(logo) Natural Genesis (logo text)
A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
Table of Contents
Introduction
Genesis Vision
Learning Planet
Organic Universe
Earth Life Emerge
Genesis Future
Glossary
Recent Additions
Search
Submit

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

B. Systems Biology Unites: EvoDevo, Genomes, Cells, Networks, Symbiosis, Homology, Inherency

Danchin, Etienne, et al. Beyond DNA: Integrating Inclusive Inheritance into an Extended Theory of Evolution. Nature Reviews Genetics. 12/7, 2011. From our retrospect, genetic studies in the later 20th century first focused on identifying and sequencing molecular nucleotides. With this in place, a systems approach is now finding equally significant network relations between these genomic components. But as a result, the agency of “hereditary” is being widely extended from epigenetic to cultural reaches. With coauthors Frances Champagne, Anne Charmantier, Alex Mesoudi, Benoit Pujol, and Simon Blanchet, a new generation of researchers from France, England, and the U.S. scope out and synthesize this expansion, as the Abstract attests. With 162 references, the paper, available on Mesoudi’s website, provides a good summary of this epochal 21st century revision and expansion. See also Danchin's 2013 paper "Avatars of Information: Towards an Inclusive Evolutionary Synthesis" in Trends in Ecology and Evolution (Online March).

Many biologists are calling for an ‘extended evolutionary synthesis’ that would ‘modernize the modern synthesis’ of evolution. Biological information is typically considered as being transmitted across generations by the DNA sequence alone, but accumulating evidence indicates that both genetic and non-genetic inheritance, and the interactions between them, have important effects on evolutionary outcomes. We review the evidence for such effects of epigenetic, ecological and cultural inheritance and parental effects, and outline methods that quantify the relative contributions of genetic and non-genetic heritability to the transmission of phenotypic variation across generations. These issues have implications for diverse areas, from the question of missing heritability in human complex-trait genetics to the basis of major evolutionary transitions. (Abstract, 475)

Daneker, Mitchell, et al. Systems Biology: Analysis and Parameter Identification via Informed Neural Networks. arXiv:2202.01723. We cite this entry by University of Pennsylvania, and Brown University “biomolecular engineers” as an example of how this integral approach is also meriting from these cerebral AI learning methods.

The dynamics of systems biological processes are usually modeled by ordinary differential equations (ODEs) with many unknown parameters that need to be inferred from noisy and sparse measurements. Here, we make avail of systems-biology informed neural networks for parameter estimation by incorporating the ODEs content into them. To complete the workflow of system identification, we describe a structural and practical analysis to identify and study salient features. We use an ultridian endocrine model for glucose-insulin interaction to demonstrate these methods and their implementation. (Excerpt)

Davidson, Eric. Evolutionary Bioscience as Regulatory Systems Biology. Developmental Biology. 357/1, 2011. The senior Caltech cell biologist makes a summary statement, that, per the second quote, can well define this 21st century integral revision. Still underway, its import is to set aside the 1950s modern synthesis of gene mutations and population drift for a novel evolution due more to the newly found prevalence of layered networks that compose genomes. It is changes in these varying systemic interconnections between nucleotides that actually influence life’s long development.

At present several entirely different explanatory approaches compete to illuminate the mechanisms by which animal body plans have evolved. Their respective relevance is briefly considered here in the light of modern knowledge of genomes and the regulatory processes by which development is controlled. Just as development is a system property of the regulatory genome, causal explanation of evolutionary change in developmental process must be considered at a system level. Here I enumerate some mechanistic consequences that follow from the conclusion that evolution of the body plan has occurred by alteration of the structure of developmental gene regulatory networks. The hierarchy and multiple additional design features of these networks act to produce Boolean regulatory state specification functions at upstream phases of development of the body plan. These are created by the logic outputs of network subcircuits, and in modern animals these outputs are impervious to continuous adaptive variation unlike genes operating more peripherally in the network. (Abstract)

The first (standard view) is the classic neo-Darwinian concept that evolution of animal morphology occurs by means of small continuous changes in primary protein sequence which in general require homozygosity to effect phenotype. The second paradigm holds that evolution at all levels can be illuminated by detailed analysis of cis-regulatory changes in genes that are direct targets of sequence level selection, in that they control variation of immediate adaptive significance. Both approaches often focus on changes at single gene loci, and both are framed within the concepts of population genetics. An entirely different way of thinking is that the evolution of animal body plans is a system level property of the developmental gene regulatory networks (dGRNs) which control ontogeny of the body plan. (35)

