(logo) Natural Genesis (logo text)
A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
Table of Contents
Introduction
Genesis Vision
Learning Planet
Organic Universe
Earth Life Emerge
Genesis Future
Glossary
Recent Additions
Search
Submit

V. Systems Evolution: A 21st Century Genesis Synthesis

Into the 2000s and the 2010s, an integrative fleshing out of an evolutionary development from an ecosmos origin to habitable bioworlds, emergent life, mind and persons in community is underway by a worldwise collaboration. This animate milieu reaches from a conducive physical ground to vital autocatalysis, nested recurrent scales, neural connectomes, ramifying intelligence, complex fractal ecosystems and onto complementary civilizations. Various “extended evolutionary synthesis” projects are underway which try to factor in epigenetics, niche construction, and more mostly remain in a (neo)Darwinian mode. From our global vantage and vista, a deeper dimension of self-organized dynamics as they spawn exemplary complexified, networked, minded creatures and groupings provide the crucial missing source code. For one example, Alan Turing’s morphogenetic programs are seen in effect from developing embryos to animal anatomies and striped patternings. In a day when one can sequence their genetic ancestry, it would seem that life’s whole development from universe to us should necessarily have its own natural genomic endowment.

As an evolution was ‘in the air’ in the 1850’s, so today there seems to be “in the Internet airwaves” a sense of life’s Earthly course as a quickening, deeply homologous, convergent gestation (a view Darwin held). Rather than a branching tree or bush, a main axis of bodily complexity, larger brains, represented information, communal cooperation, and knowing awareness is evident. As here and elsewhere, an episodic, scalar tandem of complexity and cognition is no longer a contingent meander. As guided by informed, organizational energies, an oriented direction and sequence toward phenomenal people is traced. Thus a prior ladder of Being is replaced by a temporal progression of Becoming. For a name, we offer Genesis Evolutionary Synthesis. This large section and the next four contain over 500 references and quotations in support, along with many more citations throughout. We next add via a listing of 21st century contributions, trends and advances as they may inform a 2020 worldwise genesis revolution. One name is added to each to identify and locate.

A statistical physics perspective finds condensed matter phenomena in evolutionary and organic processes. (William Bialek)

Evolutionary processes can be rooted in a fertile materiality by way of active spontaneities. (Cristina Marchetti)

The constant presence of self-organizing agencies at work prior to selective effects implies a deeper, code source for life’s cellular and cerebral evolutionary emergence. (Jamie Davies)

Networked complexities describe a scale-free, multiplex connective anatomy and physiology across somatic, cerebral, and group phases. (Albert Laszlo Barabasi)

A major evolutionary transitionsmodel describes a nested scale from genes and cells to a human phase, whence each stage has a relative code or template from replicators to language. (Eors Szathmary)

Into the 2010s, strong evidence grows for a persistent convergence of formative patterns and metabolic processes across life’s creaturely development. (George McGhee)

Life’s evolutionary gestation exhibits a deep homology whence recurrent anatomies and physiologies can be continuously traced to vertebrate and invertebrate rudimentary origins. (Neil Shubin)

Revolutionary views of whole genome phenomena beyond central dogma nucleotides such as gene regulatory networks. (James Shapiro)

Bodies and brains are composed of diverse modular wholes within wholes of semi-autonomous, labor-dividing, mosaic units for genetic, metabolic and neural utility. (Gunter Wagner)

A rational morphology or structural biology, a century after D’Arcy Thompson, serves to quantify an archetypal Bauplan by way of innate mathematical equations. (Charles Cockell)

The occasion of novel species, aka arrival of the fittest, is not due to random mutation but arises from independent, dynamical self-organizing systems. (Andreas Wagner)

A 21st century of evolution and embryology as evolutionary developmental biology or EvoDevo joins individual ontogeny with species phylogeny. (Scott Gilbert)

Innovative insights into what constitutes genetic influences have now include epigenetic factors far beyond point nucleotides. (Eva Jablonka)

Beneficial symbiotic unions across fauna and flora have become a major formative contributor for the evolution and viability of cellular, organismic, and social assemblies. (Lynn Margulis)

Beneficial cooperation beyond just competition is seen as the prevalent mode by which animal and human societies come together and are maintained. (Martin Nowak)

Life’s oriented genesis has a central tendency to increase computational intelligence and proactive behavior (Richard Watson)

Animal intelligence All manner of creaturely organisms are found to have aware personalities, clever abilities, and communicative sociality. (Lori Marino)

Niche construction. As animals evolve their tendency to modify a biotic area and build single and communal nest sites is a prime contribution. (Kevin Laland)

An evolutionary arrow occurs whence creatures achieve increasing degrees of autonomy, individuality and a semiotic freedom of choice. (Daniel Dennett)

