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

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

Linden-Santangeli, Nathaniel, et al. Increasing certainty in systems biology models using Bayesian multimodel inference.. Linden-Santangeli, Nathaniel, et al. Increasing certainty in systems biology models using Bayesian multimodel inference. arXiv:2406.11178.. UC San Diego bioscientists show how to integrate this popular research procedure with an holistic sense of metabolic vitalities.

Mathematical models are a good way to study the structure and behavior of intracellular signaling networks. As a result, the same signal pathway can be represented by multiple models, each with underlying assumptions. Here, we use Bayesian inference to develop a way to achieve increasing certainty. A case study of extracellular regulated kinase (ERK), we show that multimodel inference enhances predictive accuracy. Finally, we use multimodel inference to explain sub-cellular location-specific ERK activity dynamics. (Excerpt)

Lucocq, John, et al. Systems Biology in 3D Space – Enter the Morphome. Trends in Cell Biology. 25/2, 2015. Aided by advanced nanoimaging techniques such as electron tomography and cryomicroscopy, University of St. Andrews, University of Nottingham, and European Molecular Biology Laboratory researchers advise that cellular studies is poised to enter a new integral, three dimensional phase of complete comprehension. Search Tim Mercer for similar work from Australia.

Systems-based understanding of living organisms depends on acquiring huge datasets from arrays of genes, transcripts, proteins, and lipids. These data, referred to as ‘omes’, are assembled using ‘omics’ methodologies. Currently a comprehensive, quantitative view of cellular and organellar systems in 3D space at nanoscale/molecular resolution is missing. We introduce here the term ‘morphome’ for the distribution of living matter within a 3D biological system, and ‘morphomics’ for methods of collecting 3D data systematically and quantitatively. A sampling-based approach termed stereology currently provides rapid, precise, and minimally biased morphomics. We propose that stereology solves the ‘big data’ problem posed by emerging wide-scale electron microscopy (EM) and can establish quantitative links between the newer nanoimaging platforms such as electron tomography, cryo-EM, and correlative microscopy. (Abstract)

Malod-Dognin, Noel and Natasa Przulj. Functional Geometry of Protein Interactomes. Bioinformatics. 35/19, 2019. Barcelona Supercomputing Center life scientists show how these metabolic processes can similarly be found to exhibit common network topologies, which can then be modeled by simplical complexes just like the brain. See also Centralities in Simplical Complexes: Applications to Protein Interaction Networks by Ernesto Estrada and Grant Ross in the Journal of Theoretical Biology (438/46, 2018).

Markowetz, Florian and Michael Boutros, eds. Systems Genetics: Linking Genotypes and Phenotypes. Cambridge: Cambridge University Press, 2015. Leading researchers from Europe and the US provide a comprehensive survey of novel abilities to treat whole genomes, as now distinguished by gene regulatory networks, so as to better reveal how organisms form and flourish. A typical, notable chapter is Phenotype State Spaces and Strategies for Exploring Them by Andreas Hadjiprocopis and Rune Linding, whence evolution is an optimization endeavor due to self-organizing criticalities.

Martin, Lynn, et al, eds. Integrative Organismal Biology. New York: Wiley-Blackwell, 2012. . A major theoretical contribution to the overdue reunion of living entities with their evolutionary development. An initial chapter Plasticity, Complexity, and the Individual by editors Martin, Cameron Ghalambor and Arthur Woods states the imperative for and veracity of this spatial and temporal living systems synthesis. Typical chapter sare Evolutionary Systems Biology by Mihaela Pavlicev and Gunter Wagner, The Role of Ecological Epigenetics in Integrative Biology by Asron Schrey, et al, and Physiological Regulatory Networks: The Orchestra of Life? by Lynn Martin and Alan Cohen.

