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

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)

Mayfield, John. The Engine of Complexity: Evolution as Computation. New York: Columbia University Press, 2013. Since computers are the icon of our present cyberage, the physical cosmos and life’s emergence are methodically being reinterpreted in kind. The Iowa State University emeritus biologist achieves a conceptual survey and articulation in this regard. With Seth Lloyd (search) and others, a digital universe springs from and develops by mathematical laws as they may run and iterate. A software-like information and processing then becomes a primary source and agency. A companion approach is the theory of evolutionary or genetic algorithms, from Richard Dawkins and Daniel Dennett, along with John Holland’s complex adaptive systems. By this theme, fitter organisms with apparent purposes are the result of their relatively successful instructions.

To consider, while winnowing selection goes on, the model does enters a deeper, prior program in operation that impels life's procession. To illustrate, Mayfield cites Iowa State colleague Dan Ashlock’s work from his Evolutionary Computation for Modeling and Optimization, to distill this five step sequence: Generate a population of informational structures, Calculate relative quality, Select best structures to copy, Replace the worst with them, Generate variations, and Output the best result. And just now we optimum (or good enough) peoples pop out as the universe’s way of consciously learning this procedure and, as alluded in closing, so that might we continue such encoding and begin a new creation.

There are at least three things that make the subject of information interesting to me, a biologist, who happens also to be fascinated by larger issues. First, it is obvious to any modern biologist that a proper understanding of life is not possible without a detailed understanding of how the information stored in DNA is utilized to make new living organisms. Second, the process of evolution is very easily understood and illustrated when presented in computational terms. In this mode of thinking, evolution occurs by following a particular strategy for information manipulation and accumulation. In this book I call that strategy “the engine of complexity.” Third, complexity of any significant kind, living or not, is only possible to achieve through processes that can be broadly described as computing. (3)

Maze, Jack, et al. The Virtual Mode: a Different Look at Species. Taxon. 54/1, 2005. Rather than random genes and selection, a self-organizing dynamics serves the emergence of somatic form and function. One might reflect that while the modern synthesis was a major achievement of the mid 20th century, it is now being surpassed and expanded by a 21st century (genesis) synthesis.

Our hypothesis is that besides the aggregate gene pool and the constraining external morphological power of natural selection, there is an internal morphological function of self-organized formation that produces a novel emergence that is immediately viable and functional. (132) Our hypothesis adds another dimension to morphological generation, and, we suggest, acknowledges that our world is not mechanical and linear but complex and non-linear. (132)

McDougall, Carmel and Bernard Degnan. Modularity of Gene-Regulatory Networks Revealed in Sea-Star Development. BMC Biology. 9/6, 2011. If the actual import of these findings, among so many nowadays, can be rightly grasped, they imply a universal, independent presence for these creative dynamical system attributes, which then become instantiated in each and every genomic and cellular instance, such as the noble sea star. By these insights may be realized an implicate 21st century evolutionary program, verily that something else and more going on, that serves to orient and direct life’s emergent, quickening gestation. This is a huge advance that wholly overturns selection alone and begs an imminent Genesis Synthesis.

Evidence that conserved developmental gene-regulatory networks can change as a unit during deutersostome evolution emerges from a study published in BMC Biology. This shows that genes consistently expressed in anterior brain patterning in hemichordates and chordates are expressed in a similar spatial pattern in another deuterostome, an asteroid echinoderm (sea star), but in a completely different developmental context (the animal-vegetal axis). This observation has implications for hypotheses on the type of development present in the deuterostome common ancestor. (Abstract, 1)

This finding indicates that the genes involved in these patterning processes could be components of a conserved gene regulatory network (GRN) - a set of genes that operate together in a predicted pattern of activation or repression to control a particular process within an organism - and that this GRN is deployed regardless of developmental mode. (1) It is therefore becoming evident that the redeployment of GRNs at different times of development, in different developmental contexts, or in completely new territories within the organism, is an important process in metazoan evolution, and that the circuitry of these networks can provide more robust evolutionary information than the expression patterns of individual genes. (2)

Historically, the notion that large-scale evolution could be driven by a multiplicity of small changes in DNA sequences was theoretically challenging, as the majority of these changes are likely to be deleterious, and cause decreased fitness. The discovery of GRNs makes this conceptually less of a problem, as base-pair changes in the regulatory region of one gene could alter the binding affinities of various transcription factors, effectively placing the entire network under the operation of different drivers. One can then envisage the situation where a given gene network could be induced to turn on at a different stage of development or in a different spatial location within the organism. (3)

McGhee, George. Can Evolution be Directional Without Being Teleological? Studies in History and Philosophy of Science C. 58/93, 2016. The Rutgers University paleontologist (search 2019) weighs in on this misunderstood quandary, often due to misdefined terms, by saying that while random happenstance surely does occur, over the long haul due to structural limits and nature’s reuse of what works in kind, an ascendant course will be traversed. But it is then stated that this axial path does not imply an innate, independent aim or purpose. See also Life’s Biological Chemistry: A Destiny or Destination Starting from Prebiotic Chemistry by R. Krishnamurthy in Chemistry: A European Journal (24/63, 2018) which traces an oriented emergence from biochemicals to people, but denies any teleological direction, and Chance, Necessity and the Origins of Life by Robert Hazen (2016, 2019 search)

Convergent evolution reveals to us that the number of possibilities available for contingent events is limited, that historically evolution is constrained to occur within a finite number of limited pathways, and that contingent evolution is thus probabilistic and predictable. That is, the phenomenon of convergence proves that evolutionary processes can repeatedly produce the same, or very similar, organic designs in nature and that evolution is directional in these cases. For this reason it is argued that evolution can be directional without being teleological, and that the dichotomy that evolution must either be directionless and unpredictable or directional and predetermined (teleological) is false. (Abstract)

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