Recently, the group of McBride reported a stunning observation regarding peroxisome biogenesis: newly born peroxisomes are hybrids of mitochondrial and ER-derived pre-peroxisomes. What was stunning? Studies performed with the yeast Saccharomyces cerevisiae had convincingly shown that peroxisomes are ER-derived, without indications for mitochondrial involvement. However, the recent finding using fibroblasts dovetails nicely with a mechanism inferred to be driving the eukaryotic invention of peroxisomes: reduction of mitochondrial reactive oxygen species generation associated with fatty acid oxidation. This not only explains the (...) mitochondrial involvement, but also its apparent absence in yeast. The latest results allow a reconstruction of the evolution of the yeast's highly derived metabolism and its limitations as a model organism in this instance. As I review here, peroxisomes are eukaryotic inventions reflecting mutual host endosymbiont adaptations: this is predicted by symbiogenetic theory, which states that the defining eukaryotic characteristics evolved as a result of mutual adaptations of two merging prokaryotes. See also the video abstract here: https://youtu.be/HtyKhQ3DSxg Eukaryotic peroxisomes illustrate effects of symbiogenesis, following the non-phagocytotic merger of an archaeon and a bacterium. Internal ROS formation upon fatty acid oxidation was reduced by the invention of peroxisomes for extra-mitochondrial FA oxidation. Both peroxisomal membranes and their oldest enzymes seem ultimately derived from the pre-mitochondrion. (shrink)

Constantin Merezhkowsky is celebrated today for his theory of symbiogenesis, postulated in the early decades of the twentieth century, particularly that chloroplasts were symbiotic cyanophytes (cyanobacteria). While biologists point singularly to what they see as his heroic achievement, its neglect and subsequent rediscovery, we introduce a broader and much more complex perspective on his science, his troubled life and career. We present a view of Merezhkowsky as zoologist, anthropologist, botanist, philosopher, and novelist. We explain the genesis of his theory (...) of the origin of chloroplasts and of nucleus and cytoplasm as symbionts, as well as his depiction of the geo-chemical context of the origins and early evolution of life on earth. We also disclose his sordid social and political activities, his eugenics and racist writings, his paedophilia, and his metaphysics. Finally, we describe the context of his elaborate suicide in 1921. (shrink)

Written for non-experts, this volume introduces the mechanisms that underlie reticulate evolution. Chapters are either accompanied with glossaries that explain new terminology or timelines that position pioneering scholars and their major discoveries in their historical contexts. The contributing authors outline the history and original context of discovery of symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow, and infectious heredity. By applying key insights from the areas of molecular (phylo)genetics, microbiology, virology, ecology, systematics, immunology, epidemiology and computational (...) science, they demonstrate how reticulate evolution impacts successful survival, fitness and speciation. Reticulate evolution brings forth a challenge to the standard Neo-Darwinian framework, which defines life as the outcome of bifurcation and ramification patterns brought forth by the vertical mechanism of natural selection. Reticulate evolution puts forward a pattern in the tree of life that is characterized by horizontal mergings and lineage crossings induced by symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow, and infective heredity, making the “tree of life” look more like a “web of life.” On an epistemological level, the various means by which hereditary material can be transferred horizontally challenges our classic notions of units and levels of evolution, fitness, modes of transmission, linearity, communities, and biological individuality. The case studies presented examine topics including the origin of the eukaryotic cell and its organelles through symbiogenesis; the origin of algae through primary and secondary symbiosis and dinoflagellates through tertiary symbiosis; the superorganism and holobiont as units of evolution; how endosymbiosis induces speciation in multicellular life forms; transferrable and non-transferrable plasmids and how they symbiotically interact with their host; the means by which pro- and eukaryotic organisms transfer genes laterally (bacterial transformation, transduction and conjugation as well as transposons and other mobile genetic elements); hybridization and divergence with gene flow in sexually-reproducing individuals; current (human) microbiome and viriome studies that impact our knowledge concerning the evolution of organismal health and acquired immunity; and how symbiosis and symbiogenesis can be modelled in computational evolution. (shrink)

