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Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 46 through 60 of 131 found.


Systems Evolution: A 21st Century Genesis Synthesis

Quickening Evolution

Hazen, Robert. Chance, Necessity and the Origins of Life: A Physical Sciences Perspective. Philosophical Transactions of the Royal Society A. 375/2016.0353, 2016. We note this essay by the Carnegie Institute geochemist (search 2019) for its content and affinity to writings by the paleontologist George McGhee (2016, 2019 herein). They both reject Jacques Monod’s 1970 verdict that all is accident, and instead agree that while randomness is rife, an overall physical, geologic, biochemical, anatomic and physiologic evolution is constrained as it develops emergent scales of complexity and sentience. But any admission of an innate orthogenesis is a step that cannot yet be taken.

Earth's 4.5-billion-year history has witnessed a complex sequence of high-probability chemical and physical processes, as well as ‘frozen accidents’. Most models of life's origins similarly invoke a sequence of chemical reactions and molecular self-assemblies in which both necessity and chance play important roles. Recent research adds two important insights into this discussion. First, in the context of chemical reactions, chance versus necessity is an inherently false dichotomy—a range of probabilities exists for many natural events. Second, given the combinatorial richness of early Earth's chemical and physical environments, events in molecular evolution that are unlikely at limited laboratory scales of space and time may, nevertheless, be inevitable on an Earth-like planet at time scales of a billion years. (Abstract)

In 2015, we discovered that the diversity and global distribution of mineral species follow statistical patterns analogous to the arrangement and frequency of words in a book. Whereas a few words such as ‘a’, ‘and’ and ‘the’ are common in any book, the majority of different words are used rarely. On Earth, the resulting ‘large number of rare events’ (LNRE) distribution of minerals facilitates a calculation of the probabilities for more than 5000 chemical reactions. (2) Because this observed distribution of mineral species on Earth is analogous to that of words in a book, modification of lexical statistics facilitates application of LNRE models to characterize the diversity and distribution of Earth’s minerals. (3)

Chance versus necessity is a misleading dichotomy. Even if estimates of the four relevant parameters described above are in error by a few orders of magnitude, the implications of Earth’s combinatorial chemical richness are clear: chemical reactions that are improbable to reproduce at the short time scale and limited spatial dimensions of laboratory experiments—experiments, for example, requiring exacting physical and chemical conditions or unusual juxtaposition of several reactant molecules on an uncommon mineral surface—may be inevitable under the diverse physical and chemical environments possible at planetary scales of space and time. (7)

Quickening Evolution

McGhee, George. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. Cambridge: MIT Press, 2019. As 2020 nears, whence scientific studies in every field are coming together to presage a revolutionary vision, the Rutgers University paleontologist (search) provides an evidential treatise upon life’s propensity, aided by physical constraints, to repetitively develop and repurpose similar forms and functions across procession of myriad organisms. The first chapter, Convergence in Life Forms in the Seas and on the Land, sets the scene for creaturely internal anatomy and physiology, along with external sustenance forages, reproductive behaviors, and much more. McGhee goes on to advise that habitable exoplanets will hold to the same evolutionary convergence. He notes the Darwin’s Aliens paper by Samuel Levin, et al (International Journal of Astrobiology 18/1, 2019) to say that life’s “nested multilevel hierarchy of individuality” should generally be scaled in each instance. But he then recites the 13 reasons noted by M. Canales, et al (search) as to why our home ecoworld is so uniquely special, see third quote. In summary, it is noted while contingencies are surely in effect, an overall common trajectory will and need be followed.

Our Earth is a water world; 71 percent of the earth's surface is covered by water. The fossil record shows that multicellular life on dry land is a new phenomenon; for the vast majority of the earth's history—3,500 million years of its 4,560 million years of existence—complex life existed only in the oceans. Explaining that convergent biological evolution occurs because of limited evolutionary pathways, McGhee examines examples of convergent evolution in forms of feeding, immobility and mobility, defense, and organ systems. McGhee suggests that the patterns of convergent evolution that we see in our own water world indicate the potential for similar convergent forms in other water worlds.. (Publisher)

The first five of these strange things are Earth’s plate tectonic activity recycles ca rbon, necessary for life and habitable planetary climates, Earth’s atmosphere possesses an ozone layer which helps to shield life from solar radiation, Earth’s axial wobble is stabilized by its very large moon, which also moderates climate fluctuations, Earth’s many environmentally variable habitats aid an evolutionary diversity, and Earth’s strong magnetic field protects life from high-energy cosmic radiation and solar storms. (250)

