V. Life's Corporeal Evolution Develops, Encodes and Organizes Itself: An Earthtwinian Genesis Synthesis

Krotov, Dmitry, et al. Morphogenesis at Criticality. Proceedings of the National Academy of Sciences. 111/3683, 2014. Princeton University, Joseph Henry Laboratories of Physics and Lewis-Sigler Institute for Integrative Genomics, theorists, including William Bialek, contend that genome phenomena, as it informs developing morphologies, is effectively poised or “tuned” to a critical state. One may add, just as brains are now found to be.

Spatial patterns in the early fruit fly embryo emerge from a network of interactions among transcription factors, the gap genes, driven by maternal inputs. Such networks can exhibit many qualitatively different behaviors, separated by critical surfaces. At criticality, we should observe strong correlations in the fluctuations of different genes around their mean expression levels, a slowing of the dynamics along some but not all directions in the space of possible expression levels, correlations of expression fluctuations over long distances in the embryo, and departures from a Gaussian distribution of these fluctuations. Analysis of recent experiments on the gap gene network shows that all these signatures are observed, and that the different signatures are related in ways predicted by theory. Although there might be other explanations for these individual phenomena, the confluence of evidence suggests that this genetic network is tuned to criticality. (Abstract)

Biological networks are described by many parameters, and the behavior of a network is qualitatively different (monostable, bistable, oscillating, etc.) in different parts of parameter space. Critical points and surfaces are the borders between such qualitatively different regimes, as with phase transitions in equilibrium thermodynamics. We argue that, as expected from the thermodynamic case, genetic regulatory networks should exhibit behaviors near criticality that are independent of most molecular details. Analyzing recent experiments on the gap gene network in the early Drosophila embryo, we find that these signatures of criticality can be seen, quantitatively. This raises the question of why evolution has tuned this network to such a special point in its parameter space. (Significance)

Kul, Kaveli. Adaptive Evolution without Natural Selection. Biological Journal of the Linnean Society. Online July, 2013. The University of Tartu, Estonia, semiotics scholar advises one more way that something innately prescriptive is going on prior to selective eliminations. By this view, life’s temporal, scalar development from microbes to people is seen as most facilitated constant communicative behaviors. This proactive agency is said to deserves much merit as informing and guiding an evolutionary emergence.

A mechanism of evolution that ensures adaptive changes without the obligatory role of natural selection is described. According to this mechanism, the first event is a plastic adaptive change (change of phenotype), followed by stochastic genetic change which makes the transformation irreversible. This mechanism is similar to the organic selection mechanism as proposed by Baldwin, Lloyd Morgan and Osborn in the 1890s and later developed by Waddington, but considerably updated according to contemporary knowledge to demonstrate its independence from natural selection. Conversely, in the neo-Darwinian mechanism, the first event is random genetic change, followed by a new phenotype and natural selection or differential reproduction of genotypes. Due to the role of semiosis in the decisive first step of the mechanism described here (the ontogenic adaptation, or rearrangement of gene expression patterns and profile), it could be called a semiotic mechanism of evolution. (Abstract)

Lala, Kevin, et al. Evolution Evolving: The Developmental Origins of Adaptation and Biodiversity. Princeton: Princeton University Press, 2024. Five veteran authors, KL (nee Laland), Tobias Uller, Nathalie Feiner, Marcus Feldman and Scott Gilbert orient and advance a once and future proposal that life’s personal occasion and maturation, aka eco evo devo, across the extent of Metazoan animals should take the place of life’s central explanatory basis.

A new scientific view of evolution is emerging that questions and expands our understanding of how evolution works. Recent research shows that organisms differ in how effective they are at evolving because the process itself has changed over time. In this book, a group of leading biologists draw on the latest findings in evo-devo studies, as well as epigenetics, symbiosis and inheritance to examine the central role that developmental processes play.

