Symbiogenesis redicts the monism of the cosmos.

Symbiogenesis has been systematically exploited to understand consciousness as the aggregate of our physiology. The Symbiogenic mechanism for assimilation of factors in the environment formulates the continuum from inside the cell to the Cosmos, both consciousness and cosmology complying with the Laws of Nature. Since Symbiogenesis is 'constructive', whereas eliminating what threatens us is 'destructive', why do we largely practice Symbiogenesis? Hypothetically, Symbiogenesis recursively simulates the monism of our origin, recognizing 'something bigger than ourselves'. That perspective explains many heretofore unexplained aspects of consciousness, such as mind, epigenetic inheritance, physiology, behaviors, social systems, mathematics, the Arts, from an a priori perspective. Moreover, there is an energetic continuum from Newtonian to Quantum Mechanics, opening up to a novel way of understanding the 'true nature of our being', not as 'materialism', but instead being the serial homeostatic control of energy. The latter is consistent with the spirit of Claude Bernard and Walter B. Cannon's perspectives on physiology. Such a paradigm shift is overdue, given that materialism is causing the destruction of the Earth and ourselves.

How mitochondrial cristae illuminate the important role of oxygen during eukaryogenesis.

Inner membranes of mitochondria are extensively folded, forming cristae. The observed overall correlation between efficient eukaryotic ATP generation and the area of internal mitochondrial inner membranes both in unicellular organisms and metazoan tissues seems to explain why they evolved. However, the crucial use of molecular oxygen (O2) as final acceptor of the electron transport chain is still not sufficiently appreciated. O2 was an essential prerequisite for cristae development during early eukaryogenesis and could be the factor allowing cristae retention upon loss of mitochondrial ATP generation. Here I analyze illuminating bacterial and unicellular eukaryotic examples. I also discuss formative influences of intracellular O2 consumption on the evolution of the last eukaryotic common ancestor (LECA). These considerations bring about an explanation for the many genes coming from other organisms than the archaeon and bacterium merging at the start of eukaryogenesis.

The quantum cell.

There is a consensus that we are conscious of something greater than ourselves, as if we are derived from some other primordial set of principles. Classical or Newtonian physics is based on the Laws of Nature. Conversely, in a recent series of articles, it has been hypothesized that the cell was formed from lipid molecules submerged in the primordial ocean that covered the earth 100 million years after it formed. Since lipids are amphiphiles, with both a positively- and negatively-charged pole, the negatively-charged pole is miscible in water. Under the influence of earth's gravity, the lipid molecules stand up perpendicularly to the surface of the water, packing together until the negative charge neutralizes the Van der Waals force for surface tension, causing the lipid molecules to 'leap' into the micellar form as a sphere with a semi-permeable membrane. Particles in the water freely enter and exit such spheres based on mass action. Over time such protocells evolved Symbiogenesis, encountering factors that posed existential threats, assimilating them to form physiology to maintain homeostatic control. Importantly, when differentiated lung or bone cells are exposed to zero gravity, they lose their phenotypic identity in their evolved state, which has been interpreted as transiting from local to non-local consciousness.

Characterisation of the fig-fig wasp holobiont.

Plants and animals have long been considered distinct kingdoms, yet here a 'plant-animal' is described. An extraordinary symbiosis in which neither organism can reproduce without the other, the fig tree (Ficus) provides the habitat for its exclusive pollinator: the fig wasp (Agaonidae). Characterising the 'fig-fig wasp holobiont' acknowledges, for the first time, 'plant-animal symbiogenesis'.

The symbiotic origin of the eukaryotic cell.

Eukaryogenesis represented a major evolutionary transition that led to the emergence of complex cells from simpler ancestors. For several decades, the most accepted scenario involved the evolution of an independent lineage of proto-eukaryotes endowed with an endomembrane system, including a nuclear compartment, a developed cytoskeleton and phagocytosis, which engulfed the alphaproteobacterial ancestor of mitochondria. However, the recent discovery by metagenomic and cultural approaches of Asgard archaea, which harbour many genes in common with eukaryotes and are their closest relatives in phylogenomic trees, rather supports scenarios based on the symbiosis of one Asgard-like archaeon and one or more bacteria at the origin of the eukaryotic cell. Here, we review the recent discoveries that led to this conceptual shift, briefly evoking current models of eukaryogenesis and the challenges ahead to discriminate between them and to establish a detailed, plausible scenario that accounts for the evolution of eukaryotic traits from those of their prokaryotic ancestors.

