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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 61 through 75 of 107 found.


Ecosmomics: Independent, UniVersal, Complex Network Systems and a Genetic Code-Script Source

Cosmic Code > Genetic Info > Genome CS

Fang, Jing-Kai, et al. Divide-and-Conquer Quantum Algorithm for Hybrid de novo Genome Assembly of Short and Long Reads.. PRX Life. 2/023006, 2024. We note this contribution by BGI Research, Shenzhen, China computational geneticists as a frontier example of how genetic studies are being taken to a new dimension by virtue of quantum capabilities. An evidential result implies that life’s genomic proscription can gain an affinity with this fundamental physical phase.

Researchers have begun to apply quantum computing in genome assembly implementation, but the issue of repetitive sequences remains unresolved. Here, we propose a hybrid assembly quantum algorithm using short reads and long reads which utilizes divide-and-conquer strategies to approximate the ground state of a larger Hamiltonian while conserving quantum resources. The convergence speed is improved via the problem-inspired Ansatz based on the known information. In addition, we verify that entanglement within quantum circuits may accelerate the assembly path optimization. (Excerpt)

Life's Corporeal Evolution Develops, Encodes and Organizes Itself: An Earthtwinian Genesis Synthesis

Quickening Evolution

MacIver, Malcolm and Barbara Finlay. The neuroecology of the water-to-land transition and the evolution of the vertebrate brain. Philosophical Transactions of the Royal Society B. December, 2021. Veteran Northwestern University and Cornell University evolutionary neuroscientists make a case that this epochal movement of aquatic creatures onto dry, sunlit surfaces played a much more paramount role in life’s emergence than previously seen.

The water-to-land transition in vertebrate evolution offers a unique opportunity for computational affordances and a new ecology for the brain. As a result, a much enlarged visual sensorium owing to air versus water as a medium, then led to mobile eyes and neck. In water, the midbrain tectum coordinates approach/avoid decisions, due to water flow and the bodily state and learning. On land, the relative motions of sensory surfaces and effectors must be resolved, adding on computational architectures from the dorsal pallium. For the large-brained and long-living denizens, making the right decision allows animals to learn from experience. Integration of memorized panoramas in the basal ganglia/frontal cortex becomes a substantial cognitive habit-to-plan benefit. (Excerpt)

Quickening Evolution > Systems Biology

Linden-Santangeli, Nathaniel, et al. Increasing certainty in systems biology models using Bayesian multimodel inference.. Linden-Santangeli, Nathaniel, et al. Increasing certainty in systems biology models using Bayesian multimodel inference. arXiv:2406.11178.. UC San Diego bioscientists show how to integrate this popular research procedure with an holistic sense of metabolic vitalities.

Mathematical models are a good way to study the structure and behavior of intracellular signaling networks. As a result, the same signal pathway can be represented by multiple models, each with underlying assumptions. Here, we use Bayesian inference to develop a way to achieve increasing certainty. A case study of extracellular regulated kinase (ERK), we show that multimodel inference enhances predictive accuracy. Finally, we use multimodel inference to explain sub-cellular location-specific ERK activity dynamics. (Excerpt)

Quickening Evolution > Nest > Life Origin

Pérez-Mercader., Juan. Making Biochemistry-Free Life in a Test Tube.. Di Mauro, Ernesto, ed.. The First Steps of Life. Wiley Online, 2023. In this chapter, a senior scientist (see below) now at Origins describes evidential results which may well imply an intrinsic organism-like ecosmic fertility. See also Competitive exclusion principle among synthetic non-biochemical protocells by Sai Krishna Katla, et al (J P-M) in Cell Reports Physical Science (4/4, 2024).


As we discover many extrasolar planets it is time to ask: Is biochemistry-based life the only chemical support for life? On Earth, all living systems (i) process information, (ii) metabolize, (iii) self-reproduce and (iv) evolve. But can processes (i)-(iv) take place in a non-biochemical chemical system? We present progress resulting from experiments on a reaction during the non-equilibrium synthesis of functional polymer vesicles from small, non-biochemical molecules. Their dynamical evolution integrates metabolism, growth, reproduction, and descent with modification by implementing a polymerization induced self-assembly (PISA) scenario. Together, these results offer insights into generic chemistry-based artificial life, as well as into the origin of proto-cells enroute to proto-life and pre-LUCA living systems. (Abstract)