Integrative Organismal Biology synthesizes current understanding of the causes and consequences of individual variation at the physiological, behavioral and organismal levels. Emphasizing key topics such as phenotypic plasticity and flexibility, and summarizing emerging areas such as ecological immunology, oxidative stress biology and others, Integrative Organismal Biology pulls together information across a multitude of disciplines to provide a synthetic understanding of the role of the individual in evolution. Beginning with grounding theory highlighting the role of the individual in evolutionary and ecological processes, the book covers theory and mechanism from both classic and modern perspectives. Chapters explore concepts such as how genetic and epigenetic variation becomes physiological and phenotypic variation, homeostasis, gene regulatory networks, physiological regulatory networks, and integrators. A concluding section illustrates these concepts through a series of case studies of life processes such as aging, reproduction, and immune defense. (Publisher)

Medford, June and Diane McCarthy. Growing Beyond: Designing Plants to Serve Human and Environmental Interests. Current Opinion in Systems Biology. 5/82, 2017. In a section on Synthetic Biology, Colorado State University biologists look ahead from 20 years of molecular, cellular and system biology studies to see how they might avail an evolutionary reconception of nature’s fauna to enhance planetary viability. See also Bacterial Cancer Therapies, Protein Glycosylation in Prokaryotes, Control Systems for Diabetes.

Plant synthetic biology provides a pathway toward the design and construction of sustainable systems for life on earth. Traditional plant selection and breeding techniques have long enabled people to modify and enhance plant traits for human uses. However, these techniques are limited to traits that already exist in plants. Synthetic biology allows us to break free of this constraint and develop plants with entirely novel traits and redesigned biochemical pathways. Further, evolution itself provides a tool for the development of new and enhanced traits. While a plant's multicellular nature and long lifespan present challenges to synthetic biology research, the unique value of plant synthetic biology as a pathway toward sustainable systems outweighs the challenges. (Abstract)

Medina, Miguel. Systems Biology for Molecular Life Sciences and its Impact in Biomedicine. Cellular and Molecular Life Sciences. 70/6, 2013. A University of Malaga, Spain, biologist begins an extensive paper with historical roots from Vladimir Vernadsky, Ludwig Bertalanffy, Conrad Waddington, and Ilya Prigogine to Ramon Margalef, Per Bak, Brain Goodwin, Murray Gell-Mann, Stuart Kauffman, and others. By turns, a prior mechanistic reduction is to be now leavened through an admission of life’s equal preference for integral organisms. A signal advance of the past years is the recognition of the total extent that nested networks grace and serve anatomical and physiological vitality. Of importance is the profusion of “-omic” classes which endow a genetic essence to other forms and functions such as interactomes in cells, bodily metabolomes, and brainy connectomes. A large benefit is lately accruing by reconceptions of cellular cancers as dynamic, scale-free complexities.

Modern systems biology is already contributing to a radical transformation of molecular life sciences and biomedicine, and it is expected to have a real impact in the clinical setting in the next years. In this review, the emergence of systems biology is contextualized with a historic overview, and its present state is depicted. The present and expected future contribution of systems biology to the development of molecular medicine is underscored. Concerning the present situation, this review includes a reflection on the “inflation” of biological data and the urgent need for tools and procedures to make hidden information emerge. Descriptions of the impact of networks and models and the available resources and tools for applying them in systems biology approaches to molecular medicine are provided as well. The actual current impact of systems biology in molecular medicine is illustrated, reviewing two cases, namely, those of systems pharmacology and cancer systems biology. Finally, some of the expected contributions of systems biology to the immediate future of molecular medicine are commented. (Abstract)

Medina, Monica. Genomes, Phylogeny, and Evolutionary Systems Biology. Proceedings of the National Academy of Sciences. 102/Supplement 1, 2005. An article from a Sackler Colloquium on “Systematics and the Origin of Species: On Ernst Mayr’s 100th Anniversary” which describes “a new age of evolutionary research” made possible as genomes become sequenced and available online. This “postgenomics era” is now filling in and clarifying the eukaryotic tree of life from Genome to Transcriptome, Proteome, Interactome, Metabolome, and Phenome.

Mesarovic, M., et al. Search for Organizing Principles. IEE Proceedings – Systems Biology. 1/1, 2004. The inaugural issue of this new journal. As biological science struggles to gain theoretical roots in an inhospitable universe, a deliberate shift is underway from a reduction phase to a reassembly of all the genetic and cellular components. The same cannot be said for other fields that seem stuck in a fragment phase – there is not yet a Systems Physics, Systems Cosmology, or Systems Psychology.

