmentalization. To support these claims, computer-predicted, prebiotic syntheses of several biotic molecules as well as a multistep, self-regenerative cycle of iminodiacetic acid were validated by experiment.


2019 ◽  
Vol 15 (S350) ◽  
pp. 216-219
Author(s):  
N. F. W. Ligterink ◽  
J. Terwisscha van Scheltinga ◽  
V. Kofman ◽  
V. Taquet ◽  
S. Cazaux ◽  
...  

AbstractThe emergence of life on Earth may have its origin in organic molecules formed in the interstellar medium. Molecules with amide and isocyanate groups resemble structures found in peptides and nucleobases and are necessary for their formation. Their formation is expected to take place in the solid state, on icy dust grains, and is studied here by far-UV irradiating a CH4:HNCO mixture at 20 K in the laboratory. Reaction products are detected by means of infrared spectroscopy and temperature programmed desorption - mass spectrometry. Various simple amides and isocyanates are formed, showing the importance of ice chemistry for their interstellar formation. Constrained by experimental conditions, a reaction network is derived, showing possible formation pathways of these species under interstellar conditions.


Author(s):  
Eva Hudlicka

Computational affective models are being developed both to elucidate affective mechanisms, and to enhance believability of synthetic agents and robots. Yet in spite of the rapid growth of computational affective modeling, no systematic guidelines exist for model design and analysis. Lack of systematic guidelines contributes to ad hoc design practices, hinders model sharing and re-use, and makes systematic comparison of existing models and theories challenging. Lack of a common computational terminology also hinders cross-disciplinary communication that is essential to advance our understanding of emotions. In this chapter the author proposes a computational analytical framework to provide a basis for systematizing affective model design by: (1) viewing emotion models in terms of two core types: emotion generation and emotion effects, and (2) identifying the generic computational tasks necessary to implement these processes. The chapter then discusses how these computational ‘building blocks' can support the development of design guidelines, and a systematic analysis of distinct emotion theories and alternative means of their implementation.


2003 ◽  
Vol 9 (3) ◽  
pp. 269-316 ◽  
Author(s):  
Steen Rasmussen ◽  
Liaohai Chen ◽  
Martin Nilsson ◽  
Shigeaki Abe

Assembling non-biological materials (geomaterials) into a proto-organism constitutes a bridge between nonliving and living matter. In this article we present a simple step-by-step route to assemble a proto-organism. Many pictures have been proposed to describe this transition within the origins-of-life and artificial life communities, and more recently alternative pictures have been emerging from advances in nanoscience and biotechnology. The proposed proto-organism lends itself to both traditions and defines a new picture based on a simple idea: Given a set of required functionalities, minimize the physicochemical structures that support these functionalities, and make sure that all structures self-assemble and mutually enhance each other's existence. The result is the first concrete, rational design of a simple physicochemical system that integrates the key functionalities in a thermodynamically favorable manner as a lipid aggregate integrates proto-genes and a proto-metabolism. Under external pumping of free energy, the metabolic processes produce the required building blocks, and only specific gene sequences enhance the metabolic kinetics sufficiently for the whole system to survive. We propose an experimental implementation of the proto-organism with a discussion of our experimental results, together with relevant results produced by other experimental groups, and we specify what is still missing experimentally. Identifying the missing steps is just as important as providing the road map for the transition. We derive the kinetic and thermodynamic conditions of each of the proto-organism subsystems together with relevant theoretical and computational results about these subsystems. We present and discuss detailed 3D simulations of the lipid aggregation processes. From the reaction kinetics we derive analytical aggregate size distributions, and derive key properties of the metabolic efficiency and stability. Thermodynamics and kinetics of the ligation directed self-replication of the proto-genes is discussed, and we summarize the full life cycle of the proto-organism by comparing size, replication time, and energy with the biomass efficiency of contemporary unicells. Finally, we also compare our proto-organism picture with existing origins-of-life and protocell pictures. By assembling one possible bridge between nonliving and living matter we hope to provide a piece in the ancient puzzle about who we are and where we come from.


2019 ◽  
Vol 58 (2) ◽  
pp. 282-300
Author(s):  
Felicitas Hesselmann ◽  
Cornelia Schendzielorz

This contribution seeks to provide a more detailed insight into the entanglement of value and measurement. Drawing on insights from semiotics and a Bourdieusian perspective on language as an economy of linguistic exchange, we develop the theoretical concept of value-measurement links and distinguish three processes – operationalisation, nomination, and indetermination – as forms in which these links can be constructed. We illustrate these three processes using (e)valuation practices in science, particularly the journal impact factor, as an empirical object of investigation. As this example illustrates, measured values can function as building blocks for further measurements, and thus establish chains of evaluations, where it becomes more and more obscure which values the measurements actually express. We conclude that in the case of measured values such as impact factors, these chains are driven by the interplay between the interpretative openness of language and the seeming tendency of numbers to fixate meaning thus continually re-creating, transforming and modifying values.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kathleen Wermke ◽  
Michael P. Robb ◽  
Philip J. Schluter