The universe as it exists in our region was not improbably fashioned for odd living organisms, nor were odd living organisms made by a strange condition of the universe in our region – living organisms are the universe in one of its own manifestations. Namely, life as we know it is a manifestation of the universe at a particular point in space nd time in its evolution. And species of life on Earth that are self-aware – magpies, elephants, dolphins, apes, humans – are manifestations of the universe that has become aware of itself. (251)

Quickening Evolution

McGhee, George. Can Evolution be Directional Without Being Teleological? Studies in History and Philosophy of Science C. 58/93, 2016. The Rutgers University paleontologist (search 2019) weighs in on this misunderstood quandary, often due to misdefined terms, by saying that while random happenstance surely does occur, over the long haul due to structural limits and nature’s reuse of what works in kind, an ascendant course will be traversed. But it is then stated that this axial path does not imply an innate, independent aim or purpose. See also Life’s Biological Chemistry: A Destiny or Destination Starting from Prebiotic Chemistry by R. Krishnamurthy in Chemistry: A European Journal (24/63, 2018) which traces an oriented emergence from biochemicals to people, but denies any teleological direction, and Chance, Necessity and the Origins of Life by Robert Hazen (2016, 2019 search)

Convergent evolution reveals to us that the number of possibilities available for contingent events is limited, that historically evolution is constrained to occur within a finite number of limited pathways, and that contingent evolution is thus probabilistic and predictable. That is, the phenomenon of convergence proves that evolutionary processes can repeatedly produce the same, or very similar, organic designs in nature and that evolution is directional in these cases. For this reason it is argued that evolution can be directional without being teleological, and that the dichotomy that evolution must either be directionless and unpredictable or directional and predetermined (teleological) is false. (Abstract)

Quickening Evolution

Newman, Sturat. Inherent Forms and the Evolution of Evolution. Journal of Experimental Zoology B. Online August, 2019. The New York Medical College, Valhalla, theoretical experimentalist (search) has long studied and advocated the view that life’s creaturely forms arise from and manifest an intrinsic physical and mathematical basis. Here he comments on Bonner’s paper in this journal (June) which is a capsule of his 60 prolific years guided by this persuasion. In regard, Newman cites a growing trend to view the presence of the same structure, wing to limb, in descendent organisms. See also Inherency and Homomorphy in the Evolution of Development by SN in Current Opinion in Genetics (57/1, 2019), see third quote.

John Bonner presented a provocative conjecture that the means by which organisms evolve has itself evolved. The elements of his proposed model, namely the emergence of sex and enhanced selection pressures on larger multicellular forms, centers on a close mapping of genotypic to phenotypic change. He has also studied the intrinsic organizational properties of cell aggregates in social amoebae. By comparing the mechanistic bases of morphogenesis in the embryos of metazoans (animals), closely related holozoans, onto dictyostelids and volvocine algae, I conclude that understanding the evolution of multicellular evolution does indeed require knowledge of the inherent forms of diversifying lineages. (Abstract excerpt)

This approach stands outside of, but complements, the more gene-centric, adaptationist concepts of the major transitions in evolution scale, which are echoed in Bonner’s paper. As discussed her, and previously, the evolutionary transition from aggregates of unicellular organisms to the morphogenetically prolific Matazoa was a consequence of the acquisition of novel self-organizational capabilities, a factor that eludes selectionist explanatory frameworks. (6)

Inherency: The idea that aspects of the phenotype in development and evolution are latent in the organism’s material identity and that these features will spontaneously emerge if the conditions are appropriate.

Quickening Evolution

Powell, Russell and Maureen O’Malley. Metabolic and Microbial Perspectives on the “Evolution of Evolution". Journal of Experimental Zoology B. Online September, 2019. Boston University and University of Bordeaux philosophers of biology comment on John Bonner’s article with the above title (herein June) for a special issue. But this present paper, alongside structural biologist Bonner himself, Stuart Newman and Scott Gilbert, can illustrate a deep conceptual dichotomy. The major transitions model (see Abstract), along with the nested dimensions view of Eva Jablonka and Marion Lamb, and Newman who goes on to root life in a physical inherency, quite imply a directional procession. However P & O’M’s opening section is Broad Problem 1: Progressivism, which worries that these scalar views are at odds with past, vested denials of any teleological course and aim. As this quandary persists and resists, it begs a 21st century natural philosophy to sort out, clear up, and allow an actual evolutionary gestation to be realized. (See Powell’s new book Contingency and Convergence (MIT Press, Jan. 2020) for more.)

