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Displaying entries 46 through 60 of 88 found.

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

Lyons, Timothy, et al. Co‐evolution of early Earth environments and microbial life. Nature Reviews Microbiology. May, 2024. Akin to many current studies herein, UC Riverside, University of Alberta, Dartmouth, MIT, and University of Washington researchers can now proceed, so it seems, to recover, quantify and fill in the entire continous course from the physical ecosmos to a prokaryote milieu as it forms a viable ecosphere.

Two records of Earth history evoke the ascent of life and its co-evolving ecosystems: the geobiological and geochemical traces preserved in rocks and the evolutionary histories within genomes. In this Review, we explore the history of microbial life on Earth and the degree to which it shaped, and was shaped by, transitions in the chemical properties of the oceans, continents and atmosphere. We examine the diversity and evolution of early metabolic processes, their couplings with biogeochemical cycles and links to the oxygenation of the early biosphere. We discuss the distinction between the beginnings of metabolisms and their subsequent proliferation and their capacity to shape surface environments on a planetary scale. (Excerpts)

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.

Moody, Edmund, et al. The nature of the last universal common ancestor and its impact on the early Earth system. Nature Ecology & Evolution.. July, 2024. Nineteen paleobiochemists in the UK, across Europe and onto Okinawa, including Tim Lenton and Nick Lane, post a thorough recognition to date, bolstered by the latest instrumental and computational techniques, of this long supposed ancient, rudimentary bacterial precursor.

The nature of the last universal common ancestor (LUCA) with regard to its age and Earth system impact has been the subject of debate across diverse disciplines. Here we infer that LUCA lived ~4.2 Ga ago through divergence time analysis of pre-LUCA gene duplicates, microbial fossils and isotope records. Our results suggest LUCA was a prokaryote-grade anaerobic acetogen was part of an established ecological system. The metabolism of LUCA would have provided a niche for other microbial community members and hydrogen recycling by atmospheric photo chemistry could have supported a modestly productive early ecosystem.

Montrose, Kristopher, et al. Proteostatic tuning underpins the evolution of novel multicellular traits. Science Advances. 10/10, 2024. University of Helsinki and Georgia Tech biologists postulate still another deep, biomolecular driver of life’s insistent transition to a major whole organism phase.

The evolution of multicellularity paved the way for the origin of complex life on Earth, but little is known about the mechanistic basis of early multicellular evolution. Here, we examine its molecular basis in the long-term evolution experiment known as MuLTEE. We demonstrate that cellular elongation, a key adaptation for increased biophysical toughness and organismal size, is driven by the chaperone component Hsp90. Altogether, our results show how ancient protein folding systems can be tuned to drive rapid evolution at a new level of biological individuality by revealing novel developmental phenotype. (Excerpts)

Deng, Jie, et al. The development of ecological systems along paths of least resistance.. . Into this year, MIT, Stanford, Princeton and Universitat Pompeu Fabra theorists including Simon Levin and Ricard Sole review an advanced confluence of the environmental sciences which moves them to suggest the actual presence of independent, recurring patterns and processes that provide a general orderliness across disparate flora and fauna bioregions

A crucial question in biology is whether there are common principles that imbue the development of ecosystems independent of organismal diversity and environmental context. Ecological theory holds that these systems proceed by a sequenced orderly process from fast-growing to slow-growing taxa. However, it is possible that this is just the path of least resistance. Here, we show that the order from fast-to slow-growth is the likely path when local taxon self-organize for species survival. Using data from bacterial and metazoan systems, we quantify that ecosystems do move along paths of least effort. As simple principles come to explain a basic trend like this they portend an enhanced understanding of the collective features characterizing the prolific biosphere vitalities. (Abstract excerpt)

Historical contingency (environmental conditions) seems to modulate the dynamics of shor- term ecological systems while convergent evolution seems a plausible explanation for finding long-term solutions to an environmental challenge. Our work suggests that accounting for this feasible least resistance will be a step towards the longstanding aim of understanding the expected outcomes of repeating the tape of life. (9)

Madsen, Anastasia and Shermin de Silva. Societies with fission–fusion dynamics as complex adaptive systems: the importance of scale.. Philosophical Transactions of the Royal Society B.. July, 2024. This paper in a special Connected interactions: enriching food web research by spatial and social interactions issue by UC San Diego behavioral ecologists is a good example of how the complexity sciences can be applied to foster a new phase of integral understandings. See also herein From nets to networks: tools for deciphering phytoplankton metabolic interactions within communities and their global significance by Charlotte Nef, et al which provides a further network dimension

