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

Hedges, S. Blair, et al. Tree of Life Reveals Clock-Like Speciation and Diversification. Molecular Biology and Evolution. 32/4, 2015. An update summary by Temple University geneticists, including Sudhir Kumar, on the copious Timetree of Life project begun in 2006. A large book with this title was published in 2009 by Oxford University Press. A lavish, well arranged, educational website continues at www.timetree.org. A Foreword by James Watson notes the passage from Charles Darwin’s 1837 branching sketch to its 21st century version that spans life’s earthly origin through every kingdom and species to primates and homo sapiens. This 2015 article adds a latest depiction with a spiral shape spanning four billion years. But an unexpected result is that this integral vista shows Darwinian adaption to be a secondary effect within a broad, steady march of diverse speciation. In this revision, a methodical trend is displayed with chronological precision. While local life may be contingent and random, as a whole, by a “law of large numbers,” phyla and clades average out to a predictable procession.

Genomic data are rapidly resolving the tree of living species calibrated to time, the timetree of life, which will provide a framework for research in diverse fields of science. Previous analyses of taxonomically restricted timetrees have found a decline in the rate of diversification in many groups of organisms, often attributed to ecological interactions among species. Here, we have synthesized a global timetree of life from 2,274 studies representing 50,632 species and examined the pattern and rate of diversification as well as the timing of speciation. We found that species diversity has been mostly expanding overall and in many smaller groups of species, and that the rate of diversification in eukaryotes has been mostly constant. We also identified, and avoided, potential biases that may have influenced previous analyses of diversification including low levels of taxon sampling, small clade size, and the inclusion of stem branches in clade analyses. We found consistency in time-to-speciation among plants and animals, ∼2 My, as measured by intervals of crown and stem species times. Together, this clock-like change at different levels suggests that speciation and diversification are processes dominated by random events and that adaptive change is largely a separate process. (Abstract)

Held, Lewis. Deep Homology?: Uncanny Similarities of Humans and Flies Uncovered by Evo-Devo. Cambridge: Cambridge University Press, 2017. The Texas Tech geneticist continues his project to uncover and document the presence of many similar anatomies and forms across a widest range of creatures, in this work between homo sapiens and musca domestica (house fly). As the second quote says, the title term from Neil Shubin (search) signifies that they can be traced to an ancestral origin long ago. Typical chapters are Body Axes, Nervous System, Limbs and Vision, which altogether give an increasing credence to a singular evolutionary gestation. See a good book review by David Linz and Armin Moczek in Evolution & Development (19/277, 2017).

Humans and flies look nothing alike, yet their genetic circuits are remarkably similar. Here, Lewis I. Held compares the genetics and development of the two to review the evidence for deep homology, the biggest discovery from the emerging field of evolutionary developmental biology. Remnants of the operating system of our hypothetical common ancestor 600 million years ago are compared in chapters arranged by region of the body, from the nervous system, limbs and heart, to vision, hearing and smell. Concept maps provide a clear understanding of the complex subjects addressed, while encyclopaedic tables offer comprehensive inventories of genetic information.

Homology: 1. a similarity often attributable to common origin. 2. likeness in structure between parts of different organisms (the wing of a bat and the human arm) due to evolutionary differentiation from a corresponding part in a common ancestor. 3. similarity of nucleotide or amino acid sequence (as in nucleic acids or proteins). (Merriam-Webster)

Heyduk, Karolina, et al. The Genetics of Convergent Evolution. Nature Reviews Genetics. 20/485, 2019. Convergent evolution has been pervasive throughout the history of life. Even very complicated adaptations, such as camera eyes in animals, sex determination systems in eukaryotes and eusociality in insects, have evolved multiple times. (485) Yale University biologists open with these statements, which are a good example of 2019 conclusions that an inherent propensity repeats as similar forms and features in kind. In this paper insightful evidence from flora photosynthesis is seen to build the case that life’ development knows what it is doing and where it is going. (Look for Convergent Evolution on Earth by George McGhee due in October from MIT Press.)

The tree of life is resplendent with examples of convergent evolution, whereby distinct species evolve the same trait independently. Many highly convergent adaptations are also complex, which makes their repeated emergence surprising. In plants, the evolutionary history of two carbon concentrating mechanisms (CCMs) — C4 and crassulacean acid metabolism (CAM) photosynthesis — presents such a paradox. Here, we propose that many of the complexities often associated with C4 and CAM photosynthesis may have evolved during a post-emergence optimization phase. (Abstract excerpt)

Hidalgo, Jorge, et al. Information-Based Fitness and the Emergence of Criticality in Living Systems. Proceedings of the National Academy of Sciences. 111/10095, 2014. A Spanish, Italian, and American team, with Jayanth Banavar and Amos Maritan, continues their articulation of how nature spontaneously self-organizations into fledgling organismic complexities. As other areas also find, personal and group life succeeds best in a dynamic poise between chaos and order. As a result, “individuals in communities” are moved to evolve and emerge into collective wholes. By these insights, the fields of statistical mechanics, information theory, genetics, neuroscience, and more can be integrated in to a coherent explanation.