First, we will address the unnecessary link between symbio-studies and Gaia, asking for the historical and epistemological reasons why they become associated. In particular, we contend that the association is mediated by the common interest in large-scale physico-chemical and biochemical patterns, rather than by an emphasis on harmony, equilibrium, and cooperation (Visvader 1992). Second, we will ask what Gaia is in a metatheoretical sense: is it a scientific hypothesis, a theory, a metaphor, an inspired invention, or a resurgence of antiscientific (...) attitude? After examining some alternatives that show the importance of metatheorizing, we will define Gaia a ‘scientific narrative’, this being a technical term in a sketchy metatheory. Let us just say, for now, that by narrative we don’t mean fairytale or artistic fiction, but rather a way of telling the history of our planet. We are not going to answer the question whether or not we should ban Gaia from any scientific discourse, nor the question how symbio-students should deal with the traditional association of their field with Gaia. But we hope to frame the dilemma in which symbio-students and the scientific community at large are held in a better way than simply insisting on classic demarcations between science and non-science. (shrink)

This commentary takes issue with the idea that replication is a “fundamental element” in natural selection. Such an assumption is based on a traditional, mechanistic view of evolution. A symbiogenetic theory of evolution offers an alternative to traditional theories, emphasizing reproduction and qualitative development rather than replication and quantitative development. The issues raised by the symbiogenetic alternative may be extended to discussions of behavioral development.

The appeal to mechanisms in scientific explanation is commonplace in contemporary philosophy of science. In short, mechanists argue that an explanation of a phenomenon consists of citing the mechanism that brings the phenomenon about. In this paper, we present an argument that challenges the universality of mechanistic explanation: in explanations of the contemporary features of the eukaryotic cell, biologists appeal to its symbiogenetic origin and therefore the notion of symbiogenesis plays the main explanatory role. We defend the notion that (...) symbiogenesis is non-mechanistic in nature and that any attempt to explain some of the contemporary features of the eukaryotic cell mechanistically turns out to be at least insufficient and sometimes fails to address the question that is asked. Finally, we suggest that symbiogenesis is better understood as a pragmatic scientific law and present an alternative non-mechanistic model of scientific explanation. In the model we present, the use of scientific laws is supposed to be a minimal requirement of all scientific explanations, since the purpose of a scientific explanation is to make phenomena expectable. Therefore, this model would help to understand biologists’ appeal to the notion of symbiosis and thus is shown to be better, for the case under examination, than the mechanistic alternative. (shrink)

Of two contending models for eukaryotic evolution the “archezoan“ has an amitochondriate eukaryote take up an endosymbiont, while “symbiogenesis“ states that an Archaeon became a eukaryote as the result of this uptake. If so, organelle formation resulting from new engulfments is simplified by the primordial symbiogenesis, and less informative regarding the bacterium‐to‐mitochondrion conversion. Gradualist archezoan visions still permeate evolutionary thinking, but are much less likely than symbiogenesis. Genuine amitochondriate eukaryotes have never been found and rapid, explosive adaptive (...) periods characteristic of symbiogenetic models explain this. Mitochondrial proteomes, encoded by genes of “eukaryotic origin“ not easily linked to host or endosymbiont, can be understood in light of rapid adjustments to new evolutionary pressures. Symbiogenesis allows “expensive” eukaryotic inventions via efficient ATP generation by nascent mitochondria. However, efficient ATP production equals enhanced toxic internal ROS formation. The synergistic combination of these two driving forces gave rise to the rapid evolution of eukaryotes.Also watch the Video Abstract. (shrink)