Juan Pérez-Mercader earned his Ph.D. from the City College of New York. In 1998 he founded Spain's Centro de Astrobiología as its first Director. In 2010, he joined Harvard in the Earth and Planetary Sciences and Origins of Life Initiative, where he leads a project on the "Top-down Synthesis of an Ex-novo Chemical Artificial Living System". Some of his Research Interests are Physics of Self-organizing Behavior, Information in Non-equilibrium, Physico-chemical Systems, Chemical Computation, Quantum Field Theory, and Dynamical Renormalization Group,

Quickening Evolution > Nest > Life Origin

D'Eugeno, Francesco, et al. D'Eugenio, Francesco, et al. JADES: Carbon enrichment 350 Myr after the Big Bang in a gas-rich galaxy.. arXiv:2311.09908. As the awesome Webb telescope continues to send fantastic images from the outermost reaches of space and time, UK, USA, Australia, France, Italy, Germany, Japan, Spain report a deeper probe into the onset appearance of metallic elements and compounds which can innately engender a fertile prebiotic milieu. Into 2024 then as one may be a viewer of this ecosmic planetarium, the whole show seems to have an essential, independent life and mind of its own

Finding the first generation of metals in the early Universe and identifying their origin is an important goal of modern astrophysics. In regard, we report deep JWST/NIRSpec spectroscopy of a GS-z12 galaxy as the most distant detection of a metal transition and redshift via emission lines. We derive a super-solar carbon-to-oxygen ratio higher than the C/O measured in galaxies discovered by JWST, and higher than Type-II supernovae enrichment. Such a high C/O in a galaxy observed 350 Myr after the Big Bang may be explained by the yields of metal poor stars, and may even be the heritage of the first generation of supernovae from Population III progenitors. (Excerpt)

The appearance of the first galaxies marks a key phase transition of the Universe with the start of stellar nucleosynthesis and the diffusion of metals. Extensive theoretical work has been devoted to predicting the properties of the first generation of stars and their supernova yield. The launch of JWST enabled, for the first time, the measurement of the physical properties of galaxies. These are generally understood in terms of decreasing gas metallicity and increasing density, ionisation parameter, temperature and stochasticity of their star-formation histories. (1)

Quickening Evolution > Nest > Life Origin

Goldford, Joshua, et al. Primitive purine biosynthesis connects ancient geochemistry to modern metabolism. Nature Ecology & Evolution. 8/4, 2024. Blue Marble Space Institute, Seattle, and Earth-Life Science Institute, Tokyo researchers including Harrison Smith sketch out a long feasible course from early precursors all the way present organisms.

An open question in the origin and evolution of life is whether a continuous track from geochemical precursors to the molecular biosphere can be reconstructed from modern biochemistry. Here we identify a pathway by simulating the evolution of a biospheric metabolism via biochemical reactions and models of primitive coenzymes.. This expansion trajectory leads to hypotheses about the tempo and mode pathway of metabolic enhanceent. An evident concordance between biological and geological analyses suggests a plausible evolutionary history for the majority of core biochemistry. (Excerpt)

Quickening Evolution > Nest > Life Origin

Harrison, Stuart, et al. Life as a Guide to Its Own Origins. Harrison, Stuart, et al. Life as a Guide to Its Own Origins. Annual Review. Volume 54, 2023. Centre for Life's Origins and Evolution, University College London biotheorists including Nick Lane at once add new nuances as to how early living systems might have spontaneously come into being, but still do so within a mechanical frame.

The origin of life entails a continuum from prebiotic chemistry to molecular machinery. Using Here we consider how selection could promote increased complexity before replicative genes. Far-from-equilibrium environments such as hydrothermal systems drive reactions between CO2 and H2 that self-organize into protocells and prefigure the universal core of metabolism. Patterns in the genetic code show that genes and proteins arose through direct biophysical interactions between amino acids and nucleotides in this protometabolic network. Random genetic sequences template nonrandom peptides, producing selectable function in growing protocells. (Excerpt)

Quickening Evolution > Nest > Life Origin

López-Díaz, Amahury Jafet , et al. The Origin of Information Handling. arXiv:2404.04374. Binghamton University, New York theorists including Hiroki Sayama and Carlos Gershenson consider and finesse another algorithm-like component as life gets its well proscribed act altogether. In regard, core guidance is provided by Howard Pattee, Juan Perez-Mercader, Chiara Marletto and Matthew Egbert. Once again something and someone seems in gestation, as long foreseen.