Del Moral, Raquel, et al. From Genomics to Scientomics: Expanding the Bioinformation Paradigm. Information. 2/4, 2011. With coauthors Monica Gonzalez, Jorge Navarro, and Pedro Marijuan of the Bioinformation and Systems Biology Group, Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain, an article from a special issue of Selected Papers from FIS (Frontiers of Information Science) 2010 Beijing. The online journal, conference, and this paper are revolutionary signs realization, after science fills in all the parts, and their complex connections, that what is actually going on is nature’s persistent, creative cross-communication. As the authors note, not only has this view take hold in molecular genetics, but similarly across neuronal studies, and on to cultural discourse, as a distinctive attribute which is informational in kind. In regard, the “–omics” connotation can be carried into every realm, whence worldwide scientific collaboration becomes akin to genomic activity. This newly perceived quality appears in the same, repetitive fashion from proteins to people, which begs the presence and discovery of the innate, parent to child, genetic code of a genesis universe.

Contemporary biological research (particularly in systems biology and the “omic” disciplines) is factually answering some of the poignant questions associated with the information concept and the limitations of information theory. Here, rather than emphasizing and persisting on a focalized discussion about the i-concept, an ampler conception of “informational entities” will be advocated. The way living cells self-produce, interact with their environment, and collectively organize multi-cell systems becomes a paradigmatic case of what such informational entities consist of. Starting with the fundamentals of molecular recognition, and continuing with the basic cellular processes and subsystems, a new interpretation of the global organization of the living cell must be assayed, so that the equivalents of meaning, value, and intelligence will be approached along an emerging “bioinformational” perspective.

The great advantage fuelling the expansion of the bioinformation paradigm is that, today, cellular information processes may be defined almost to completion at the molecular scale (at least in the case of prokaryotic cells). Concretely, the crucial evolutionary phenomenon of protein-domain recombination—knowledge recombination—will be analyzed here as a showcase of, and even as a model for, the interdisciplinary and multidisciplinary mixing of the sciences so prevalent in contemporary societies. Scientomics will be proposed as a new research endeavor to assist advancement. Informationally, the “society of enzymes” appears as a forerunner of the “society of neurons”, and even of the “society of individuals”. (651, Abstract)

The creation of knowledge is always an informational process, ultimately derived from knowledge recombination processes in the cerebral “workspace” of individuals. Reliable knowledge mediates action/perception cycles of individuals and prolongs them, supra-individually, making possible a more cogent and integrated closure at the social scale. The scientific method itself appears from this perspective as the conditions to be met for a coherent decomposition of problems by communities of problem-solvers whose workings are separated in time and space. Standards, measurements, mathematical operations, formalizations, and so on, become ways and means to extract mental operations out of the individual’s nervous system and directly interconnect perceptions and actions at a vast institutional-social scale. We really see a “collective nervous system”, a “social workspace” in action. (663)

It can be argued that the growth of informational complexity of cells, nervous systems, and societies along their respective evolutionary, ontogenetic, and historical trajectories has been based on the cumulative consequences of knowledge recombination phenomena. Very limited “agents” are capable of developing a collective processing that goes far beyond the computing bounds of each single agential entity; and their collective processing includes the dynamics of knowledge recombination in all the different information realms. It is amazing that among the procedures to create novelty in those repositories, a central strategy becomes the swapping of knowledge “chunks” from one construct to another, so that new cognitive constructs emerge and new adaptive capabilities are deployed. We have seen how this occurs evolutionarily in cellular protein-domain recombination, and how mental constructs seem to be handled in a similar way. From a highly macroscopic point of view, the different disciplines would also partake in this common strategy of knowledge recombination. (667-668)

Depew, David and Bruce Weber. The Fate of Darwinism: Evolution after the Modern Synthesis. Biological Theory. 6/1, 2012. The University of Iowa and California State University philosophers of biology have for two decades been at the forefront of a measured effort to update and change evolutionary theory in accord with advances in nonlinear sciences. The paper opens with a synoptic history since Darwin’s selection, Mendel’s mutations, their 1950s melding, a later molecular basis, which arrives at a “population genetics” unable explain very much, e.g. novel species. Two major revisions are merited. A 19th century emphasis on embryonic gestation and organism maturation, set aside for most of the Darwinian 20th, is steadily being reunited via developmental system theories, an “eco-evo-devo” persuasion, epigenetic and environmental influences, and so on. But the prime revolution is to admit and factor in complex systems of “autopoietic, self-formative, and self-organizing” forces, prior to selection, so as to recognize nature’s independent dynamic spontaneity.