A central trend of brain size, neuron number, network density, concerted and mosaic socialized capacities define an encephalization of increasing acuity. (Suzana Herculano-Houzel)

Another cerebral discovery is a steady scale of bicameral hemispheres with the same part/field attributes across life’s entire sentient ascent. (Giorgio Vallortigara)

A perception of biosemiotic activity by biologic code significations other than genetic that process and communicate vital information. (Marcello Barbieri)

New affinities between ontogeny and phylogeny are seen not only for corporeal form but for cognitive ability, motor skills, behaviors and language learning. (Arhat Abzhanov)

2020: With some 330+ references, this chapter reports and documents an overdue extended and revised evolutionary synthesis. This main course correction is in the air as evolution itself was for Darwin. As the introductory list of novel reasons cites, the project involves a (re)integration of developmental stages, aka evo-devo, major transitions scale, network topologies, symbiosis and modularity, an axial trend for brains, intelligence and knowledge, cooperative behaviors, free members in mutual groups, song, dance and protolanguage, deep anatomic homologies, and so on.

Another prime quality, quite absent from the old synthesis, is the procreative presence of natural, independent, self-organizing complex source codings. Statistical physics inputs as a common ground are also being recognized. By way of a cognizant personsphere, (the premise of this site and our worldwise selfie) life’s encoded, fleshed out, quickening, ever learning, oriented ascent that got us creatures and peoples well now takes on a guise of a maternal embryonic gestation. So this surmise may proceed from a once Darwin’s day to our current and future promise of a 21st century genesis synthesis.


Agrawal, Anurag. Toward a Predictive Framework for Convergent Evolution. American Naturalist. 190/S1, 2017.

Bonduriansky, Russell and Troy Day. Extended Heredity: A New Understanding of Inheritance and Evolution. Princeton: Princeton University Press, 2018.

Bonner, John T. The Evolution of Evolution. Journal of Experimental Zoology B. 332/8, 2020.

Cohen, Irun and Assaf Marron. The Evolution of Universal Adaptations of Life is Driven by Universal Properties of Matter: Energy, Entropy and Interaction. F1000Research. July 30, 2020.

Davies, Jamie. Life Unfolding: How the Human Body Creates Itself. Oxford: Oxford University Press, 2014.

Gissis, Snait and Eva Jablonka, eds. Transformations of Lamarckism. Cambridge: MIT Press, 2011.

Held, Lewis. Deep Homology?: Uncanny Similarities of Humans and Flies Uncovered by Evo-Devo. Cambridge: Cambridge University Press, 2017.

Jain, Kavita and Luca Peliti. Special Issue on a Statistical Theory of Biological Evolution. Journal of Statistical Physics. 172/1, 2018.

Laland, Kevin, et al. The Extended Evolutionary Synthesis. Proceedings of the Royal Society B. Vol. 282/Iss. 1813, 2015.

Manrubia, Susanna, et al. From Genotypes to Organisms: State of the Art and Perspectives of a Cornerstone in Evolutionary Dynamics. arXiv:2002:00363.

McGhee, George. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. Cambridge: MIT Press, 2019.

Ostachuk, Agustin. What is It Like to be a Crab? A Complex Network Analysis of Eucaridan Evolution. Evolutionary Biology. Online May 2019.

Orgogozo, Virginie. Replaying the Tape of Life in the Twenty-First Century. Interface Focus. 5/20150057, 2015.

Shapiro, James. Evolution: A View from the 21st Century. Upper Saddle River, NJ: FT Press Science, 2011.

Vermeij, Geerat. Power, Competition, and the Nature of History. Paleobiology. Online October, 2019.

Wagner, Andreas. Arrival of the Fittest. New York: Current/Penguin, 2014.



View the 341 Bibliographic Entries

A. A Major Evolutionary Transitions Scale

We chose the cover of this 1995 book by John Maynard Smith and Eors Szmathary which introduced their conceptual notice of a nested, developmental sequence because it depicts life’s creaturely evolution as proceeding to our human phase. The image has been criticized as an olden “great scale of nature” since currently a teleological goal denied, nor is it permitted. But if newly due to a worldwise sapienence coming to her/his (Charlotte and Charles EarthWin) own knowledge, an oriented, central course may indeed be quantified and set in place.

As this site tracks the broad field of evolutionary biology, into the 2010s this model has gained acceptance because it well defines life’s episodic emergence from replicative biomolecules to human linguistic societies. This section offers a diverse array of studies, tweaks, adjustments both at specific levels and for the whole procession. A notable aspect is that each phase is seen to possess a novel genetic-like code version. Here is an example where a prior neoDarwinian aimless, contingent, selection scheme exists side by side with a genesis synthesis which has not yet been fully articulated.

