I. Our Planatural Edition: A 21st Century PhiloSophia, Earthropo Ecosmic PediaVersion

C. An Earthumanity Era: A 2020s Global Cognizance Proceeds as a Knowsphere by Her/His Bicameral Self

Daniels, Bryan, et al. Identifying a Developmental Transition in Honey Bees Using Gene Expression Data. bioRxiv, November 7, 2022. A latest paper by Arizona State University and Banner Health, Phoenix complexity theorists including Robert Page describes how dynamic genome studies now reveal critically poised bistable states even in this prescriptive phase. This –omic occurrence of self-organized criticalities can well establish nature’s 2020s universal preference for this optimum poise. See also Social Networks Predict the Life and Death of Honey Bees by Benjamin Wile, et al in Nature Communications 12/1, 2021 and Self-Organization and the Evolution of Division of Labor by R. Page and Sandra Mitchell in Apidologie (29/1, 1998).

In many organisms, interactions among genes lead to multiple functional states, while other interactions can transition into new modes, maybe by way of critical bifurcations in dynamical systems. Here, we develop a statistical theory to identify a bistability near a transition event from gene expression data. We apply the method to honey bees where a known developmental occurrence between bees performing tasks in the nest and leaving to forage. Our approach is able to predict the emergence of bistability and link it to genes involved in the behavioral transition. (Abstract excerpt)

Social insects represent well-known examples of adaptive collective systems, combining the efforts of many individual actors to produce robust and adaptive aggregate behavior. The allocation of tasks to individuals often displays a sophisticated organization that promotes collective success. This distributed coordination of effort is the result of a complicated process reaching from the level of gene regulation to social relations. (1) To summarize, the generality of this phenomenology suggests that such critical transitions may be a common mechanism within biology, making use of the emergent properties of strongly interacting dynamical networks to generate reproducible diversity. (14)

Evans, Constantine, et al. Pattern Recognition in the Nucleation Kinetics of Non-Equilibrium Self-Assembly. arXiv:2207.06399. This intricate, frontier posting by Cal Tech and University of Chicago computational biologists including Erik Winfree is able to graphically describe an expansive, self-similar consistency from molecules all the way to minds. Its deep neural net operations are found to well apply across these domains to an extent life’s spatial and temporal developmental panorama and self-observation well appears as a procreative genesis.

Inspired by biology's best computer, the brain, neural networks achieve a profound reformulation of computational principles. Analogous high-dimensional, interconnected architectures also arise within information-processing molecular systems inside living cells,. Might neuromorphic collective modes be thus found broadly in other physical and chemical processes such as protein synthesis, metabolism, or structural self-assembly? Here we examine nucleation of animate structures to show that complex patterns can be classified similar to neural network computation. Specifically, we design a set of 917 DNA tiles that can self-assemble in three alternative ways such that competitive nucleation depends on the co-localization of tiles within the three structures. This success suggests that ubiquitous physical phenomena, such as nucleation, may hold powerful information processing capabilities when scaled up to more intricate systems. (Abstract excerpt)

From Computation to Life: The Challenge of a Science of Organization. www.walterfontana.zone/writings. This entry is the Inaugural Lecture for the Chair in Informatics and Computational Sciences 2019-2020 at the Collège de France, Paris by the veteran Harvard Medical School systems biologist (see website). He was notably the coauthor with Leo Buss of The Arrival of the Fittest (1994, search) about an innate evolutionary course. Some 25 years later, this richly composed edition proceeds to describe a deep integration of chemical phenomena with complexity theories and physical substrates which altogether can be expressed b informative computer programs. As the quotes convey, along with a catalytic force, the whole package can well presage a natural genesis synthesis with a global 2020s research agenda. For a current example, see Representing Catalytic Mechanisms with Rule Composition by Jakob Andersen, WF, et al at arXiv:2201.04515,

(3) In addition to statistical models, researchers also construct mechanistic models to gain insight into the dynamical processes that generate the system state reflected in the data. Analyzing the behavior of a molecular interaction network is helpful for understanding how and why a biological system might function. Such networks are modeled at various levels of abstraction. One recent approach represents each interaction as an instruction in a purpose-made programming language. A model then effectively represents a biological system as a program. This is more subtle than just using a computer; it is about representing a complex system using ideas from computation. (E-1)

(4) At a more fundamental level, many systems in nature are composed of components that mutually construct each other in a way that glues them together into a unit: metabolisms, cells, organisms, ecologies, cognitive systems, economies, cultures. All these systems are functional organizations. What kind of dynamics produces organizations of this sort? How much of their architecture is contingent and how much of it is inevitable? The idea of computation is the modern formalization of the idea of mechanism. However, unlike its predecessors, the clockwork and the steam engine, computation emphasizes a constructive aspect of interaction. (E-1)

