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Displaying entries 46 through 60 of 104 found.

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

Chojnacki, Leilee, et al. Chojnacki, Leilee, et al. Gravitational wave analogues in spin nematics and cold atoms. Physical Review B. 109/L220407, 2024. Theory of Quantum Matter Unit, Okinawa Institute of Science and Technology, University of Tokyo, Keio University, Japan and Rice University physicists cleverly draw upon an apparent affinity between an atomic state and gravity waves as a way to study this celestial phenomena. See also Statistical Patterns in the Equations of Physics and the Emergence of a Meta-Law of Nature by Andrei Constantin, et al at arXiv:2408.11065 for another current instance. Once again, into the mid-2020s, 80 years after WWII, a steady, recurrent consilience is becoming evident across the widest infinities.

Many large-scale phenomena in our Universe, such as gravitational waves, are difficult to reproduce in laboratory settings. However, parallels with condensed matter systems can provide an alternative experimental accessibility. Here we show how spin nematic phases provide a low-energy route for accessing the physics of linearized gravity. We show at the level of the action that the low-energy effective field theory describing a spin nematic is in correspondence with that of linearized gravity. We then cite a microscopic model of a spin-1 magnet whose excitations in the low energy limit disperse, massless spin-2 Bosons which are in one-to-one correspondence with gravitational waves.

Thus far, several condensed matter systems have been suggested to mimic features of gravity, with much focus on reproducing the effects of curved spacetimes. Tensor analogs leading to rich gravitational phenomena exist, and have been measured, in the context of superfluid 3He. Acoustic analogs of gravitational phenomena were suggested and later measured, with further promising experimental can didates in semimetals, in quantum Hall systems, in optics [10,11] and in cold atoms. In this Letter, we identify a parallel between gravitational waves and the Goldstone modes of quantum spin nematics, and suggest two routes for their experimental real ization.. (1)

Madhanagopal, Bharath, et al. The unusual structural properties and potential biological relevance of switchback DNA. Nature Communications. 5/6636, 2024. A team of eight biogeneticists at SUNY Albany avail the latest instrumental methods and computational visualizations to come upon and illume a polar opposite version of the DNA helical coil. As a result, they can proceed with a retinue of novel properties.

Synthetic DNA motifs form the basis of nucleic acid nanotechnology. Here, we present a detailed characterization of switchback DNA, a globally left-handed structure composed of two parallel DNA strands. Compared to a conventional duplex, this form shows lower thermodynamic stability but exhibits enhanced biostability. Strand competition and strand displacement experiments show that component sequences have a preference for duplex complements. We hypothesize a potential role for switchback DNA as an alternate structure in sequences containing short tandem repeats which can open new avenues in biology and nanotechnology. (Excerpt)

In this work, we present a detailed characterization of a DNA motif called switchback DNA. Although the motif and its self-assembly into a lattice were recently reported, the biochemical and biophysical prop erties of this molecule are unknown. The impact of the unusual left-handed topology and parallel strand orientation on the physico-chemical properties of the motif is of potential interest in nucleic acid structure in general. We hypothesize that short tandem repeats may have the propensity to form switchback DNA as an alternate DNA structure and consider its potential role in biology and prospects in DNA nanotechnology. (2)

The RNA Institute at SUNY Albany is positioned to make significant contributions towards understanding the role of RNA in fundamental biological processes, developing RNA as a tool for science, and harnessing this knowledge to improve human health. The Institute brings together teams of researchers from multiple Departments and Universities with expertise in Biology, Bioinformatics, Chemistry, Engineering, Genetics, and Structural Biology.

Karollus, Alexander, et al. Species-aware DNA language models capture regulatory elements and their evolution. Genome Biology.. Vol. 25/Art 83, 2024. In this BMC journal, Technical University of Munich geneticists introduce an effective synthesis of these premier nucleotide and narrative code-script domains. By so doing, a cross-assimilation is achieved of these biomolecular and linguistic text phases to an extent they can be seen as the same descriptive process in different sequential venues. See also How do Large Language Models understand Genes and Cells Chen Fang, et al in bioRxiv preprints for March 27, 2024 and Gene and RNA Editing at arXiv:2409.09057.

Large-scale multi-species genome sequencing promises to shed new light on gene regulatory instructions. To this end, algorithms are needed that can leverage conservation while accounting for their evolution. Here, we introduce species-aware DNA language models trained on 800 species spanning 500 million years of evolution. We show that DNA language models distinguish transcription factor and RNA-binding protein motifs from background non-coding sequence. These results show that species-aware DNA language models are a powerful, flexible, and scalable tool to integrate information from large compendia of highly diverged genomes. (Abstract)

A typical eukaryotic genome contains large regions of non-coding DNA. Tese are not translated into proteins but contain regulatory elements which control gene expression in response to environmental cues. Finding these regulatory elements and elucidating how their combinations and arrangements determine gene expression is a major goal of genomics research and is of great utility for synthetic biology and personalized medicine. (1)

ConclusionIn this study, we trained language models on the genomes of hundreds of fungal species, spanning more than 500 million years of evolution. We specifically directed our attention to non-coding regions, examining the ability of the models to acquire meaningful species-specific and shared regulatory attributes when trained on the genomes of many species. To our knowledge, we are the first to show that LMs are able to transfer these attributes to unseen species.