L'eucaryogenèse représente une transition évolutive majeure qui a conduit à l'émergence de cellules complexes à partir d'ancêtres plus simples. Pendant plusieurs décennies, le scénario le plus accepté impliquait l'évolution d'une lignée indépendante de proto-eucaryotes dotée d'un système endomembranaire, comprenant un compartiment nucléaire, un cytosquelette développé et la phagocytose, qui aurait permis d'incorporer l'ancêtre alphaprotéobactérien des mitochondries. Cependant, la découverte récente par des approches métagénomiques et culturales des archées Asgard, qui partagent de nombreux gènes avec les eucaryotes et sont leurs plus proches parents dans des arbres phylogénomiques, soutient plutôt les scénarios basés sur la symbiose d'une archée de type Asgard et d'une ou plusieurs bactéries à l'origine de la cellule eucaryote. Nous passons ici en revue les découvertes récentes qui ont conduit à ce changement conceptuel, en évoquant brièvement les modèles actuels d'eucaryogenèse, et les défis pour discriminer entre ces derniers et établir un scénario plausible détaillé qui rende compte de l'évolution des traits eucaryotes à partir de ceux de leurs ancêtres procaryotes.

Genome assembly of the acoel flatworm Symsagittifera roscoffensis, a model for research on body plan evolution and photosymbiosis.

Symsagittifera roscoffensis is a well-known member of the order Acoela that lives in symbiosis with the algae Tetraselmis convolutae during its adult stage. Its natural habitat is the eastern coast of the Atlantic, where at specific locations thousands of individuals can be found, mostly, lying in large pools on the surface of sand at low tide. As a member of the Acoela it has been thought as a proxy for ancestral bilaterian animals; however, its phylogenetic position remains still debated. In order to understand the basic structural characteristics of the acoel genome, we sequenced and assembled the genome of aposymbiotic species S. roscoffensis. The size of this genome was measured to be in the range of 910-940 Mb. Sequencing of the genome was performed using PacBio Hi-Fi technology. Hi-C and RNA-seq data were also generated to scaffold and annotate it. The resulting assembly is 1.1 Gb large (covering 118% of the estimated genome size) and highly continuous, with N50 scaffold size of 1.04 Mb. The repetitive fraction of the genome is 61%, of which 85% (half of the genome) are LTR retrotransposons. Genome-guided transcriptome assembly identified 34,493 genes, of which 29,351 are protein coding (BUSCO score 97.6%), and 30.2% of genes are spliced leader trans-spliced. The completeness of this genome suggests that it can be used extensively to characterize gene families and conduct accurate phylogenomic reconstructions.

From macroevolution's "independence proclamation" to the "act of independence". / Del "grito de independencia" de la macroevolución al "acto independentista"

J. Gould constantly argues against the Neodarwinian conception of macroevolution as a "reductionist and trivialized" perspective. Currently this conception is still prevalent; as can be noted on the conceptualization of macroevolutionary process, as just a mere gradualist interpolation of the microevolutionary process. The claims for the theoretical independence of the macroevolution, mainly exposed by Gould and Eldredge in what they call "the ontological maturation of biology", defending an ontological status of the hierarchical nature of biological organization, in opposition of a mere descriptive-epistemological scheme, were largely ignored or relegated as part of the philosophical problem of the units of selection. Perhaps, the absence of a convincing evolutionary mechanism or mode in the upper levels of the biological organization -as species-, that was non-reducible to the genetic level might explain the lack of interest of evolutionary biologist. However, current developments in the multilevel selection theory, as the concept of evolutionary transitions in individuality, together with symbiogenetic theory of evolution provides a better conceptualization of macroevolution, that might overcome the "claim" to the "act" of ontological independence. A re-conceptualization possible by the recognition of a non-reducible upper-level mode and tempo of evolution, in the sense of vertical evolutionary mechanisms or transitions of individuality by means of persistent symbiosis, as viral chronic-infections or any other symbiogenetic agent.

