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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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V. Life's Corporeal Evolution Develops, Encodes and Organizes Itself: An Earthtwinian Genesis Synthesis

3. Cellular Self-Organization and Holobiont Symbiogenesis

Igamberdiev, Abir, et al, eds. Symbiogenesis and Progressive Evolution. Biosystems. April, 2021. is a special collection edited by AI, Richard Gordon, and George Mikhailovsky which into the 2020s seeks to report frontier insights and evidence that nature’s constant preference for a mutual convergent synthesis of diverse members is in primary procreative effect everywhere. We note in this issue From Empedocles to Symbiogenetics: Lynn Margulis's Revolutionary Influence on Evolutionary Biology by Dorion Sagan and Symbiogenesis as a Driving Force of Evolution: The Legacy of Boris Kozo-Polyansky by Vladimir Agafonov, et al, Serial Endosymbiosis Theory: From Biology to Astronomy and Back to the Origin of Life by Predrag Slijepcevic (search) and Archaeal Origins of Eckaryotic Cells by Frantisek Baluska and Sherrie Lyons.

Symbiogenesis played a crucial role in the origin of eukaryotic cells and onto life’s emergence. It led to a complexification of coding systems as a result of merging individual genomes of prokaryotic cells. This issue will explore the role of horizontal gene transfer and symbiogenesis onto complex multicellular organisms. The papers herein will seek to understand the role of symbiogenesis in the evolutionary process and suggest computational models to describe the emergence of complex biological systems. The issue is dedicated to the founders of the concept of symbiogenesis Boris Kozo-Polyansky (1890-1957) and Lynn Margulis (1938-2011), the former chief editor of BioSystems, who proved this concept and introduced it into the mainstream of evolutionary theory. (Issue Introduction excerpt)

Karr, Jonathan, et al. A Whole-Cell Computational Model Predicts Phenotype from Genotype. Cell. 150/2, 2012. Nine Stanford University and Craig Venter Institute computational biophysicists illuminate the presence of a mathematical domain that in addition to familiar metabolic, microbial components graces and enhances a cell’s relational interactive development.

Understanding how complex phenotypes arise from individual molecules and their interactions is a primary challenge in biology that computational approaches are poised to tackle. We report a whole-cell computational model of the life cycle of the human pathogen Mycoplasma genitalium that includes all of its molecular components and their interactions. An integrative approach to modeling that combines diverse mathematics enabled the simultaneous inclusion of fundamentally different cellular processes and experimental measurements. We conclude that comprehensive whole-cell models can be used to facilitate biological discovery. (Abstract)

Kiers, Toby and Stuart West. Evolving New Organisms Via Symbiosis. Science. 348/392, 2015. Vrije Universiteit, Amsterdam, and Oxford University, zoologists proceed to integrate the well accepted fact that cellular creatures arose by way of mutual reciprocities with the popular major evolutionary transition scale of relative individualities, within which such symbiotic ways become even more valid.

Kooijman, S., et al. Quantitative Steps in Symbiogenesis and the Evolution of Homeostasis. Biological Reviews. 78/3, 2003. A dynamic energy budget (DEB) model is proposed for the reciprocal endosybiotic process.

Kravchenko-Balasha, Nataly, et al. On a Fundamental Structure of Gene Networks in Living Cells. Proceedings of the National Academy of Sciences. 109/4702, 2012. In similar fashion to work by Keith Farnsworth, et al, and Melody Morris, et al (search each) Hebrew University of Jerusalem, UCLA, Weizmann Institute of Science Israel, and Universite de Liege, Belgium proceed by way of computational logics with deeper perceptions into these dynamic, sustaining topologies from genomics to cellularity phases.

Computers are organized into hardware and software. Using a theoretical approach to identify patterns in gene expression in a variety of species, organs, and cell types, we found that biological systems similarly are comprised of a relatively unchanging hardware-like gene pattern. Orthogonal patterns of software-like transcripts vary greatly, even among tumors of the same type from different individuals. Two distinguishable classes could be identified within the hardware-like component: those transcripts that are highly expressed and stable and an adaptable subset with lower expression that respond to external stimuli. Importantly, we demonstrate that this structure is conserved across organisms. The approach provides a conceptual thermodynamic-like framework for the analysis of gene expression levels and networks and their variations in diseased cells. (Abstract)

The analogy that we make with computer architecture is complementary to the well-developed characterization of local motifs in transcription networks. The aim in characterizing local motifs is to discern connections between a few genes that act like simple logic gates. Here, instead, we examine the flow of information in the whole genome to identify large groups of transcripts that act in concert. (4702)

Lake, James. Evidence for an Early Prokaryotic Endosymbiosis. Nature. 460/967, 2009. Although the evolutionary formation of nucleated eukaryotic cells is now well attributed to mutual joinings and engulfments of diversified bacteria, that these simpler components also arose in such manner has not been considered. Here a UCLA astrobiologist “presents evidence that the double-membrane, gram negative prokaryotes were formed as the result of a symbiosis between an ancient actinobacterium and an ancient clostridium.” Lake closes this feature article by musing that such a reconstructed pathway of life’s cellular procession seems so apt that it could not have occurred by accident.