Zhao, Xiangyi, et al. Irreversibility in Bacterial Regulatory Networks. arXiv:2409.04513. In a paper to appear in Science Advances, Northwestern University and University of Texas Southwestern Medical Center researchers including Adilson Motter take advantage of a widest compass to achieve an exemplary affinity for microbial and genetic phases with deep physical phenomena. In regard, here is another 2024 instance which roots living personal systems a whole scale encoded universality.

Irreversibility, in which a transient perturbation leaves a system in a new state, is an emergent property in systems of interacting entities. This feature has well-established implications in statistical physics but remains underexplored in biological phases. Focusing on the regulatory network of Escherichia coli, we examine responses to transient single-gene perturbations and find that irreversibility increases with the proximity of the perturbed gene to positive circuits. (Excerpt)

A common goal in both statistical physics and systems biology is to connect the attributes of microscopic entities with observable macroscopic properties. Of particular interest are macroscopic properties that are emergent—including pattern formation and synchronization because they arise from interactions between system entities and can therefore enable new system-level functionality. In statistical physics, an important property is the irreversibility of macroscopic processes, where entropy—a state function—can increase despite the time-reversibility of the microscopic dynamics. (1)

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

Duran-Nebreda, Salva, et al. Duran-Nebreda, Salva, et al. On the multiscale dynamics of punctuated evolution.. Trends in Ecology and Evolution. 39/8, 2024. Institut de Biologia Evolutiva, Barcelona, University of Tennessee, Vilnius University, Lithuania, American Museum of Natural History and Texas A&M University including Blai Vidiella, Sergi Valverde and Nils Eldredge himselfwho in 1972 along with Stephen Jay Gould formulated the original theory that life’s long developmental course seems to have proceeded by way of extended quiet periods interrupted by bursts of novel forms and properties. After a half century of wide and deep quantitative studies, this review indeed finds a broad semblance of such episodic patterns.

For five decades, paleontologists, paleobiologists, and ecologists have investigated patterns of punctuated equilibria in biology. Here, we step outside those fields and summarize recent advances in the theory of and evidence for this phenomena gathered from current observations in geology, molecular biology, genetics, anthropology, and sociotechnology. Altogether, our findings lead to a more general theory that we refer to as punctuated evolution. The quality of recent datasets support this expanded view in a way that can be modeled across a vast range from mass extinctions in ages past to the possible Anthropocene futures. (Abstract)

Prokopenko, Mikhail, et al. Biological arrow of time: Emergence of tangled information hierarchies and self-modelling dynamics. arXiv:2409.12029. By later 2024, ten coauthors from astrophysicists to computational biologists at the University of Sydney, ASU, University of Sussex, UCL, and Oxford including Paul Davies, Joseph Lizier, Geraint Lewis and Fernando Rosas can now post a comprehensive application of 21st century complex network systems theory to an equally expansive synthesis of life’s evolutionary emergence to be at last able to discern a central, orthogenesis-like course. In regard, the major sequential transitions scale provides a definitive, vectorial ascent mostly distinguished by relative genetic prescriptions and regnant individuality at each nested stage. See also On the roles of function and selection in evolving systems by Michael Wong, et al at PNAS (120/43, 2023) for another current intimation.

We study open-ended evolution by focusing on computational and information-processing dynamics underlying major evolutionary transitions. In doing so, we consider biological organisms as hierarchical dynamical systems that generate regularities in their phase-spaces through interactions with an environment. These emergent information patterns can then be encoded within an organism. Our main conjecture is that when macro-scale patterns continue on to micro-scale components, it creates tensions between what is encodable at an evolutionary stage and what may be realisable in the environment. This computation-theoretic argument can then be seen to trace a biological arrow of time. (Abstract excerpt)

In consideration of what the nested transitions have in common, they each involve major changes in individuality and how it perpetuates itself by novel inheritance modes of storing and transmitting information. Examples include replicating molecules which form cells as independent replicators, the DNA genetic code and proteins as enzymes; prokaryotes evolving into eukaryotes with a nucleus, and so on towards multicellularity and eusociality, as well as language and sociocultural evolution. (3)
Finally, we suggested that the biological arrow of time generates an oriented course of “information self-creation” by way of three canonical elements of computation: information preservation (memory/storage), information modification (processing), and information usage (communication). We propose that, in terms of dynamical systems, it is precisely this defined quality that forms a dimension for major evolutionary transitions along the biological arrow of time (23)

Slijepcevic, Predrag. Slijepcevic, Predrag.Principles of cognitive biology and the concept of biocivilisations... Biosystems. January, 2024. The Brunel University London biophilosopher provides an article synopsis of his 2023 book Biocivilisations: A New Look at the Science of Life. (London: Chelsea Green) which this abstract well conveys.

A range of recent studies promote the cognitive aspects of life: all organisms, from bacteria to mammals, are capable of sensing/perception, decision-making, problem-solving, learning, and other functions. In this paper I present a scientific and philosophical synthesis which is expressed through the four principles: (1) sentience and consciousness, (2) autopoiesis, (3) free energy and relational biology, and (4) behavioral repertoire. The principles reinforce themselves so that hierarchical and heterarchical shifts are widespread in the biosphere. As a result, I developed the concept of biocivilisations to identify and introduce a non-human social intelligence with equivalents of communication, engineering, science, medicine, art, and agriculture, in all kingdoms of life.

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.

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