Variation, adaptation, heredity and fitness, constraints and affordances, speciation, and extinction form the building blocks of the (Neo-)Darwinian research program, and several of these have been called “Darwinian principles.” Here, we suggest that caution should be taken in calling these principles Darwinian because of the important role played by reticulate evolutionary mechanisms and processes in also bringing about these phenomena. Reticulate mechanisms and processes include symbiosis, symbiogenesis, lateral gene transfer, infective heredity mediated by genetic and organismal mobility, and hybridization. (...) Because the “Darwinian principles” are brought about by both vertical and reticulate evolutionary mechanisms and processes, they should be understood as foundational for a more pluralistic theory of evolution, one that surpasses the classic scope of the Modern and the Neo-Darwinian Synthesis. Reticulate evolution moreover demonstrates that what conventional (Neo-)Darwinian theories treat as intra-species features of evolution frequently involve reticulate interactions between organisms from very different taxonomic categories. Variation, adaptation, heredity and fitness, constraints and affordances, speciation, and extinction therefore cannot be understood as “traits” or “properties” of genes, organisms, species, or ecosystems because the phenomena are irreducible to specific units and levels of an evolutionary hierarchy. Instead, these general principles of evolution need to be understood as common goods that come about through interactions between different units and levels of evolutionary hierarchies, and they are exherent rather than inherent properties of individuals. (shrink)

It has been said that new discoveries and developments in the human, social, and natural sciences hang “in the air” (Bowler, 1983; 2008) prior to their consummation. While neo-Darwinist biology has been powerfully served by its mechanistic metaphysic and a reductionist methodology in which living organisms are considered machines, many of the chapters in this volume place this paradigm into question. Pairing scientists and philosophers together, this volume explores what might be termed “the New Frontiers” of biology, namely contemporary areas (...) of research that appear to call an updating, a supplementation, or a relaxation of some of the main tenets of the Modern Synthesis. Such areas of investigation include: Emergence Theory, Systems Biology, Biosemiotics, Homeostasis, Symbiogenesis, Niche Construction, the Theory of Organic Selection (also known as “the Baldwin Effect”), Self-Organization and Teleodynamics, as well as Epigenetics. Most of the chapters in this book offer critical reflections on the neo-Darwinist outlook and work to promote a novel synthesis that is open to a greater degree of inclusivity as well as to a more holistic orientation in the biological sciences. (shrink)

This chapter introduces the main research schools and paradigms along which the field of evolutionary biology has been developing. Evolutionary thinking was originally founded upon the Neo-Darwinian paradigm that combines the teachings of traditional Darwinism with those of the Modern Synthesis. The Neo-Darwinian paradigm has since further diversified into the Micro-, Meso-, and Macroevolutionary schools, and it has also started to integrate the school of Ecology. Together, these schools establish the paradigm called Ecological Evolutionary Developmental Biology (Eco-Evo-Devo). A final school (...) studies Reticulate Evolution as it occurs by means of symbiosis, symbiogenesis, lateral gene transfer, infective heredity, and hybridization. This chapter reviews the major tenets and points of differentiation that exist between these distinct evolution schools. The chapter ends by looking into how evolution can be defined and how distinct units, levels, and mechanisms underlie theorizing on evolutionary hierarchies and evolutionary causation. The following chapter examines how the different evolution schools are implemented into the symbolic sciences. (shrink)

In the field of biosemiotics in our time, Ferdinand de Saussure's theory of semiology has been dismissed for its glottocentric, anthropocentric, and dyadic characteristics and as such unsuitable for the said field. Such accusation is symptomatic of an extremely narrow view of Saussure, which ignores the efforts he made in tackling problems concerning the unification of biology and semiotics . A broader view of Saussure, emerging from the newly-discovered orangery manuscripts along with his thought-provoking course lectures, reveals that his epistemology (...) is actually grounded in evolutionary differences and the concept of uniformitarianism. In order to demonstrate the value of his ideas, this paper proceeds through five sections. To begin with, the understandings and misunderstandings of key terms are summarized while seeking to reconcile arbitrary and relatively arbitrary modes of consciousness within the network of differences that Saussure proposes in his manuscripts. My study points out how such a network blurs disciplinary or systematic boundaries between language and non-verbal systems and how it might serve as a framework for appreciating true analogies between natural sciences and the science of language. The paradox of analogy, torn between the synchronic and diachronic schemes of time, is discussed. This unravels several strings that have made the functioning of analogy into such a delicate point in Saussure's theory of evolution. The concept of état de langue is made comprehensive in relation to appropriations of Darwinian model and Neo-Darwinian ideas. Saussure's model of evolution explicates the phenomenon of symbiogenesis, which is non-linear, non-adaptive, non-restrictive as regards localities, yet claims certain truths about nature and culture. Finally, my study draws attention to the implications of conceptualizing non-linear evolution within and across systems. There are indeed disparities between Saussure's epistemology and that of biosemiotics: nineteenth-century confused epistemology reoccurred within biosemiotics in its early phase. (shrink)

