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Displaying entries 46 through 60 of 84 found.

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

Wong, Michael, et al. On the roles of function and selection in evolving systems. PNAS. 120/43, 2023. Into the mid 2020s, nine Carnegie Institution for Science and University of Colorado senior scientists including Carol Cleland and Robert Hazen can now see fit to discern a central, definitive evolutionary course in terms of a relative increase in “functional information.” The paper provides an early technical description but also view 2024 talks by RH (google terms) for latest summaries. The text first introduces the very idea that any such temporal quantitative vector may now be evident at all, which has long been ruled out in biological schools.

The universe is replete with complex evolving systems, but the existing macroscopic physical laws do not seem to adequately describe these systems. Recognizing that the identification of conceptual equivalencies among disparate phenomena were foundational to developing previous laws of nature, we approach a potential “missing law” by looking for equivalencies among evolving systems. We suggest that all evolving systems—including but not limited to life—are composed of diverse components that can combine into configurational states that are then selected for or against based on function. We then identify the fundamental sources of selection—static persistence, dynamic persistence, and novelty generation—and propose a time-asymmetric law that states that the functional information of a system will increase over time when subjected to selection for function(s). (Significance)

A more deeply rooted factor in the absence of a law of evolution may be the reluctance of scientists to consider “function” and “context” in their formulations. A metric of information that is based on functionality suggests that considerations of the context of a system alters the outcome of a calculation, and that this context results in a preference for configurations with greater degrees of function. An asymmetric trajectory based upon functionality may seem antithetical to scientific analysis. Nevertheless, we conjecture that selection based on static persistence, dynamic persistence, and novelty generation is a universal process that results in systems with increased functional information. (Conclusion)

Yadav, Manush, et al. Evolution beats random chance: Performance-dependent network evolution for enhanced computational capacity.. arXiv:2403.15869. As historic mechanism, computational, and organismic schools now proceed to cross-inform and assimilate each other within an ecosmic revolution, Cyber-Physical Systems, Technische Universit Berlin and Indian Institute of Science Education and Research, Punjab theorists advance new evolutionary perceptions as the living system sciences become distinguished and defined by complex network dynamics and deep algorithmic programs.

The quest to understand structure-function relationships in networks across scientific disciplines has intensified. However, the optimal architecture remains elusive for complex information processing. We investigate how specific structures form to solve distinct tasks using a novel method of performance-dependent network evolution by way of reservoir computing principles. Our findings not only serve an understanding of process-specific network evolution but also shed light on the optimum design of complex information processing mechanisms. (Abstract)

García-Valdecasas, Miguel and Terrence Deacon. Origins of biological teleology: how constraints represent ends. Synthese. August, 2024. University of Navarra, Spain and a UC Berkeley (search) anthropologists propose a latest integrity of biomolecular autopoietic processes with personal purpose across evolution as a further basis for life’s oriented course.

To naturalize the concept of teleological causality in biology one needs to specify how the causality of organisms is distinct from designed artifacts or the increase of entropy. Historically, this oriented view has been based on an analogy with purposeful action. In this regard, to bridge the gap between biology and human agency we describe a simple molecular process called autogenesis that shows how complementary self-organizing processes can give rise to higher-order relations that resemble goal-like dispositions. Because the autogenic model is described in sufficient detail to be empirically realizable, it provides a proof of principle for a basic form of teleological causality.

Our molecular model described by autogenesis satisfies the five criteria for teleological causality in Section 1. First, its target-direction is not reducible to external factors, but due to the holistic constraints on its self-organizing processes that maintain its discrete individuality. Second, is constitutive because the linkage between these reciprocal constraint-generating processes by a molecule that makes them co-dependent. Third, it is disposed to prevent its component self-organizing processes from reaching their terminal states. Fourth, it is normative, so as to maintain the causal capacity of which it is its own beneficiary. And fifth, its hologenic nature can impose what might be considered the general description of an end onto new physical substrates. (24)

Huang, Wentao, et al. Near-collapse of the geomagnetic field may have contributed to atmospheric oxygenation and animal radiation in the Ediacaran Period. Communications Earth & Environment. Vol. 5/Art. 207,, 2024. A seventeen member international team at the University of Rochester, across the US onto Brazil and South Africa perceptively identify and qualify an additional planet scale factor which seems to have influenced life’s often stochastic but oriented evolutionary development.

