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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
Table of Contents
Genesis Vision
Learning Planet
Organic Universe
Earth Life Emerge
Genesis Future
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V. Life's Corporeal Evolution Develops, Encodes and Organizes Itself: An Earthtwinian Genesis Synthesis

Aguirre, Jacobo, et al. On the Networked Architecture of Genotype Spaces and its Critical Effects on Molecular Evolution. Open Biology. July, 2018. In this Royal Society journal, Barcelona and Madrid systems theorists including Susanna Manrubia make a thorough case with over 200 references for a dynamic synthesis by way of ubiquitous network phenomena. The paper goes on to establish ways that these topologies can inherently arise from animate physical systems. Their presence is especially evident as whole genomes translate and array into creaturely physiologies. A “multlscape” is thus achieved with abilities to quickly adapt to external changes. In regard, a 21st century genesis revolution gains a broad outline by this deep inclusion of a complex, exemplary source as it arrays everywhere.

In this Royal Society journal, Barcelona and Madrid systems theorists including Susanna Manrubia make a thorough case with over 200 references for a dynamic synthesis by way of ubiquitous network phenomena. The paper goes on to establish ways that these topologies can inherently arise from animate physical systems. Their presence is especially evident as whole genomes translate and array into creaturely physiologies. A “multlscape” is thus achieved with abilities to quickly adapt to external changes. In regard, a 21st century genesis revolution gains a broad outline by this deep inclusion of a complex, exemplary source as it arrays everywhere.

Ananthaswamy, Anil. Chemistry Guides Evolution, Claims Theory. New Scientist. January 18, 2003. A report on scientists who believe that Earth’s early chemistry channeled life to form bounded vesicles and to proceed in a predictable way from cells to animals. A comment by Harold Morowitz sums up:

It’s part of a quiet paradigm revolution going on in biology, in which the radical randomness of Darwinism is being replaced by a much more scientific law-regulated emergence of life. (12)

Ao, Ping. Global View of Bionetwork Dynamics: Adaptive Landscape. Journal of Genetics and Genomics. 36/2, 2009. The emeritus University of Washington bioengineer is presently at the Systems Biology Laboratory, Shanghai Center for Systems Biomedicine. Also known as a “fitness landscape,” this popular map-like metaphor from Sewall Wright in 1932, variously by Theodosius Dobzhansky, George Simpson, Conrad Waddington, and others, attempts to graphically display the active evolutionary and organismic traverses, as if attractors, of creaturely genotypes and/or phenotypes. This 21st century survey covers five areas of population genetics, developmental biology, gene regulation and genetic switch, neural dynamics and computing, and protein folding via current complex network theories. For more background and discussion, see the edited volume The Adaptive Landscape in Evolutionary Biology, (Oxford UP, 2012) And while reading one wonders if a similar presence and expansion of such a ground of being and becoming might extended to life’s fertile celestial realms, as if a conducive cosmic spacescape.

Based on recent work, I will give a nontechnical brief review of a powerful quantitative concept in biology, adaptive landscape, initially proposed by S. Wright over 70 years ago, reintroduced by one of the founders of molecular biology and by others in different biological contexts, but apparently forgotten by modern biologists for many years. Nevertheless, this concept finds an increasingly important role in the development of systems biology and bionetwork dynamics modeling, from phage lambda genetic switch to endogenous network for cancer genesis and progression. It is an ideal quantification to describe the robustness and stability of bionetworks. Here, I will first introduce five landmark proposals in biology on this concept, to demonstrate an important common thread in theoretical biology. Then I will discuss a few recent results, focusing on the studies showing theoretical consistency of adaptive landscape. From the perspective of a working scientist and of what is needed logically for a dynamical theory when confronting empirical data, the adaptive landscape is useful both metaphorically and quantitatively, and has captured an essential aspect of biological dynamical processes. Though at the theoretical level the adaptive landscape must exist and it can be used across hierarchical boundaries in biology, many associated issues are indeed vague in their initial formulations and their quantitative realizations are not easy, and are good research topics for quantitative biologists. I will discuss three types of open problems associated with the adaptive landscape in a broader perspective. (Abstract)