The appeal to mechanisms in scientific explanation is commonplace in contemporary philosophy of science. In short, mechanists argue that an explanation of a phenomenon consists of citing the mechanism that brings the phenomenon about. In this paper, we present an argument that challenges the universality of mechanistic explanation: in explanations of the contemporary features of the eukaryotic cell, biologists appeal to its symbiogenetic origin and therefore the notion of symbiogenesis plays the main explanatory role. We defend the notion that (...) symbiogenesis is non-mechanistic in nature and that any attempt to explain some of the contemporary features of the eukaryotic cell mechanistically turns out to be at least insufficient and sometimes fails to address the question that is asked. Finally, we suggest that symbiogenesis is better understood as a pragmatic scientific law and present an alternative non-mechanistic model of scientific explanation. In the model we present, the use of scientific laws is supposed to be a minimal requirement of all scientific explanations, since the purpose of a scientific explanation is to make phenomena expectable. Therefore, this model would help to understand biologists’ appeal to the notion of symbiosis and thus is shown to be better, for the case under examination, than the mechanistic alternative. (shrink)

Nigel Clark’s ‘ex-orbitant globality’ concerns the incalculability of other-than-human forces we typically fail to acknowledge, yet which haunt all considerations of environmental change. This article considers Gaia theory as a useful heuristic to register the ubiquity of bacteria to environmental activity and regulation. Bacteria are Gaia theory’s fundamental actants, and through symbiosis and symbiogenesis, connect life and matter in biophysical and biosocial entanglements. Emphasizing symbiosis might invoke the expectation of a re-inscription of the human insofar as the ubiquitous inter-connectivity (...) of life ultimately connects everything to the human. I want to argue toward the opposite conclusion: that bacterial liveliness suggests a profound indifference to human life. As such, symbiosis does not efface difference, nor its vigorous refusal to be absorbed within human formulations of world-remaking, including environmental change. Bacterial indifference’s radical asymmetry suggests the need for non-human centred theories of globality. (shrink)

Biopolitics and necropolitics have used animals as a concept to illustrate a particular human biopolitical situation, much in the “tradition” of Aristotle’s provisional biopolitics. In the Western context, not only our understanding of politics but also tropology and the conceptual apparatus itself are haunted by this ancient legacy, which underlies a vertical ontology tied to processes of spatialization and containment, a vertical ontology that enables an intelligibility of figurative translation. The article considers tropological systems as systems embedded in particular forms (...) of governmentality, forms of the violent administration of life and death. To show how certain bodies are marked as animal or animal-like and used in the (metaphorical) processes of exclusion/inclusion, it focuses on Giorgio Agamben’s thoughts on Carolus Linnaeus and Zakiyyah Iman Jackson’s analysis of metaphorics in the most recent (r)evolutionary theory, symbiogenesis, developed by Lynn Margulis. Moreover, to radically disturb the graduated ontological premises of traditional stylistics and tropology, we move beyond existing conceptualizations of the body and the sovereign, all of which are based on de-borderization, intersections, movements, and transfigurations. (shrink)

This article outlines a research agenda that addresses the question of how contemporary interactive arts practice can evolve new strategies or ways of facilitating the development and representation of subjective experiences that induce an embodied felt sense of the humanmachine co-evolution. To help answer this question, the term symbiogenic has been created as a shorthand or umbrella term to better discuss these types of experiences and the concepts they introduce. The term symbiogenic is taken from symbiogenesis, the evolutionary theory (...) introduced in 1909 by Russian biologist Konstantin Mereschkowsky and expanded in the modern era by Dr. Lynn Margulis (1993, 1981). This theory emphasizes cooperation and other more complex interactions between organisms that go beyond mere competition. The research starts from the conception that there currently exists a range of interactive artworks that examine and engage with the increasing cooperation and co-evolution that humans are experiencing with their technological environment. However, what is proposed is that interactive or technological art can go further and provoke a bodily felt sense of this dynamic and thus bring into greater consciousness the co-dependent and co-evolutionary path of our relationship with technology. It is believed that these experiences can be both developed and identified within an artistic context but they lack a cohesive conceptual framework from which to study and analyse them. (shrink)