Auto-catalysis is relevant in origin-of-life scenarios, because it concentrates the mass of a system in the autocatalytic loop, while suppressing many side reactions that could be a kinetic threat. It would be of great interest to understand whether, given hypotheses about the chemical substances and the chemical rules available 3.5–4 billion years ago, this cycle was the only solution in the accessible chemical space, or whether there are other paths. In other words: is the universality in the functional organization of metabolism that we observe today one of many options, or is it necessary? (E-11)

In closing, I would like to take in the whole picture. I tried to span an arc between three chemistries and representations of their interactions founded on ideas from computer science. When endowed with dynamics, all three give rise to aspects I associate with functional organization. At the beginning I asked about such aspects as self-maintaining organizations of logic whose change is constrained, the auto-catalytic chemical networks present in living systems, and the causal structures that organize the signaling processes in cells. These dynamics are a constructive force based on interactions that directly build new objects with new interactive properties. The challenge of a science of (chemical) organization consists in formalizing and understanding this constructive dynamics. (E-16, 17)

Frank, Adam, et al. Intelligence as a Planetary Scale Process. International Journal of Astrobiology. February, 2022. Veteran astroscholars AF, University of Rochester, David Grinspoon, Planetary Science Institute and Sara Walker, Arizona State University provide a latest admission, description and affirmation of the actual evolutionary emergence a worldwise cerebral faculty. As the quotes engage, a mindfulness to allow something going on by own agencies, such an appearance and fulfillment now becomes readily evident.

Intelligence is usually seen as an individual faculty. Here, we broaden the idea of intelligence as a collective group property and extend it to the planetary scale. We consider the ways in which a relative technological intelligence may represent a kind of planetary scale transition, much as the origin of life itself may be seen as a global phenomenon. Our approach follows many researchers today that the correct scale to understand key aspects of life and its evolution is planetary, beyond traditional focus on individual species. (Abstract excerpt)

A transition to planetary intelligence, as we described here, would achieve its operative presence at a global scale. Such a mindful world could steer the future evolution of Earth, acting in concert with and guided by a deep understanding of natural systems. If other civilizations that may exist in the universe undergo such a transition, we would expect to see a marked difference in their biosignatures due to a sustainable, global intelligence versus those that not been able to attain this emergent phase. (27)

We propose five properties required for a world to show knowing cognitive activity operating across planetary scales. These are: (1) emergence ,(2) dynamics of networks, (3) networks of semantic information, (4) appearance of complex adaptive systems, (5) autopioesis. Different degrees of these properties appear as a world evolves from abiotic (geosphere) to biotic (biosphere) to technologic (technosphere). (33)

Furtak, Marcin, et al. The Forest, the Trees, or Both? Hierarchy and Interactions between Gist and Object Processing during Perception of Real-world Scenes. Cognition. Vol. 221, April, 2022. Into this year, Polish Academy of Sciences and Tel Aviv University neuropsychologists can draw upon their own research along with a review of past 21st century work to an extent that they can presently reach a strong conclusion. Taken together, these studies join our results in supporting the global to local accounts, suggesting that gist (field) is processed more readily, and earlier, than objects. (5) As reported across the website, a temporal sequence appears to go on for both evolution and an entity. A sighted occasion is viewed by way of these dual archetypal modes, whereby a contextual scene is perceived first, after which item details are noticed and situated.

The global-to-local theories of perception assume that the gist of a scene is computed early and automatically, whereas recognition of objects occurs at a later stage, requires attentional resources, and is primed by the representation of whole. To test these views, we investigated the sequence of gist- and object-recognition. We generally found that backgrounds were classified more accurately than foreground objects, while wider fields influenced object recognition. Thus these findings support global-to-local theories, implying that gists are more readily seen than details, and at an earlier stage. (Abstract excerpt)

Gagler, David, et al. Scaling Laws in Enzyme Function Reveal a New Kind of Biochemical Universalit. PNAS. 119/9, 2022. Arizona State University bioscientists including Sara Walker, Chris Kempes and Hyunju Kim enter a good example of novel Earthuman abilities which can now find life’s deeper phases to also be distinguished by common, recurrent, self-similar patterns as everywhere else. A further implication is that such a result can be traced to and rooted in physical phenomena. A section heading is Universal Scaling Laws Define the Behavior of Enzyme Classes Across Diverse Biochemical Systems. A graphic depicts how the same forms hold from Archaea and Bacteria to Eukaryotes and Metagenomes, independently of specific components. We wonder again at our emergent EarthWise faculty whom can just now come to these discoveries.

