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

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)

McGhee, George. Convergent Evolution on Earth: Lessons for the Search for Extraterrestrial Life. Cambridge: MIT Press, 2019. As 2020 nears, whence scientific studies in every field are coming together to presage a revolutionary vision, the Rutgers University paleontologist (search) provides an evidential treatise upon life’s propensity, aided by physical constraints, to repetitively develop and repurpose similar forms and functions across procession of myriad organisms. The first chapter, Convergence in Life Forms in the Seas and on the Land, sets the scene for creaturely internal anatomy and physiology, along with external sustenance forages, reproductive behaviors, and much more. McGhee goes on to advise that habitable exoplanets will hold to the same evolutionary convergence. He notes the Darwin’s Aliens paper by Samuel Levin, et al (International Journal of Astrobiology 18/1, 2019) to say that life’s “nested multilevel hierarchy of individuality” should generally be scaled in each instance. But he then recites the 13 reasons noted by M. Canales, et al (search) as to why our home ecoworld is so uniquely special, see third quote. In summary, it is noted while contingencies are surely in effect, an overall common trajectory will and need be followed.

Our Earth is a water world; 71 percent of the earth's surface is covered by water. The fossil record shows that multicellular life on dry land is a new phenomenon; for the vast majority of the earth's history—3,500 million years of its 4,560 million years of existence—complex life existed only in the oceans. Explaining that convergent biological evolution occurs because of limited evolutionary pathways, McGhee examines examples of convergent evolution in forms of feeding, immobility and mobility, defense, and organ systems. McGhee suggests that the patterns of convergent evolution that we see in our own water world indicate the potential for similar convergent forms in other water worlds.. (Publisher)

The first five of these strange things are Earth’s plate tectonic activity recycles ca rbon, necessary for life and habitable planetary climates, Earth’s atmosphere possesses an ozone layer which helps to shield life from solar radiation, Earth’s axial wobble is stabilized by its very large moon, which also moderates climate fluctuations, Earth’s many environmentally variable habitats aid an evolutionary diversity, and Earth’s strong magnetic field protects life from high-energy cosmic radiation and solar storms. (250)

The universe as it exists in our region was not improbably fashioned for odd living organisms, nor were odd living organisms made by a strange condition of the universe in our region – living organisms are the universe in one of its own manifestations. Namely, life as we know it is a manifestation of the universe at a particular point in space nd time in its evolution. And species of life on Earth that are self-aware – magpies, elephants, dolphins, apes, humans – are manifestations of the universe that has become aware of itself. (251)

McGhee, George. Convergent Evolution: Limited Forms Most Beautiful. Cambridge: MIT Press, 2011. The author is Professor of Paleobiology in the Department of Earth and Planetary Sciences at Rutgers University. Evolutionary theory is today beset and impeded by deep quandaries due to a tacit natural selection paradigm that denies or cannot contain any sense of an intrinsic, independent development. While evidence from molecules to minds, and every creaturely species in between, confirms that organisms converge upon similar patterns and processes over and over, as this book avers, the fact remains at conceptual odds with this vested 1950s Modern Synthesis. Following colleague Simon Conway Morris, McGhee provides the most thorough, organized documentation across genes, proteins, metabolism, animals, plants, ecosystems, and behavior, of this reality so far. All of which begs the impression that something is going on by itself, as if a once and future developmental gestation due to innate genetic propensities. An important book.