AbstractIn early infancy, melody provides the most salient prosodic element for language acquisition and there is huge evidence for infants’ precocious aptitudes for musical and speech melody perception. Yet, a lack of knowledge remains with respect to melody patterns of infants’ vocalisations. In a search for developmental regularities of cry and non-cry vocalisations and for building blocks of prosody (intonation) over the first 6 months of life, more than 67,500 melodies (fundamental frequency contours) of 277 healthy infants from monolingual German families were quantitatively analysed. Based on objective criteria, vocalisations with well-identifiable melodies were grouped into those exhibiting a simple (single-arc) or complex (multiple-arc) melody pattern. Longitudinal analysis using fractional polynomial multi-level mixed effects logistic regression models were applied to these patterns. A significant age (but not sex) dependent developmental pattern towards more complexity was demonstrated in both vocalisation types over the observation period. The theoretical concept of melody development (MD-Model) contends that melody complexification is an important building block on the path towards language. Recognition of this developmental process will considerably improve not only our understanding of early preparatory processes for language acquisition, but most importantly also allow for the creation of clinically robust risk markers for developmental language disorders.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Oliver R. Maguire ◽  
Iris B. A. Smokers ◽  
Wilhelm T. S. Huck

AbstractThe incorporation of orthophosphate from scarce geochemical sources into the organic compounds essential for life under mild conditions is a fundamental challenge for prebiotic chemistry. Here we report a prebiotic system capable of overcoming this challenge by taking inspiration from extant life’s recycling of orthophosphate via its conversion into kinetically stable thermodynamically activated (KSTA) nucleotide triphosphates (e.g. ATP). We separate the activation of orthophosphate from its transfer to organic compounds by, crucially, first accumulating a KSTA phosphoramidate. We use cyanate to activate orthophosphate in aqueous solution under mild conditions and then react it with imidazole to accumulate the KSTA imidazole phosphate. In a paste, imidazole phosphate phosphorylates all the essential building blocks of life. Integration of this chemistry into a wet/dry cycle enables the continuous recycling of orthophosphate and the accretion of phosphorylated compounds. This system functions even at low reagent concentrations due to solutes concentrating during evaporation. Our system demonstrates a general strategy for how to maximise the usage of scarce resources based upon cycles which accumulate and then release activated intermediates.


2020 ◽  
Author(s):  
Andrea Fossati ◽  
Chen Li ◽  
Peter Sykacek ◽  
Moritz Heusel ◽  
Fabian Frommelt ◽  
...  

AbstractProtein complexes, macro-molecular assemblies of two or more proteins, play vital roles in numerous cellular activities and collectively determine the cellular state. Despite the availability of a range of methods for analysing protein complexes, systematic analysis of complexes under multiple conditions has remained challenging. Approaches based on biochemical fractionation of intact, native complexes and correlation of protein profiles have shown promise, for instance in the combination of size exclusion chromatography (SEC) with accurate protein quantification by SWATH/DIA-MS. However, most approaches for interpreting co-fractionation datasets to yield complex composition, abundance and rearrangements between samples depend heavily on prior evidence. We introduce PCprophet, a computational framework to identify novel protein complexes from SEC-SWATH-MS data and to characterize their changes across different experimental conditions. We demonstrate accurate prediction of protein complexes (AUC >0.99 and accuracy around 97%) via five-fold cross-validation on SEC-SWATH-MS data, show improved performance over state-of-the-art approaches on multiple annotated co-fractionation datasets, and describe a Bayesian approach to analyse altered protein-protein interactions across conditions. PCprophet is a generic computational tool consisting of modules for data pre-processing, hypothesis generation, machine-learning prediction, post-prediction processing, and differential analysis. It can be applied to any co-fractionation MS dataset, independent of separation or quantitative LC-MS workflow employed, and to support the detection and quantitative tracking of novel protein complexes and their physiological dynamics.


Life ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 12 ◽  
Author(s):  
Paul Rimmer ◽  
Oliver Shorttle

There are two dominant and contrasting classes of origin of life scenarios: those predicting that life emerged in submarine hydrothermal systems, where chemical disequilibrium can provide an energy source for nascent life; and those predicting that life emerged within subaerial environments, where UV catalysis of reactions may occur to form the building blocks of life. Here, we describe a prebiotically plausible environment that draws on the strengths of both scenarios: surface hydrothermal vents. We show how key feedstock molecules for prebiotic chemistry can be produced in abundance in shallow and surficial hydrothermal systems. We calculate the chemistry of volcanic gases feeding these vents over a range of pressures and basalt C/N/O contents. If ultra-reducing carbon-rich nitrogen-rich gases interact with subsurface water at a volcanic vent they result in 10 − 3 – 1 M concentrations of diacetylene (C4H2), acetylene (C2H2), cyanoacetylene (HC3N), hydrogen cyanide (HCN), bisulfite (likely in the form of salts containing HSO3−), hydrogen sulfide (HS−) and soluble iron in vent water. One key feedstock molecule, cyanamide (CH2N2), is not formed in significant quantities within this scenario, suggesting that it may need to be delivered exogenously, or formed from hydrogen cyanide either via organometallic compounds, or by some as yet-unknown chemical synthesis. Given the likely ubiquity of surface hydrothermal vents on young, hot, terrestrial planets, these results identify a prebiotically plausible local geochemical environment, which is also amenable to future lab-based simulation.


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