J. Gould criticó constantemente la concepción de la macroevolución por parte del neodarwinismo, como "reduccionista y trivializadora". No obstante, esta es la concepción vigente en la actualidad, como se evidencia en la conceptualización del proceso macorevolutivo, como interpolación gradualista de los procesos microevolutivos. Los gritos a favor de la independencia teórica de la macroevolución principalmente esgrimidos por Eldredge y Gould en lo que llamaron, la "maduración ontológica de la biología", reclamaban reconocer a la organización jerárquica biológica como esquema ontológico y no, como mero concepto descriptivo-epistemológico, fueron ignorados o relegados al interminable debate de la unidad de selección. Quizás, a razón de la ausencia de la identificación de un mecanismo o modo evolutivo convincente y propio de niveles de orden superior al nivel genético. Sin embargo, gracias a los desarrollos de la teoría de selección en múltiples niveles, como el concepto de transiciones evolutivas en individualidad, junto a la teoría simbiogenética de evolución, en el presente trabajo se plantea que una reconceptualización en el seno de dichos desarrollos permitiría avanzar del "grito" al "acto" independentista de la macroevolución. El carácter autónomo o la particularidad del tempo y modo residirían en mecanismos evolutivos verticales como las transiciones en individualidad mediadas por simbiosis persistentes, como las infecciones virales crónicas o por otros agentes simbiogenéticos.

Symbiosis and the Anthropocene.

Recent human activity has profoundly transformed Earth biomes on a scale and at rates that are unprecedented. Given the central role of symbioses in ecosystem processes, functions, and services throughout the Earth biosphere, the impacts of human-driven change on symbioses are critical to understand. Symbioses are not merely collections of organisms, but co-evolved partners that arise from the synergistic combination and action of different genetic programs. They function with varying degrees of permanence and selection as emergent units with substantial potential for combinatorial and evolutionary innovation in both structure and function. Following an articulation of operational definitions of symbiosis and related concepts and characteristics of the Anthropocene, we outline a basic typology of anthropogenic change (AC) and a conceptual framework for how AC might mechanistically impact symbioses with select case examples to highlight our perspective. We discuss surprising connections between symbiosis and the Anthropocene, suggesting ways in which new symbioses could arise due to AC, how symbioses could be agents of ecosystem change, and how symbioses, broadly defined, of humans and "farmed" organisms may have launched the Anthropocene. We conclude with reflections on the robustness of symbioses to AC and our perspective on the importance of symbioses as ecosystem keystones and the need to tackle anthropogenic challenges as wise and humble stewards embedded within the system.

The drawbridge of nature: Evolutionary complexification as a generation and novel interpretation of coding systems.

The phenomenon of evolutionary complexification corresponds to the generation of new coding systems (defined as а codepoiesis by Marcello Barbieri). The whole process of generating novel coding statements that substantiate organizational complexification leads to an expansion of the system that incorporates externality to support newly generated complex structures. During complexifying evolution, the values are assigned to the previously unproven statements via their encoding by using new codes or rearranging the old ones. In this perspective, living systems during evolution continuously realize the proof of Gödel's theorem. In the real physical world, this realization is grounded in the irreversible reduction of the fundamental uncertainty appearing in the self-referential process of internal measurement performed by living systems. It leads to the formation of reflexive loops that establish novel interrelations between the biosystem and the external world and provide a possibility of active anticipatory transformation of externality. We propose a metamathematical framework that can account for the underlying logic of codepoiesis, outline the basic principles of the generation of new coding systems, and describe main codepoietic events in the course of progressive biological evolution. The evolutionary complexification is viewed as a metasystem transition that results in the increase of external work by the system based on the division of labor between its components.

Zombie ideas about early endosymbiosis: Which entry mechanisms gave us the "endo" in different endosymbionts?

Recently, a review regarding the mechanics and evolution of mitochondrial fission appeared in Nature. Surprisingly, it stated authoritatively that the mitochondrial outer membrane, in contrast with the inner membrane of bacterial descent, was acquired from the host, presumably during uptake. However, it has been known for quite some time that this membrane was also derived from the Gram-negative, alpha-proteobacterium related precursor of present-day mitochondria. The zombie idea of the host membrane still surrounding the endosymbiont is not only wrong, but more importantly, might hamper the proper conception of possible scenarios of eukaryogenesis. Why? Because it steers the imagination not only with regard to possible uptake mechanisms, but also regarding what went on before. Here I critically discuss both the evidence for the continuity of the bacterial outer membrane, the reasons for the persistence of the erroneous host membrane hypothesis and the wider implications of these misconceptions for the ideas regarding events occurring during the first steps towards the evolution of the eukaryotes and later major eukaryotic differentiations. I will also highlight some of the latest insights regarding different instances of endosymbiont evolution.

The role of symbiosis in the first colonization of the seafloor by macrobiota: Insights from the oldest Ediacaran biota (Newfoundland, Canada).