Laland, Kevin, et al. The Extended Evolutionary Synthesis: Its Structure, Assumptions and Predictions. Proceedings of the Royal Society B. Vol. 282/Iss. 1813, 2015. Within growing realizations that the 1950s Modern Evolutionary Synthesis, which remains in place, has become quite inadequate, leading theorists including Eva Jablonka, Gerd Muller, and Kim Sterelny continue their efforts to scope out an appropriate 21st century version. Older random mutation and post selection alone can be amended and surpassed by a “reciprocal causation” between organism and environment such as niche construction, epigenetic inheritance, directional phenotypic variation, evolutionary developmental biology, and so on. Something else and far more is going on which is not accidental, but still in need, we add, of a physical rooting in a cosmic, self-organizing, vivifying genesis. See also Schism and Synthesis at the Royal Society, a review by KL of the November, 2016 meeting New Trends in Evolutionary Biology (Trends in Ecology and Evolution February 2017).

Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the ‘extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism–environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology. (Abstract)

Landis, Michael and Joshua Schraiber. Pulsed Evolution Shaped Modern Vertebrate Body Sizes. Proceedings of the National Academy of Sciences. 114/13224, 2017. We cite this paper by Yale and Temple University biologists to show how evolutionary theorists are finding an independent mathematical process as it generates and guides corporeal creatures across widely diverse clades. See also in Systematic Biology Phylogenetic Analysis Using Levy Processes by Landis, et al (62/2, 2013) and Inference of Evolutionary Jumps in Large Phylogenies Using Levy Processes by Pablo Duchin, et al (66/6, 2017).

The diversity of forms found among animals on Earth is striking. Despite decades of study, it has been difficult to reconcile the patterns of diversity seen between closely related species with those observed when studying single species on ecological timescales. We propose a set of models, called Lévy processes, to attempt to reconcile rapid evolution between species with the relatively stable distributions of phenotypes seen within species. These models, which have been successfully used to model stock market data, allow for long periods of stasis followed by bursts of rapid change. We find that many vertebrate groups are well fitted by Lévy models compared with models for which traits evolve toward a stationary optimum or evolve in an incremental and wandering manner. (Significance)

Lane, Nick, et al. Energy, Genes and Evolution: Introduction to an Evolutionary Synthesis. Philosophical Transactions of the Royal Society B. 368/20120253, 2013. An overview for this special issue on Energy Transduction and Genome Function: An Evolutionary Synthesis. As the Abstract excerpts sample, life’s ancient evolutionary heritage keeps expanding beyond just mutation and selection and deeper into its dynamic substrate of a physical cosmos. The thesis and claim is that a proper, complete understanding need have a bioenergetic, thermodynamic dimension and source. Salient papers could be “The Inevitable Journey to Being” by Michael Russell, et al, “Early Biochemical Evolution” by Filipa Sousa, et al, and “Why did Eukaryotes Evolve only Once? Genetic and Energetic Aspects of Conflict and Conflict Mediation” by Neil Blackstone. See also a companion issue “The Evolutionary Aspects of Bioenergetic Systems” in Biochimica et Biophysica Acta - Bioenergetics (1827/2, 2013) with some of the same authors.

Life is the harnessing of chemical energy in such a way that the energy-harnessing device makes a copy of itself. No energy, no evolution. The ‘modern synthesis’ of the past century explained evolution in terms of genes, but this is only part of the story. While the mechanisms of natural selection are correct, and increasingly well understood, they do little to explain the actual trajectories taken by life on Earth. From a cosmic perspective—what is the probability of life elsewhere in the Universe, and what are its probable traits?—a gene-based view of evolution says almost nothing. Irresistible geological and environmental changes affected eukaryotes and prokaryotes in very different ways, ones that do not relate to specific genes or niches. Questions such as the early emergence of life, the morphological and genomic constraints on prokaryotes, the singular origin of eukaryotes, and the unique and perplexing traits shared by all eukaryotes but not found in any prokaryote, are instead illuminated by bioenergetics. If nothing in biology makes sense except in the light of evolution, nothing in evolution makes sense except in the light of energetics. This Special Issue of Philosophical Transactions examines the interplay between energy transduction and genome function in the major transitions of evolution, with implications ranging from planetary habitability to human health. (Abstract, Lane, et al)