All life on Earth uses a shared set of chemical compounds and reactions which provides a detailed model for universal biochemistry. Here, we introduce a more generalizable concept that is more akin to the kind of universality found in physics. We show how enzyme functions form universality classes with common scaling behavior. Together, our results establish the existence of a new kind of biochemical universality, independent of the details of life on Earth’s component chemistry. (Abstract excerpt)

In physics, the notion of coarse-graining is critical to identifying universality classes, because it allows ignoring most details of individual systems in favor of uncovering systematic behavior across different systems. (3)

Garcia-Sanchez, Miguel, et al. The Emergence of Interstellar Molecular Complexity Explained by Interacting Networks. Proceedings of the National Academy of Sciences. 119/30, 2022. Centro de Astrobiologia (CSIC/INTA), Torrejon de Ardoz, Spain and Swedish University of Agricultural Science researchers including Jacobo Aguirre contribute a frontier synthesis by adding and applying such equally real and vitally present interlinking webworks to nature’s intrinsic formation of nodal biomolecules. This integration is achieved and demonstrated by through novel NetWorld algorithmic computations. As the quote says, an especial value accrues by virtue of a quantified perception of commonly recurrent processes and vivifying anatomies.

The road to life is punctuated by transitions toward complexity, from astrochemistry to biomolecules and eventually, to living organisms. But studies of these original phases remain a challenge to which complexity and network theory has not been much applied. We introduce a computational framework whereby simple networks simulate the most basic elements of life as they interact to form complex structures. We observe a resultant explosion of diversity when the parameter representing the environment reaches a critical value. While this model is abstract, its predictions well mimic the molecular evolution in the interstellar medium during the emergence of chemical complexity. Altogether our work suggests that the rules leading to biological complexity may be relatively simple as they engender universal patterns. (Abstract/Significance)

All in all, we believe that (i) the similarities between the results in [30], based on models that are firmly rooted in classical ecological theory and checked with real data, (ii) those obtained from molecular abundances in interstellar clouds, and (iii) the ones introduced by our computational environment, derived from a simple framework with no a priori ecological or chemical assumptions, are not coincidental. They instead hint that the long path from the creation of the basic prebiotic compounds in the interstellar medium to the origin of life and its evolution on the early Earth could show universal patterns and common phenomena at all scales and across all stages. (8)

Gontier, Nathalie, et al. Introduction: Language and Worldviews. Topoi. 41/3, 2022. University of Lisbon, Barcelona, Porto, Seville and Pavia scholars introduce the issue’s topical subject and survey some 15 contributions, see Abstract for more. Its reach by design traces all the way back to Animal Minds and the Evolution of Communication and Language. A major essay by the lead editor well summarizes, posted next. For example see Language: The Ultimate Artifact to Build, Develop and Update Worldviews by Lorenzo Magnani, The Work of Words: Poetry, Language and the Dawn of Community by Ricardo Santos-Alexandre and Language, Thought and the History of Science by Carmela Chateau-Smith. See also Evolutionary Epistemology by Nathalie Gontier and Michael Bradie in the Journal for General Philosophy of Science. (52/2, 2021) for an issue on this companion endeavor.

This special issue on Language and Worldviews grew out of a workshop on Language Throughout the Ages (Google) that was organized by the Applied Evolutionary Epistemology Lab (appeel.fc.ul.pt) at the University of Lisbon in 2019. Language and worldviews are favorite topoi for philosophers of language or mind, science, or religion, epistemology or logic. How language establishes, mediates, constructs, or enacts a contextual milieu amongst peoples, and between basic physical, sociocultural, and biological aspects is a huge, vital realm. (Excerpt)

Gosak,, Marko, et al. Networks Behind the Morphology and Structural Design of Living Systems. Physics of Life Reviews. March, 2022. As a good example of timely abilities to achieve a convergent synthesis of nonlinear, animate complexities, five University of Maribor, Slovenia theorists including Matjaz Perc post a 40 page, 250 reference article with regard to life’s ubiquitous connectivities across every anatomic and physiological instance. For example intercellular and multicellular interaction patterns, fluid flows, neural nets and all else can be seen to exhibit similar topological dynamics. Today collaborative teams in every land, on a daily basis, altogether compose a speciesphere scientific endeavor going on by itself. But with insane carnage not far away, such a learning, thinking Earthuman faculty whom is achieving these revolutionary findings is still unknown. For such reasons, the evident presence of an independent, universal mathematic source in manifest effect still cannot be implied. See also Dynamics of Higher Order Networks by this collegial team including Matjaz Perc at arXiv:2203.06601 for a similar exercise.