The earliest record of animal life comes from the Ediacaran of Newfoundland, including dm scale fossil organisms, most of which are inferred to have been epibenthic immotile eumetazoans. This work introduces the palaeobiology of the major fossil groups in the Newfoundland assemblages including strange fractal-like taxa and addresses some of biogeochemical challenges such as sulfide buildup that could most easily have been overcome by symbiogenesis. Specifically, the epibenthic reclining nature of some of the Ediacaran biota-with their fractal-like high surface area lower surfaces-are considered to have been well designed for gaining nutriment from chemosynthetic, sulfur-oxidizing bacteria. This view constitutes a shift away from the view that most of the biota were anomalously large osmotrophs.

Symbiogenesis is driven through hierarchical reorganization of an ecosystem under closed or semi-closed conditions.

Ecosystems generate selective environments and function as sources of various metabolic systems for symbiogenesis. In this study, we have explored how symbiogenesis occurs in the living world, from a holistic perspective, by observing a long-term experimental culture of an ecosystem model (CET microcosm) and using related findings in laboratory and field studies of endosymbiosis between auto- (photo-) and heterotrophic organisms. The results obtained suggest that symbiogenesis can occur in the mature stages of semi-closed ecosystems and lead to a new ecosystem-oriented perspective of symbiogenesis. Symbiogenesis is an aspect of ecosystem evolution in which whole ecosystem dynamics generate selective conditions operating on the component species, favoring symbiotic associations among some of them. The development of symbiotic associations then modifies the organization and material/energy flow structure of the ecosystem, which, in turn, modifies their selective environments.

Symbiogenesis as a driving force of evolution: The legacy of Boris Kozo-Polyansky.

We analyze evolutionary views of Boris Kozo-Polyansky (1890-1957) who was the first who formulated the symbiotic theory of evolution as a concept in his book, Symbiogenesis: A New Principle of Evolution (1924). Later, starting from 1967, Lynn Margulis independently formulated and further developed the concept of symbiogenesis. Although the ideas on the symbiotic origin of chloroplasts and mitochondria appeared earlier, the book of Kozo-Polyansky presented symbiogenesis as the main factor of complexification in the course of evolution, not only in relation to the origin of eukaryotic cell. Kozo-Polyansky incorporated the ideas of symbiogenesis into a broader paradigm that anticipated the important concepts of the modern Extended Evolutionary Synthesis such as the idea of net of life, the evolutionary role of apoptosis, the ideas of punctuated equilibrium, and the concept of metasystem transition.

Why the third way of evolution is necessary.

The Third Way of Evolution was founded in 2014 to make the public aware that contemporary evolution science is not limited to the neo-Darwinian Modern Synthesis of the past century. This was important to do because evolution was challenged as incapable of explaining biological complexity by the Intelligent Design movement. Expounding biological theories like the Modern Synthesis is always subject to limited empirical evidence, fundamental concepts that inevitably change over time, and conceptual preferences that often prove to be misleading. The Modern Synthesis was based on Darwin's preference for the phyletic gradualism necessary to elevate Natural Selection as the sole force determining the direction of evolutionary change. In contradiction to this principle, agricultural crop breeding, direct observation in nature, and genomics have shown that genome change following symbiogenetic cell fusions or interspecific hybridization, not selection, are empirically the most effective methods for originating novel life forms and new species. By asserting that the accumulation of random "slight" variations was the basic mode of both short-term and long-term evolutionary change, the Modern Synthesis also ignored the distinction between (1) microevolutionary change within species by localized mutations and (2) macroevolutionary origination of new species and taxa by genome restructuring. In so doing, the Modern Synthesis failed to recognize the evolutionary importance of cellular capacities to generate large-scale genome changes. By focusing on individual protein-coding genes as the fundamental units of genetic information, the Modern Synthesis did not successfully incorporate either the full non-coding informa tion content in genomes or the major evolutionary potential of mobile DNA elements to generate multisite intragenomic networks necessary for the development of complex organisms. When all of the phenomena overlooked by the Modern Synthesis are taken into consideration, it is not difficult to answer Intelligent Design arguments and show that science is making real progress in understanding the evolution of biological complexity.

Lynn Margulis and Boris Kozo-Polyansky: How the Symbiogenesis was translated from Russian.

This contribution details the complex history of the early work by Boris Kozo-Polyansky (1924) that became available in English translation 86 years after it was published in Russian. The great American naturalist Lynn Margulis-whose serial endosymbiosis theory was presciently predated by Kozo-Polyansky by four decades-was instrumental in organizing this resurrection and 'horizontal transfer' of knowledge, forgotten by that time even in Russia.

The origin of symbiogenesis: An annotated English translation of Mereschkowsky's 1910 paper on the theory of two plasma lineages.

