V. Life's Corporeal Evolution Encodes and Organizes Itself: An EarthWinian Genesis Synthesis

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)

Arthur, Wallace. The Emerging Conceptual Framework of Evolutionary Developmental Biology. Nature. 415/757, 2002. In the latter 19th century evolution and embryology were unified as a subject but went separate ways as quantitative studies in each field diverged. Around 1980 a reconvergence began with the discovery of the homeobox gene complex and of epigenetic influences. Arthur provides a lucid review of how developmental and phylogenetic findings now reinforce each other. What results is a reciprocity of discrete gene and field or topological features along with a “broadly recapitulatory” parallel between individual ontogenetic maturation and the long course of evolution.

Looked at in one way, development is programmed by genes. But this is too limited a view. There is a complementary process, the epigenetic programme, through which genes are controlled by developmental agents of diverse kinds, including transcription factors and secreted morphogens. (759)

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. 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.

Bapteste, Eric and Philippe Huneman. Towards a Dynamic Interaction Network of Life to Unify and Expand the Evolutionary Theory. BMC Biology. 16/56, 2018. In a unique contribution to a genesis synthesis, Sorbonne University philosophers of biology describe the pervasive, innate presence of network topologies as they serve to link altogether prior organismic parts across biomolecular, cellular, and organism phases. This late addition is seen to bolster the holobiont symbiosis model, and accord with scaffolded, process, and chimeric gene aspects. Once again, if by a philosophia mind to allow and view, life’s homologous developmental course takes on a webwork anatomy, physiology and neural appearance. With this in place, a shift toward network thinking, as everywhere else, would advance and unify evolutionary theory. See also Testing the “(Neo-) Darwinian” Principles against Reticulate Evolution by Nathalie Gontier in Information (11/7, 2020).

The classic Darwinian theory and the Synthetic evolutionary theory and their linear models, while invaluable to study the origins and evolution of species, are not primarily designed to model the evolution of organisations, typically that of ecosystems, nor that of processes. How could evolutionary theory better explain the evolution of biological complexity and diversity? Inclusive network-based analyses of dynamic systems could retrace interactions between (related or unrelated) components. This theoretical shift from a Tree of Life to a Dynamic Interaction Network of Life, which is supported by diverse molecular, cellular, microbiological, organismal, ecological and evolutionary studies, would further unify evolutionary biology. (Abstract)

Barberousse, Anouk, et al, eds. Mapping the Future of Biology. Berlin: Springer, 2009. (Boston Studies in the Philosophy of Science: Volume 266). A premier collection, introduced by Richard Lewontin, from a 2006 meeting (see quote) that was actually open to real revisions of the 1950s modern evolutionary synthesis. Although some authors circle wagons around Darwinian selection alone, Susan Oyama (search) offers a chapter on how a deep informational source, a once and future “Biologos,” might be a crucial enrichment. Mark Bedau (search) goes on to refute the vested view that “if life’s tape was run again it would not repeat” by reference to a robust complex systems milieu. Scott Gilbert goes on to advocate eco-evo-devo, while John Olding-Smee makes a case for niche construction. As opposed to Massimo Pigliucci’s 2010 edited work on the Altenberg 16 meeting, which does not mention self-organization in the index, a novel portal is here entered unto an much overdue expansion, a genesis synthesis.

When planning to organize Paris 2006 workshop on the role of models and theories in today’s biology, our impression was that the most important issues were coming from new general theoretical approaches, namely that the theories of self-organization, niche construction or epigenetics, were to be seen as alternative approaches to neo-Darwinism. However, the conference proved that neo-Darwinism is still the only unifying theoretical approach to the living world and that the newer trends have to be conceived of as complementing neo-Darwinism, rather than as competing with it. (editors, 7)

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