We trace the history of the Modern Evolutionary Synthesis, and of genetic Darwinism generally, with a view to showing why, even in its current versions, it can no longer serve as a general framework for evolutionary theory. The main reason is empirical. Genetical Darwinism cannot accommodate the role of development (and of genes in development) in many evolutionary processes. We go on to discuss two conceptual issues: whether natural selection can be the “creative factor” in a new, more general framework for evolutionary theorizing; and whether in such a framework organisms must be conceived as self-organizing systems embedded in self-organizing ecological systems. (89)

Di Ventura, Barbara and Victor Sourjik. Self-Organized Partitioning of Dynamically Localized Proteins in Bacterial Cell Division. Molecular Systems Biology. 7/457, 2011. In an exemplary article for this online journal, University of Heidelberg biologists propose that such formative dynamics now being discovered vitally at work everywhere ought to be then appreciated and availed upon as nature’s independent, intrinsic propensity. We offer two quotes, and a note about the journal.

How cells manage to get equal distribution of their structures and molecules at cell division is a crucial issue in biology. In principle, a feedback mechanism could always ensure equality by measuring and correcting the distribution in the progeny. However, an elegant alternative could be a mechanism relying on self-organization, with the interplay between system properties and cell geometry leading to the emergence of equal partitioning. Our findings reveal a novel and effective mechanism of protein partitioning in dividing cells and emphasize the importance of self-organization in basic cellular processes. (457)

Given its simplicity and low evolutionary cost, self-organized partitioning may be a widely used strategy, and self-organization has indeed been shown to be the driving force of spindle assembly in eukaryotes and of the distribution of chemoreceptor clusters in bacteria. Well recognized to be important in many aspects of multicellular biology—from embryogenesis to formation of animal social structures—self-organization is thus likely to have a similarly important role in the regulation of even the simplest intracellular processes. (10-11)

Molecular Systems Biology covers all aspects of the rapidly growing and interdisciplinary field of systems biology at the molecular level, and will attract and help shape the highest quality research in the evolving areas of genomics, proteomics, metabolomics, bioinformatics, microbial systems, and the integration of cell signaling and regulatory networks. The journal will work together with the systems biology community to establish guidelines, standards and metrics for global complex datasets.

DiFrisco, James and Johannes Jaeger. Genetic Causation in Complex Regulatory Systems: An Integrative Dynamic Perspective. BioEssays. 42/6, 2020. A biological studies advance, KU Leuven philosopher and a Complexity Science Hub, Vienna systems biologist seek to add a relational network vista which can inform the historic turn from discrete nucleotides to whole entities, be it genomes or organisms.

The logic of genetic discovery remains in place, but the focus of biology is shifting from genotype–phenotype relationships to complex metabolic, physiological, developmental, and behavioral traits. In light of this, the reductionist view of genes as privileged causes is re‐examined. The scope of genetic effects in complex regulatory systems, in which dynamics are driven by feedback and hierarchical interactions across levels, are considered. This review argues that genes can be treated as specific difference‐makers for the molecular regulation of their expression. However, they are not stable, proportional or specific as causes of the behavior of regulatory networks. Proper dynamical models can illuminate cause‐and‐effect in complex biological systems so to gain an integrative understanding of underlying complex phenotypes. (Abstract edit)

Faragalla, Kyrillos, et al. From Gene List to Gene Network: Recognizing Functional Connections that Regulate Behavioral Traits. Journal of Experimental Zoology B. Online November, 2018. Western University, Ontario biologists in coauthor Graham Thompson’s group post a decisive review of the need to shift from a particulate nucleotide phase, which winds up with long tabulations, to equally real multiplex interrelations. The paper uniquely goes on to extend a “network ladder” of node first, interactions next onto protein, neuronal, social and ecosystem stages, which appear as emergent radiations of the same dynamic topology.

The study of social breeding systems is often gene focused, and the field of insect sociobiology has been successful at assimilating tools and techniques from molecular biology. One common output from sociogenomic studies is a gene list, which is readily generated from microarray, RNA sequencing, or other molecular screens. Gene lists, however, are limited because the tabular information does not explain how genes interact with each other, or how they change in real time circumstances. Here, we promote a view from molecular systems biology, where gene lists are converted into gene networks that better describe these functional connections that regulate behavioral traits. We argue that because network analyses are not restricted to “genes” as nodes, their implementation can connect multiple levels of biological organization into a single, progressively complex study system. (Abstract excerpt)

Fu, Pengcheng and Sven Panke, eds. Systems Biology and Synthetic Biology. Hoboken, NJ: Wiley, 2009. A significant tome which covers not only theory and practice, but also the philosophical implications of being able to begin a new biological creation via this informational revolution. In such regard, Cliff Hooker, the University of Newcastle, Australia director of its Complex Adaptive Systems Research Group, (Google) along with Fu, contributes papers to the extent that a novel dynamical paradigm, essentially a newly appreciated conducive, animate cosmos, will be required going forward.