Arber, Werner. Horizontal Gene Transfer among Bacteria and its Role in Biological Evolution. Life. 4/217, 2014. As an example of how senior scientists can hold opposite conceptions, a situation that presages a paradigm shift, the University of Basel microbiologist and 1978 Nobel laureate in Medicine endorses the prior influence of a ubiquitous “natural self-organization” which serves to drive and guide life’s oriented emergence. This is especially evident in microbial genome and cellular dynamics as they share and process information. Apropos, octogenarian Werner Arber is also President of the Pontifical Academy of Sciences at the Vatican. In this capacity he has chaired recent international conferences in Rome such as the 2012 Complexity and Analogy in Science and in May 2014 Sustainable Humanity, Sustainable Nature: Our Responsibility with Pope Francis (Google each). At the latter meeting, Arber’s presentation in The Broader Context section was Human-Nature Co-Evolution.

This is a contribution to the history of scientific advance in the past 70 years concerning the identification of genetic information, its molecular structure, the identification of its functions and the molecular mechanisms of its evolution. Particular attention is thereby given to horizontal gene transfer among microorganisms, as well as to biosafety considerations with regard to beneficial applications of acquired scientific knowledge. (Abstract) As a contribution to the history of scientific investigations, we trace here a sequence of steps of conceptual and experimental approaches to understand microbial evolution at the molecular level. This shall allow us to extrapolate to generally valid laws of nature guiding biological evolution by self-organization. (218)

Evolutionary Inventiveness of Nature’s Self-Organization Our present scientific insights into the evolution of life and of appropriate habitats reveal a remarkable degree of invention concerning different specific molecular processes that contribute to the generation of a rich diversity of forms of life living in a large number of different habitats. It becomes more and more known that many specific molecular mechanisms can contribute to a slow but steady evolutionary progress of living organisms. We have become aware that mechanistic insights into specific steps of genetic variation obtained in the work with one kind of bacteria cannot be generalized for all kinds of bacteria. On the other hand, it seems to us that the three defined natural strategies of genetic variation (local sequence change, intragenomic rearrangement of DNA segments, horizontal gene transfer) can best contribute to conceptually understand the self-organized natural process of the slow but steady evolution of life to a rich biodiversity within a global system of interdependencies. (221-222)

Aria, Cedric. Macroevolutionary Patterns of Body Plan Canalization in Euarthropods. Paleobiology. October, 2020. A University of Toronto biologist meticulously analyzes datasets for these diverse invertebrates as they appeared in the prolific Cambrian era (~540 my ago). He concludes that their swift rise was mostly due to the buildup of genetic regulatory networks. See also Early Fossil Record of Euarthropoda and the Cambrian Explosion by Allison Daley, et al in PNAS (115/5325, 2018.)

Arnoldt, Hinrich, et al. Toward the Darwinian Transition: Switching Between Distributed and Speciated States in a Simple Model of Early Life. Physical Review E. 92/052909, 2015. Arnoldt, and Marc Timme, MPI Dynamics and Self-Organization, with Steven Strogatz, Cornell University find stochastic condensed matter physics can help explain how life arose from an initial communal phase onto distinct, evolving organisms.

