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

Losos, Jonathan. Improbable Destinies: How Predictable is Evolution? New York: Penquin, 2017. A Harvard University, Organismic and Evolutionary Biology professor alludes that while evolutionary developments do converge upon similar forms, a constant, quirky contingency which causes life to ever splay into arbitrary directions seems to rule. While local pathways may be followed, an overall drive and direction and aim does not exist, we are a lucky fluke.

Love, Alan, ed. Conceptual Change in Biology: Scientific and Philosophical Perspectives on Evolution and Development. Dordrecht: Springer, 2015. Select papers from a 2010 Dahlem Workshop held at the MPI for History of Science, Berlin, as a 30 year retrospect after a 1981 meeting that began explorations of an Evo-Devo unification. Topics such as adaptation, allometry, heterochrony, homoplasy, plasticity, constraint, hierarchies, are discussed by leading researchers David Wake, Fred Nijhout, Marc Kirschner, Rudolf Raff, Gunter Wagner, Wallace Arthur, Stuart Newman and more. But the focus seemed to be more on conceptual theories rather than an inquiry upon what life’s long phylogeny is doing and becoming by its own innate propensities.

Lu, Qiaoying and Pierrick Bourrat. The Evolutionary Gene and the Extended Evolutionary Synthesis. British Journal for the Philosophy of Science. Online June, 2017. Macquarie University and University of Sydney philosophers of biology consider how such revisions are influenced by on-going malleable definitions of what this nucleotide molecule actually is and does. Along with the quotes, see also, e.g., The Human Microbiome and the Missing Heritability Problem by Santiago Sandoval-Motta, et al (2017 search).

Advocates of an ‘extended evolutionary synthesis’ have claimed that standard evolutionary theory fails to accommodate epigenetic inheritance. The opponents of the extended synthesis argue that the evidence for epigenetic inheritance causing adaptive evolution in nature is insufficient. We suggest that the ambiguity surrounding the conception of the gene represents a background semantic issue in the debate. Starting from Haig’s gene-selectionist framework and Griffiths and Neumann-Held’s notion of the evolutionary gene, we define senses of ‘gene’, ‘environment’, and ‘phenotype’ in a way that makes them consistent with gene-centric evolutionary theory. We argue that the evolutionary gene, when being materialized, need not be restricted to nucleic acids but can encompass other heritable units such as epialleles. If the evolutionary gene is understood more broadly, and the notions of environment and phenotype are defined accordingly, current evolutionary theory does not require a major conceptual change in order to incorporate the mechanisms of epigenetic inheritance. (Abstract)
Epiallele and Epigene: An epiallele is one of a number of alternative difference makers, such as alternative epigenetic modifications, that cause epigenetic inheritance. The set of epialleles that leads to the same phenotypic difference (at a given grain of description) represents an epigene. (4)

Even if the term ‘gene’ comes to be used to refer to the molecular gene exclusively, and theorists employ another term (such as ‘replicator’) when referring to our concept of evolutionary gene, the conceptual analysis we provide will still be valuable insofar as it highlights two things: First researchers should define the concepts they use and carefully interpret works from different fields; this is crucial for productive interdisciplinary discussion. Second, the discovery of DNA as the material basis for genetic information, understood in the evolutionary sense, does not mean that it is the only basis for it. Hence, we are confident that current evolutionary theory is resilient and adaptive enough to incorporate new hereditary materials without requiring profound conceptual changes. (20-21)

Mabee, Paula. Integrating Evolution and Development: The Need for Bioinformatics in Evo-Devo. BioScience. 56/4, 2006. An overview of this historic reintegration of genotype and phenotype, known as evolutionary developmental biology, which studies transformations in morphology over time. In this regard, a major aspect is a pervasive modularity in genetic, embryonic, and evolutionary domains, for …modules are the units of evolution. A systems or network understanding can be further facilitated by computer ontologies, along with improved visualization methods. If a tendency to form pattern and process modules is so constant, and since complex adaptive self-organization is known to generate nested modular structures and entities, one then wonders such presence in life’s progression could be attributed to an independent, universal source.

Makarieva, Anastassia, et al. Energetics of the Smallest: Do Bacteria Breathe at the Same Rate as Whales? Proceedings of the Royal Society B. 272/2219, 2005. A power law scale invariance for metabolic rates has been established across the range of multicellular organisms, but until now prokaryotic microbes have not been studied. This study reports that the same pattern continues for prokaryote cells whose volumes vary over a million fold in size.