Empirical evidence suggesting that living systems might operate in the vicinity of critical points, at the borderline between order and disorder, has proliferated in recent years, with examples ranging from spontaneous brain activity to flock dynamics. However, a well-founded theory for understanding how and why interacting living systems could dynamically tune themselves to be poised in the vicinity of a critical point is lacking. Here we employ tools from statistical mechanics and information theory to show that complex adaptive or evolutionary systems can be much more efficient in coping with diverse heterogeneous environmental conditions when operating at criticality.

Analytical as well as computational evolutionary and adaptive models vividly illustrate that a community of such systems dynamically self-tunes close to a critical state as the complexity of the environment increases while they remain non-critical for simple and predictable environments. A more robust convergence to criticality emerges in co-evolutionary and co-adaptive set-ups in which individuals aim to represent other agents in the community with fidelity, thereby creating a collective critical ensemble and providing the best possible trade-off between accuracy and flexibility. Our approach provides a parsimonious and general mechanism for the emergence of critical-like behavior in living systems needing to cope with complex environments or trying to efficiently coordinate themselves as an ensemble. (Abstract)

Hoelzer, Guy, et al. On the Logical Relationship between Natural Selection and Self-Organization. Journal of Evolutionary Biology. 19/6, 2006. I have met two of the authors, Hoelzer (University of Nevada) and John Pepper (University of Arizona), who along with Eric Smith (Santa Fe Institute) are working to articulate an expanded evolutionary synthesis that can assimilate real nonlinear drivers prior to selective effects. The article abstract provides a good capsule.

Most evolutionary biologists cherish Darwin's theory of natural selection (NS) as the process of adaptive evolution more than 140 years after publication of his first book on the subject. However, in the past few decades the study of self-organization (SO) in complex dynamical systems has suggested that adaptation may occur through intrinsic reorganization without NS. In this study, we attempt to describe the logical framework that relates the general process of SO to the specific process of NS. We describe NS as a mechanism that coordinates the coevolution of species in an ecosystem to effectively capture, process and dissipate solar energy into the earth's shadow. Finally, we conclude that NS is an emergent process founded on the same thermodynamic imperatives that are thought to underlie all SO. This perspective suggests that the theory of self-organizing systems offers a broader physical context in which to understand the process of NS, rather than contesting it. It even suggests the possibility that there may be a physical basis for understanding the origin of the process of NS. Rather than being merely a fluke of nature, the origin of NS that may be driven by energy flows across gradients.

Hoffmeyer, Jesper. Origin of Species by Natural Translation. Petrilli, Susan, ed. Translation Translation. Amsterdam: Rodopi, 2003. A contribution to the perceptual shift from a particulate, gene-centered emphasis in evolutionary theory to include Baldwin effect-like environmental influences. By Hoffmeyer’s semiotic approach, nature is seen to be most engaged in an activity of translation or interpretation, not selection alone.

The usual identification of biological information with digitally coded sequential information carried in nucleic acids (DNA and RNA) has tended to blind us to the analogly coded kinds of information present in the form of cytoplasmic architecture and membrane bound processes. The perpetual transmission down through generations of ontogenetic “messages” shuffled back and forth between digital and analog codes is the root form of natural translation. Ultimately these messages assure the evolutionarily acquired semiotic competence of natural systems in managing the genotype-envirotype translation processes. (329)

Hofmann, Klaus, et al. Building Functional Modules from Molecular Interactions. Trends in Biochemical Sciences. 31/9, 2006. Another recognition of persistent modularity in cellular metabolism. But this is set within a mechanical metaphor via “protein machines” which go about their assemblies as if in a factory. So once more, a conflation of regnant life within an inappropriate physical universe. With Breuker, et al above, these unexamined philosophical lapses and lacunae inhibit both biology and physics.

Hogeweg, Paulien. Interlocking of Self-Organization and Evolution. Hemelrijk, Charlotte, ed. Self-Organization and Evolution of Social Systems. Cambridge: Cambridge University Press, 2005. The Utrecht University information biologist achieves one more reconception of life’s evolutionary rise as a manifestation of self-organizing dynamics. This prior drive before selection results in a multi-level emergence from genomes to societies, which one may add, is the typical spatial pattern of such complexifying systems. A practical case of how self-organization works is then proposed: TODO – “do what there is to do” - whence each local, individual agent does just that – repair the nest, clean the burrow, weed the garden, and so on.