A major challenge when describing the origin of life is to explain how instructional information systems emerge naturally from mere molecular dynamics. Based on recent experimental results showing that chemical computations does not require a biological basis, we elucidate the origin and evolution of information processes by automata, computation and storage and transmission. In contrast to theories that assume initial complex structures, our narrative starts from early interactive self-replicators. By way of describing these primordial transitions, our metaphor can be translated to other models to explore biological phenomena at multiple spatial and temporal scales. (Excerpt)

We can imagine our planet as a big parallel, quasi-universal Turing machine capable of simulating a huge variety of functions (programs). Of course, natural resources are finite, and this is a limitation for life to emerge. Under this perspective, the first organisms on the planet could be described as some kind of automata which were running in these primitive environments. As a result of the geophysical and geochemical constraints, which we could call the primeval ecosystem language, elementary bimolecular reactions emerged. These chemical reactions are capable of recognizing regular languages, a task that does not involve counting or memory. (1, 2)

Quickening Evolution > Nest > Life Origin

Lu, Heng, et al. Small-molecule autocatalysis drives compartment growth, competition and reproduction. Nature Chemistry. August 7, 2023. Fifteen investigators mainly at the Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, and Université PSL, Paris, France, along with Eors Szathmary (Centre for Ecological Research, Budapest) post novel insights into how a network of small-molecule autocatalytic reactions, without genetic material and enzymes, can foster and grow into protocellular compartments. The result is said to be fundamental to the experimental verification of the principles of systems chemistry and points the way forward in the study of the origin of life. So once more in a major study nature’s propensity to boot itself up through auto-spontaneous means is well quantified.

Sustained autocatalysis coupled to compartment growth and division is a key step in the origin of life, but an experimental demonstration of this phenomenon in an artificial system has proven elusive. We show that autocatalytic reactions within compartments drive osmosis and diffusion resulting in vesicle growth. Our work indicates how a combination of properties of living systems (growth, division, variation, competition, rudimentary heredity and selection) can arise from simple physical–chemical processes and may have paved the way for the emergence of evolution by natural selection. (Excerpt)

Quickening Evolution > Nest > Life Origin

Mauro, Ernesto, ed.. The First Steps of Life. Wiley Online, 2023. This edited, authoritative collection is published as an ebook edition. Typical chapters are The Emergence of Life-Nurturing Conditions in the Universe by Juan Vladilo, The Role of Formamide in Prebiotic Chemistry (Raffaele Saladino), A Praise of Imperfection: Emergence and Evolution of Metabolism (Juli Pereto), and Making Biochemistry-Free Life in a Test Tube by Juan Perez-Mercader (see review). Here again, a dozen diverse chapters convey and integrate strong evidence that a veritable proof an in fact confirm a revolutionary ecosmic procreation.


Origin of Life studies have a retrospective goal: understanding nature through the comprehension of its origins and its complexities. This book proposes both an overview of this large area and an in-depth look at the opinions and results obtained by some of the active contributors. The topics occur a bottom-up order from the habitability of the universe to a meaningful prebiotic chemistry, the problem of chirality, and on through the role of minerals in biogenesis, fertile environments, cellular vesicles, replicative codes, the structure of LUCA and on their way to the evolution of information and complexity. (EDM)

Ernesto Di Mauro is a Molecular Biology professor and vice-president of the Académie Européenne Interdisciplinaire des Sciences, France. His research focuses on structural codes for complex molecular interactions in DNA topology, RNA-polymerases and DNA-topoisomerases.

Quickening Evolution > Nest > Life Origin

Rout, Saroj, et al. An Analysis of Nucleotide–Amyloid Interactions Reveals Selective Binding to Codon-Sized RNA.. J. Am. Chem. Soc.. 145/21915, 2023. This recent posting by fourteen ETH Zurich and Aachen University biochemists including Roland Riek contends that rather than a single prebiotic path, several companion, catalytic reactivities and replicators were merging altogether toward a long vivid traverse to our retrospective curiosity. Into these 2020s then, by virtue of ever stronger evidence like this, a sufficient veracity may have been reached so as to confirm a phenomenal presence of an ecosmic procreativity.