Identifying and theorizing major turning points in the history of life generates insights not only into epochal events but also the processes that bring them about. In his treatment of these issues, John Bonner identifies the evolution of sex, multicellularity, and nervous systems as enabling the “evolution of evolution,” which involves transformations in how life develops. By comparing his framework with two decades of major transitions scale theory, we identify some issues between Bonner's view and the prevailing literature. These problems include implicit progressivism, conceptual disunity, and a limited ability to explain major transformations. In contrast with the “vertical” focus on replication, hierarchy, and morphology that preoccupies most literature on major transitions, we propose a “horizontal” dimension in which metabolism and microbial innovations play an explanatory role in the broad‐scale organization of life. (Abstract)

Quickening Evolution

Sela, Itamar, et al. Selection and Genome Plasticity as the Key Factors in the Evolution of Bacteria. Physical Review X. 9/031018, 2018. In this physics journal, aided by current affirmations of a common repetition in kind everywhere, National Center for Biotechnology Information theorists I. Sela, Yuri Wolf and Eugene Koonin report that genomic phenomena takes on the form of a nested scale across many domains or classes. As their Summary below notes, the present re-unification and re-rooting of life in an increasingly fertile cosmos is well served by such evidential findings. See also a reference Family Specific Scaling Laws in Bacterial Genomes by Eleonora De Lazzari, et al in Nucleic Acids Research (45/13, 2017, second quote).

Sela, Itamar, et al. Selection and Genome Plasticity as the Key Factors in the Evolution of Bacteria. Physical Review X. 9/031018, 2019. In this physics journal, aided by current affirmations of a common repetition in kind everywhere, National Center for Biotechnology Information theorists I. Sela, Yuri Wolf and Eugene Koonin report that genomic phenomena takes on the form of a nested scale across many domains or classes. As their Summary below notes, the present re-unification and re-rooting of life in an increasingly fertile cosmos is well served by such evidential findings. See also a reference Family Specific Scaling Laws in Bacterial Genomes by Eleonora De Lazzari, et al in Nucleic Acids Research (45/13, 2017, second quote). OK

In microbes, different functional classes of genes, such as those involved in information processing, metabolism, and regulation, show scaling exponents with the genome size. However, there is no general theory to explain these “universal laws” of microbial genome evolution. Here, we describe a mathematical model that recovers the differential scaling of functional gene classes in bacterial genomes, includes only two parameters to characterize genomes, selection coefficient and plasticity. After testing the model against genomic data, we conclude that genome plasticity is a key evolutionary factor. Our findings suggest that at least some key aspects of genome evolution can be captured by general theoretical models akin to those widely used in physics. (Sela Summary)

Among several quantitative invariants found in evolutionary genomics, one of the most striking is the scaling of the overall abundance of proteins, or protein domains, which share a specific functional annotation across genomes of given size. The size of these functional categories change, on average, as power-laws in the total number of protein-coding genes. Here, we show that such regularities are not restricted to the behavior of high-level functional categories, but exist at the level of single evolutionary families of protein domains. Under the common assumption that selection is driven solely or mainly by biological function, these findings point to fine-tuned and interdependent roles of specific protein domains. (De Lazzari Abstract)

Quickening Evolution

Svorcova, Jana and Anton Markos. Epigenetic Processes and the Evolution of Life. Boca Raton: CRC Press, 2019. Charles University, Prague theoretical biologists (search AM) achieve a consummate review to date of life’s oriented, stirring “planetogenesis.” The inclusive survey set within a biospheric milieu proceeds from rudimentary metabolic and/or replicator origins onto unicells and organisms, with an emphasis upon evolving phases of genetic heredity. An informational, semiotic quality is emphasized along with a pervasive symbiosis which leads to an I, Holobiont model. With all this in place, an extended evolutionary synthesis in the air is well scoped out.

The book covers the possible story of emergence of life and its subsequent evolution, emphasizing the necessary evolutionary step negotiation of a common "language set" which kept all inhabitants in the biosphere together, ensuring a basic level of understanding among them. The book focuses on "protocols of communication" (both genetic and epigenetic) representing norms shared and understood across the whole biosphere, enabling a plethora of holobiotic relationships. Cooperative nature of organismal evolution and epigenetic processes as a major force in evolution are also covered.