In this article, we argue that social systems with fission–fusion (FF) dynamics are best characterized within a complex adaptive systems (CAS) framework. We discuss how endogenous and exogenous factors drive scale-dependent network properties across temporal, spatial and social domains. Importantly, this view treats the dynamics themselves as objects of study. CAS theories allow us to interrogate FF activities in taxa that do not conform to prior views of sociality and suggest new questions regarding stability and change in social systems, that would lead to system-level reorganization. (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)

Koch, Christof. Then I Am Myself the World: What Consciousness Is and How to Expand It. New York: Dutton,, 2024. The natural neuroscientist philosopher (search) continues his quest for a viable understanding of our very human sentient, knowledgeable awareness. His subjects are both his own emotional senses and their essential situation within a conducive cosmos. .In regard, his main thematic guide is integrated-information theory see section) which he endorses and embellishes. In all, the 2020s contribution illumes and presages our personal and planetary awakening to a new, phenomenal procreativity.

In his latest contribution, Christof Koch explores the only thing we directly experience: consciousness. The text proceeds to investigate the physical origins in the brain and how this basis can be used to measure consciousness in natural and artificial systems.   He explains when and where can degrees of consciousness exists, in consideration of major social and scientific questions: When does a fetus first become self-aware? Can psychedelic and mystical experiences transform lives? What happens to consciousness in near-death experiences? Why will generative AI ultimately be able to do the very thing we can do, yet never feel any of it? And do our experiences reveal a single, objective reality?

The brain is the most complex piece of self-organized matter in the known universe. By no coincidence, it is the organ of consciousness. Unlike advances in genomics and astrophysics, progress in understanding the brain and mind directly relates to who we are, our strengths and infirmities and whether we partake of some larger, ultimate reality which we can and will discover. (13)

Christof Koch is a neuroscientist at the Allen Institute and the Tiny Blue Dot Foundation, and a former professor at the California Institute of Technology.

Sameul, Sigal. What if absolutely everything is conscious?.. vox.com/future-perfect/353430/what-if-absolutely-everything-is-conscious.. Scientists spent ages mocking panpsychism. Now, some are warming to the idea that plants, cells, and even atoms are conscious. We record this essay because it is a well-researched, wide ranging, sensitive survey of this historic, once and future revision. Along the way the views of Galen Strawson, Audrey Dussutour, Michael Levin and others are considered. An ecosmic consciousness now seems to be dawning, this time with scientific and philosophical groundings as a prime revolutionary basis.

Sigal Samuel is a senior reporter for Vox’s Future Perfect. She writes primarily about the future of consciousness, tracking advances in artificial intelligence and neuroscience along with ethical implications. Before joining Vox, Sigal was the religion editor at the Atlantic.

Mendoza-Halliday, Diego, et al. A ubiquitous spectrolaminar motif of local field potential power across the primate cortex.. Nature Neuroscience. 27/3, 2024. Seventeen neuroresearchers mainly based at MIT and Vanderbilt University along with others in the Netherlands, China and Canada report the presence of a second stratified array of cerebral functions across several relative species all the way to human cogitation.

The mammalian cerebral cortex is anatomically organized into a six-layer motif. But it is unknown whether a laminar motif of neuronal activity patterns exists across the cortex. Here we report such a motif in the power of local field potentials (LFPs). Using laminar probes, we recorded LFPs from 14 cortical areas across the cortical hierarchy in five macaque monkeys. We found a ubiquitous spectrolaminar pattern with a deep-to-superficial layer gradient of high-frequency power and a superficial-to-deep gradient of alpha-beta power. Laminar recordings from other species showed that this pattern is highly preserved among primates—macaque, marmoset and human. (Excerpt)

Nern, Aljoscha, et al. Connectome-driven neural inventory of a complete visual system.. bioRxiv.. Some sixty Janelia Research Campus, Howard Hughes Medical Institute neuroscientists achieve a first overall quantification of this cerebral faculty with both detail and expanse. A surmise is then made that although performed on an archetypal insect model its generic format seems extend through life’s evolutionary procession to our curious selves.