It has been hypothesized that in the era just before the last universal common ancestor emerged, life on earth was fundamentally collective. Ancient life forms shared their genetic material freely through massive horizontal gene transfer (HGT). At a certain point, however, life made a transition to the modern era of individuality and vertical descent. Here we present a minimal model for stochastic processes potentially contributing to this hypothesized “Darwinian transition.” The model suggests that HGT-dominated dynamics may have been intermittently interrupted by selection-driven processes during which genotypes became fitter and decreased their inclination toward HGT. Stochastic switching in the population dynamics with three-point interactions may have destabilized the HGT-dominated collective state and essentially contributed to the emergence of vertical descent and the first well-defined species in early evolution. A systematic nonlinear analysis of the stochastic model dynamics covering key features of evolutionary processes (such as selection, mutation, drift and HGT) supports this view. (Abstract)

Arthur, Wallace. Biased Embryos and Evolution. Cambridge: Cambridge University Press, 2004. A zoologist at the National University of Ireland carefully sorts through the convergence of the population genetics/natural selection basis of the 20th century modern synthesis with new understandings from the study of embryological development. But this reunion of phylogeny and ontogeny requires an admission of internal, epigenetic factors acting prior to selection which then give a directional bias. An accessible work that argues the monolithic Darwinism has widened into a delta with many parallel streams or schools of thought that beg for a new (Genesis?) synthesis.

But many of us feel that something is missing; that selection is not enough; that the actualization of some creatures, together with the failure of others to emerge from the realm of the possible, requires something else – something internal that interacts with selection in a particular way. (25) I like to think of this book as a contribution to a growing movement whose goal is to transform the ‘modern’ synthesis that is appropriate for the twenty-first. (191) …evolution and development are indeed the two great processes of biological creation. One has created organisms with trillions of cells from a single-cell starting point over a period of about a billion years. The other repeatedly achieves the same thing over a single lifetime. (199)

Auletta, Gennaro. A Paradigm Shift in Biology? Information. 1/1, 2010. A Pontifical Gregorian University philosopher joins the chorus calling for a creation-friendly science to move beyond a sterile mechanics whereof life and person are reduced to chemistry and physics. The way forward will involve complex, self-organizing systems, along with an informational source and essence, channeling constraints, so as to allow a teleonomy and teleology. By this path, an evolutionary “epigeny” can gain novel witness and admission. See also Auletta’s 2011 book Cognitive Biology, for much more, albeit technical, views upon this revolution.

The growing perception is that the traditional conceptual framework of biology, which has been drawn from classical mechanics, is no longer adequate. According to this traditional approach, any biological functionality can be explained in pure chemical or mechanical terms. (29) In the following, I shall show that the language of physics cannot remain centered on notions like mass, energy, speed of reaction, etc., but should be expressed with the help of concepts like constraints, degenerate states and processes, differential timing and irreversible dissipative events, dynamical itinerancy, information sharing and selecting, equivalence classes, i.e., in a non-strictly mechanistic conceptual framework. (29)

Avise, John and Francisco Ayala. In the Light of Evolution I: Adaptation and Complex Design. Proceedings of the National Academy of Sciences. 104/Supplement 1, 2007. An introduction to this Sackler Colloquium whose content could exemplify a welling transformation of evolutionary thought. Three themes were covered: Approaches to Biocomplexity Assessment, From Ontogeny to Symbiosis (A Hierarchy of Complexity), and Dissecting Complex Phenotypes (Case Studies). As a public institution the papers are online, just Google: ‘PNAS light evolution.’ But a curious conflation seems to occur. The first two theory sections tacitly argue that while life’s advance does involve modular, cooperative, nested, dynamic networks, it can still be explained by an expanded Darwinian mutation and selection. Francisco Ayala’s lead article takes this tact, along one by Michael Lynch. Yet these structural and functional features reflect an intrinsic self-organization which this old mold or paradigm, and its moribund universe substrate, can not recognize or permit.

Babajanyan, Sanasar, et al. Coevolution of reproducers and replicators at the origin of life and the conditions for the origin of genomes. PNAS. 12/14, 2023. An international team posted at the National Library of Medicine, NIH, the Yerevan Physics Institute, and CNRS, University of Paris including Eugene Koonin offers this latest proposal, reviewed by Eors Szathmary, of a 2023 convergent synthesis across the full span of life’s cellular and organism emergence within an evidently conducive ecosmic universe. By this integral vista, an oriented developmental process seems to unfold along a scalar sequence from biochemical precursors through some manner of hereditaries all the way to our Earthuman retrospective sapience.