Our main website premise, which a new 2021 introduction reiterates, is the occurrence of a further consummate, spherical stage. So the section will also gather entries that glimpse a continuance of this pattern and process onto a nascent Earthkinder. But it is important to enter a caveat and distinction. While this planetary occasion is especially manifest via its cerebral, informative sapiensphere, and sometimes alluded to as a super-organic phase, we do not here imply an homogeneous globalization. Rather as described in Sustainable Ecovillages in chapter VIII, a next evident stage actually seems to be social protocells, in a way akin to viable protocells at life’s origin.

2020: A major revision since 1995 is a theoretical view that life’s developmental evolution can be characterized by a nested, episodic, recurrent, directional sequence of being and becoming. Although life’s course through myriad forms and stages does meander with many extinctions, a regnant, scalar procession from gene replicators all the way to talkative peoples is now widely applied. As such it provides skeletal orientation for a genesis synthesis.


Andersson, Claes and Petter Tornberg. Toward a Macroevolutionary Theory of Human Evolution: The Social Protocell. Biological Theory. 14/2, 2019.

Calcott, Brett and Kim Sterelny, ed. The Major Transitions in Evolution Revisited. Cambridge: MIT Press, 2011.

Carmel, Yohay and Ayelet Shavit. Operationalizing Evolutionary Transitions in Individuality. Proceedings of the Royal Society B. February, 2020.

Clarke, Ellen. Origins of Evolutionary Transitions. Journal of Biosciences. 39.2, 2017.

Evolving a Major Transition in the Internet Age. evolution-institute.org/evolving-a-major-transition-in-the-internet-age.

Furukawa, Hikaru and Sara Imari Walker. Major Transitions in Planetary Evolution. Ikegami, Takashi, et al, eds. ALIFE 2018 Conference Proceedings. Cambridge: MIT Press, 2018.

Hoffecker, John. Modern Humans: Their African Origin and Global Dispersal. New York: Columbia University Press, 2017.

Kesebir, Selin. The Superorganism Account of Human Sociality. Personality and Social Psychology Review. 16/3, 2012.

Rosslenbroich, Bernd. On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Heidelberg: Springer, 2014.

Sandora, McCullen and Joseph Silk. Biosignature Surveys to Exoplanet Yields and Beyond. arXiv:2005.04005.

Suki, Bela. The Major Transitions of Life from a Network Perspective. Frontiers in Fractal Physiology. 3/Article 94, 2012.

Szathmary, Eors. Toward Major Evolutionary Transition Theory 2.0. Proceedings of the National Academy of Sciences. 112/10104, 2015.

West, Stuart, et al. Major Evolutionary Transitions in Individuality. Proceedings of the National Academy of Sciences. 112/10112, 2015.


View the 49 Bibliographic Entries

B. Systems Network Biology and Genetics

This section will report the significant turn in genetics and biology since the 2001 Human Genome Project to reassemble and reconceive the many biomolecule pieces and components into an integral whole. With their initial occurrence and identity in place, the presence of equally real interrelations in between, and the information they carry and convey, can be admitted and quantified. By this inclusive scope, the dynamic web of life can shed a mechanistic, machinery cast for a phenomenal emergent vitality.

Into the 2010s the network revolution has joined and deepened the systems approach by which further to reunite animate phenomena. Life’s nested wholes within wholes thus become braced and graced by the same multiplex topologies and dynamics as found everywhere else from quantome to neurome and epitome.

2020: Since the 2001 human genome sequence, a broad movement has sought to quantify and involve the equally real regulatory and vivifying connectivities between the biomolecular nucleotides. Recent endeavors factor in network topologies and involve deep learning methods. As the 130 sample references convey, an international effort aided by online advances in technique and computation is well along with an integral understanding of 3D and 4D organismic epi/genomes and metabolomes.

Alvarez-Buylla, Elena, et al. Systems Biology Approaches to Development beyond Bioinformatics. BioScience. 66/5, 2016.

Cavagna, Andrea, et al. Physical Constraints in Biological Collective Behavior. Current Opinion in Systems Biology. 9/49, 2018.

Davidson, Eric. Evolutionary Bioscience as Regulatory Systems Biology. Developmental Biology. 357/1, 2011.

DiFrisco, James and Johannes Jaeger. Genetic Causation in Complex Regulatory Systems: An Integrative Dynamic Perspective. BioEssays. 42/6, 2020.

Gazestani, Vahid and Nathan Lewis. From Genotype to Phenotype: Augmenting Deep Learning with Networks and Systems Biology. Current Opinion in Systems Biology. 15/68, 2019.

Gilpin, William, et al. Learning Dynamics from Large Biological Data Sets: Machine Learning Meets Systems Biology. Current Opinion in Systems Biology. July 30, 2020.

Gosak, Marko, et al. Network Science of Biological Systems at Different Scales. Physics of Life Reviews. November, 2017.

Ingalls, Brian. Mathematical Modeling in Systems Biology. Cambridge: MIT Press, 2020.