Earth’s magnetic field is known to be in an unusual state when macroscopic animals of the Ediacara Fauna diversified and thrived (635 – 540 MYA). But any connection between these events remains unclear. Here, we present single crystal paleointensity data from pyroxenites and gabbros that define an intensity decline from a strong Proterozoic field like today to an Ediacaran value 30 times weaker. This concurrence raises the question of whether enhanced H ion loss in a reduced magnetic field contributed to the oxygenation, ultimately allowing diversi fication of macroscopic and mobile animals.

Mathis, Cole, et al. Self-Organization in Computation & Chemistry: A Return to AlChemy. arXiv:2408.12137. Arizona State University, University of Michigan, and Santa Fe Institute complexity theorists including Stephanie Forrest provide a 30 year update to an original attempt to inform reaction networks with novel computational aspects. As the Abstract says, the approach can presently yield new insights into nature’s seemingly innate propensity to engender complex, viable, evolving entities.

How do complex adaptive systems such as life emerge from constituent parts? In the 1990s Walter Fontana and Leo Buss proposed an approach based on a computation model known as λ calculus whereby simple rules within in large space of possibilities could yield complex, dynamic stable biochemical reaction networks. Here, we revisit this classic model, called AlChemy, to study those results using current computing resources. Our analysis now reveals that complex, stable organizations emerge more frequently than expected, and are robust against collapse. We conclude with applications of AlChemy to self-organization in programming languages and to the origin of life.

Rimmer, Paul and Oliver Shorttle. A Surface Hydrothermal Source of Nitriles and Isonitriles. Life. 14/4, 2024. Cavendish Laboratory and University of Cambridge astrobiologists cite even more apparent biomaterial occasions and reasons for life’s inexorable coming together int increasingly complex, ascendant vitalities. See also Symmetry breaking and chiral amplification in prebiotic ligation reactions Min Deng, et al in Nature (626/1019, 2024).

Giant impacts can generate transient hydrogen-rich but carbon poor atmospheres. The result is that local regions of the Hadean crust were plausibly saturated with graphite. We explore the consequences for a prebiotic surface hydrothermal vent scenario. The equilibrium with graphite purifies the leftover gas, resulting in substantial quantities of nitriles and isonitriles relevant for biochemical precursors. We use these results to predict gas-phase concentrations of methyl isocyanide of ∼1 ppm which can participate in the non-enzymatic activation of the monomeric building blocks of life. (Excerpt)

Kacar, Betul. Reconstructing Early Microbial Life.. Annual Review of Microbiology. August, 2024. In this comprehensive status paper, a University of Wisconsin bacteriologist (search) describes the latest views about life’s prokaryotic biosphere from its ancient, foundational onset all the way to our human microbiomes and beyond to a new phase of a beneficial makeover.

For more than 3.5 billion years, life experienced environmental extremes on Earth such as shifts to oxygenated atmospheres, hothouse conditions and global glaciations. Meanwhile, an ecological revolution took place. Earth evolved from only microbial life to the plants and animals that are familiar today. However, the incorporation of molecular genetics, population biology, and evolutionary biology approaches into the study of Precambrian biota remains a significant challenge. This review synthesizes our current knowledge of early microbial life and describes a frontier area that integrates microbiology, paleobiology, and evolutionary synthetic biology to reconstruct ancient biological innovations. (Abstract)

Sher, Daniel, et al. Quantitative principles of microbial metabolism shared across scales.. . . Nature Microbiology., 2024. By this year, our Earthuman collective studies of life’s prokaryotic foundation now enables Boston University and MIT researchers to discern common, recurrent characteristics across its multifaceted film-like assemblies. See also Recent advances in deep learning and language models for studying the microbiome by Binghao Yan, et al. arXiv:2409.10579 for a concurrent survey.