These findings indicate that the mass-specific metabolic rates of living cells vary within universal limits that are on a large scale independent of the size of the organism to which they belong. (2222)

Malagon, Nicolas and Ellen Larsen. Heredity and Self-Organization: Partners in the Generation and Evolution of Phenotypes. International Review of Cell and Molecular Biology. Volume 315, 2015. University of Toronto biologists present a latest survey of how pervasively this natural propensity graces all aspects of evolutionary life. Since the “physical-chemical world is (now known to be) self-organized,” by this paradigm shift genomes and organisms will also be formed by and express this quality.

In this review we examine the role of self-organization in the context of the evolution of morphogenesis. We provide examples to show that self-organized behavior is ubiquitous, and suggest it is a mechanism that can permit high levels of biodiversity without the invention of ever-increasing numbers of genes. We also examine the implications of self-organization for understanding the “internal descriptions” of organisms and the concept of a genotype-phenotype map. (Abstract)

Mameli, Matteo. The Inheritance of Features. Biology and Philosophy. 20/2-3, 2005. A philosopher of biology at King’s College sets aside an older emphasis on DNA alone, from which organisms “unfold,” in favor of an expanded appreciation of a number of epigenetic factors such as environment contexts during development. Mameli uses an example of baking a cake, which comes with a recipe, but whose final product depends on which kind of oven is used. We can witness in papers like this, and many others herein, a historic shift to a new evolutionary genesis synthesis.

This paper…argues that (given what we know about developmental processes and genetic activity) the DNA-centric theory should be abandoned in favor of a pluralistic (but not holistic) theory of the inheritance of features. According to this pluralistic theory, the reliable reoccurrence of phenotypes must be explained by appealing not only to processes responsible for the reliable reoccurrence of genetic developmental factors but also to processes responsible for the reliable reoccurrence (or persistence) of non-genetic developmental factors. (365)

Manrubia, Susanna, et al. From Genotypes to Organisms: State of the Art and Perspectives of a Cornerstone in Evolutionary Dynamics. arXiv:2002:00363. Eighteen coauthors including Jose Cuesta, Sebastian Ahnert, Lee Altenbery, Paulien Hogeweg, Ard Louis, and Joshua Payne (search each) post a 44 page composite paper with 383 references from a CECAM (search) workshop at the University of Zaragoza in March 2019. The endeavor was an attempt to meld rapidly moving fields such as RNA and protein structures, gene regulatory and metabolic networks, computational algorithms, synthetic biology and so on as they may come together to explain how a phenotype creature arises or “maps” from a genomic source. A notice of “universal” occurrences is apparent, along with much evidence that generative forces are indeed in play before any selective effects. Into 2020, this is a good example of a filling in and acknowledgement of a “natural genesis” that this website has long sought to document.

Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is a major missing piece in a fully predictive theory of evolution. Though we are far from achieving a complete picture of these relationships, our understanding of simpler aspects such as structures induced in the space of genotypes by sequences traced to molecular genotype-phenotype maps has revealed important facts about the dynamical description of evolutionary processes. Empirical evidence supporting such relevant features as phenotypic bias is growing as well, while the synthesis of concept and experiment leads to questioning the nature of evolutionary dynamics. This work reviews with a critical and constructive attitude our current knowledge of how genotypes map onto phenotypes and organismal functions, and discusses theoretical and empirical avenues to broaden and improve this comprehension. (Abstract excerpt)

In other words, natural selection can only act on variation that has been pre-sculpted by the GP map. (14) We have identified a patchwork of processes that in principle are able to shape the variational properties of the GP map for phenotypes at the level of whole organisms, where complex integration leaves us unable to derive the properties from physical first-principles. This is an area in which evolutionary theory needs much greater development. At levels of complexity where reductionist modelling is impossible, we have surveyed efforts that attempt to analyse how evolutionary processes shape the GP map. The body of results described, while not a fully fleshed-out theory, is sufficient to demonstrate that this process-based approach can inform a research program for the GP map at the whole organism level. (32)

Marcot, Jonathan and Daniel McShea. Increasing Hierarchical Complexity throughout the History of Life. Paleobiology. 33/2, 2007. Although the paper begins with a good recognition of a nested, emergent progression, obviously there, as biologists immersed in or inhibited by an evolutionary paradigm that denies any drive or direction, it does not take it further.

