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

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)

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.

Lewitus, Eric and Helene Morlon. Natural Constraints to Species Diversification. PLoS Biology. Online August, 2016. As the extended Abstract explains, École Normale Supérieure, Paris, biologists employ the latest analytic and geometric measures to discern the presence of inherent universal principles and patterns that are found to array across and distinguish life’s long developmental ascent to our worldwide ability to discover this.

Identifying modes of species diversification is fundamental to our understanding of how biodiversity changes over evolutionary time. Diversification modes are captured in species phylogenies, but characterizing the landscape of diversification has been limited by the analytical tools available for directly comparing phylogenetic trees of groups of organisms. Here, we use a novel, non-parametric approach and 214 family-level phylogenies of vertebrates representing over 500 million years of evolution to identify major diversification modes, to characterize phylogenetic space, and to evaluate the bounds and central tendencies of species diversification. We identify five principal patterns of diversification to which all vertebrate families hold. These patterns, mapped onto multidimensional space, constitute a phylogenetic space with distinct properties.

Firstly, phylogenetic space occupies only a portion of all possible tree space, showing family-level phylogenies to be constrained to a limited range of diversification patterns. Secondly, the geometry of phylogenetic space is delimited by quantifiable trade-offs in tree size and the heterogeneity and stem-to-tip distribution of branching events. Finally, both the constrained range and geometry of phylogenetic space are established by the differential effects of macroevolutionary processes on patterns of diversification. Given these properties, we show that the average path through phylogenetic space over evolutionary time traverses several diversification stages, each of which is defined by a different principal pattern of diversification and directed by a different macroevolutionary process. The identification of universal patterns and natural constraints to diversification provides a foundation for understanding the deep-time evolution of biodiversity. (Abstract)

Lipson, Hod, et al. On the Origin of Modular Variation. Evolution. 56/8, 2002. Computer simulations reveal why functional modules inherently form and evolve.

Lister, Adrian. Behavioural Leads in Evolution: Evidence from the Fossil Record. Biological Journal of the Linnean Society. Online October, 2013. A senior Natural History Museum, London, zoologist marshals copious evidence to claim that across the Metazoan kingdoms, creatures engage in proactive conduct to survive, reproduce and prevail, which then drives and influences life’s evolutionary trajectory.

There has been much discussion of the role of behaviour in evolution, especially its potential to lead morphological evolution by placing the organism in a novel selective environment. Many adaptations of living species can be imagined to have originated in this way, although documented examples are relatively few. A fruitful arena for testing hypotheses about behavioural innovation is the fossil record. Traditionally, the behaviour of fossil species has been deduced from their morphology, precluding the observation of a behavioural lead preceding morphological evolution. This circularity can be broken by examining behavioural proxies independent of the adaptive morphology itself. Examples applicable to fossil remains include dietary information (e.g. wear traces on teeth, stable isotopes) and trace fossils indicating locomotor mode (footprints). The signature of a behavioural lead would be an observed shift in behaviour from one horizon (or taxon) to another, followed later by a functionally-related morphological change.

This pattern can be sought either in finely-stratified anagenetic sequences of fossils (stratophenetic approach) or among fossils with well-resolved species-level phylogenies (cladistic approach). An array of case studies from the literature is presented. These include feeding shifts in finely-resolved sequences of vertebrates ranging from freshwater fish to terrestrial ungulates, as well as locomotor changes crucial to major evolutionary transitions in the origin of tetrapods, birds, and humans. The latter examples highlight the role of behaviour in initiating exaptation (the requisitioning of structure for a new function). The case studies also illustrate the challenges of using fossil sequences to elucidate behavioural roles, including insufficient stratigraphic resolution and uncertainty over the adaptive function of observed traits. By the same token, they suggest criteria for choosing promising cases for research, as well as for formulating testable hypotheses about evolutionary modes. (Abstract)