A metabolism is the complex network of chemical reactions within every cell and organism, maintaining life and mediating ecosystems. Here we highlight principles that exhibit commonalities across scales, which could help achieve an integrated perspective on microbial life. The mechanisms underlying these flows, such as enzyme–substrate interactions, often are represented by equations like those that characterize cells and resources or predators and prey. We propose that these formal similarities reflect shared principles and discuss how their investigation may contribute to a common language for studying microbial metabolism across scales.

Yan, Binghao, et al. Recent advances in deep learning and language models for studying the microbiome.. arXiv:2409.10579. Akin to advances in genetic studies, University of Pennsylvania, Vanderbilt University Medical Center, University of South Florida and University of Pittsburgh investigators report how novel AI linguistic methods can be readily adapted for better analytic understandings of bacterial communities.

Recent progress in deep learning and large language models (LLMs) have revolutionized how researchers study microbiome and metagenomics data. Microbial protein and genomic sequences, like natural languages, form a language of life, enabling the adoption of LLMs to extract useful insights from complex microbial ecologies. We review applications of deep learning and language models in analyzing microbiome and metagenomics data with an overview of protein/genomic language modeling and microbiome studies. We also discuss novel viromics language modeling, biosynthetic gene cluster prediction, and knowledge integration for metagenomics studies. (Abstract)

The microbiome refers to the collective genomes of microorganisms residing in a specific habitat, such as human body sites (e.g., gut, skin, airway) and environments (e.g., air, soil, water). Metagenomics research involves the direct profiling and analysis of these microbial communities’ genomic sequences, bypassing the need for isolating and culturing individual members. This approach allows for a comprehensive assessment of microbial diversity, functions, and dynamics within their natural contexts. (1)

Araujo, Gui, et al. A mechanistic framework for complex microbe-host symbioses. Trends in Microbiology.. September, 2024. Swansea University, Swansea, UK, Theoretical and Experimental Ecology Station, CNRS, France, University of New South Wales, and University of Tasmania contribute to the current, revived admission of nature’s pervasive utility of active mutual reciprocities across every organismic domain in their relative evolutionary environs. But they still need to couch it, so it seems, in an inorganic basis to avoid any sense of a vitalist milieu.

Virtually all multicellular organisms live in symbiotic associations with complex microbial communities, aka the microbiome. Recently, the analyses of numerous microbiomes have revealed an incredible diversity of symbionts. Here we explore and summarise the suite of ecological and evolutionary mechanisms identified as relevant to microbiomes. complexity and diversity. We argue that microbiome assembly is a dynamic product of ecology and evolution at various spatio-temporal scales. We develop a cohesive foundation for the theoretical understanding of the combined effects of ecology and evolution on the assembly of complex symbioses.

Crockett, William, et al.. Physical constraints during Snowball Earth drive the evolution of multicellularity. Proceedings of the Royal Society B. June, 2024. With regard to this major biological transition event, WC, MIT, Jack Shaw and Chris Kempes, Sante Fe Institute and Carl Simpson, University of Colorado factor in a global environmental influence which they say impelled microorganisms to band together for sheer survival. As the quotes advise, in retrospect as the whole scenario becomes filled in and fleshed out it does seem to reveal an innate, sequential drive and direction across life’s stratified emergence. See also Experimental Snowball Earth Viscosity Drives the Evolution of Motile Multicellularity by Andrea Halling, et al in bioRxiv (February 8, 2024).

Molecular and fossil evidence suggests that complex eukaryotic multicellularity evolved during the late Neoproterozoic era, coincident with Snowball Earth glaciations, where ice sheets covered most of the globe. During this period, environmental conditions were extreme with significant effects on resource availability and optimal phenotypes. By testing novel hypotheses, we show how multicellularity was likely acquired differently in eukaryotes and prokaryotes owing the biophysical and metabolic regimes they inhabit. These results suggest that adverse conditions during Snowball Earth glaciations gave multicellular eukaryotes an evolutionary advantage, paving the way for the complex organism lineages that followed. (Excerpt)

Each new level of life’s organization can be associated with an event in evolutionary history that changed the state of the evolutionary game. By adding a new hierarchical level to the organization of organisms, these major transitions in individuality added new niches to the ecosystem (e.g. trophic) and introduced new phenotypes. Such transitions include the origin of cells, eukaryotes, multicellularity, and colonial and social organisms. (1)