Quickening Evolution

Vermeij, Geerat. Power, Competition, and the Nature of History. Paleobiology. Online October, 2019. In this capsule essay, the UC Davis biogeologist draws on his many years of steady research which enables him to recognize and define the presence of a central evolutionary course, as the Abstract and quotes explain. It is really evident that this must be the case from microbes to a metropolis, but natural history has often avoided or denied this admission. See also recent writings by Robert Hazen and George McGhee for similar takes.

Historians have debated whether pathways and events from the past to the present are influenced by contingency, the dependence of outcomes on particular prior conditions, or whether there is long-term emergent directional change. Using evidence from the fossil record and the metabolic evolution of organisms, I show here that power (total energy taken up and expended per unit time) has increased stepwise over time at ecosystem and global scales due to the ratchet-like, cumulative effects of competition and cooperation and to the influence of top competitors and opportunistic species. The history of life thus exhibits an emergent directionality at larger ecosystem phases. (Abstract)

Both sides of this debate (chance/course) focus on participants – lineages and clades in the case of evolution – rather than on the processes to which they are subjected. I suggest that that this emphasis on actors rather than interactions is misplaced, and that a reorientation toward interactions and their outcomes resolves and eliminates the apparent conflict between a contingent and a directional view of history. (2)

Finally, the increasing concentration of power over time might characterize all emergent systems and interacting particles. Although the underlying mechanisms proposed here apply to metabolizing organisms, it is an open question whether life is essential for generating directionality. Gravity ensures that larger bodies exert disproportionate influences on their neighborhoods, suggesting a mechanism for concentrating mass and power at large scales to some point defined by black holes. As in the biosphere, contingency reigns at the scale of movements and positions of particles, while interactions among them generate emergent patterns that are more predictably. (12)

Quickening Evolution > Systems Biology

Malod-Dognin, Noel and Natasa Przulj. Functional Geometry of Protein Interactomes. Bioinformatics. 35/19, 2019. Barcelona Supercomputing Center life scientists show how these metabolic processes can similarly be found to exhibit common network topologies, which can then be modeled by simplical complexes just like the brain. See also Centralities in Simplical Complexes: Applications to Protein Interaction Networks by Ernesto Estrada and Grant Ross in the Journal of Theoretical Biology (438/46, 2018).

Quickening Evolution > Systems Biology

Malod-Dognin, Noel and Natasa Przulj. Functional Geometry of Protein Interactomes. Bioinformatics. 35/19, 2019. Barcelona Supercomputing Center life scientists show how these metabolic processes can similarly be found to exhibit common network topologies, which can then be modeled by simplical complexes just like the brain. See also Centralities in Simplical Complexes: Applications to Protein Interaction Networks by Ernesto Estrada and Grant Ross in the Journal of Theoretical Biology (438/46, 2018).

Quickening Evolution > Biosemiotics

Hendin, Yogi Hale. Meeting Report: The 18th Annual Biosemiotics Gathering. Biosemiotics. 12/2, 2019. An Erasmus University, Rotterdam philosopher reviews this UC Berkeley June convocation, organized by Terence Deacon and the author (Google title for more info and a 70 page book of abstracts). Some talks were Quantum origins of ontic emergence by Michael Epperson, Creation of the relative next by Donald Favareau, Can truth and love prevail? by Gerald Ostdick, and Do cell sing to each other? by Mark Johnson.

Over June 17–20, 2018, from dozens of countries, biosemioticians converged at the University of California, Berkeley to discuss the state of the art of Biosemiotics. The syncretic gathering, like the discipline itself, brought together scholars in natural science, social science, and the humanities, to further develop what Danish chemist and ur-biosemiotian Jesper Hoffmeyer calls “the life of signs, and the signs of life.” The conferees examined the hermeneutics of biological communication, its relevance to the Extended Evolutionary Synthesis, and went on to address primordial questions such as What is life, What Is Semiosis, and much more. (Abstract excerpt)

Quickening Evolution > Biosemiotics

Witzany, Guenther, ed. Biocommunication of Animals. Dordrecht: Springer, 2914. The Austrian biophilosopher gathers another volume about how flora and fauna across all evolutionary scales are distinguished by constant conversations, a natural talk show. Chapters span spiders, kangaroo rats, crows, wolves, catfish, elephants, ants, chimpanzees, nematodes, parrots and more. See especially How Corals Coordinate and Organize by Pierre and GW which about the presence of semio-physical symbioses, fractal self-similarity and modular networks.