Meyers, Robert A., ed. Systems Biology. Weinheim: Wiley-VCH, 2012. Among the spate of editions as this approach flourishes, a 700 page tutorial volume with main sections on its biological basis, evolution, modeling, medicine and disease, organisms. After conceptual overviews, topics include Embryogenomics, Interactome, Systematics, Proteins, Neuronal Dynamics, Plants, Synthetic Biology, and so on. Chapters such as Fractals in Biology and Medicine, and Chaos in Biochemistry and Physiology show how well the complexity and networks sciences describe integral genomes, cells and persons.

Minelli, Alessandro. An Evo-Devo Perspective on Analogy in Biology. Philosophies. 4/1, 2019. In a special collection from the Second World Congress on Analogy at Adam Mickiewicz University, Poland in May 2017, the University of Padova senior biologist and author (search) describes new appreciations of life’s tendency to draw upon and repeat patterns and processes (aka homology, homoplasy, convergence, etc.) in creaturely kind across life’s evolution. As a result, this long, episodic emergence is increasingly becoming seen as a developmental gestation.

To explain the amazing morphological and biomechanical analogy between two distantly related vertebrates as a dolphin and a shark, framed only in terms of adaptation (i.e., Darwinian survival of the fittest) is far from satisfactory. The same is true of any other structurally similar, but phylogenetically unrelated organisms. An evolutionary argument does not say how the developmental processes of their ancestors could evolve so as to produce these phenotypes (the arrival of the fittest). To address the evolution of possible forms, we cannot ignore that these are products of development. This invites an integrated perspective, currently known as evolutionary developmental biology, or evo-devo. Paths through living forms are not satisfactorily explained in terms of geometrical transformations or the adaptive value of the phenotypes. The emergence of form is dependent on the intrinsic evolvability of developmental processes that translate the genotype into phenotypes. As a consequence, development makes analogous structures more likely to evolve than a purely adaptationist view would ever suggest. (Abstract)

This Special Issue follows the intention of the congress to promote interdisciplinary research, philosophical reflection, and discourse across multiple methodological perspectives about analogy. There are many definitions and conceptions of analogy, but it is always considered as a universal tool that enables us to discover, explore, compare, analyze, understand and illustrate similarities and differences. Formally speaking, analogy can be defined as a relation between relations; it is connected with proportions and remains pervasive in science, art and religion. If we agree that inter-cultural, inter-ideological and inter-religious dialogue is a crucial issue, the humanistic approach to analogy seems to be of the greatest importance. (Summary)

Moczek, Armin, et al. The Significance and Scope of Evolutionary Developmental Biology: A Vision for the 21st Century. Evolution & Development. 17/3, 2015. Some twenty-two scientists such as Scott Gilbert, Brian Hall, Angelika Stollewerk, and Karen Sears provide, as the Abstract notes, an update survey of this Evo-Devo reunion since the 1980s and 1990s. Life’s temporal course from earliest rudiments to our human retrospective can thus be perceived as a deep homologous conservation of regulatory networks, anatomic forms, robustness, convergence, neural systems, phenomic processes, and so on. By this confluence, although not directly stated, a strong sense of earthly evolution as an embryonic gestation becomes increasingly evident. The comprehensive paper goes on to suggest ways to inform biology education, along with benefits for health and agriculture.

Evolutionary developmental biology (evo-devo) has undergone dramatic transformations since its emergence as a distinct discipline. This paper aims to highlight the scope, power, and future promise of evo-devo to transform and unify diverse aspects of biology. We articulate key questions at the core of eleven biological disciplines—from Evolution, Development, Paleontology, and Neurobiology to Cellular and Molecular Biology, Quantitative Genetics, Human Diseases, Ecology, Agriculture and Science Education, and lastly, Evolutionary Developmental Biology itself—and discuss why evo-devo is uniquely situated to substantially improve our ability to find meaningful answers to these fundamental questions. We posit that the tools, concepts, and ways of thinking developed by evo-devo have profound potential to advance, integrate, and unify biological sciences as well as inform policy decisions and illuminate science education. We look to the next generation of evolutionary developmental biologists to help shape this process as we confront the scientific challenges of the 21st century. (Abstract)

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