Kutschera, Ulrich. Systems Biology of Eukaryotic Superorganisms and the Holobiont Concept. Theory in Biosciences. Online June, 2018

O’Malley, Maureen, et al. A Philosophical Perspective on Evolutionary Systems Biology. Biological Theory. 10/1, 2015.

Radde, Nicole and Marc-Thorsten Hutt. The Physics behind Systems Biology. EPJ Nonlinear Biomedical Physics. Online August, 2016.

Soyer, Orkun, ed. Evolutionary Systems Biology. Berlin: Springer, 2012.

View the 131 Bibliographic Entries

C. Evoinformatics: A Biosemiotic Quality

Akin to movements such as an algorithmic nature and information paradigm, since around 2000 a central presence and role for communicative aspects of living systems has gained prominence. The title term arose from the broader field of semiotics, the study of significations as they distinguish, engender, and vitalize from evolution to ecologies. A pioneer initiator was Thomas Sebeok (1920-2001) at Indiana University, where a loquacious group has since gone forth. Into the 21st century a leading sponsor has been Marcello Barbieri (see above), via an initial book The Organic Codes (2003) among many and a steady embellishment of articles.

As the endeavor grew, inspired by articulations of life’s dialogic essence, an International Society for Biosemiotic Studies formed with annual international conferences and other activities. A stream of volumes such as Biosemiotics: An Examination into the Signs of Life and the Life of Signs (2009) by Jesper Hoffmeyer, and Towards a Semiotic Biolog (2011) edited by Claus Emmeche and Kaveli Kull helped build a representative library. The London Metropolitan University scholar Wendy Wheeler has set up a Living Books about Life web page with writings by Terrence Deacon, Mary Catherine Bateson, and others, accessible from the Society home page.

2020: By way of a Biosemiotics book series (Springer), a journal by this name, international conferences and advocates such as Marcello Barbieri and Jesper Hoffmeyer, an informational, communicative presence and role has been found and articulated for many code versions beyond genes alone. An array of microbial, cellular, metabolic sensings, signings and relative cross-talk across evolutionary organisms has been well scoped out and confirmed.

Barbieri, Marcello. Code Biology, Peircean Biosemiotics, and Rosen’s Relational Biology. Biological Theory. 14/1, 2019.

Marcello, Barbieri. The Semantic Theory of Language. Biosystems. January, 2020.

Deacon, Terrence. Reconsidering Darwin’s “Several Powers.”. Biosemiotics. Online March, 2016.

Emmeche, Claus and Kalevi Kull, eds. Towards a Semiotic Biology: Life is the Action of Signs. London: Imperial College Press, 2011

Hoffmeyer, Jesper. The Semiome: From Genetic to Semiotic Scaffolding. Semiotica. 198/11, 2014.

Hofmeyr, Jan-Hendrik. The First Special Issue on Code Biology. BioSystems. 164/11, 2018.

Pattee, Howard and Joanna Raczaszek-Leonardi. Laws, Language and Life. Berlin: Springer, 2012.

Velmezova, Ekaterina, et al, eds. Biosemiotic Perspectives on Language and Linguistics.International: Springer, 2015.

Wheeler, Wendy. Expecting the Earth: Life/Culture/Biosemiotics. London: Lawrence & Wishart, 2016.

View the 48 Bibliographic Entries

D. An Evolutionary Intelligence Arises

2020: Since 2015 we have reported a growing sense that as life evolves it does so by a directional emphasis on cerebral and cognitive qualities more so than somatic anatomy. An implication is that a developmental gestation seems to be skewed to and involved with becoming smarter and more informed. In this way, one can become a self-aware member in a coherent community.

Chaistain, Erick, at al. Algorithms, Games, and Evolution. Proceedings of the National Academy of Sciences. 111/10620, 2014.

de Vladar, Harold and Eors Szathmary. Neuronal Boost to Evolutionary Dynamics. Interface Focus. 5/6, 2015.

Hasson, Uri, et al. Direct Fit to Nature: An Evolutionary Perspective on Biological and Artificial Neural Networks. Neuron. 105/3, 2020.

Hochberg, Michael, et al.Innovation: An Emerging Focus from Cells to Societies. Philosophical Transactions of the Royal Society B. Vol. 372/Iss. 1736, 2017.

Kouvaris, Kostas, et al. How Evolution Learns to Generalize. arXiv:1508.06854.

Oudeyer, Pierre-Yves and Linda Smith. How Evolution May Work Through Curiosity-Driven Development Process. Topics in Cognitive Science. 8/2, 2016.

Watson, Richard and Eors Szathmary. How Can Evolution Learn? Trends in Ecology & Evolution. 31/2, 2016.

Watson, Richard, et al. Evolutionary Connectionism. Evolutionary Biology. Online December, 2015.

View the 36 Bibliographic Entries