Advances in imaging techniques and biometric data methods have enabled us to apply the topological network properties to organelles, organs, and tissues, as well as the coordinations among them that yield a healthy, whole organism. We review research dedicated to these advances with a focus on networks between cells, the topology of multicellular structures, neural interactions, fluid transportation, and anatomies. The percolation of blood vessels, brain geometries, bone porosity, and relations between various parts of the human body are some examples we explore in detail. (Abstract excerpt)

Tools from the armamentarium of the complex network theory are nowadays recognized as a general and powerful theoretical framework for assessing real-world systems. Their wide applicability is to a significant extent a consequence of their natural suitability to represent and study the relations between individual components in virtually any discrete system. For these reasons, we are witnessing in the last two decades an explosion of multidisciplinary studies in which the complex network methods are applied to social sciences [223-229], linguistics [230-232], ecological systems [233-235], economics [236, 237], and a wide range of engineered and technological systems. (23)

Grossberg, Stephen. Conscious Mind, Resonant Brain: How Each Brain Makes a Mind. New York: Oxford University Press,, 2022. The octogenarian Boston University poly-neuroscientist was often asked to write a summary work about his luminous studies (search). As a result, this large format, illustrated, 700 page volume proceeds to substantiate and explain his Complementary Computation theory of dynamic cerebral processes and cognitive features. As the quotes describe, into the 21st century and 2020s a vital finding can now be established. Our human neural facility, awareness and responsive behavior is distinguished by a double basis of opposite but reciprocal functions and qualities. One version is the What/Where model of object view and spatial place, which draws on dual cortical streams. Another instance, of course, is our hemispheric halves with their archetypal contrast of dot/connect, node/link, the litany goes all the way to male and female compete/cooperate aspects.

Malleable network topologies, as they serve to inform and communicate are noted to play a significant role. In further regard, as noted in an Introduction (7), Chapter 17 traces our emergent, personal brain/mind epitome deep down to the original complex dynamics of a physical source stage. Sections such as A Universal Developmental Code, Complementarity Biological and Physical Laws, A Universal Measurement Device of and in the World express how active neural cognizance can be found to self-organize in similar accord with physical principles and phenomena. Along with April entries like The Bifocal Stance Theory of Cultural Evolution (Jagiello) and Novelty and Imitation within the Brain (Czegel), such quantified proof of a true bicameral uniVerse could provide an urgent resolve as the two poles lock into mutual war.

The work embodies a revolutionary Principia of Mind that clarifies how autonomous adaptive intelligence is achieved. Because brains embody a universal developmental code, further insights emerge about shared law in living cells from primitive to complex and onto how networks of interacting cells support developmental and learning processes in all species. These novel brain design principles of complementarity, uncertainty, and resonance are then traced to the physical world with which our brains ceaselessly interact, and which enable our brains to incrementally learn to understand those laws, thereby enabling humans to understand the world scientifically. (Publisher)

A question concerns how the complementarity organization of our brains may be related to the complementary properties of the physical world. Here I will note that this occurrence was first proposed in the 1920s by the physicist Niels Bohr from quantum mechanics. The phenomena involves different aspects such as position and momentum for waves and particles. If the brain is a kind of universal measurement system of physical environs such as light, heat and pressure. This fact raises the question of whether brains may have assimilated basic physical principles throughout evolution. (7)

What and Where Cortical Processing Streams These two types of learning, perceptual/cognitive vs. spatial motor, to on in different brain systems. The ventral>/i> stream processes information that enables us to recognize objects. It is thus called the What version. Thedorsal phase provides information about where objects are in space and how to act upon them. It is accordingly called the Where and How mode. (28) I will suggest in Figure 1.19 how they obey “computationally complementary” laws. Complementarity implies the need to balance the capabilities of each version against those of the other. (aka herein as a Golden Mean). (28)

Complementary Processing Streams for Perception/cognition and Space/action. I have called this paradigm Complementary Computing because it describes how the brain is organized into complementary parallel processing streams whose interactions generate biologically intelligent behaviors. A singly cortical stream can compute some properties well, but cannot, by itself, process orther computationally complementary properties. Pairs of cortical streams interact, using multiple stages, to generat emergent features that overcome their complementary deficiencies to compute complete information with which to represent or control some intelligent faculty. (29)

Universal Design for Self=Organizing Measurements and Prediction Systems. Implicit in these conclusions is the fact that principles, mechanisms and architectures in this book are about fundament problems of measurement and how a self-organizing system and represent and predict outcomes in a changing world. Mind and brain are explained by these theories because they are natural computational embodiments of these occasions. (34)