Life is evolutionarily the most complex of the emergent symmetry-breaking, macroscopically organized dynamic structures in the Universe. Members of this cascading series of disequilibria-converting systems, or engines in Cottrell's terminology, become ever more complicated—more chemical and less physical—as each engine extracts, exploits and generates ever lower grades of energy and resources in the service of entropy generation. Each one of these engines emerges spontaneously from order created by a particular mother engine or engines, as the disequilibrated potential daughter is driven beyond a critical point. Exothermic serpentinization of ocean crust is life's mother engine. It drives alkaline hydrothermal convection and thereby the spontaneous production of precipitated submarine hydrothermal mounds. (Abstract, Russell et al)

Life is the harnessing of chemical energy in such a way that the energy-harnessing device makes a copy of itself. This paper outlines an energetically feasible path from a particular inorganic setting for the origin of life to the first free-living cells. The sources of energy available to early organic synthesis, early evolving systems and early cells stand in the foreground, as do the possible mechanisms of their conversion into harnessable chemical energy for synthetic reactions. In terms of the main evolutionary transitions in early bioenergetic evolution, we focus on: (i) thioester-dependent substrate-level phosphorylations, (ii) harnessing of naturally existing proton gradients at the vent–ocean interface via the ATP synthase, (iii) harnessing of Na+ gradients generated by H+/Na+ antiporters, (iv) flavin-based bifurcation-dependent gradient generation, and finally (v) quinone-based (and Q-cycle-dependent) proton gradient generation. (Abstract, Sousa, et al)

According to multi-level theory, evolutionary transitions require mediating conflicts between lower-level units in favour of the higher-level unit. By this view, the origin of eukaryotes and the origin of multicellularity would seem largely equivalent. Yet, eukaryotes evolved only once in the history of life, whereas multicellular eukaryotes have evolved many times. Examining conflicts between evolutionary units and mechanisms that mediate these conflicts can illuminate these differences. Energy-converting endosymbionts that allow eukaryotes to transcend surface-to-volume constraints also can allocate energy into their own selfish replication. This principal conflict in the origin of eukaryotes can be mediated by genetic or energetic mechanisms. Genome transfer diminishes the heritable variation of the symbiont, but requires the de novo evolution of the protein-import apparatus and was opposed by selection for selfish symbionts. By contrast, metabolic signalling is a shared primitive feature of all cells. Aspects of metabolic regulation may have subsequently been coopted from within-cell to between-cell pathways, allowing multicellularity to emerge repeatedly. (Abstract, Blackstone)

Lau, Emily, et al. An Integrative Understanding of Evolutionary Convergence Across Organisms and Biological Scales. Integrative and Comparative Biology. 64/5, 2024. EL and Rebecca Varney, UC Santa Barbara and Jessica Goodheart, AMNH introduce this Society of Integrative and Comparative Biologists (SICB) seminar which seems to be an endeavor to find ways to define and express the clear, pervasive evidence that life uses the same pattern and processes in kind over and over. As a result, somewhat contrary to neoDarwinian currency, there is an inherent degree of expectation and constancy across Metazoan organisms. Typical papers are Physiological Basis of Convergent Evolution in Animal Communication SystemsGet access by Nigel Anderson, et al, Phenotypic Convergence Is Stronger and More Frequent in Herbivorous Fishes by M. Kolmann, et al and Does Phenotypic Integration Promote Convergent Evolution? by Tristan Stayton. See also in this issue Introduction to the 2024 Chordate Origins, Evolution, and Development by Billie Swalla for another SICB Symposium

The extent to which evolution is predictable is a long-standing question in biology, with implications for biological issues such as viral evolution, antibiotic resistance in bacteria, and organismal responses to climate change. Convergent evolution, the phylogenetically independent evolution of similar phenotypes, provides biological replicates for exploring patterns of predictability. To this end, we organized a SICB symposium entitled “Integrating research on convergent evolution across levels of biological organization, organisms, and time.” Here, we introduce findings from papers in this symposium issue, identify common themes, emerging questions, and more so to better understand nature’s reuse of similar forms and features. (Abstract)

Laubichler, Manfred and Jane Maienschein, eds. From Embryology to Evo-Devo. Cambridge: MIT Press, 2007. A 550 page tome on “the history of developmental evolution” by the main engaged theorists and historians of science. Lengthy summaries are provided by Brian Hall, Gerd Muller, and Gunter Wagner. If so set in the past century from the early 1900s partition of ontogeny and phylogeny, their analytical quantifications since, unto the present holistic reunion, a singular evolutionary recapitulation akin to a gestational genesis becomes broadly evident. A door is also ajar in several places for inherent self-organizational influences.