Charles Darwin famously concluded On the Origin of Species with a vision of “endless forms most beautiful” continually evolving. More than 150 years later many evolutionary biologists see not endless forms but the same, or very similar, forms evolving repeatedly in many independent species lineages. In this book, George McGhee describes the ubiquity of the phenomenon of convergent evolution and connects it directly to the concept of evolutionary constraint - the idea that the number of evolutionary pathways available to life are not endless, but quite limited. Convergent evolution occurs on all levels, from tiny organic molecules to entire ecosystems of species. McGhee demonstrates its ubiquity in animals, both herbivore and carnivore; in plants; in ecosystems; in molecules, including DNA, proteins, and enzymes; and even in minds, describing problem-solving behavior and group behavior as the products of convergence. (Publisher)

In summary, convergent evolution occurs across the entire spectrum of molecules that make up life. We have studied examples of the convergent evolution of identical nucleotide substitutions in nuclear and mtDNA molecules of distantly related organisms, similar amino acid sequences in unrelated protein molecules, similar structural geometries in proteins with different amino acid sequences, and similar protein functions by gene sharing; the convergent evolution of the same enzyme function produced by the convergent evolution of the same protein producing that function;….and the convergent evolution of the same macromolecular structure in unrelated enzymes. The number of molecular evolutionary pathways available to life is not endless but is quite restricted, and convergent evolution is the direct result. (206-207)

McMenamin, Mark. The Garden of Ediacara. New York: Columbia University Press, 1998. The Mount Holyoke College paleontologist relates his discoveries of Precambrian fossil microorganisms in the Ediacaran region of Australia. These findings prompt McMenamin to propose a convergent view of evolution most characterized by an emergent sentience which was present even in that ancient era.

With evidence in our hands of convergently evolved protective skeletons and eusocial animals, plus numerous cases of iterative evolution, and not only the convergent evolutionary enlargements of brains but perhaps even iterative evolution of the brain itself, we must now accept a neovitalistic view of evolutionary change. (267) Please don’t misunderstand me; with neovitalism I am not invoking some type of mystical force to accomplish these changes. Rather, there must be something about the structure of the material world that causes matter to organize in this particular and very interesting way. In other words, it would appear that life evokes mind. There is indeed some kind of evolutionary directionality and vital potency. (270)

McShea, Dan. A Universal Generative Tendency toward Increase Organismal Complexity. Hallgrimsson, Benedikt and Brian Hall, eds. Variation. Amsterdam: Elsevier, 2005. A careful argument for a vectorial rise in “internal variance” as organisms evolve which produces cellular and organ components with greater complexity, defined as parts which are more differentiated from each other.

Rather, it is that the variational possibilities, the raw materials so to speak, supplied to selection will be increasingly complex, and an eye is the result of the differential survival of the subset of these ever more complex options that are functional. (437)

McShea, Daniel. The Hierarchical Structure of Organisms. Paleobiology. 27/2, 2001. An important summary of how evolution proceeds by nested spheres of whole entities from prokaryotes to cells, organisms, and ‘individuated metazoan colonies.’ By this reckoning the passage of life is not a gradual drift or meander, rather a central trend of stratified complexity is evident where each subsequent stage is an autopoietic, symbiotically formed individuation.

The degree of hierarchical structure of organisms - the number of levels of nesting of lower-level entities within higher-level individuals - has apparently increased a number of times in the history of life, notably in the origin of the eukaryotic cell from an association of prokaryotic cells, of multicellular organisms from clones of eukaryotic cells, and of integrated colonies from aggregates of multicellular individuals. (405)

McShea, Daniel and Mark Changizi. Three Puzzles in Hierarchical Evolution. Integrative and Comparative Biology. 43/1, 2003. In contrast to the standard tree or bush model of an arbitrarily branching evolution, a novel understanding of life’s ascent is coming together in the synthesis conveyed by the new journal title for the former American Zoologist. By this perspective, the development of earth life is seen to proceed as a nested scale of individuated, semi-autonomous entities: bacteria within cells within organisms, which go on to aggregate into societies. Whereas the old model has no central direction, the new version defines a vectorial, repetitive emergence.

The maximum degree of hierarchical structure of organisms has risen over the history of life, notably in three transitions: the origin of the eukaryotic cell from symbiotic associations of prokaryotes; the emergence of the first multicellular individuals from clones of eukaryotic cells; and the origin of the first individuated colonies from associations of multicellular organisms. (74)

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