I cannot help but notice that the existence of the double-membrane structure immediately suggests a possible mechanism for its formation and for the observed genome transfers from Clostridia and Actinobacteria to the double-membrane prokaryotes – endosymbiosis. I believe that this agreement should not be ascribed to chance. (970)

Lane, Christopher and John Archibald. The Eukaryotic Tree of Life. Trends in Ecology and Evolution. 23/5, 2008. Canadian biologists contend that an appreciation of the pervasive role of endosymbiotic activity amongst the evolution and nature of nucleated cells will require a revision of life’s branching course. A companion article The Prokaryotic Tree of Life by James McInerney, et al, goes on to wonder if the “tree” motif which harks back to Lamarck and Haeckel is appropriate at all, rather a web-like “network” may be better. But such approaches remain constrained by their purview of molecular gene and corporeal soma alone. If a cerebral intelligence is added, a directional trunk accrues, which changes everything.

Latorre, Amparo, et al. The Role of Symbiosis in Eukaryotic Evolution. Gargaud, Muriel, et al, eds. Origins and Evolution of Life: An Astrobiological Perspective. Cambridge: Cambridge University Press, 2011. With coauthors Ana Durban, Andres Moya and Juli Pereto of the Institut Cavanilles de Biodiversitat I Biologia Evolution, Valencia, a succinct chapter about the latest insights into nature’s preference for mutual assemblies of disparate components across a broad realm of living functions and activities. And as we log this on November 29, 2011, we want to record the sudden passing on November 22 at age 73 of Lynn Margulis, the redoubtable founder of this theory and advocate of life’s propensity to join, evolve, and emerge by persistent symbiosis. I had heard her introduce Robert Hazen just two weeks before when he spoke at near by University of Massachusetts at Amherst, where Lynn was professor of biology. She was tireless in her defense of this now proven theory, and in her enthusiasm with and time for students. The University and scientific community are in a state of shock at the loss of this international superstar.

In a broad sense, symbiosis could be defined as a long-term association between two or more organisms of different species at the behavioural, metabolic or genetic level. (326)

The symbiotic origin of the eukaryotic cell is not widely accepted. Mitochondria and other derived organelles during parallel adaptation to anacrobiosis have a bacterial origin. The same is true for plastids of plants, algae and protists. We cannot disregard the discovery of new instances of endosymbionts currently en route to become organelles or fully fledged eukaryotic compartments of bacterial origin. (339) We are now closer than before, due to the advent of the omics methodologies, not only to further unraveling of the steps towards the origin of the eukaryotic cell, but also to assessing the question as to how much eukaryotic complexity is originated through evolutionary innovations be symbiogenesis. (339)

Lim, Shen Jean and Seth Bordenstein. An Introduction to Phylosymbiosis. Proceedings of the Royal Society B. Vol. 287/Iss. 1922, 2020. Vanderbilt University biologists (search SB) describe and illustrate this new found way that life well avails the benefits of myriad microbe-host communities. The survey covers, for example, plant roots, insect guts, aquatic creatures, land animals such as rodents and primates, and more. See also A Bird’s Eye View of Phylosymbiosis by Brian Trevelline, et al in this journal, Issue 1923, which reports upon avian instances.

Phylosymbiosis was formulated to support a hypothesis-driven framework for the characterization of a cross-system trend in host-associated microbiomes. Defining phylosymbiosis as ‘microbial community relationships that recapitulate the phylogeny of their host’, we review its literature and data. Quantitative proof is provided by statistical methods evaluating higher microbiome variation between host species than within host species, and a positive association between host genetic relationships and microbiome beta diversity. Significant degrees of phylosymbiosis are prevalent in microbiomes of plants and animals from terrestrial and aquatic habitats. Its pervasiveness carries several important implications for advancing knowledge of eco-evolutionary processes that impact host–microbiome interactions and future applications of precision microbiology. (Abstract excerpt)

Lloyd, Elisabeth and Michael Wade. Criteria for Holobionts from Community Genetics. Biological Theory. 14/3, 2019. We note this entry by a veteran Indiana University philosopher and biologist as a thorough, evenhanded review of this increasingly popular symbiotic concept of organisms from critters to sapiens. After some clarifications and caveats, by a proper understanding of life’s levels of selection, the holobiont model is a viable model of internal and external mutualisms.

Lopez-Garcia, Purificacion and David Moreira. Selective Forces for the Origin of the Eukaryotic Nucleus. BioEssays. 28/5, 2006. Further confirmations on how symbiotic syntheses serve to form the nucleated cell.

We propose here an evolutionary scenario that reconciles both an ancestral endosymbiotic origin of the eukaryotic nucleus with an autogenous generation of the contemporary nuclear membrane and ER (endoplasmic reticulum) from the bacterial membrane. (525)

Ma’ayan, Avi, et al. Toward Predictive Models of Mammalian Cells. Annual Review of Biophysics and Biomolecular Structure. 34/319, 2005. In this century of systems biology, a new understanding of cells is in process as more than the collection of parts we learned in high school. Many approaches now describe equally real interrelations between resident networks and modules whereby cells become another microcosm of universal self-organization and autopoietic self-maintenance. Among other topics, the chapter surveys small-world network principles, nested modularity, a constant cross-talk, and how to represent and predict cellular intra- and inter-activities.

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