Laubichler, Manfred and Jurgen Renn. Extended Evolution: A Conceptual Framework for Integrating Regulatory Networks and Niche Construction. Journal of Experimental Zoology B. Online June, 2015. In this journal edited by Gunter Wagner, Arizona State University and Max Planck Institute, History of Science biologists add a further aspect to a 21st century synthesis by way of the pervasive, relational presence of systemic networks. These integrative propensities can be identified all the way from dynamic genomes to eusocial animal groupings as they actively prevail in and arrange their environment.

This paper introduces a conceptual framework for the evolution of complex systems based on the integration of regulatory network and niche construction theories. It is designed to apply equally to cases of biological, social and cultural evolution. Within the conceptual framework we focus especially on the transformation of complex networks through the linked processes of externalization and internalization of causal factors between regulatory networks and their corresponding niches and argue that these are an important part of evolutionary explanations. This conceptual framework extends previous evolutionary models and focuses on several challenges, such as the path-dependent nature of evolutionary change, the dynamics of evolutionary innovation and the expansion of inheritance systems. (Abstract)

Lenton, Timothy, et al. Revolutions in Energy Input and Material Cycling in Earth History and Human History. Earth System Dynamics. 7/353, 2016. . Lenton, University of Exeter, with Peter-Paul Pitcher, Potsdam Institute for Climate Impact Research, and Helga Weisz, Humboldt University, trace life’s advance from early anoxygenic and oxygenic photosynthesis, eukaryotic land colonization, Paleolithic and Neolithic fire usage, and onto the anthropo industrial age. From our late vantage, a further remedial phase of a solar-powered recycling revolution is evident and imperative. The paper is available in full on this site, see also The Energy Expansions of Evolution by Olivia Judson (2017) for a biospheric version.

Major revolutions in energy capture have occurred in both Earth and human history, with each transition resulting in higher energy input, altered material cycles and major consequences for the internal organization of the respective systems. In Earth history, we identify the origin of anoxygenic photosynthesis, the origin of oxygenic photosynthesis, and land colonization by eukaryotic photosynthesizers as step changes in free energy input to the biosphere. In human history we focus on the Palaeolithic use of fire, the Neolithic revolution to farming, and the Industrial revolution as step changes in free energy input to human societies. Looking ahead, a prospective sustainability revolution will require scaling up new renewable and decarbonized energy technologies and the development of much more efficient material recycling systems – thus creating a more autotrophic social metabolism. Such a transition must also anticipate a level of social organization that can implement the changes in energy input and material cycling without losing the large achievements in standard of living and individual liberation associated with industrial societies. (Abstract excerpts)

Lenton, Timothy, Kenneth Caldeira and Eors Szathmary. Major Transitions and Role of Disturbances in the Evolution of Life and of the Earth System. Schellnhuber, Hans Joachim, et al, eds. Earth System Analysis for Sustainability. Cambridge: MIT Press, 2004. The chapter essay confirms an emergent nest of genetic information from molecules to language and adds new parallel transitions in the use of matter and energy.

Major transitions share a number of recurring features, including the emergence of higher-level units of evolution, the evolution of novel inheritance systems, and an increase in complexity.(34) .…multicellular organisms depend on a second (epigenetic) inheritance system: a liver cell and a white blood cell are genetically almost identical; the difference between them is caused by which genes are on (i.e., expressed) and which are off (silent). (35) It is amazing how much harm the human race has done within so little harm. The Earth must consciously be transformed into a unit as if it had been shaped by evolution at that level, for we have only one Earth. (49)

Levine, George. Darwin Loves You: Natural Selection and the Re-Enchantment of the World. Princeton: Princeton University Press, 2006. A Rutgers University scholar contends that Charles’ work has been distorted and misrepresented. His thought and writings could just as readily support a cooperative, teleological view of life. In so doing, Levine aligns with Robert Richards who believes that Darwin was as much a Romantic akin to Alexander von Humboldt with whom he corresponded, than a Newtonian mechanic. Such a “Kinder, Gentler” Darwin might then inspire a less combative, more emphatic sense of a life and people-friendly nature.

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