Systems biology…aims at system-level understanding of biological processes and biochemical networks as a whole. This “system-oriented” new biology is shifting our focus from examining particular molecular details to studying the information flows at all biological levels: Genomic DNA, mRNA, proteins, informational pathways, and regulatory networks. (Fu, 2) These examples illustrate that we are able to not only “read” the genetic code to understand living systems but also “write” the message for the creation of new life forms. (Fu, 4)

Fusco, Giuseppe, ed. Perspectives on Evolutionary and Developmental Biology. Padova: University of Padova Press, 2019. . This 420 page volume of essays for the Italian biologist and author Alessandro Minelli’s (search) 70th birthday is online in full, just Google title + Padova. With such entries a Towards a Developmental Biology of Holobionts by Scott Gilbert, An Evolutionary Biology for the 21st Century by Armin Moczek, Evo-Devo’s Challenge to the Modern Synthesis by Gerd Muller, The Evolutionary Relationships of Neural Structures in Arthropods by Angelika Stollewerk, Humans of the Middle Pleistocene by Giorgio Manzi, and Dynamic Structures in Evo-Devo by Johannes Jaeger, the work offers a latest evocation of this overdue (re)union of phylogeny and ontogeny. This 21st century synthesis is reinforced by a pervasive notice of symbiotic mutualities from eukaryotes to organisms and groups. In addition, a “self-constructing” essence is seen in process from physical origins to social peoples.

Evolutionary developmental biology (evo-devo) has revolutionized our understanding of why and how evolution unfolds the way it does. At the same time, much of evo-devo remains steeped in traditional perspectives and established dichotomies; these need to be overcome if evo-devo is to remain relevant in the coming century. In particular our conception of developmental evolution has to embrace the nature and consequences of developmental bias, the self-constructing nature of living systems, and the reciprocal interdependencies of development and environment in evolution. (Moczek abstract)

Evolution does not act on particular stages in the life of an organism. Instead, it alters developmental processes and life cycles in response to environmental conditions to bring about phenotypic change. The structure of these processes determines evolvability, the capacity of organisms to adapt. They lead us to fundamentally reconsider the active role of organisms in evolutionary change, which raises the possibility of a new agent-based theory of evolution in which organisms and their perceived environments co-construct each other in a radically innovative dialectic dynamic. (Jaeger abstract)

Garcia-Ojalvo, Jordi. Physical Approaches to the Dynamics of Genetic Circuits. Contemporary Physics. 52/5, 2011. As another instance of both the discovery in genomes of pervasive regulatory networks, and their association with and rooting in statistical mechanics, a Universitat Politècnica de Catalunya, Terrassa, Spain physicist provides a lengthy tutorial introduction. A growing number of such projects and papers are on their way to a whole scale reconception of the nature of genotype and phenotype, and by an affinity with a nonlinear materiality, to imply a conducive genesis cosmos.

Cellular behaviour is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have been studied for decades using the tools of statistical and nonlinear physics. The goal of this introductory tutorial is to show how approaches traditionally used in physics can help in reaching a systems-level understanding of living cells. (Abstract, 439)

One of the main questions to be answered in the quest towards understanding life is how structure relates with function in living systems, in particular in cells. A substantial amount of evidence has recently pointed to the relevance of a ‘mesoscopic’ description, at the level of networks of interacting genes and proteins that coordinately govern most cellular processes. This picture has relegated the notion of ‘one gene, one function’ (and frequently one disease) that guided much of genetics and molecular biology in most of the twentieth century. (439)

Cells, both in unicellular and multicellular organisms, possess multiple mechanisms of communicating with one another, in a process that is critical for the survival of any species. From bacterial biofilms to the more sophisticated animal tissues, cells coordinate their behavior in order to function and dynamics is not an exception. (458)

Garcia-Sancho, Miguel. Biology, Computing, and the History of Molecular Sequencing. New York: Palgrave Macmillan, 2012. A Spanish National Research Council historian of genetics provides a thorough course from Frederick Sanger’s 1950s rudimentary techniques to 1960s basic instrumentation, later 1980-1990s automation onset and onto 21st century rapid, large-scale machine computations. But we include because this worldwide collaborative, cumulative project can quite appear as our human phenomenal way that a genesis uniVerse tries to read its own genetic code.

Previous   1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10  Next  [More Pages]