An interpretive system for the IBM 704 computer permitting interpretation of the genetic pattern of a numeric symbioorganism as a game strategy has been developed. Selection for best performance in a simple game has been applied in a preliminary experiment. An objective method to measure the quality of a game played is described. The results presented in the article show a small but significant improvement of game quality during a period of 2300 generations.The general characteristics of the phenomena observed are (...) similar to those of preceding evolution experiments . However, a startling infection process caused by a parasite whose behaviour was influenced by the game competition is described. The parasite never developed an independent game strategy to any degree of efficiency and was entirely dependent on its host organism for game competitions with, and transmission of the infection to, uninfected hosts.The consequences of substituting the reproduction and mutation rules used in the preceding evolution experiments are discussed. Particularly, the use of rules applying the reproduction pattern ofDNA-molecules is considered, and the theoretic aspects of symbiogenetic evolution experiments based onDNA-norm are discussed. A few inferences concerning the origin and history of terrestrial life suggested by the results of the symbiogenesis experiments are presented.Ein interpretierendes System für die IBM 704 Rechenmaschine, dass Interpretation des genetischen Modells von einem numerischen Symbio-organismus wie eine Spiel Strategie, erlaubt, wurde entwickelt. Eine Forführung für Fähigkeit in einem einfachen Spiel wurde angewandt in einem preliminarisches Experiment. Eine objektive Methode zur Messung der Qualität des betreffenden Spiels wurde beschrieben. Die in dem Artikel angegebenen Resultate zeigen eine kleine, aber bedeutende Verbesserung der Spiel-Qualität während einr Periode von 2300 Generationen.Die allgemeinen Kennziechen von den beobachteten Phänomenen sind denen von vorhergehenden Evolutions-Experimenten ähnlich . Jedoch, ein überraschender Infektions-Prozess, verursacht durch einen Parasit, wessen Verhalten beinflusst wurde durch die Spiel-Konkurrenz, wurde beschrieben. Der Parasit entwickelte niemals eine unabhängige Spiel-Strategie zu irgendeinem Masze von Fähigkeit und war ganz abhängig von seinem Gastherr-Organismus für Spiel-Konkurrenz mit, und Überbringung von der Infektion auf, uninfektierte Gäste.Die Folgerungen von dem Ersetzen der Fortpflanzung und Mutations-Regeln , angewandt in vorhergehenden Evolutions-Experimente wurden besprochen. Besonders der Gebrauch von Regeln welche das FortpflanzungsModell von DNA-Molekülen anwenden wurde betrachtet, und die theorethischen Aspekte von Symbiogenetischen Evolutions-Experimenten basiert auf DNA-Norm wurden besprochen. Einige Schlussfolgerungen in Bezug auf die Entstehung und Geschichte von dem Erdenleben suggeriert durch die Resultate von den Symbiogenese-Experimenten wurden gezeigt. (shrink)

Lynn Margulis’s writing about symbiosis has profoundly influenced contemporary evolutionary theory, as well as continental and analytic philosophy of science, the materialist turn, and new materialism. Nonetheless, her work, and all symbiosis or evolution, is founded on a paradox: symbiosis fictionalizes customary accounts of the origin and evolution of species, yet it is impossible to speak of symbiosis (cross-species association) unless species-boundaries have been posited in advance. Thus, a tension is legible throughout Margulis’s work between the drive to surpass the (...) limits of species-definitions as they have been traditionally understood, and a need to maintain them in order that there can be “symbiosis” at all. Margulis criticized neo-Darwinian accounts of evolution in part because she saw symbiogenesis as debunking the theory that life was defined by individualistic competition. More recently, Myra Hird has suggested that the gift, such as it has been theorized by certain anthropologists and philosophers, could adequately figure symbiosis and the ethical relations founded on it. I turn to Derrida’s writing on the gift to suggest that, if a gift worthy of the name chances to happen, it necessarily exceeds scientific, theoretical, and philosophical knowledge. (shrink)