Vision provides animals with detailed information such as color, form, and movement across the visual scene. Computing these spatial features requires a large, diverse network of neurons, such that in animals as distant as flies and humans, these regions comprise half the brain’s volume. Here, we report a new connectome mapping of the right optic lobe from a male Drosophila central nervous system. Altogether, this comprehensive set of tools and data unlock new possibilities for systematic investigations of vision in Drosophila, a foundation for a deeper understanding of sensory processing. (Excerpt)

Ros‑Rocher, Nuria and Thibaut Brunet.. What is it like to be a choanoflagellate? Sensation, processing and behavior in the closest unicellular relatives of animals. Animal Cognition. 26/1767, 2024. In this convergent year, Evolutionary Cell Biology and Evolution of Morphogenesis Unit, Institut Pasteur, Université Paris neuroresearchers contribute to analyses of life’s consistent neural and cognitive embellishment beginning with their deepest rudimentary yet acute stirrings.

All animals evolved from a single lineage of unicellular precursors more than 600 million years ago. Thus, the biological and genetic foundations for animal sensation, cognition and behavior must necessarily have arisen by modifications of pre-existing features in their unicellular ancestors. Here, we reconstruct the perceptive environs inhabited by choanoflagellates, a group of aquatic microeukaryotes. Existing evidence shows that they are capable of chemo, photos and mechano-sensation processes that resemble those in animal sensory cells. We discuss how facultative multicellularity in choanoflagellates might help us understand how evolution displaced the locus of decision-making from a single cell to a collective, and how a new space of behavioral complexity might have become accessible in the process. (Abstract)

Discussion: From microbial behavior to animal cognition Although data remain scarce, it is already clear that choanoflagellates have complex perceptive abilities and behaviors: they display at least eight sensory modalities, and as many behavioral outputs (Fig. 2). Almost inevitably, many more must exist, as suggested by the complex molecular repertoire of putative sensory receptors encoded in the choanoflagellate genomes and transcriptomes.

Venditti, Chris. et al. Co-evolutionary dynamics of mammalian brain and body size. Nature Ecology & Evolution. 8/8, 2024. University of Reading and Durham University bioanthropologists including Robert Barton (search) describe a latest geometric measurement technique by which to quantify this title timeline. We record to acknowledge and consider.

Despite decades of comparative studies, puzzling aspects of the relationship between mammalian brain and of body mass continue to defy satisfactory explanation. Here we show that several issues arise from fitting log-linear models to the data because, as we argue, the correlated evolution of brain and body mass is in fact log-curvilinear. By way of scaling relationships, we document varying rates of relative brain mass evolution across the mammalian phylogeny. As a result, we find a trend in only three orders, with the strongest in primates as it sets the stage for the rapid directional increase that produced the computational powers of the human brain.

Mitchell, Kevin and Nick Cheney. The Genomic Code: The genome instantiates a generative model of the organism. . . Into 2024, a Trinity College, Dublin neuro-geneticist (search) and a University of Vermont computational biologist (see NC website) propose to join neural net learning methods with views of life’s cognitive emergence, as this section conveys, to advance an integral understanding.

dynamic relationship between the genome and organismal form. Here, we propose a new analogy inspired by machine learning and neuroscience whence the genome becomes a compressed space of latent variables which are DNA sequences that specify the biochemical properties of encoded proteins. Collectively, these comprise a connectionist network that is encoded by an evolutionary learning algorithm. An energy landscape then constrains a self-organising development so as to produce a new individual, akin to Conrad Waddington’s epigenetic landscape. (Abstract)

Rosslenbroich, Bernd, et al. Agency as an Inherent Property of Living Organisms. Biological Theory.. August, 2024. Institute of Evolutionary Biology and Morphology Centre, Witten/Herdecke University, Germany contribute a current, definitive explanation and endorsement of manifest evolutionary scales and degrees of personal, proactive liberties all the way to ourselves.

A central characteristic of living organisms is their intrinsic activity with regard to basic life processes and behavior in the environment. While some debate goes on, we contend that such agency is immanent in living organisms. In regard, we identify several organismic levels to capture different qualities that occur or transform during evolution. An example is an ontogenetic level of directed agency that includes preconceived goals. An enhanced physiological and behavioral autonomy then extends the evolutionary scope of self-generated, flexible actions and reactions.

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