Livnat, Adi. Interaction-Based Evolution: How Natural Selection and Nonrandom Mutation Work Together. Biology Direct. Online October, 2013. In a 43 page essay, a Virginia Tech assistant professor of biological sciences with a 2006 doctorate in Ecology and Evolutionary Biology from Princeton University delves into a revisionary expansion of the Modern Synthesis. This online journal edited by Eugene Koonin, Laura Landweber and David Lipman provides articles with peer reviews, in this case Nigel Goldenfeld, Jurgen Brosius, and Ford Doolittle. As the quotes convey, the composite posting could exemplify the state of evolutionary theory. At the outset Livnat feels obligated to say that his approach is “mechanistic” in kind, and will not detract from natural selection as the lone operative. As other works at this frontier, he then proceeds to do the opposite. While not Lamarckian, epigenetic influences are quite in effect beyond the molecular genome. Further novel aspects are broached but it is averred they do not carry any sense of teleology. Conversations with Gunter Wagner, Simon Levin, Marc Feldman, others, are acknowledged, and affinities with the work of James Shapiro, Lynn Caporale and Arlin Stoltzfus (search), so his views are representative. Goldenfeld found the article “provocative and stimulating,” and to Brosius it was “eye-opening,” but Doolittle was “very irritated.” To wit while some “nonrandom, non-accidental” stimulus does seem at work, selection will not to be parted with until this evident prior agency can be fully explained by a robust, understandable theory. And a tacit impediment remains an alien physical cosmos sans any enlivening, generative program of its own.

Here I address these questions from a unified perspective, by means of a new mechanistic view of evolution that offers a novel connection between selection on the phenotype and genetic evolutionary change (while relying, like the traditional theory, on natural selection as the only source of feedback on the fit between an organism and its environment). I hypothesize that the mutation that is of relevance for the evolution of complex adaptation—while not Lamarckian, or “directed” to increase fitness—is not random, but is instead the outcome of a complex and continually evolving biological process that combines information from multiple loci into one. This allows selection on a fleeting combination of interacting alleles at different loci to have a hereditary effect according to the combination’s fitness. (Hypothesis)

My general approach will be as follows. I will continue to assume that selection is the only source of feedback on the fit between an organism and its environment. However, I will revisit the question of the nature of the mutation that drives evolution. Here, I will continue to assume that mutation is not Lamarckian, and that a given mutation is not more likely to occur in an environment where it increases fitness than in an environment where it does not. However, I will show that there is another alternative, which has not been attended to yet, which is neither accidental mutation nor mutation that violates our core assumptions. Revisiting the question of the nature of mutation, I will construct a new theory of how adaptive evolution happens, based on selection, but also on a new connection between selection on the phenotype and genetic evolutionary change. I will show that this approach addresses the unresolved problems of sex and interactions from a unifying perspective, and at the same time begins to propose a mechanism at the point where traditional theory relies only on pure chance. (4)

This paper holds that the mutation that drives evolution is not a result of random accident but an outcome of a mutational writing phenotype. This phenotype itself evolves, like anything else inherent to the organism. It absorbs the information that comes from selection and guides selection further by providing further variation. (38) The process described here is “Kantian” in that it shows that evolution is driven not only by external forces. It is not random accident that generates the variance that selection operates on. Rather, a phenotype causing syntactic internal change is absorbing information from the outside world—from natural selection—and changes itself in the process. (39)

Livnat, Adi. Simplification, Innateness, and the Absorption of Meaning from Context. Evolutionary Biology. Online March, 2017. The University of Haifa theorist continues his project (search) to achieve a better explanation of life’s evolution as due in some way to algorithmic computations, network propensities, genome – language affinities, neural net deep learning, and more. By enlisting these current insights, an advance beyond Darwinian natural selection as the only agency is proposed so as to identify and explain an actual non-random or non-accidental innate essence. We quote at length to convey the substantial contribution. An earlier posting is available at arXiv:1605.03440.