In a macroevolutionary timescale, evolvability itself evolves. Lineages are sorted based on their ability to generate adaptive novelties, which leads to the optimization of their genotype-phenotype map. The system of translation of genetic or epigenetic changes to the phenotype may reach significant horizontal and vertical complexity, and may even exhibit certain aspects of learning behaviour. This continuously evolving semiotic system probably enables the origin of complex yet functional and internally compatible adaptations. However, it also has a second, “darker”, side. As (...) was pointed out by several authors, the same process gradually reduces the probability of the origination of significant evolutionary novelties. In a similar way to the evolution of societies, teachings, or languages, in which the growing number of internal linkages gradually solidifies their overall structure and the structure or interpretation of their constitutive elements, the evolutionary potential of lineages decreases during biological evolution. Possible adaptations become limited to small “peripheral” modifications. According to the Frozen Evolution theory, some of the proximate causes of this “macroevolutionary freezing” are more pronounced or present exclusively in sexual lineages. Sorting based on the highest evolvability probably leads to the establishment of certain structural features of complex organisms, e.g. the modular character of their development and morphology. However, modules also “macroevolutionary freeze” whereas the hypothetical “thawing” of modules or their novel adaptive combinations becomes rarer and rarer. Some possible ways out of this dead end include the rearrangement of individual development, e.g. neoteny, radical simplification, i.e. sacculinization, and transition to a higher level of organization, e.g. symbiosis or symbiogenesis. The evolution of evolvability is essentially a biosemiotic process situated at the intersection of the genocentric modern synthesis and the evo-devo-centric extended synthesis. Therefore, evolvability may eventually connect these three not necessarily contradictory approaches. (shrink)

This paper investigates how reticulate evolution contributes to a better understanding of human sociocultural evolution in general, and community formation in particular. Reticulate evolution is evolution as it occurs by means of symbiosis, symbiogenesis, lateral gene transfer, infective heredity, and hybridization. From these mechanisms and processes, we mainly zoom in on symbiosis and we investigate how it underlies the rise of (1) human, plant, animal, and machine interactions typical of agriculture, animal husbandry, farming, and industrialization; (2) diet-microbiome relationships; and (...) (3) host-virome and other pathogen interactions that underlie human health and disease. We demonstrate that reticulate evolution necessitates an understanding of behavioral and cultural evolution at a community level, where reticulate causal processes underlie the rise of synergistic organizational traits. (shrink)

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. (shrink)

A theoretical framework is provided to explore teleonomy as a problem of self-causation, distinct from upward, downward and reticulate causation. Causality theories in biology are often formulated within hierarchy theories, where causation is conceptualized as running up or down the rungs of a ladder-like hierarchy or, more recently, as moving between multiple hierarchies. Research on the genealogy of cosmologies demonstrates that in addition to hierarchy theories, causality theories also depend upon ideas of time. This paper explores the roots and impact (...) of both time and hierarchy thinking on causal reasoning in the evolutionary sciences. Within evolutionary biology, the Neodarwinian synthesis adheres to a linear notion of time associated with linear hierarchies that portray upward causation. Eco-evo-devo schools recognize the importance of downward causation and consequently receive resistance from the standard view because downward causation is sometimes understood as backward causation, considered impossible by adherents of a linear time model. In contrast, downward causation works with a spatial or presential time notion. Hybridization, lateral gene transfer, infective heredity, symbiosis and symbiogenesis require recognition of reticulate causation occurring in both space and time, or spacetime, between distinct and interacting ontological hierarchies. Teleonomy is distinct from these types of causation because it invokes the problem of self-causation. By asking how the focal level in a hierarchy can persist through time, self-causation raises philosophical concerns on the nature of duration, identity and individuality. (shrink)