The history of life is punctuated by a number of major transitions in hierarchy, defined here as the degree of nestedness of lower-level individuals within higher-level ones: the combination of single-celled prokaryotic cells to form the first eukaryotic cell, the aggregation of single eukaryotic cells to form complex multicellular organisms, and finally, the association of multicellular organisms to form complex colonial individuals. These transitions together constitute one of the most salient and certain trends in the history of life, in particular, a trend in maximum hierarchical structure, which can be understood as a trend in complexity. (182)

Margulis, Lynn and Dorion Sagan. What Is Life? New York: Simon & Schuster, 1995. An innovative attempt to answer this question as posed by Erwin Schrodinger in his 1944 book which leads to a wide-ranging, imaginative survey of animate properties and essence. More than mobile protoplasm, living entities from bacteria to the biosphere are most distinguished by their recurrent, symbiotic, self-sustained autopoietic organization and sentience.

The ‘fractals’ of life are cells, arrangements of cells, many-celled organisms, communities of organisms, and ecosystems of communities. (14) Self-transforming, holarchic life “breaks out” into new forms that incorporate formerly self-sufficient individuals as integral parts of greater identities. The largest of these levels is the planetary layer, the biosphere itself. Each level reveals a different kind of ‘organic being.’ (20)

Mind and body, perceiving and living, are equally self-referring, self-reflexive processes already present in the earliest bacteria….Life on earth is a complex, photosynthetically based, chemical system fractally arranged into individuals at different levels of organization. (178)

Mattick, John. A New Paradigm for Developmental Biology. Journal of Experimental Biology. 210/9, 2007. In a special issue on Post-Genomic and Systems Approaches to Comparative and Integrative Physiology, (see also Eivind Almass) a University of Queensland geneticist contends that much more is going on than previously thought. Genetic programs were long attributed to analogue protein components, but now with sequencing by digital systems, it is evident that regulatory RNA networks also carry much generative information.

I propose that the epigenetic trajectories of differentiation and development are primarily programmed by feed-forward RNA regulatory networks and that most of the information required for multicellular development is embedded in these networks… (1526)

Mattick, John. The Central Role of RNA in Human Development and Cognition. FEBS Letters. 585/11, 2011. (FEBS = Federation of European Biochemical Societies) Citing our advanced, post-sequence age, a University of Queensland geneticist proposes two main modes or courses for genomic research. A prior stage, necessary to identify all the nucleotide components, is inadequate to explain consequent evolutionary and organismic complexity and intelligence. As the systems biology turn studies, a network domain of regulatory connections between the biomolecules is where the real generative action is. While people, primates and invertebrates may have similar numbers of genes, our unique human difference and acumen is due to this “progressive” genomic intricacy and information efficiency as these dynamic nested networks are refined over life’s developmental emergence.

It appears that the genetic programming of humans and other complex organisms has been misunderstood for the past 50 years, due to the assumption that most genetic information is transacted by proteins. However, the human genome contains only about 20,000 protein-coding genes, similar in number and with largely orthologous functions as those in nematodes that have only 1000 somatic cells. By contrast, the extent of non-protein-coding DNA increases with increasing complexity, reaching 98.8% in humans. The majority of these sequences are dynamically transcribed, mainly into non-protein-coding RNAs, with tens of thousands that show specific expression patterns and subcellular locations, as well as many classes of small regulatory RNAs. Moreover it appears that animals, particularly primates, have evolved plasticity in these RNA regulatory systems, especially in the brain. Thus, it appears that what was dismissed as ‘junk’ because it was not understood holds the key to understanding human evolution, development, and cognition. (Abstract)

The third great surprise, which was entirely contrary to expectations, is that the number and repertoire of protein-coding genes remains relatively static across the metazoan lineage, despite enormous increases in developmental and cognitive complexity. The simple nematode has almost 20,000 protein-coding genes, similar to that in the human. (1801) Moreover, despite some interesting expansions and innovations, such as RNA editing in vertebrates, the majority of these genes are orthologous (i.e., have similar functions, even in sponge, the most primitive metazoan. That is, all animals have a similar protein toolkit, and therefore the relevant information that programs progressively more complex organisms must lie elsewhere in the genome, presumably in an expanded regulatory architecture. (1801)

The emerging evidence suggests that evolution has shaped the human genome in far more sophisticated ways than ever imagined, and that most of the information it holds is involved in complex regulatory processes that underpin development and brain function. This includes the vast numbers of non-coding RNAs and transposons, which rather than being junk, appear to provide the regulatory power and plasticity required to program our ontogeny and cognition. (1610) Moreover, it seems that the major challenge that evolution had to overcome to evolve developmentally complex organisms was regulatory, and that the barriers imposed by the rising cost of regulation were overcome by moving to a hierarchical RNA-based regulatory system. (1610)

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