Every coordination within or between animals depends on communication processes. Although the signaling molecules, vocal and tactile signs, gestures and its combinations differ throughout species due to their evolutionary origins and adaptation processes, certain levels of biocommunication can be found throughout such as environmental indices (temperature, light, water, etc.), trans-specific communication with non-related organisms, species-specific communication, and intraorganismic communication, i.e., sign-mediated coordination within the body of the organism.(Summary)

Earth Life Emergence: Development of Body, Brain, Selves and Societies

Earth Life > Common Code

Cofre, Rodrigo, et al. A Comparison of the Maximum Entropy Principle Across Biological Spatial Scales. Entropy. 21/10, 2019. University of Valparaiso, Pontifical Catholic University, Chile and Imperial College London mathematical physicists cite another perceptive method to discern nature’s recurrent geometries as they track and rise from life’s origin to we peoples. See also Quantifying High-Order Interdependencies via Mutual Information (Rosas 2019 herein) for a companion effort. The endeavor and its findings are quite timely as public demonstrations rile Chilean cities, and many other nations, for better governmental, economic, and climatic policies.

Despite their differences, biological systems arrayed as nested levels tend to exhibit common organizational patterns. But these commonalities are often hard to grasp due to the specialized nature of modern science and parcelled terminology employed by scientific sub-disciplines. To explore these organizational features, this paper provides a comparative study of diverse applications of the maximum entropy principle, which has found many uses at different biological stages ranging from amino acids up to societies. By presenting these studies under an accessible approach and language, our aim is to establish a unified view over these seemingly heterogeneous scenarios. (Abstract)

One of the most powerful features of the MEP is its generality, which enables its use over an extremely broad range of scenarios. This section explores six case studies of the application of the MEP in biology at different spatial scales, employing a unified methodology and notation. The cases are amino acids in proteins, retinal ganglion cells, whole brain networks, plant communities, macroecologic biodiversity, and human vote interactions in the US Supreme Court. (4-5)

Earth Life > Common Code

Rosas, Fernando. Quantifying High-Order Interdependencies via Multivariate Extensions of the Mutual Information. Physical Review E. 100/032305, 2019. Imperial College London mathematicians including Henrik Jensen report a technical exercise about ways to perceive and express nature’s emergent, animate scales. A prime feature seems to be an intrinsic synergy between all manner of entities and their informed, cooperative behaviors. A similar motif in musical compositions is offered as an example, indeed a true music and harmony of the spheres, and oour creaturely lives does play. See also Tangled Worldview Model of Opinion Dynamics by this group at arXiv:1901.06372.

This article introduces a model-agnostic approach to study statistical synergy, a form of emergence in which patterns at large scales are not traceable from lower scales. Our framework leverages various multivariate extensions of Shannon's mutual information, and introduces the O-information as a metric capable of representing synergy- and redundancy-dominated systems. We develop key analytical properties of the O-information, and study how it relates to other metrics of high-order interactions from the statistical mechanics and neuroscience literature. Finally, as a proof of concept, we use the proposed framework to explore the relevance of statistical synergy in Baroque music scores. (Abstract)

A unique opportunity in the era of “big data” is to make use of the abundant data to deepen our understanding of the high-order interdependencies that are at the core of complex systems. Plentiful data is nowadays available about e.g. the orchestrated activity of multiple brain areas, the relationship between various econometric indices, or the interactions between different genes. What allows these systems to be more than the sum of their parts is not in the nature of the parts, but in the structure of their interdependencies. (1)

Synergy: the interaction or cooperation of two or more organizations, substances, or other agents to produce a combined effect greater than the sum of their separate effects.

Earth Life > Nest > Geological

Sun, HongGuang, et al. Fractal Nature of Groundwater Level Fluctuations Affected by Riparian Zone Vegetation Water Use. Nature Scientific Reports. 9/15383, 2019. State Key Laboratory of Hydrology-Water Resources and University of Wyoming engineers provide a latest mathematical and geometric analysis by way of these intrinsic common, nested complexities. Whenever could it finally dawn upon us that all this facile phenomena actually has an independent existence of its own as it engenders everywhere this anatomy and physiology of Earth’s animate bio/noosphere.

Groundwater systems affected by various factors can exhibit complex fractal behaviors, whose characterization is not straightforward. This study explores their fractal scaling affected by plant water use and river stage fluctuations in the riparian zone, using multifractal detrended fluctuation analysis. The results show that the water level variations of the Colorado River, USA, exhibit multifractals caused by the memory of time series of the water level fluctuations. For the site with high-density plants the groundwater level fluctuation becomes persistent in spring and summer, since the plants have the most sustained influence in these seasons. (Abstract excerpts)

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