While each of these features plays an important role in differentiating eukaryotic and prokaryotic multicellularity, none provides a definitive answer for the 1.5 billion year gap between eukaryogenesis and the emergence of complex multicellular lineages. The Neoproterozoic Snowball Earth glacial events provide an environmental driver that our models show would have selected for multicellular morphologies during this time period, helping explain the lag between eukaryogenesis and the proliferation of complex multicellularity. (9)

Parker, Joseph. Parker, Joseph. Organ Evolution: Emergence of Multicellular Function.. Annual Review of Cell and Developmental Biology.. June, 2024. As the abstract notes, a CalTech bioengineer contributes new reasons how and why segmented, modular living systems came together for mutual benefit on this course of nested complexity.

Instances of multicellularity across the tree of life have fostered the evolution of complex organs composed of distinct cell types that cooperate and produce emergent biological functions. To study how organs originate I propose a cell- to organ-level transitions framework, whereby a division of labor sets in between cell types by functional niche creation, cell type and ratcheting of cell interdependencies. These discrete components of functional variation may be deployed or combined within cells to introduce new properties into multicellular niches, or partitioned across cells to establish division of labor. (Excerpt)

Reeves, Jonathan, et al. Searching for the earliest archaeological record: insights from chimpanzee material landscapes.. Journal of the Royal Society Interface. August, 2024. JR, Lydia Luncz and Tomos Proffitt, Technological Primates Research Group, MPI Evolutionary Anthropology and Soiret Serge Pacome, Laboratoire de Zoologie et de Biologie Animale, Université Félix Houphouët-Boigny, Côte d’Ivoire, West Africa provide a latest detailed recovery of how our primate forebears learned how to make these initial implements.

The origin of tool use is a central issue in human evolutionary studies. Plio-Pleistocene core and flake methods represent the earliest evidence of tool use in the human lineage. Here, we present a landscape-scale study of the chimpanzee (Pan troglodytes verus) material culture from the Djouroutou Chimpanzee Project, Taï Forest, Cote d’Ivoire. This study explores the interplay between behavioural and environmental factors in shaping the stone record of nut cracking. We gain insight into the range of signatures that may be associated with a pre-core and flake archaeological record, providing new expectations for an earlier record of tool use. (Excerpt)

Life’s Cerebral Cognizance Becomes More Complex, Smarter, Informed, Proactive, Self-Aware

Frank, Steven A.. Circuit design in biology and machine learning.. arXiv:2408.09604.. A latest entry by the UC Irvine evolutionary biologist. See his website for a lifetime stream of insightful papers.

Current biomedicine focuses on the genetic components of cells and their biochemical dynamics. This approach views an emergent complexity, which constrains any micro-intervention in living hardware. Here, I explore a recent complementary field: diverse intelligence, which studies how a wide range of systems reach specific goals. Using tools from behavioral science and multiscale neuroscience, we address development, regenerative repair, and cancer as behaviors of a collective intelligence of cells as it navigates possible morphologies, transcriptional and physiological states.

A biological circuit is a neural or biochemical cascade, taking inputs and producing outputs. This article steps through two classic machine learning models to set the foundation for analyzing broad questions about the design of biological circuits. One observance is the central role of internal models of the environment embedded within biological circuits, illustrated by dimensional reduction and trend prediction. Overall, many challenges in biology have machine learning analogs, suggesting hypotheses about how biology's circuits are designed. (Excerpts)

Goff, Philip. Why? The Purpose of the Universe. Oxford: Oxford University Press, 2024.. Oxford: Oxford University Press, 2024. A latest insightful volume by a Durham University, UK philosopher who senses that the real presence of ascendant life and mind in an apparent conducive cosmos must have some intrinsic place and significance.

Why are we here? What's the point of existence? On the 'big questions' of meaning and purpose, Western thought has been stuck with the dichotomy of traditional religion and secular atheism. Through an exploration of contemporary cosmology and new research on consciousness, Goff argues for cosmic purpose: the idea that the universe is directed towards certain goals, such as the emergence of life. Ultimately, the work outlines a way of living in hope that some universal creativity is still unfolding, which appears to involve human beings.

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