Next I will focus on two aspects of the concurrence of self-organization and evolution, namely (1) how, in an eco-evolutionary context, spatial self-organization generates new levels of selection, and thereby directs evolution of the basic replicating entities into unexpected directions, and (2) how cellular self-organization occurs as a consequence of the interlocking of intra- and intercellular dynamics, and how this causes genomic self-organization, and, in a sense, ‘directed’ evolution. (170)

Holland, John. Biology’s Gift to a Complex World. The Scientist. September, 2008. The University of Michigan systems wizard recounts in this “Magazine of the Life Sciences” the steps and path that led to his several advances in complexity theory. Holland first realized it is the recombination of genes in reproduction, rather than random mutations, that is the main driving force of evolution. This factor was next appreciated to have a mathematical basis, which he conceived as the now widely employed “genetic algorithms.” With stints at the Santa Fe Institute, such innate genome dynamics could be further modeled as “complex adaptive systems” composed of individual agents engaged in communicative interaction, from which a higher order emerges. In an expansion beyond molecules, CAS phenomena can be seen universally present from neural networks to immune reactions to financial economies. A good summary of Holland’s corpus and the welling shift to a genesis evolutionary synthesis.

Hoyal Cuthill, Jennifer and Simon Conway Morris.. Fractal branching organizations of Ediacaran rangeomorph fronds reveal a lost Proterozoic body plan. PNAS. 111/36, 2014. Cambridge University paleobiologists report a pre-Cambrium presence of a physiological fractal geometry whose self-similarity served to improve creaturely sustenance.

Rangeomorph fronds characterize the late Ediacaran Period (575–541 Ma), representing some of the earliest large organisms. As such, they offer key insights into the early evolution of multicellular eukaryotes. However, their extraordinary branching morphology differs from other organisms and is highly enigmatic. Here we provide a unified mathematical model, allowing us to reconstruct 3D morphologies of 11 taxa and measure their functional properties. This reveals an adaptive radiation of fractal morphologies which maximized body surface area, consistent with diffusive nutrient uptake. Rangeomorphs were adaptively optimal for the low-competition, high-nutrient conditions of Ediacaran oceans. (Abstract)

Hsieh, Shannon, et al. The Phanerozoic Aftermath of the Cambrian Information Revolution. Paleobiology. 48/3, 2022. Akin to Cellular Self-Organization: An Overdrive in Cambrian Diversity by Filip Vujovic, et al in BioEssays (July 2022), University of Illinois, Chicago and University of Connecticut paleoecologists including Roy Plotnick achieve a similar perception of rapid, wide-spread cerebral and cognitive advances as organic forms suddenly leapt forward from simpler stages. Many studies from the Burgess Shale to Devonian phases of “nervous system complexities” provided an empirical basis. As a result, a graphic radiation can be sketched from no CNS to ganglia onto a relative brain. In their rare purview, soma and sensory together are seen to constitute life’s radical emergent, quicker transition (on its way to our late planetary reconstruction).

The Cambrian information revolution describes how biotic increases in signals, sensory abilities, behavioral interactions, and landscape spatial complexity led to a rapid increase in animal cognition concurrent with the Cambrian radiation. Here, we compare neural and cognitive complexity in pre- and post-Cambrian marine ecosystems. We do not find a trend in this regard, nor in macroscopic sense organs These results suggest that sophisticated information processing was already common in early Phanerozoic ecosystems, comparable with behavioral evidence from the trace fossil record. The overall rise in cognitive sophistication in the Cambrian was likely a unique event in the history of life. (Abstract)

Comparisons of faunal lists from Cambrian and post-Cambrian ecosystems reveal similarly high shares of animal genera with brains as well as macroscopic sensory organs. Our results show that the Cambrian radiation generated ecosystems that were “modern” in sensory- and information-processing complexity, comparable to ecosystems in the later Phanerozoic. A major difference, however, is that most sensorially and cognitively complex animals in the Cambrian were panarthropods, since chordates and mollusks had not yet diversified. In both Cambrian and recent times, nervous systems permitted a variety of life modes, but the most active are associated with brains, which first appear in the Cambrian. (414-415)

Huneman, Philippe. Revisiting Darwinian Teleology: A Case for Inclusive Fittness as Design Explanation. Studies in History and Philosophy of Biological and Biomedical Sciences. Online July, 2019. The University of Paris Sorbonne evolutionary theorist offers a latest attempt sort and clarify ways to view life’s relative appearance as having some innate directional course. That is to say, how to thread a narrow path between its olden mainstream rejection and the fact that something must be going on which resulted in our human presence.

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