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

Hallgrimsson, Benedikt and Brian Hall, eds. Variation. Amsterdam: Elsevier, 2005. In this collection are for the first time many papers which consider how and why the biological hierarchy across genetic, developmental, organismal, species, population, and community/ecological levels changes in time and form. The studies are aided by new insights and tools from bioinformatics and computational biology. The second quote is from a concluding article by Hallgrimsson, Hall and Yardley Brown. See also the Dan McShea article.

This volume appears at a time when the synthesis of developmental and evolutionary biology (evo-devo) is reaching a mature phase. Indeed, the prospect for a new synthesis bridging genetics, development, ecologic, and evolutionary biology now seems more likely than at any time in the past. (6) The developmental genetic basis for variability most likely resides in emergent properties of the genetic networks that regulate development such as nonlinearity, thresholds, and redundancy. It is our view that understanding the sources of phenotypic variation and the causes of phenotypic variability will converge into a single area of study as we develop a systems understanding of how variation is generated and regulated within developmental systems. (548)

Harmon, Luke. Contingent Predictability in Mammalian Evolution. Current Biology. 27/11, 2017. A review of a Geography of Ecological Niche Evolution in Mammals article by French, Swiss, and Italian biologists in the same issue who find a common convergence to persist amongst disparate animal spatial environments.

Convergence of distantly related species to similar forms speaks to the predictability of evolution, but we still lack general insights into whether convergence is more common or rare than we would expect. Using a global dataset of mammalian species, Mazel and colleagues find that both convergence and divergence occur more often than expected. Convergence was especially common at broad scales that involved Australia, speaking to the extraordinary replicate mammalian communities found there.

Hazen, Robert. Chance, Necessity and the Origins of Life: A Physical Sciences Perspective. Philosophical Transactions of the Royal Society A. 375/2016.0353, 2016. We note this essay by the Carnegie Institute geochemist (search 2019) for its content and affinity to writings by the paleontologist George McGhee (2016, 2019 herein). They both reject Jacques Monod’s 1970 verdict that all is accident, and instead agree that while randomness is rife, an overall physical, geologic, biochemical, anatomic and physiologic evolution is constrained as it develops emergent scales of complexity and sentience. But any admission of an innate orthogenesis is a step that cannot yet be taken.

Earth's 4.5-billion-year history has witnessed a complex sequence of high-probability chemical and physical processes, as well as ‘frozen accidents’. Most models of life's origins similarly invoke a sequence of chemical reactions and molecular self-assemblies in which both necessity and chance play important roles. Recent research adds two important insights into this discussion. First, in the context of chemical reactions, chance versus necessity is an inherently false dichotomy—a range of probabilities exists for many natural events. Second, given the combinatorial richness of early Earth's chemical and physical environments, events in molecular evolution that are unlikely at limited laboratory scales of space and time may, nevertheless, be inevitable on an Earth-like planet at time scales of a billion years. (Abstract)

In 2015, we discovered that the diversity and global distribution of mineral species follow statistical patterns analogous to the arrangement and frequency of words in a book. Whereas a few words such as ‘a’, ‘and’ and ‘the’ are common in any book, the majority of different words are used rarely. On Earth, the resulting ‘large number of rare events’ (LNRE) distribution of minerals facilitates a calculation of the probabilities for more than 5000 chemical reactions. (2) Because this observed distribution of mineral species on Earth is analogous to that of words in a book, modification of lexical statistics facilitates application of LNRE models to characterize the diversity and distribution of Earth’s minerals. (3)

Chance versus necessity is a misleading dichotomy. Even if estimates of the four relevant parameters described above are in error by a few orders of magnitude, the implications of Earth’s combinatorial chemical richness are clear: chemical reactions that are improbable to reproduce at the short time scale and limited spatial dimensions of laboratory experiments—experiments, for example, requiring exacting physical and chemical conditions or unusual juxtaposition of several reactant molecules on an uncommon mineral surface—may be inevitable under the diverse physical and chemical environments possible at planetary scales of space and time. (7)

Hazen, Robert, et al. Functional Information and the Emergence of Biocomplexity. Proceedings of the National Academy of Sciences. 104/Supplement 1, 2007. The various papers tend to emphasize a certain quality, in this case the symbolic informational content of animate systems such as RNA sequences.

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)

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