Aspects of peroxisome evolution, uncoupling, carnitine shuttles, supercomplex formation, and missing neuronal fatty acid oxidation (FAO) are linked to reactive oxygen species (ROS) formation in respiratory chains. Oxidation of substrates with high FADH2/NADH (F/N) ratios (e.g., FAs) initiate ROS formation in Complex I due to insufficient availability of its electron acceptor (Q) and reverse electron transport from QH2, e.g., during FAO or glycerol‐3‐phosphate shuttle use. Here it is proposed that the Q‐cycle of Complex III contributes to enhanced ROS formation going (...) from low F/N ratio substrates (glucose) to high F/N substrates. This contribution is twofold: 1) Complex III uses Q as substrate, thus also competing with Complex I; 2) Complex III itself will produce more ROS under these conditions. I link this scenario to the universally observed Complex III dimerization. The Q‐cycle of Complex III thus again illustrates the tension between efficient ATP generation and endogenous ROS formation. This model can explain recent findings concerning succinate and ROS‐induced uncoupling. (shrink)

Eukaryotic origins are heavily debated. The author as well as others have proposed that they are inextricably linked with the arrival of a pre‐mitochondrion of alphaproteobacterial‐like ancestry, in a so‐called symbiogenic scenario. The ensuing mutual adaptation of archaeal host and endosymbiont seems to have been a defining influence during the processes leading to the last eukaryotic common ancestor. An unresolved question in this scenario deals with the means by which the bacterium ends up inside. Older hypotheses revolve around the application (...) of known antagonistic interactions, the bacterium being prey or parasite. Here, in reviewing the field, the author argues that such models share flaws, hence making them less likely, and that a “pre‐symbiotic stage” would have eased ongoing metabolic integration. Based on this the author will speculate about the nature of the (endo) symbiosis that started eukaryotic evolution–in the context of bacterial entry being a relatively “early” event–and stress the differences between this uptake and subsequent ones. He will also briefly discuss how the mutual adaptation following the merger progressed and how many eukaryotic hallmarks can be understood in light of coadaptation. Also see the video abstract here https://youtu.be/ekqtNleVJpU. (shrink)

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. (shrink)

One of the current problems in microbiology concerns the understanding of fitness in host-symbiont systems. A great deal of research and conceptual work has analysed how the host benefits from such associations; however, very little of this work has attempted to take the microbial perspective. Nevertheless, some scientists have argued that we should conduct more comparative studies of both microorganisms that interact with a host and their free-living counterparts in order to determine whether or not symbiosis is beneficial for these (...) microorganisms. In this paper, by means of analysing heritable symbiosis as a case study, I intend to provide a different perspective on this subject. Mainly, I argue that asking how the fitness of a given microorganism was changed during the evolution of heritable symbiosis may be theoretically unjustified at both the early and late stages of this process. The reason for this, I argue, is that, during the evolution of heritable symbiosis, the fitness of a microorganism becomes incommensurable with that of its free-living counterparts because their contexts become radically different; therefore, comparing their fitness makes little sense. My analysis is driven by the use of the ecological concept of fitness; accordingly, my conclusions are bound to this specific interpretation of fitness. (shrink)

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. (shrink)

Translation: How did life originate? What were the first life forms? How did the cells of our body evolve? Is natural selection the only mechanism whereby evolution occurs? What did Darwin mean with the term natural selection and do we still use that definition today? Does evolution occur slow or fast? Are we determined by our genes? We all ask ourselves these questions from time to time. Scientists however often get too technical and philosophers too speculative in their answers. This (...) book aims to form a bridge between the life and human sciences. Questions on the origin and evolution of life are analyzed critically from within different disciplines. The result is a state of the art, accessible for philosophers and scientists as well as non-academics. Many of the answered proposed can thereby be understood as complements, deviations and alternatives to the standard paradigm of biology, the Modern Synthesis. These deviating statements are bundles into 15 theses. The question then becomes in how far the Modern Synthesis should become the subject of revision based upon these theses. Original: Hoe is leven ontstaan? Welke vorm nam het eerste leven aan? Hoe ontstonden de cellen waaruit ons lichaam is opgebouwd? Is natuurlijke selectie het enige mechanisme waarlangs evolutie zich voordoet? Wat bedoelde Darwin met natuurlijke selectie en gebruiken we deze definitie vandaag nog? Voltrekt evolutie zich traag of snel? Worden we gedetermineerd door onze genen? We stellen ons allemaal deze vragen wel eens. Wetenschappers worden echter algauw te technisch en filosofen te speculatief bij het beantwoorden ervan. Dit boek wil een brug slaan tussen de natuurwetenschappen en de menswetenschappen en de vragen omtrent de oorsprong en evolutie van leven, kritisch en nuchter, vanuit verschillende disciplines analyseren. Het resultaat is een huidige stand van zaken, leesbaar, zowel voor filosofen als wetenschappers en ook voor de leek. Vele van de voorgestelde antwoorden kunnen daarbij begrepen worden als aanvullingen, afwijkingen of alternatieven van het standaardparadigma in de biologie: de Moderne Synthese. Deze afwijkende stellingen werden gebundeld in 15 thesen. De vraag is in hoeverre de Moderne Synthese, in relatie met deze thesen, onderwerp voor herziening moet zijn. (shrink)