The origin of life, which is equivalent to the origin of cells, is arguably the greatest enigma in biology. The intricate complexity of the simplest extant cells could only evolve from simpler, prebiological entities, but how to reconstruct. Here we present an evolutionary scenario in which cells evolved via symbiosis between protocells composed of protometabolic reaction networks could divide and become subject to selection, but as yet without primordial genetic elements (GE). Mathematical models can describe conditions for the survival of such symbionts and the origin of modern-type genomes, in particular, coordination of the rates of protocell division and replication. (Significance)

Ball, Philip. How Life Works: A User’s Guide to the New Biology. Chicago: University of Chicago Press,, 2023. A latest 500 page edition by the prolific British science writer and polyscholar which has a primary intent of finally setting aside and correcting the olden machine model. Into these 2020s, a true to life version is now ready to replace and invigorate. It can do so by an array of integral features that include Complexity, Redundancy, Modularity, Robustness, Networks, Hierarchy, Agency, Purpose, Self-Organization, Combinatorial Logic, each explained in turn. The contribution thus stands as the strongest, comprehensive statement to date. See also a review Genes are not the blueprint for life by Denis Noble in Nature (626/254, 2024), with a quote below.

But as a sad note, on November 6, 2023 (a year later) an article by PB in Nautilus says he now has prostate cancer, which moves him to write a luminous mediation on what living beingness and wearing out may possibly be about, see second quote. (The malady may yet be treatable in some manner at this point.)

Biology is undergoing a quiet but profound transformation. Several aspects of the standard picture of how life works—the genome as a blueprint, of proteins as molecular machines, cells with fixed identities, and more—have been exposed as incomplete, misleading, or wrong. How Life Works, explores a new biological scene which reveals life to be a far richer, more ingenious affair than we had ever guessed. It explains that there is no unique place to look for an answer. Living beings are composed of many levels such as genes, proteins, cells, tissues along with immune and nervous systems. With this knowledge come new possibilities. As we discover the conditions that dictate the forms into which cells organize themselves, our ability to guide and select the outcomes becomes extraordinary. (Publisher)

Later in the book, Ball grapples with the philosophical question of what makes an
organism alive. Agency — the ability of an organism to bring about change to itself or its environment to achieve a goal — is the author’s central focus. Such agency, he argues, is attributable to whole organisms, not just to their genomes. Genes, proteins and processes such as evolution don’t have goals, but a person certainly does. (Noble review)

For what truly distinguishes living organisms as self-organized knots of energy and matter, spinning in the universe, is that they acquire meaning and purpose. Those words can often disturb many biologists because they convey teleological and even theological connotations. But this is a fundamental misunderstanding of what life is, of why we are not “nothing but atoms.” Not only can meaning and purpose be scientific concepts, but they need to become that if we are ever to get to the core of what life is. (How Life Really Works. Nautilus Nov. 6, 2023.)

Ball, Philip. The Strange Inevitability of Evolution. Nautilus Quarterly. Issue 20, 2015. Also online at http://nautil.us/issue/20/creativity. The British science writer surveys the work of Andreas Wagner, Manfred Eigen, Susanna Manrubia, Johannes Jaeger, Peter Schuster, and others as they integrate the frontiers of evolutionary theory with complex system, informational and statistical physics features. As a result, the rise of life, mind and people increasingly seems to be written into the natural cosmos.

These ideas suggest that evolvability and openness to innovation are features not just of life but of information itself. That is a view long championed by Schuster’s sometime collaborator, Nobel laureate chemist Manfred Eigen, who insists that Darwinian evolution is not merely the organizing principle of biology but a “law of physics,” an inevitable result of how information is organized in complex systems. And if that’s right, it would seem that the appearance of life was not a fantastic fluke but almost a mathematical inevitability.

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