Interactions between RNA and proteins form the basis of many biological processes from transcription and translation to gene regulation, yet little is known about their ancient origins. We hypothesize that peptide amyloids played a role whose repetitive structure lends itself to building interfaces with other polymers. Here, we report that short RNA binds in a sequence-dependent manner to peptide amyloids. Sequence-specific RNA–peptide interactions of this kind may then provide a path to understand how genetic code replication came to be. (Excerpt)

Quickening Evolution > Nest > Life Origin

Walton, Craig, et al. Cosmic dust fertilization of glacial prebiotic chemistry on early Earth. Nature Astronomy. 8/5, 2024. ETH Zürich, Cambridge University and Oxford University enter a novel proposal that a lack of vital biochemicals could have been made up by hitched rides across the dusty ISM so to reach and fertilize our Archean era surfaces.

Earth’s surface lacks many elements considered vital for prebiotic chemistry. In contrast, extraterrestrial rocky objects are rich in these ingredients, which may have been delivered to our planet. However, the way by which they were supplied remains unclear. Today, the flux of extraterrestrial matter to Earth is mainly fine-grained cosmic dust. Although rarely discussed in a prebiotic context, cosmic deposits are known to form by sedimentary processes. Here we combine constraints on this aspect with simulations of dusty accretions to show that localized sediments could well have accumulated in early Earth environments such as glacial cryoconite materials. (Excerpt)

However, although these mechanisms operate across different spatial scales and timescales, they are not mutually exclusive. Thermally processed deposits of exogenous organic matter may have degassed HCN into lake systems fed by glacial meltwater rich in P and S sourced from locally dissolving cosmic dust. Taken together with recent findings from geology, astronomy and prebiotic chemistry, our results provide sup port for the fertilization of prebiotic chemistry by cosmic dust on early Earth. Furthermore, cosmic dust is potentially a widespread and flexible planetary fertilizer, being accreted in quantities that may be assessed by observation9,65 to potentially habitable exoplanets. (7)

Quickening Evolution > Nest > Microbial

Biswas, Kuheli and Naama Brenner. Universality of phenotypic distributions in bacteria. Physical Review Research. 6/L022043, 2024. We record this paper in a physics journal by Network Biology Research Laboratory, Technion - Israel Institute of Technology bioengineers as an exemplary verification this year of a recurrent consistency which distinguishes this vast prokaryotic phase. Once again, a doubleness of an overt domain which arises from and is guided by an independent ecode source is quite evident.

Some phenotypic properties in bacteria exhibit recurrent statistics, with distributions collapsing under scaling. The extent and origins of such a universality are not well understood. By way of models for growth and division, we identify compound “shape factors” that describe the distributions throughout a large set of single-cell data. We find that the emergence of common distributions is associated with robust shape factors across many conditions which explain the universal cell sizes, and highly expressed protein content.

Quickening Evolution > Nest > Microbial

Kacar, Betul. Foundations for reconstructing early microbial life.. arXiv:2406.09354. A University of Wisconsin bacteriologist proposes that a better comprehension of how this primal prokaryotic stage originally managed to survive and thrive as a guide to our present climate stresses.

For more than 3.5 billion years, life had extreme environmental conditions which include shifts from oxygen-less to over-oxygenated atmospheres and cycling between hothouse Earth and glaciations. Meanwhile, the planet evolved from a long microbial stage to plants and animals. Many cellular attributes evolved which collectively define our biosphere and now concern our human fate. In regard, a new disciplinary synthesis is needed to learn how microbes survived an ever changing globe over deep time. This review describes an emerging area in microbiology and evolutionary synthetic biology so to reconstruct the earliest microbial innovations.

Quickening Evolution > Nest > Microbial

Puri, Devina and Kyle Allison. Escherichia coli self-organizes developmental rosettes. PNAS. 121/23, 2024. Emory University and Georgia Institute of Technology biomedical engineers are able to discern the further presence of these cellular metabolic patternings in a prokaryotic microbe. Akin to embryonic somitogenesis, living systems of every kind are being found to to arrange and array themselves by way of iconic similarities.

Rosettes are self-organizing, circular multicellular communities that initiate developmental processes like organogenesis and embryogenesis in complex organisms. Though common in eukaryotes, this multicellular behavior has not been reported in bacteria. In this study, we found that Escherichia coli forms rosettes by active sister-cell repositioning. We went on to show that proper rosette formation was required for morphogenesis of multicellular chains, rpoS gene expression, and hydrostatic clonal-chain biofilms. These findings establish self-organization of clonal rosettes by a prokaryote and have implications for evolutionary biology, synthetic biology, and medical microbiology. (Excerpt)

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