In 1910, the Russian biologist Konstantin Sergejewitch Mereschkowsky (Константин Сергеевич Мережковский, in standard transliterations also written as Konstantin Sergeevic Merezkovskij and Konstantin Sergeevich Merezhkovsky) published a notable synthesis of observations and inferences concerning the origin of life and the origin of nucleated cells. His theory was based on physiology and leaned heavily upon the premise that thermophilic autotrophs were ancient. The ancestors of plants and animals were inferred as ancestrally mesophilic anucleate heterotrophs (Monera) that became complex and diverse through endosymbiosis. He placed a phylogenetic root in the tree of life among anaerobic autotrophic bacteria that lack chlorophyll. His higher level classification of all microbes and macrobes in the living world was based upon the presence or absence of past endosymbiotic events. The paper's primary aim was to demonstrate that all life forms descend from two fundamentally distinct organismal lineages, called mykoplasma and amoeboplasma, whose very nature was so different that, in his view, they could only have arisen independently of one another and at different times during Earth history. The mykoplasma arose at a time when the young Earth was still hot, it later gave rise to cyanobacteria, which in turn gave rise to plastids. The product of the second origin of life, the amoeboplasma, arose after the Earth had cooled and autotrophs had generated substrates for heterotrophic growth. Lineage diversification of that second plasma brought forth, via serial endosymbioses, animals (one symbiosis) and then plants (two symbioses, the second being the plastid). The paper was published in German, rendering it inaccessible to many interested scholars. Here we translate the 1910 paper in full and briefly provide some context.

A cosmic virosphere.

The concept of a cosmic virosphere that serves as the repository of information for all life on Earth and throughout the Universe is discussed. Recent studies in geology, astronomy and biology point to an intimate connection between the evolution of life and a cosmic virosphere/biosphere.

Debating Eukaryogenesis-Part 2: How Anachronistic Reasoning Can Lure Us into Inventing Intermediates.

Eukaryotic origins are inextricably linked with the arrival of a pre-mitochondrion of alphaproteobacterial-like ancestry. However, the nature of the "host" cell and the mode of entry are subject to heavy debate. It is becoming clear that the mutual adaptation of a relatively simple, archaeal host and the endosymbiont has been the defining influence at the beginning of the eukaryotic lineage; however, many still resist such symbiogenic models. In part 1, it is posited that a symbiotic stage before uptake ("pre-symbiosis") seems essential to allow further metabolic integration of the two partners ending in endosymbiosis. Thus, the author argued against phagocytic mechanisms (in which the bacterium is prey or parasite) as the mode of entry. Such positions are still broadly unpopular. Here it is explained why. Evolutionary thinking, especially in the case of eukaryogenesis, is still dominated by anachronistic reasoning, in which highly derived protozoan organisms are seen as in some way representative of intermediate steps during eukaryotic evolution, hence poisoning the debate. This reasoning reflects a mind-set that ignores that Darwinian evolution is a fundamentally historic process. Numerous examples of this kind of erroneous reasoning are given, and some basic precautions against its use are formulated. Also see the video abstract here https://youtu.be/ekqtNleVJpU.

Bacterial Genes Outnumber Archaeal Genes in Eukaryotic Genomes.

Eukaryotes are typically depicted as descendants of archaea, but their genomes are evolutionary chimeras with genes stemming from archaea and bacteria. Which prokaryotic heritage predominates? Here, we have clustered 19,050,992 protein sequences from 5,443 bacteria and 212 archaea with 3,420,731 protein sequences from 150 eukaryotes spanning six eukaryotic supergroups. By downsampling, we obtain estimates for the bacterial and archaeal proportions. Eukaryotic genomes possess a bacterial majority of genes. On average, the majority of bacterial genes is 56% overall, 53% in eukaryotes that never possessed plastids, and 61% in photosynthetic eukaryotic lineages, where the cyanobacterial ancestor of plastids contributed additional genes to the eukaryotic lineage. Intracellular parasites, which undergo reductive evolution in adaptation to the nutrient rich environment of the cells that they infect, relinquish bacterial genes for metabolic processes. Such adaptive gene loss is most pronounced in the human parasite Encephalitozoon intestinalis with 86% archaeal and 14% bacterial derived genes. The most bacterial eukaryote genome sampled is rice, with 67% bacterial and 33% archaeal genes. The functional dichotomy, initially described for yeast, of archaeal genes being involved in genetic information processing and bacterial genes being involved in metabolic processes is conserved across all eukaryotic supergroups.