The year 2009 has been a year of numerous commemorations of both scientific and non-scientific achievements that contributed to the advancement of human kind. Protestants celebrated the 500th anniversary of the birth of Calvin; literary critics celebrated the 200th anniversary of the poet Edgar Allan Poe; and the musical genius Felix Mendelssohn-Bartholdy was also born 200 years ago. 2009 further marked the bicentennial of the birth of Louis Braille, the inventor of Braille; and Abraham Lincoln, the 16th president of the (...) United States, who founded the National Academy of Sciences. Pierre Curie, famous for his work on radioactivity that he conducted together with his wife Marie Curie, was born 150 ago; as was John Dewey, a philosopher and psychologist who is recognized as one of the founding fathers of both pragmatism as well as functional psychology. UNESCO and the International Astronomical Union dubbed 2009 the International Year of Astronomy. By doing so, astronomers celebrated the 400th anniversary of Galileo Galilei’s telescopic observations as well as the publication of Johannes Kepler’s Astronomia nova wherein he formulated the first two laws of planetary motion. 2009 also marked the last of a 3-year-long celebration of Planet Earth, another UNESCO-governed initiative. However, for evolutionary biologists and philosophers of science, 2009 will be largely remembered for its worldwide commemorations of the 200th anniversary of the birth of Charles Darwin, and the 150th anniversary of the publication of his magnum opus On the origin of species by means of natural selection. Footnote1 In order to pay tribute to Darwin’s major contribution to the advancement of evolutionary science, the International Union of Biological Sciences and the International Union of History and Philosophy of Science have called the year 2009 the Darwin Year. Given that so many scientific discoveries were commemorated, COPUS, the Coalition on the Public Understanding on Science, called out 2009 as the Year of Science, in the hope to pay equal tribute to both the field of biology as well as astronomy. 2009 was indeed a year of biology. Somewhat overshadowed by the big Darwin celebrations, smaller-scaled events were held to commemorate the 200th anniversary of the publication of Lamarck’s Philosophie Zoologique; and the 150th anniversary of the death of Alexander von Humboldt, the father of biogeography. In 1910, Constantin Mereschkowsky wrote his article on symbiogenesis entitled ‘The Theory of Two Plasmas as the Basis of Symbiogenesis, a New Study for the Origins of Organisms’. The article was published in the German Biologisches Zentralblatt, the journal that would later evolve into the current Theory in Biosciences. Somewhat forgotten, but equally important for the field of symbiogenesis, was the 200th anniversary of the birth of Pierre-Joseph Van Beneden, a Belgian paleontologist and zoologist famous for distinguishing parasitism from commensalism. Finally, Henry Bergson, known for inventing the currently rejected notion of élan vital, was born 150 years ago. In order to memorialize the important role these biologists played in the advancement of our understanding of the evolutionary process, a 2-day international conference was organized entitled: Evolution today and tomorrow, Darwin evaluated by contemporary evolutionary and philosophical theories. The conference was organized by The Centre for Philosophy of Science of the University of Lisbon (Portugal), in collaboration with the Centre for Environmental Biology of the same university, and the Lisbon Centre for Applied Psychology. The articles presented here are a spin-off of this conference. The current volumes contain the peer-reviewed articles of a selection of the plenary and invited speakers, as well as those of scholars who were additionally invited to contribute to the volumes. (shrink)