Considering all the above, we can now describe a main point of this paper. Evolution is a bottomless system. One cannot define all words in the dictionary in terms of other words without getting into a circularity. Ultimately, the meaning of words comes from the context of their usage; that is how language is learned and even how it evolves. The genes are similar in this regard. Their meaning comes from their context of usage. They themselves are nodes in a network, in development as well as in evolution. The upshot of this is that the bottom of the hierarchy of biological interactions - the genetic sequence - is not a stable ground upward of which life is built. Mutation is not a local accident that brings innovation all on its own as though there is no living network that it needs to connect to. The process of genetic change is a complex one where the connections between nodes in the network become stronger and weaker as they form modules that absorb meaning from context. (9)

4.15 The Engine of Evolution Interaction-based evolution argues that the process whereby a population converges on an adaptation is a process that converts information from a less orderly to a more orderly state. It proceeds from a fuzzy to a sharp, well-working and stereotyped state. However, evolution is not only a fuzzy-to-sharp process, in that the fuzzy source must first arise. The progress from fuzzy to sharp is therefore only a half of a cycle of the “engine of creativity" that is evolution. The other half is that previously made sharp elements come together at a high level to make the new fuzzy source from which new sharp elements can be made. I argued that simplification under performance pressure connects the two parts of the cycle. The simple elements it creates not only are improvements but also come together in new complex interactions which serve as the raw material for the next round of simplification. Thus, novelty arises not from accident, but from evolutionary work. (29)

Furthermore, the fact that the output of a mutational event at one generation, namely the mutation itself, can serve as an input into mutational events at later generations means that the mutation-writing phenotype creates a network of information flow through the generations, from many genes into any one gene and from any one gene to many. Other examples of networks of information flow and computation include the brain, and what computer scientists call a circuit (one instance of which is an artificial neural network). Thus, according to interaction-based evolution, genetic evolution can be seen as the result of the workings of a network, itself evolving over time. (37)

The philosophical move that is required from the perspective of interaction-based evolution is to let go of the notion that random mutation and novelty from a point are at the bottom of things - that they provide a stable ground upward from which a conceptual edifice can be built; and to accept instead that the action is at the network level: that both the meaning and origin of genetic and phenotypic elements comes from the higher levels of organization - it comes from the network - from above. This move opens up the study of evolution substantially; because while the notion of random mutation means that there is nothing of importance to be studied about the causes of mutation from an evolutionary perspective, the concept of non-accidental mutation provided by interaction-based evolution implies instead a whole world of biological mechanisms open to investigation. (38-40)

Lobkovsky, Alexander, et al. Predictability of Evolutionary Trajectories in Fitness Landscapes. PLoS Computational Biology. 7/12, 2011. National Center for Biotechnology Information, NIH, systems biologists including Yuri Wolf, and Eugene Koonin, provide, among a growing chorus, one more entry into and evidence via protein gyrations of a nascent genesis synthesis beyond random, aimless selection, whereby life’s emergent development is indeed found to track a repeatable, oriented pathway.

Is evolution deterministic, hence predictable, or stochastic, that is unpredictable? What would happen if one could ‘‘replay the tape of evolution’’: will the outcomes of evolution be completely different or is evolution so constrained that history will be repeated? Arguably, these questions are among the most intriguing and most difficult in evolutionary biology. In other words, the predictability of evolution depends on the fraction of the trajectories on fitness landscapes that are accessible for evolutionary exploration. Because direct experimental investigation of fitness landscapes is technically challenging, the available studies only explore a minuscule portion of the landscape for individual enzymes. We therefore sought to investigate the topography of fitness landscapes within the framework of a previously developed model of protein folding and evolution where fitness is equated with robustness to misfolding. We show that model-derived and experimental landscapes are significantly smoother than random landscapes and resemble moderately perturbed additive landscapes; thus, these landscapes are substantially robust to mutation. The model landscapes show a deficit of suboptimal peaks even compared with noisy additive landscapes with similar overall roughness. Thus, the smoothness and substantial deficit of peaks in fitness landscapes of protein evolution could be fundamental consequences of the physics of protein folding. (2)

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